From fb24c4a3ed2915e4cbefcfc929e17724c7299c4b Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Fri, 9 May 2025 17:14:10 -0700 Subject: [PATCH 01/11] Implement modular benchmarking pipeline for patient graph evaluation --- requirements.txt | 7 +- requirements.txt.license | 5 + src/benchmark/batch_run.py | 63 ++ src/benchmark/generate_visuals.py | 68 ++ src/benchmark/main.py | 48 ++ .../__init__.py} | 0 src/benchmark/modules/config.py | 26 + src/benchmark/modules/embedding.py | 107 +++ src/benchmark/modules/evaluation.py | 152 ++++ src/benchmark/modules/io_utils.py | 160 ++++ src/benchmark/modules/logging_utils.py | 29 + src/benchmark/modules/reconstruction.py | 176 ++++ src/benchmark/modules/regex_utils.py | 59 ++ src/benchmark/modules/run_benchmark.py | 147 ++++ src/benchmark/modules/visualization_utils.py | 72 ++ src/benchmark/output/results/results0.json | 795 ++++++++++++++++++ src/benchmark/requirements.txt | 7 + src/benchmark/requirements.txt.license | 5 + src/benchmark/setup_env.sh | 22 + 19 files changed, 1946 insertions(+), 2 deletions(-) create mode 100644 requirements.txt.license create mode 100644 src/benchmark/batch_run.py create mode 100644 src/benchmark/generate_visuals.py create mode 100644 src/benchmark/main.py rename src/benchmark/{similarity_eval.py => modules/__init__.py} (100%) create mode 100644 src/benchmark/modules/config.py create mode 100644 src/benchmark/modules/embedding.py create mode 100644 src/benchmark/modules/evaluation.py create mode 100644 src/benchmark/modules/io_utils.py create mode 100644 src/benchmark/modules/logging_utils.py create mode 100644 src/benchmark/modules/reconstruction.py create mode 100644 src/benchmark/modules/regex_utils.py create mode 100644 src/benchmark/modules/run_benchmark.py create mode 100644 src/benchmark/modules/visualization_utils.py create mode 100644 src/benchmark/output/results/results0.json create mode 100644 src/benchmark/requirements.txt create mode 100644 src/benchmark/requirements.txt.license create mode 100755 src/benchmark/setup_env.sh diff --git a/requirements.txt b/requirements.txt index c2dac38..cf5427c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ asyncer==0.0.8 attrs==25.3.0 backoff==2.2.1 beautifulsoup4==4.13.4 -biopython==1.85 +bert-score>=0.3.13 blis==1.3.0 cachetools==5.5.2 catalogue==2.0.10 @@ -28,7 +28,8 @@ dill==0.3.8 diskcache==5.6.3 distro==1.9.0 dotenv==0.9.9 -dspy @ git+https://github.com/stanfordnlp/dspy.git@b7375196ba95215dc6237175490302fb8e5976df +dspy @ git+https://github.com/stanfordnlp/dspy.git@ab340835d1a83f62fb18f86c5b17fdfb9d172713 +dspy-ai>=2.3.3 en_core_web_sm @ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.8.0/en_core_web_sm-3.8.0-py3-none-any.whl#sha256=1932429db727d4bff3deed6b34cfc05df17794f4a52eeb26cf8928f7c1a0fb85 exceptiongroup==1.2.2 fastapi==0.115.12 @@ -64,6 +65,7 @@ mdurl==0.1.2 multidict==6.4.2 multiprocess==0.70.16 murmurhash==1.0.12 +networkx>=3.1 numpy==2.0.2 openai==1.61.0 optuna==4.2.1 @@ -107,6 +109,7 @@ tiktoken==0.9.0 tokenizers==0.21.1 tomli==2.2.1 tomlkit==0.13.2 +transformers>=4.37 tqdm==4.67.1 typer==0.15.2 typing-inspection==0.4.0 diff --git a/requirements.txt.license b/requirements.txt.license new file mode 100644 index 0000000..f1e5619 --- /dev/null +++ b/requirements.txt.license @@ -0,0 +1,5 @@ +This source file is part of the Daneshjou Lab projects + +SPDX-FileCopyrightText: 2024 Stanford University and the project authors (see AUTHORS.md) + +SPDX-License-Identifier: MIT \ No newline at end of file diff --git a/src/benchmark/batch_run.py b/src/benchmark/batch_run.py new file mode 100644 index 0000000..16c4b3c --- /dev/null +++ b/src/benchmark/batch_run.py @@ -0,0 +1,63 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +""" +Run the full benchmarking pipeline on a batch of graph files in JSON format. +Each graph is benchmarked for information fidelity, topology structure, +and trajectory representation. +""" + +from pathlib import Path +import os + +# Local application imports +from benchmark.modules.io_utils import ( + load_graph_from_file, + save_results, +) +from benchmark.modules.run_benchmark import run_pipeline +from benchmark.modules.logging_utils import setup_logger + +logger = setup_logger(__name__) + + +# Replace this with your actual text used as reference +ORIGINAL_TEXT = ( + "A patient presents with chest pain. ECG was abnormal. " + "Treated and sent to cath lab." +) + +GRAPH_INPUT_DIR = "samples/json_output/am_journal_case_reports_2024" +RESULTS_OUTPUT_DIR = "output/graphs" + +os.makedirs(RESULTS_OUTPUT_DIR, exist_ok=True) + +if __name__ == "__main__": + input_dir = Path(GRAPH_INPUT_DIR) + + for fpath in input_dir.glob("*.json"): + graph_id = fpath.stem + logger.info(f"Running pipeline on: {fpath.name}") + + graph, ok = load_graph_from_file(fpath) + if not ok: + logger.error(f"Skipping {fpath.name} due to load error.") + continue + + cfg = { + "reconstruct_params": {"include_nodes": True, "include_edges": True}, + "bertscore": True, + "topology": True, + "trajectory_embedding": True, + } + + results = run_pipeline(graph, ORIGINAL_TEXT, cfg) + + output_file = Path(RESULTS_OUTPUT_DIR) / f"{graph_id}.json" + save_results(results, output_file) + + logger.info("Batch benchmarking completed.") diff --git a/src/benchmark/generate_visuals.py b/src/benchmark/generate_visuals.py new file mode 100644 index 0000000..074b3ef --- /dev/null +++ b/src/benchmark/generate_visuals.py @@ -0,0 +1,68 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +"""This module generates visualizations for the results of the benchmark pipeline.""" + +import os +import json +import numpy as np + +from benchmark.modules.visualization_utils import ( + plot_bertscore_f1, + plot_tsne_embeddings, + plot_topology_distributions, + summarize_metrics_table +) + +RESULTS_DIR = "output/" + +# Lists to collect metrics +graph_ids = [] +bertscore_f1s = [] +trajectory_embeddings = [] +node_counts = [] +edge_counts = [] + +# Iterate over each result file +for fname in os.listdir(RESULTS_DIR): + if fname.endswith(".json"): + graph_id = fname.replace(".json", "") + with open(os.path.join(RESULTS_DIR, fname), "r", encoding="utf-8") as f: + result = json.load(f) + + graph_ids.append(graph_id) + + # Get BERTScore F1 + f1 = result.get("bertscore", {}).get("f1", [np.nan])[0] + bertscore_f1s.append(f1) + + # Get embedding + emb = result.get("trajectory_embedding") + if emb: + trajectory_embeddings.append(emb) + + # Get topology stats + topo = result.get("topology", {}) + node_counts.append(topo.get("node_count", 0)) + edge_counts.append(topo.get("edge_count", 0)) + +# Convert embedding list to numpy array if not empty +if trajectory_embeddings: + trajectory_embeddings = np.array(trajectory_embeddings) + +# Generate Visualizations + +plot_bertscore_f1(graph_ids, bertscore_f1s) + +if len(trajectory_embeddings) > 1: + plot_tsne_embeddings(trajectory_embeddings, graph_ids) + +plot_topology_distributions(node_counts, edge_counts) + +summary_df = summarize_metrics_table(graph_ids, bertscore_f1s, node_counts, edge_counts) +print("\n=== Summary Table ===") +print(summary_df) diff --git a/src/benchmark/main.py b/src/benchmark/main.py new file mode 100644 index 0000000..c4e7087 --- /dev/null +++ b/src/benchmark/main.py @@ -0,0 +1,48 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +""" +This script runs the full benchmarking pipeline on a single patient graph. +Intended for validating information extraction, structure, and representation quality. +""" + +import sys +from pathlib import Path +sys.path.append(str(Path(__file__).resolve().parents[1])) # Adds 'src' to sys.path + + +# Local application imports +from benchmark.modules.io_utils import ( + load_graph_from_file, + save_results, + data_display, +) +from benchmark.modules.run_benchmark import run_pipeline +from benchmark.modules.logging_utils import setup_logger + +logger = setup_logger(__name__) + +ORIGINAL_TEXT = ( + "A patient presents with chest pain. ECG was abnormal." + "Treated and sent to cath lab." +) + + +if __name__ == "__main__": + current_graph_path = "/Users/bikia/Documents/Code/DynamicData/samples/json_output/am_journal_case_reports_2024" + graph, ok = load_graph_from_file(current_graph_path) + + if ok: + cfg = { + "reconstruct_params": {"include_nodes": True, "include_edges": True}, + "bertscore": True, + "topology": True, + "trajectory_embedding": True, + } + results = run_pipeline(graph, ORIGINAL_TEXT, cfg) + # data_display(results) + save_results(results, "output/results/results0.json") diff --git a/src/benchmark/similarity_eval.py b/src/benchmark/modules/__init__.py similarity index 100% rename from src/benchmark/similarity_eval.py rename to src/benchmark/modules/__init__.py diff --git a/src/benchmark/modules/config.py b/src/benchmark/modules/config.py new file mode 100644 index 0000000..17b4c76 --- /dev/null +++ b/src/benchmark/modules/config.py @@ -0,0 +1,26 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +"""This module contains configuration settings for the DSPy LLM and BERTScore models.""" + +import networkx as nx + +# Graph type alias +Graph = nx.DiGraph + +# Let's change this to GEMINI +# DSPy LLM settings +LM_MODEL = "ollama/llama3.2" +LM_API_BASE = "http://localhost:11434" +LM_API_KEY = "" # or your local key if required + +# BERTScore settings +BERTSCORE_MODEL = "bert-base-uncased" + +# Trajectory Embedding settings +TRAJECTORY_EMBEDDING_MODEL = "emilyalsentzer/Bio_ClinicalBERT" +TEXT_FIELD_PATH = ["data", "commentary"] # e.g., node["data"]["commentary"] diff --git a/src/benchmark/modules/embedding.py b/src/benchmark/modules/embedding.py new file mode 100644 index 0000000..3347dc2 --- /dev/null +++ b/src/benchmark/modules/embedding.py @@ -0,0 +1,107 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +"""This module contains the TrajectoryEmbedder class for embedding patient trajectories.""" + +# Standard library imports +from typing import Optional + +# Third-party library imports +import torch +from transformers import AutoTokenizer, AutoModel +import networkx as nx + +# Local application imports +from .logging_utils import setup_logger +from .config import TRAJECTORY_EMBEDDING_MODEL + +logger = setup_logger(__name__) + + +class TrajectoryEmbedder: + """ + Embeds a patient trajectory graph by pooling embeddings of textual node content. + Uses a transformer model (e.g., Bio_ClinicalBERT) and extracts node-level text + based on a configurable path (e.g., ["data", "commentary"]). + + Attributes: + model_name (str): Hugging Face model ID used for embedding. + text_path (list[str]): Path to the text field in node + attributes (e.g., ["data", "commentary"]). + device (str): Computation device ('cuda' or 'cpu'). + """ + + def __init__( + self, + model_name=TRAJECTORY_EMBEDDING_MODEL, + text_path=None, + device=None, + ): + """ + Initializes the TrajectoryEmbedder with a specified model and text path. + Args: + model_name (str): Hugging Face model ID used for embedding. + text_path (list[str]): Path to the text field in node + attributes (e.g., ["data", "commentary"]). + device (str): Computation device ('cuda' or 'cpu'). + """ + self.model_name = model_name + self.text_path = text_path or ["content"] # Default to flat structure + self.device = device or ("cuda" if torch.cuda.is_available() else "cpu") + self.text_path = text_path + logger.info("Loading embedding model: %s on %s", model_name, self.device) + self.tokenizer = AutoTokenizer.from_pretrained(model_name) + self.model = AutoModel.from_pretrained(model_name).to(self.device) + self.model.eval() + + def embed_text(self, text: str) -> torch.Tensor: + """"Embeds a single text string using the transformer model. + Args: + text (str): Text to be embedded. + Returns: + torch.Tensor: The embedding of the text. + """ + inputs = self.tokenizer( + text, return_tensors="pt", truncation=True, padding=True + ).to(self.device) + with torch.no_grad(): + outputs = self.model(**inputs) + return outputs.last_hidden_state[0][0] + + def extract_text(self, data: dict) -> Optional[str]: + """Extracts text from the node attributes based on the specified path. + Args: + data (dict): Node attributes. + Returns: + Optional[str]: Extracted text or None if not found. + """ + try: + for key in self.text_path: + data = data[key] + return data if isinstance(data, str) else None + except (KeyError, TypeError): + return None + + def embed_graph(self, graph: nx.DiGraph) -> Optional[torch.Tensor]: + """Embeds a graph by pooling the embeddings of its nodes. + Args: + graph (nx.DiGraph): The graph to be embedded. + Returns: + Optional[torch.Tensor]: The pooled embedding of the graph. + """ + texts = [] + for _, data in graph.nodes(data=True): + t = self.extract_text(data) + if t: + texts.append(t) + + if not texts: + logger.warning("No valid node texts found for embedding.") + return None + + node_embs = torch.stack([self.embed_text(t) for t in texts]) + return node_embs.mean(dim=0).cpu() diff --git a/src/benchmark/modules/evaluation.py b/src/benchmark/modules/evaluation.py new file mode 100644 index 0000000..22a61fd --- /dev/null +++ b/src/benchmark/modules/evaluation.py @@ -0,0 +1,152 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +# pylint: disable=too-few-public-methods + +"""This module contains evaluation classes for BERTScore and graph topology validation.""" +from typing import Any +from transformers import AutoTokenizer, AutoModel +import networkx as nx +from bert_score import score + +# Local application imports +from .config import Graph +from .logging_utils import setup_logger + +logger = setup_logger(__name__) + + +class BERTScoreEvaluator: + """ + Computes BERTScore (precision, recall, F1) between original and reconstructed texts. + + Usage: + evaluator = BERTScoreEvaluator(model_type="BERTSCORE_MODEL") + results = evaluator.evaluate( + refs=["ground truth text"], + cands=["model generated text"] + ) + # results -> {"precision": [...], "recall": [...], "f1": [...]} + """ + + def __init__(self, model_type: str, device: str = None): + self.model_type = model_type + self.device = device # 'cuda', 'cpu', or None for auto-detection + + # ── Ensure the checkpoint is available locally ── + # This will pull the tokenizer & model into ~/.cache/huggingface if missing. + AutoTokenizer.from_pretrained(self.model_type) + AutoModel.from_pretrained(self.model_type) + + def evaluate(self, refs: list[str], cands: list[str]) -> dict[str, list[float]]: + """ + Args: + refs: list of reference texts. + cands: list of candidate texts. + + Returns: + Dict with keys "precision", "recall", "f1" mapping to lists of scores. + """ + if not refs or not cands: + logger.warning("Empty references or candidates list") + return {"precision": [], "recall": [], "f1": []} + + if len(refs) != len(cands): + logger.warning( + f"Mismatched list lengths: refs={len(refs)}, cands={len(cands)}" + ) + + try: + precision, recall, f1_score = score( + cands, + refs, + model_type=self.model_type, + device=self.device, + verbose=False, + ) + + return { + "precision": precision.tolist(), + "recall": recall.tolist(), + "f1": f1_score.tolist(), + } + except Exception as e: + logger.error(f"BERTScore evaluation failed: {str(e)}") + raise + + +# GRAPH TOPOLOGY VALIDATION + + +class TopologyValidator: + """ + Validates DAG properties: acyclicity, timestamp order, connectivity stats. + + Usage: + validator = TopologyValidator(graph) + stats = validator.run() + # stats -> {"is_acyclic": bool, "timestamps_in_order": bool, ...} + """ + + def __init__(self, graph: Graph): + self.graph_s = graph + + def run(self) -> dict[str, Any]: + """ + Returns: + A dict with structural validation results. + """ + if not self.graph_s or self.graph_s.number_of_nodes() == 0: + logger.warning("Empty graph in topology validator") + return { + "is_acyclic": True, # Empty graphs are technically acyclic + "timestamps_in_order": True, + "weakly_connected_components": 0, + "avg_in_degree": 0.0, + "node_count": 0, + "edge_count": 0, + "density": 0.0, + } + + is_acyclic = nx.is_directed_acyclic_graph(self.graph_s) + + # Check if timestamps exist in all nodes + timestamp_attr = "timestamp" + all_have_timestamps = all( + timestamp_attr in data for _, data in self.graph_s.nodes(data=True) + ) + + timestamps_ok = False + if all_have_timestamps: + try: + topo_nodes = list(nx.topological_sort(self.graph_s)) + timestamps = [self.graph_s.nodes[n][timestamp_attr] for n in topo_nodes] + timestamps_ok = timestamps == sorted(timestamps) + except nx.NetworkXUnfeasible: + # Graph has cycles, can't do topological sort + logger.warning("Cannot check timestamp order: graph has cycles") + timestamps_ok = False + else: + logger.warning("Not all nodes have timestamp attributes") + + components = nx.number_weakly_connected_components(self.graph_s) + node_count = self.graph_s.number_of_nodes() + edge_count = self.graph_s.number_of_edges() + + avg_in_deg = sum(dict(self.graph_s.in_degree()).values()) / max(1, node_count) + density = nx.density(self.graph_s) + + return { + "is_acyclic": is_acyclic, + "timestamps_in_order": timestamps_ok, + "all_nodes_have_timestamps": all_have_timestamps, + "weakly_connected_components": components, + "node_count": node_count, + "edge_count": edge_count, + "avg_in_degree": avg_in_deg, + "density": density, + } diff --git a/src/benchmark/modules/io_utils.py b/src/benchmark/modules/io_utils.py new file mode 100644 index 0000000..0d99b36 --- /dev/null +++ b/src/benchmark/modules/io_utils.py @@ -0,0 +1,160 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +# pylint: disable=broad-exception-caught + +"""This modules containes I/O utilities for loading and saving data.""" + +import json +import os +from typing import Any +import networkx as nx +from networkx.readwrite import json_graph + +# Local application imports +from .logging_utils import setup_logger + +logger = setup_logger(__name__) +UTF_8 = "utf-8" + +def load_graph_from_file(path: str) -> tuple[nx.DiGraph, bool]: + """ + Load a graph from a JSON file using networkx's node-link format. + Args: + path (str): Path to the JSON file containing the graph data. + Returns: + tuple: A tuple containing the loaded graph and a boolean indicating success. + """ + try: + with open(path, encoding=UTF_8) as f: + data = json.load(f) + converted_data = convert_to_node_link_format(data) + return json_graph.node_link_graph(converted_data, directed=True), True + except Exception as e: + logger.error("Error loading graph: %s", e) + return nx.DiGraph(), False + +def save_results(results: dict, path: str) -> None: + """ + Save the pipeline results to a JSON file. + Args: + results (dict): The results to save. + path (str): The path to the output file. + """ + os.makedirs(os.path.dirname(path), exist_ok=True) + with open(path, "w", encoding=UTF_8) as f: + json.dump(results, f, indent=2) + +def data_display(results: dict[str, Any]) -> None: + """ + Pretty-print the pipeline results as structured tables for easy terminal viewing. + Narrative is shown first, followed by status and individual metric tables. + + Args: + results: The dict returned by run_pipeline. + """ + # Header + print("\n========== Pipeline Results ==========\n") + + # 1) Reconstructed Narrative first + if "reconstructed_narrative" in results: + print("Reconstructed Narrative:") + print(results["reconstructed_narrative"]) + print() + + # 2) Status + status = results.get("status") + if status: + print(f"Status: {status}\n") + + # 3) BERTScore table + if "bertscore" in results: + bs = results["bertscore"] + print("BERTScore:") + print(f"{'Metric':<12} {'Score':>10}") + print("-" * 22) + for metric, scores in bs.items(): + val = scores[0] if scores else float("nan") + print(f"{metric:<12} {val:>10.4f}") + print() + + # 4) Topology table + if "topology" in results: + topo = results["topology"] + print("Topology Validation:") + print("-" * 22) + key_width = max(len(k) for k in topo) + for key, val in topo.items(): + print(f"{key:<{key_width}} : {val}") + print() + + # 5) Regex checks table + if "regex" in results: + rgx = results["regex"] + print("Regex Checks:") + print("-" * 22) + key_width = max(len(k) for k in rgx) + for key, val in rgx.items(): + print(f"{key:<{key_width}} : {val}") + print() + + # 6) Any other top-level keys + other_keys = { + k: v for k, v in results.items() + if k not in {"status", "bertscore", "topology", "regex", "reconstructed_narrative"} + } + if other_keys: + print("Additional Data:") + for key, val in other_keys.items(): + print(f"{key}: {val}") + print() + +def convert_to_node_link_format(original_json: dict) -> dict: + """ + Convert a custom-formatted graph JSON with 'node_id' and 'edges' + into NetworkX node-link format with 'id' and 'links'. + + Args: + original_json (dict): Your original graph dictionary. + + Returns: + dict: A transformed JSON compatible with networkx.node_link_graph(). + """ + converted = { + "directed": True, + "graph": {}, + "nodes": [], + "links": [] + } + + for node in original_json.get("nodes", []): + new_node = dict(node) # copy + new_node["id"] = new_node.pop("node_id", None) + converted["nodes"].append(new_node) + + for edge in original_json.get("edges", []): + new_edge = dict(edge) # copy + new_edge["source"] = new_edge.pop("from_node", None) + new_edge["target"] = new_edge.pop("to_node", None) + converted["links"].append(new_edge) + + return converted + +def save_embedding_vector(vec: list[float], out_path: str, metadata: dict = None): + """ + Save an embedding vector to a JSON file, appending it to the file if it already exists. + Args: + vec (list[float]): The embedding vector to save. + out_path (str): The path to the output file. + metadata (dict, optional): Additional metadata to include in the JSON object. + """ + row = metadata or {} + for i, v in enumerate(vec): + row[f"dim_{i}"] = v + with open(out_path, "a", encoding=UTF_8) as f: + json.dump(row, f) + f.write("\n") diff --git a/src/benchmark/modules/logging_utils.py b/src/benchmark/modules/logging_utils.py new file mode 100644 index 0000000..445bbfd --- /dev/null +++ b/src/benchmark/modules/logging_utils.py @@ -0,0 +1,29 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +"""This module contains logging utilities for standardized logging across the application.""" + +import logging + +def setup_logger(name: str) -> logging.Logger: + """ + Initializes and returns a logger with standardized settings. + + Args: + name: Usually __name__ from the calling module. + + Returns: + Configured logger instance. + """ + logger = logging.getLogger(name) + if not logger.hasHandlers(): + handler = logging.StreamHandler() + formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') + handler.setFormatter(formatter) + logger.addHandler(handler) + logger.setLevel(logging.INFO) + return logger diff --git a/src/benchmark/modules/reconstruction.py b/src/benchmark/modules/reconstruction.py new file mode 100644 index 0000000..b9577a3 --- /dev/null +++ b/src/benchmark/modules/reconstruction.py @@ -0,0 +1,176 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +"""This module provides functionality to reconstruct a clinical narrative from +a graph using a DSPy-compatible LLM.""" + +# pylint: disable=(broad-exception-caught, too-few-public-methods, too-many-arguments, too-many-positional-arguments) + +# Standard library imports +import json +from typing import Any, Optional + +# Third-party imports +import networkx as nx +import dspy + +# Local application imports +from .config import Graph +from .logging_utils import setup_logger + +logger = setup_logger(__name__) + +"""This module provides functionality to reconstruct a clinical narrative from +a graph using a DSPy-compatible LLM. +""" + + +class LLMReconstructor: + """ + Uses a DSPy-compatible LLM to reconstruct a narrative from selected parts of a graph. + + Usage: + reconstructor = LLMReconstructor( + model_name = LM_MODEL, + api_base = LM_API_BASE, + api_key= LM_API_KEY + ) + narrative = reconstructor.reconstruct( + graph, + include_nodes=True, + include_edges=False, + node_ids=["n1", "n2"], + node_attrs=["content"], + ) + """ + + def __init__( + self, + model_name: str, + api_base: str, + api_key: str, + prompt_tpl: str = ( + "Reconstruct the clinical case report from this data:\n\n{payload}\n\n" + "Write a coherent narrative including patient demographics, " + "timeline of diagnoses, treatments, and outcomes." + ), + max_retries: int = 3, + ): + try: + self.lm = dspy.LM(model_name, api_base=api_base, api_key=api_key) + self.prompt_tpl = prompt_tpl + self.max_retries = max_retries + except Exception as e: + logger.error("Error initializing LLM: %s", e) + raise + + def _build_payload( + self, + graph: Graph, + include_nodes: bool, + include_edges: bool, + node_ids: Optional[list[str]], + node_attrs: Optional[list[str]], + edge_attrs: Optional[list[str]], + ) -> dict[str, Any]: + """Build a structured payload from the graph.""" + payload: dict[str, Any] = {} + + if include_nodes: + payload["nodes"] = [] + for nid, attrs in graph.nodes(data=True): + if node_ids and nid not in node_ids: + continue + entry = {"id": nid} + for k in node_attrs or list(attrs.keys()): + if k in attrs: # Only include existing attributes + entry[k] = attrs[k] + payload["nodes"].append(entry) + + if include_edges: + payload["edges"] = [] + for src, tgt, attrs in graph.edges(data=True): + # Skip edges if we're filtering nodes and either endpoint is filtered out + if node_ids and (src not in node_ids or tgt not in node_ids): + continue + entry = {"source": src, "target": tgt} + for k in edge_attrs or list(attrs.keys()): + if k in attrs: # Only include existing attributes + entry[k] = attrs[k] + payload["edges"].append(entry) + + return payload + + def reconstruct( + self, + graph: Graph, + *, + include_nodes: bool = True, + include_edges: bool = True, + node_ids: Optional[list[str]] = None, + node_attrs: Optional[list[str]] = None, + edge_attrs: Optional[list[str]] = None, + ) -> str: + """ + Build a custom payload from the graph and call the LLM. + + Args: + graph: networkx.DiGraph with node/edge attributes. + include_nodes: include a list of nodes in the payload. + include_edges: include a list of edges in the payload. + node_ids: list of node IDs to include (default: all). + node_attrs: list of node attribute names to include (default: all). + edge_attrs: list of edge attribute names to include (default: all). + + Returns: + A string containing the reconstructed clinical narrative. + """ + if not graph: + logger.warning("Empty graph provided") + return "No data available to reconstruct narrative." + + # Verify graph is a DiGraph + if not isinstance(graph, nx.DiGraph): + logger.warning("Expected DiGraph, got %s", type(graph)) + if isinstance(graph, nx.Graph): + logger.info("Converting undirected graph to directed") + graph = nx.DiGraph(graph) + else: + raise TypeError("Input must be a networkx Graph or DiGraph") + + payload = self._build_payload( + graph, include_nodes, include_edges, node_ids, node_attrs, edge_attrs + ) + + if not payload.get("nodes") and not payload.get("edges"): + logger.warning("No nodes or edges in payload") + return "Insufficient data to reconstruct narrative." + + payload_json = json.dumps(payload, indent=2) + prompt = self.prompt_tpl.format(payload=payload_json) + + # Retry mechanism + for attempt in range(self.max_retries): + try: + resp_list = self.lm(messages=[{"role": "user", "content": prompt}]) + # dspy returns a list type of responses; + # by default that list contains exactly one completion, + # so resp_list[0] is the single response you want + return resp_list[0].strip() + except Exception as e: + logger.warning( + "LLM call failed (attempt %d/%d): %s", + attempt + 1, + self.max_retries, + e, + ) + if attempt == self.max_retries - 1: + logger.error("All LLM call attempts failed") + raise + + # This should never be reached due to the exception above, but added for completeness + return "Failed to reconstruct narrative due to LLM service errors." diff --git a/src/benchmark/modules/regex_utils.py b/src/benchmark/modules/regex_utils.py new file mode 100644 index 0000000..33b0d8d --- /dev/null +++ b/src/benchmark/modules/regex_utils.py @@ -0,0 +1,59 @@ +# pylint: disable=broad-exception-caught,too-few-public-methods + +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +""" +Provides lightweight regex-based validation for JSON-encoded graph data. +Used to catch structural formatting issues before processing. +""" + +import re +import logging + +logger = logging.getLogger(__name__) + + +class RegexValidator: + """ + Lightweight regex checks on the raw JSON string to catch common formatting issues. + + Usage: + json_str = json.dumps(json_graph.node_link_data(graph)) + validator = RegexValidator(json_str) + results = validator.run() + """ + + PATTERNS = { + "nodes_array": r'"nodes"\s*:\s*\[', + "edges_array": r'"edges"\s*:\s*\[', + "no_trailing_commas": r",\s*\]", + "node_entry": r'\{\s*"id".+?\}', + "edge_entry": r'\{\s*"source".+?"label".+?\}', + } + + def __init__(self, json_str: str): + self.s = json_str + + def run(self) -> dict[str, bool]: + """ + Returns: + Dict[str, bool]: Mapping of pattern checks to pass/fail status. + """ + if not self.s or not isinstance(self.s, str): + logger.warning("Invalid input to RegexValidator: %s", type(self.s)) + return {name: False for name in self.PATTERNS} + + results: dict[str, bool] = {} + for name, pat in self.PATTERNS.items(): + try: + found = bool(re.search(pat, self.s)) + results[name] = not found if name == "no_trailing_commas" else found + except Exception as e: + logger.error("Regex check '%s' failed: %s", name, str(e)) + results[name] = False + return results diff --git a/src/benchmark/modules/run_benchmark.py b/src/benchmark/modules/run_benchmark.py new file mode 100644 index 0000000..7007c8a --- /dev/null +++ b/src/benchmark/modules/run_benchmark.py @@ -0,0 +1,147 @@ +# pylint: disable=broad-exception-caught + +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +# pylint: disable=too-many-branches, too-many-statements + +"""This modules runs the benchmark pipeline for a single patient graph.""" + +import json +from typing import Any +import networkx as nx +from networkx.readwrite import json_graph + +# Local application imports +from .reconstruction import LLMReconstructor +from .evaluation import BERTScoreEvaluator, TopologyValidator +from .embedding import TrajectoryEmbedder +from .regex_utils import RegexValidator +from .config import ( + LM_MODEL, + LM_API_BASE, + LM_API_KEY, + BERTSCORE_MODEL, + TEXT_FIELD_PATH, + TRAJECTORY_EMBEDDING_MODEL, + Graph, +) +from .logging_utils import setup_logger + +logger = setup_logger(__name__) + + +def run_pipeline( + graph: Graph, original_text: str, config: dict[str, Any] +) -> dict[str, Any]: + """ + Benchmark pipeline for a single patient graph. + + Evaluates: + 1. LLM-based narrative reconstruction + 2. BERTScore (fidelity) + 3. Graph topology validation + 4. Optional regex check + 5. Trajectory-level embedding + + Returns: + dict: Structured results with intermediate metrics. + """ + results = {"status": "success", "errors": []} + + # Validate input types + if not isinstance(graph, (nx.Graph, nx.DiGraph)): + msg = f"Invalid graph type: {type(graph)}" + logger.error(msg) + return {"status": "error", "errors": [msg]} + + if not isinstance(original_text, str): + msg = "original_text must be a string" + logger.error(msg) + return {"status": "error", "errors": [msg]} + + # LLM Narrative Reconstruction + narrative = None + if "reconstruct_params" in config: + try: + logger.info("Starting narrative reconstruction") + reconstructor = LLMReconstructor( + model_name=LM_MODEL, api_base=LM_API_BASE, api_key=LM_API_KEY + ) + narrative = reconstructor.reconstruct(graph, **config["reconstruct_params"]) + results["reconstructed_narrative"] = narrative + logger.info("Narrative reconstruction completed") + except Exception as e: + msg = f"Narrative reconstruction failed: {str(e)}" + logger.error(msg) + results["status"] = "partial" + results["errors"].append(msg) + + # Fidelity Evaluation using BERTScore + if config.get("bertscore") and narrative: + try: + logger.info("Starting BERTScore evaluation") + model_name = config.get("bertscore_model", BERTSCORE_MODEL) + evaluator = BERTScoreEvaluator(model_type=model_name) + results["bertscore"] = evaluator.evaluate( + refs=[original_text], cands=[narrative] + ) + logger.info("BERTScore evaluation completed") + except Exception as e: + msg = f"BERTScore evaluation failed: {str(e)}" + logger.error(msg) + results["status"] = "partial" + results["errors"].append(msg) + + # Graph Topology Validation + if config.get("topology"): + try: + logger.info("Starting topology validation") + results["topology"] = TopologyValidator(graph).run() + logger.info("Topology validation completed") + except Exception as e: + msg = f"Topology validation failed: {str(e)}" + logger.error(msg) + results["status"] = "partial" + results["errors"].append(msg) + + # Optional Regex Validation + if config.get("regex"): + try: + logger.info("Starting regex validation") + json_str = json.dumps(json_graph.node_link_data(graph)) + results["regex"] = RegexValidator(json_str).run() + logger.info("Regex validation completed") + except Exception as e: + msg = f"Regex validation failed: {str(e)}" + logger.error(msg) + results["status"] = "partial" + results["errors"].append(msg) + + # Trajectory Embedding + if config.get("trajectory_embedding"): + try: + logger.info("Starting trajectory embedding") + embedder = TrajectoryEmbedder( + model_name=TRAJECTORY_EMBEDDING_MODEL, text_path=TEXT_FIELD_PATH + ) + emb = embedder.embed_graph(graph) + results["trajectory_embedding"] = emb.tolist() if emb is not None else None + logger.info("Trajectory embedding completed") + except Exception as e: + msg = f"Embedding failed: {str(e)}" + logger.error(msg) + results["status"] = "partial" + results["errors"].append(msg) + + if results["errors"]: + if results["status"] == "success": + results["status"] = "partial" + else: + results.pop("errors", None) + + return results diff --git a/src/benchmark/modules/visualization_utils.py b/src/benchmark/modules/visualization_utils.py new file mode 100644 index 0000000..b80aff2 --- /dev/null +++ b/src/benchmark/modules/visualization_utils.py @@ -0,0 +1,72 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# + +""" This module provides functions to visualize and summarize the results of the benchmarking +pipeline. It includes functions to plot BERTScore F1 scores, t-SNE embeddings, and topology +distributions, as well as to create a summary table of key metrics.""" + +import os +import matplotlib.pyplot as plt +import seaborn as sns +import pandas as pd +from sklearn.manifold import TSNE + +PLOTS_DIR = "output/plots" + +os.makedirs(PLOTS_DIR, exist_ok=True) + +def plot_bertscore_f1(graph_ids, bertscore_f1): + """Bar plot of BERTScore F1 for each graph.""" + _, ax = plt.subplots() + sns.barplot(x=graph_ids, y=bertscore_f1, ax=ax) + ax.set_title("BERTScore F1 per Graph") + ax.set_ylabel("F1 Score") + ax.set_ylim(0, 1) + plt.xticks(rotation=45) + plt.tight_layout() + plt.savefig(os.path.join(PLOTS_DIR, "bertscore_f1_barplot.png")) + plt.close() + + +def plot_tsne_embeddings(embeddings, graph_ids): + """2D t-SNE scatterplot for graph embeddings.""" + tsne_results = TSNE(n_components=2, perplexity=2, random_state=42).fit_transform(embeddings) + _, ax = plt.subplots() + sns.scatterplot(x=tsne_results[:, 0], y=tsne_results[:, 1], hue=graph_ids, s=100, ax=ax) + ax.set_title("t-SNE of Trajectory Embeddings") + ax.set_xlabel("Dimension 1") + ax.set_ylabel("Dimension 2") + plt.legend(bbox_to_anchor=(1.05, 1), loc='upper left') + plt.savefig(os.path.join(PLOTS_DIR, "trajectory_tsne.png")) + plt.close() + + +def plot_topology_distributions(node_counts, edge_counts): + """Histograms for node and edge counts across graphs.""" + _, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5)) + sns.histplot(node_counts, bins=5, ax=ax1, kde=True) + ax1.set_title("Node Count Distribution") + ax1.set_xlabel("Number of Nodes") + + sns.histplot(edge_counts, bins=5, ax=ax2, kde=True) + ax2.set_title("Edge Count Distribution") + ax2.set_xlabel("Number of Edges") + + plt.tight_layout() + plt.savefig(os.path.join(PLOTS_DIR, "topology_distributions.png")) + plt.close() + + +def summarize_metrics_table(graph_ids, bertscore_f1, node_counts, edge_counts): + """Create and return a summary DataFrame of key metrics per graph.""" + df = pd.DataFrame({ + "Graph ID": graph_ids, + "BERTScore F1": bertscore_f1, + "Nodes": node_counts, + "Edges": edge_counts + }) + return df diff --git a/src/benchmark/output/results/results0.json b/src/benchmark/output/results/results0.json new file mode 100644 index 0000000..37ec246 --- /dev/null +++ b/src/benchmark/output/results/results0.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 37-year-old male with bilateral painless testicular masses. His age and gender are noted in the initial diagnosis (node A).\n\n**Initial Diagnosis (2015-12-01T00:00:00Z):**\nThe patient presented with bilateral macro-orchitis and multifocal hyperechoic lesions on ultrasound, followed by intense contrast enhancement on MRI. The initial presentation was characterized as \"bilateral testicular masses.\" The patient's laboratory results showed normal levels of AFP, b-hCG, and LDH.\n\n**Surgical Intervention (2015-12-01T00:00:00Z):**\nThe patient underwent testis-sparing surgery, which revealed a benign large-cell calcifying Sertoli cell tumor. The histological diagnosis confirmed the presence of a benign tumor with no atypia.\n\n**Metastatic Disease (2021-06-01T00:00:00Z):**\nApproximately 6 years after the initial diagnosis, the patient's condition worsened, and lymph node metastases were detected. A bilateral radical orchiectomy and lymphadenectomy were performed to manage the disease. The histological examination revealed malignant LCCSCT with vascular permeation and spermatic cord invasion.\n\n**Progression to Terminal Stage (2021-11-01T00:00:00Z):**\nDespite chemotherapy, the patient's disease progressed further, with the development of pleural metastases, pulmonary nodules, and spine lesions. The patient received multiple rounds of chemotherapy, including vinblastine, cisplatin, ifosfamide, and paclitaxel.\n\n**Clinical Trial (2022-12-01T00:00:00Z):**\nIn an attempt to manage the disease, a clinical trial was initiated with axitinib and pazopanib. However, this treatment approach proved ineffective.\n\n**Terminal Stage (2023-07-01T00:00:00Z):**\nThe patient's condition continued to deteriorate, and he progressed to a terminal stage. The patient received palliative care, and unfortunately, passed away.\n\nIn summary, the patient presented with bilateral testicular masses in 2015 and underwent successful surgical intervention. However, the disease eventually progressed to metastatic disease, which was managed with chemotherapy and clinical trials. Despite these efforts, the patient's condition continued to worsen, ultimately leading to a terminal stage and death.", + "bertscore": { + "precision": [ + 0.31829699873924255 + ], + "recall": [ + 0.5213518738746643 + ], + "f1": [ + 0.39527177810668945 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.20442374050617218, + 0.08089178055524826, + -0.024914061650633812, + -0.03979193791747093, + 0.0259078536182642, + 0.2874663174152374, + 0.0590699277818203, + 0.1804632693529129, + 0.678746223449707, + -0.3412137031555176, + 0.09028627723455429, + -0.126709446310997, + -0.49773454666137695, + -0.3380317687988281, + -0.11197445541620255, + 0.31535783410072327, + -0.4333740174770355, + 0.27163252234458923, + -0.03901287913322449, + 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+++ b/src/benchmark/requirements.txt.license @@ -0,0 +1,5 @@ +This source file is part of the Daneshjou Lab projects + +SPDX-FileCopyrightText: 2024 Stanford University and the project authors (see AUTHORS.md) + +SPDX-License-Identifier: MIT \ No newline at end of file diff --git a/src/benchmark/setup_env.sh b/src/benchmark/setup_env.sh new file mode 100755 index 0000000..095f3c2 --- /dev/null +++ b/src/benchmark/setup_env.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# Exit immediately if a command fails +set -e + +echo "Creating virtual environment with Python 3.11..." +/opt/homebrew/bin/python3.11 -m venv .venv + +source .venv/bin/activate + +echo "Upgrading pip..." +pip install --upgrade pip + +if [ -f "requirements.txt" ]; then + echo "Installing dependencies from requirements.txt..." + pip install -r requirements.txt +else + echo "No requirements.txt found. Skipping dependency installation." +fi + +echo "Running main..." +python3 main.py \ No newline at end of file From b792b8ece0b35978921639e2637043d69e4bfe95 Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Fri, 9 May 2025 19:33:32 -0700 Subject: [PATCH 02/11] Update --- src/benchmark/batch_run.py | 82 +- src/benchmark/generate_visuals.py | 6 +- src/benchmark/main.py | 7 +- src/benchmark/modules/embedding.py | 50 +- src/benchmark/modules/io_utils.py | 92 +- src/benchmark/modules/run_benchmark.py | 4 +- .../output/plots/bertscore_f1_barplot.png | Bin 0 -> 16630 bytes .../output/plots/topology_distributions.png | Bin 0 -> 32789 bytes .../output/plots/trajectory_tsne.png | Bin 0 -> 19219 bytes src/benchmark/output/results/graph_013.json | 795 ++++++++++++++++++ src/benchmark/output/results/graph_029.json | 795 ++++++++++++++++++ src/benchmark/output/results/graph_044.json | 795 ++++++++++++++++++ src/benchmark/output/results/graph_068.json | 795 ++++++++++++++++++ src/benchmark/output/results/graph_087.json | 795 ++++++++++++++++++ src/benchmark/requirements.txt | 6 +- src/benchmark/setup_env.sh | 7 +- .../graphs/{ => mapping}/graph_metadata.csv | 0 .../graphs/{ => mapping}/graph_metadata.json | 0 .../{ => mapping}/graph_metadata_true.json | 0 19 files changed, 4161 insertions(+), 68 deletions(-) create mode 100644 src/benchmark/output/plots/bertscore_f1_barplot.png create mode 100644 src/benchmark/output/plots/topology_distributions.png create mode 100644 src/benchmark/output/plots/trajectory_tsne.png create mode 100644 src/benchmark/output/results/graph_013.json create mode 100644 src/benchmark/output/results/graph_029.json create mode 100644 src/benchmark/output/results/graph_044.json create mode 100644 src/benchmark/output/results/graph_068.json create mode 100644 src/benchmark/output/results/graph_087.json rename webapp/static/graphs/{ => mapping}/graph_metadata.csv (100%) rename webapp/static/graphs/{ => mapping}/graph_metadata.json (100%) rename webapp/static/graphs/{ => mapping}/graph_metadata_true.json (100%) diff --git a/src/benchmark/batch_run.py b/src/benchmark/batch_run.py index 16c4b3c..fc18995 100644 --- a/src/benchmark/batch_run.py +++ b/src/benchmark/batch_run.py @@ -11,13 +11,16 @@ and trajectory representation. """ +import sys from pathlib import Path -import os +sys.path.append(str(Path(__file__).resolve().parents[1])) # Adds 'src' to sys.path # Local application imports from benchmark.modules.io_utils import ( load_graph_from_file, save_results, + build_graph_to_text_mapping, + extract_original_text_from_html ) from benchmark.modules.run_benchmark import run_pipeline from benchmark.modules.logging_utils import setup_logger @@ -27,37 +30,68 @@ # Replace this with your actual text used as reference ORIGINAL_TEXT = ( - "A patient presents with chest pain. ECG was abnormal. " - "Treated and sent to cath lab." + "Starry starry night, " + "Paint your palette blue and grey, " + "Look out on a summer's day, " + "With eyes that know the darkness in my soul. " + "Shadows on the hills, " + "Sketch the trees and daffodils, " + "Catch the breeze and winter chills, " + "In colors on the snowy linen land. " + "Now I understand, " + "What you tried to say to me, " + "And how you suffered for your sanity, " + "And how you tried to set them free. " + "They would not listen, they did not know how, " + "Perhaps they'll listen now. " ) -GRAPH_INPUT_DIR = "samples/json_output/am_journal_case_reports_2024" -RESULTS_OUTPUT_DIR = "output/graphs" +# Input directory: All graph files +GRAPH_INPUT_DIR = Path(__file__).resolve().parents[2] / "webapp/static/graphs" -os.makedirs(RESULTS_OUTPUT_DIR, exist_ok=True) +# Output directory: Results +RESULTS_OUTPUT_DIR = Path("output/results") +RESULTS_OUTPUT_DIR.mkdir(parents=True, exist_ok=True) + +# Paths +metadata_csv = "webapp/static/graphs/mapping/graph_metadata.csv" +html_root_dir = "webapp/static/pmhc_html" + +# graph_to_html = build_graph_to_text_mapping(metadata_csv, html_root_dir) if __name__ == "__main__": - input_dir = Path(GRAPH_INPUT_DIR) + graph_files = list(GRAPH_INPUT_DIR.glob("*.json")) + + if not graph_files: + logger.warning("No JSON files found in input directory.") + else: + for fpath in graph_files[:5]: # Limit to first 5 files for demonstration + graph_id = fpath.stem + # html_path = graph_to_html.get(graph_id) - for fpath in input_dir.glob("*.json"): - graph_id = fpath.stem - logger.info(f"Running pipeline on: {fpath.name}") + # if not html_path: + # logger.warning(f"No HTML path found for {graph_id}") + # continue + + # reference_case_text = extract_original_text_from_html(html_path) + reference_case_text = ORIGINAL_TEXT - graph, ok = load_graph_from_file(fpath) - if not ok: - logger.error(f"Skipping {fpath.name} due to load error.") - continue + logger.info(f"Running pipeline on: {fpath.name}") - cfg = { - "reconstruct_params": {"include_nodes": True, "include_edges": True}, - "bertscore": True, - "topology": True, - "trajectory_embedding": True, - } + graph, ok = load_graph_from_file(fpath) + if not ok: + logger.error(f"Skipping {fpath.name} due to load error.") + continue - results = run_pipeline(graph, ORIGINAL_TEXT, cfg) + cfg = { + "reconstruct_params": {"include_nodes": True, "include_edges": True}, + "bertscore": True, + "topology": True, + "trajectory_embedding": True, + } - output_file = Path(RESULTS_OUTPUT_DIR) / f"{graph_id}.json" - save_results(results, output_file) + results = run_pipeline(graph, reference_case_text, cfg) + output_path = RESULTS_OUTPUT_DIR / f"{graph_id}.json" + save_results(results, output_path) - logger.info("Batch benchmarking completed.") + logger.info("Batch benchmarking completed.") \ No newline at end of file diff --git a/src/benchmark/generate_visuals.py b/src/benchmark/generate_visuals.py index 074b3ef..cc1c00e 100644 --- a/src/benchmark/generate_visuals.py +++ b/src/benchmark/generate_visuals.py @@ -11,6 +11,10 @@ import json import numpy as np +import sys +from pathlib import Path +sys.path.append(str(Path(__file__).resolve().parents[1])) # Adds 'src' to sys.path + from benchmark.modules.visualization_utils import ( plot_bertscore_f1, plot_tsne_embeddings, @@ -18,7 +22,7 @@ summarize_metrics_table ) -RESULTS_DIR = "output/" +RESULTS_DIR = "output/results" # Lists to collect metrics graph_ids = [] diff --git a/src/benchmark/main.py b/src/benchmark/main.py index c4e7087..76acf22 100644 --- a/src/benchmark/main.py +++ b/src/benchmark/main.py @@ -27,13 +27,12 @@ logger = setup_logger(__name__) ORIGINAL_TEXT = ( - "A patient presents with chest pain. ECG was abnormal." - "Treated and sent to cath lab." + "A patient" ) if __name__ == "__main__": - current_graph_path = "/Users/bikia/Documents/Code/DynamicData/samples/json_output/am_journal_case_reports_2024" + current_graph_path = "/Users/bikia/Documents/Code/DynamicData/webapp/static/graphs/graph_001.json" graph, ok = load_graph_from_file(current_graph_path) if ok: @@ -45,4 +44,4 @@ } results = run_pipeline(graph, ORIGINAL_TEXT, cfg) # data_display(results) - save_results(results, "output/results/results0.json") + save_results(results, "output/results/results_001.json") diff --git a/src/benchmark/modules/embedding.py b/src/benchmark/modules/embedding.py index 3347dc2..50c876f 100644 --- a/src/benchmark/modules/embedding.py +++ b/src/benchmark/modules/embedding.py @@ -35,12 +35,7 @@ class TrajectoryEmbedder: device (str): Computation device ('cuda' or 'cpu'). """ - def __init__( - self, - model_name=TRAJECTORY_EMBEDDING_MODEL, - text_path=None, - device=None, - ): + def __init__(self, model=TRAJECTORY_EMBEDDING_MODEL, text_field_path="content", device=None): """ Initializes the TrajectoryEmbedder with a specified model and text path. Args: @@ -49,15 +44,28 @@ def __init__( attributes (e.g., ["data", "commentary"]). device (str): Computation device ('cuda' or 'cpu'). """ - self.model_name = model_name - self.text_path = text_path or ["content"] # Default to flat structure self.device = device or ("cuda" if torch.cuda.is_available() else "cpu") - self.text_path = text_path - logger.info("Loading embedding model: %s on %s", model_name, self.device) - self.tokenizer = AutoTokenizer.from_pretrained(model_name) - self.model = AutoModel.from_pretrained(model_name).to(self.device) + self.text_field = text_field_path + logger.info(f"Loading embedding model: {model} on {self.device}") + self.tokenizer = AutoTokenizer.from_pretrained(model) + self.model = AutoModel.from_pretrained(model).to(self.device) self.model.eval() + def _get_nested_text(self, data: dict) -> Optional[str]: + """Extracts text from a nested dictionary based on the specified path. + Args: + data (dict): Node attributes. + Returns: + Optional[str]: Extracted text or None if not found. + """ + try: + keys = self.text_field.split(".") + for k in keys: + data = data[k] + return data if isinstance(data, str) else None + except Exception: + return None + def embed_text(self, text: str) -> torch.Tensor: """"Embeds a single text string using the transformer model. Args: @@ -65,9 +73,7 @@ def embed_text(self, text: str) -> torch.Tensor: Returns: torch.Tensor: The embedding of the text. """ - inputs = self.tokenizer( - text, return_tensors="pt", truncation=True, padding=True - ).to(self.device) + inputs = self.tokenizer(text, return_tensors="pt", truncation=True, padding=True).to(self.device) with torch.no_grad(): outputs = self.model(**inputs) return outputs.last_hidden_state[0][0] @@ -93,15 +99,13 @@ def embed_graph(self, graph: nx.DiGraph) -> Optional[torch.Tensor]: Returns: Optional[torch.Tensor]: The pooled embedding of the graph. """ - texts = [] - for _, data in graph.nodes(data=True): - t = self.extract_text(data) - if t: - texts.append(t) - + texts = [ + self._get_nested_text(data) + for _, data in graph.nodes(data=True) + if self._get_nested_text(data) + ] if not texts: logger.warning("No valid node texts found for embedding.") return None - node_embs = torch.stack([self.embed_text(t) for t in texts]) - return node_embs.mean(dim=0).cpu() + return node_embs.mean(dim=0).cpu() \ No newline at end of file diff --git a/src/benchmark/modules/io_utils.py b/src/benchmark/modules/io_utils.py index 0d99b36..cf6e7ba 100644 --- a/src/benchmark/modules/io_utils.py +++ b/src/benchmark/modules/io_utils.py @@ -9,6 +9,8 @@ """This modules containes I/O utilities for loading and saving data.""" +# Standard library imports +import csv import json import os from typing import Any @@ -33,7 +35,8 @@ def load_graph_from_file(path: str) -> tuple[nx.DiGraph, bool]: with open(path, encoding=UTF_8) as f: data = json.load(f) converted_data = convert_to_node_link_format(data) - return json_graph.node_link_graph(converted_data, directed=True), True + normalized_data = normalize_graph_for_networkx(converted_data) + return json_graph.node_link_graph(normalized_data, directed=True), True except Exception as e: logger.error("Error loading graph: %s", e) return nx.DiGraph(), False @@ -115,14 +118,11 @@ def data_display(results: dict[str, Any]) -> None: def convert_to_node_link_format(original_json: dict) -> dict: """ - Convert a custom-formatted graph JSON with 'node_id' and 'edges' - into NetworkX node-link format with 'id' and 'links'. - + Convert a JSON object to the node-link format used by networkx. Args: - original_json (dict): Your original graph dictionary. - + original_json (dict): The original JSON object. Returns: - dict: A transformed JSON compatible with networkx.node_link_graph(). + dict: The converted JSON object in node-link format. """ converted = { "directed": True, @@ -133,17 +133,49 @@ def convert_to_node_link_format(original_json: dict) -> dict: for node in original_json.get("nodes", []): new_node = dict(node) # copy - new_node["id"] = new_node.pop("node_id", None) + new_node["id"] = ( + new_node.get("node_id") + or new_node.get("id") + or new_node.get("customData", {}).get("node_id") + ) converted["nodes"].append(new_node) for edge in original_json.get("edges", []): new_edge = dict(edge) # copy - new_edge["source"] = new_edge.pop("from_node", None) - new_edge["target"] = new_edge.pop("to_node", None) + new_edge["source"] = new_edge.pop("from", None) + new_edge["target"] = new_edge.pop("to", None) converted["links"].append(new_edge) return converted + +def normalize_graph_for_networkx(raw_graph: dict) -> dict: + """ + Normalize the graph for use with networkx. + Args: + raw_graph (dict): The raw graph data. + Returns: + dict: The normalized graph data. + """ + for node in raw_graph["nodes"]: + # Promote content and timestamp from customData + if "customData" in node: + custom = node["customData"] + if "content" in custom: + node["content"] = custom["content"] + if "timestamp" in custom: + node["timestamp"] = custom["timestamp"] + node.update(custom) + del node["customData"] + + for edge in raw_graph["links"]: + if "from" in edge: + edge["source"] = edge.pop("from") + if "to" in edge: + edge["target"] = edge.pop("to") + + return raw_graph + def save_embedding_vector(vec: list[float], out_path: str, metadata: dict = None): """ Save an embedding vector to a JSON file, appending it to the file if it already exists. @@ -158,3 +190,43 @@ def save_embedding_vector(vec: list[float], out_path: str, metadata: dict = None with open(out_path, "a", encoding=UTF_8) as f: json.dump(row, f) f.write("\n") + +def build_graph_to_text_mapping(metadata_csv_path: str, html_root_dir: str) -> dict[str, str]: + """ + Build a mapping from graph ID (e.g., 'graph_006') to full HTML file path. + + Args: + metadata_csv_path (str): Path to the graph_metadata.csv file. + html_root_dir (str): Base path for the HTML files. + + Returns: + dict: Mapping from graph ID to corresponding HTML file path. + """ + graph_to_html = {} + + with open(metadata_csv_path, newline='', encoding='utf-8') as csvfile: + reader = csv.reader(csvfile) + for row in reader: + graph_id = row[0].strip() + html_rel_path = row[2].strip().replace("./pmc_htmls", html_root_dir) + graph_to_html[graph_id] = html_rel_path + + return graph_to_html + +def extract_original_text_from_html(html_path: str) -> str: + """ + Placeholder function to extract original case report text from HTML. + + Args: + html_path (str): Path to the HTML file. + + Returns: + str: Raw text extracted (currently placeholder). + """ + try: + with open(html_path, encoding='utf-8') as f: + html = f.read() + # TODO: replace with BeautifulSoup parsing + return f"[PLACEHOLDER] Text extracted from: {Path(html_path).name}" + except Exception as e: + return f"[ERROR] Failed to extract from {html_path}: {e}" \ No newline at end of file diff --git a/src/benchmark/modules/run_benchmark.py b/src/benchmark/modules/run_benchmark.py index 7007c8a..68fc2b8 100644 --- a/src/benchmark/modules/run_benchmark.py +++ b/src/benchmark/modules/run_benchmark.py @@ -126,9 +126,7 @@ def run_pipeline( if config.get("trajectory_embedding"): try: logger.info("Starting trajectory embedding") - embedder = TrajectoryEmbedder( - model_name=TRAJECTORY_EMBEDDING_MODEL, text_path=TEXT_FIELD_PATH - ) + embedder = TrajectoryEmbedder() emb = embedder.embed_graph(graph) results["trajectory_embedding"] = emb.tolist() if emb is not None else None logger.info("Trajectory embedding completed") diff --git a/src/benchmark/output/plots/bertscore_f1_barplot.png b/src/benchmark/output/plots/bertscore_f1_barplot.png new file mode 100644 index 0000000000000000000000000000000000000000..e3d768e081339e2faddc7f7bed715fb4515c10c1 GIT binary patch literal 16630 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The patient's demographic information is not explicitly provided in the data, but based on the clinical presentation and treatment plan, it can be inferred that the patient is likely an older adult.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient was diagnosed with stage III NSCLC and upper esophageal stricture around the same time.\n2. **Step 2 (Two months later):** An initial MRI performed revealed no abnormalities, but the patient's diagnosis of NSCLC remained active.\n3. **Step 3 (One year after Step 1):** Follow-up CT scans showed metastatic spread throughout the brain after presentation to the ED with neurological weakness.\n4. **Step 4:** The patient was admitted to hospital and started on dexamethasone, continued treatment for hypokalemia, and placed on neutropenic precautions. Pantoprazole and enoxaparin sodium were initiated due to possible hemorrhages and deep vein thrombosis prophylaxis.\n5. **Step 5:** MRI confirmed multiple new brain metastases with vasogenic edema and possible hemorrhagic components. The patient's oncologist confirmed metastasis to the brain and bone, and dexamethasone was increased to 6 mg every eight hours. Enoxaparin sodium was discontinued due to possible hemorrhages; mechanical prophylaxis started with thromboembolic deterrent stockings and sequential compression devices.\n6. **Step 6:** The patient tolerated radiation therapy well and docetaxel was re-initiated.\n7. **Step 7 (Refractory disease):** CT scans revealed new developments in the liver and possibly pancreas, indicating refractory disease to second-line docetaxel.\n8. **Step 8 (Hospice care recommendation):** The oncologist discussed a third-line option and recommended hospice care.\n\n**Timeline of Treatments:**\n\n1. **Dexamethasone:** Initially started at 4 mg twice daily, increased to 6 mg every eight hours due to metastasis.\n2. **Docetaxel:** Re-initiated after radiation therapy, with no specified dosage or frequency.\n3. **Pantoprazole and Enoxaparin Sodium:** Initiated for possible hemorrhages and deep vein thrombosis prophylaxis.\n\n**Outcomes:**\n\n1. **Radiation Therapy:** The patient tolerated the treatment well, indicating a positive response to radiation therapy.\n2. **Hospice Care Recommendation:** The oncologist recommended hospice care due to refractory disease, indicating a poor prognosis for the patient's overall health and quality of life.\n\nIn conclusion, this patient was diagnosed with stage III NSCLC accompanied by an upper esophageal stricture and underwent multiple treatments, including radiation therapy, dexamethasone, docetaxel, pantoprazole, and enoxaparin sodium. Despite initial positive responses to treatment, the patient's disease progressed, leading to a recommendation for hospice care due to refractory disease.", + "bertscore": { + "precision": [ + 0.3270224332809448 + ], + "recall": [ + 0.4040271043777466 + ], + "f1": [ + 0.3614691495895386 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.24155695736408234, + 0.21537359058856964, + -0.07995787262916565, + 0.12391994893550873, + -0.0372464694082737, + 0.15261226892471313, + -0.11476530134677887, + 0.32324033975601196, + 0.4738871157169342, + -0.23460787534713745, + -0.20247039198875427, + -0.08712716400623322, + -0.6125581860542297, + -0.031501494348049164, + -0.20453636348247528, + 0.20022889971733093, + -0.16431254148483276, + 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history of palmoplantar pustulosis. She presented with a breast mass and a chest mass, which led to further investigation and diagnosis.\n\n**Initial Diagnosis (Step 1):**\nThe patient's initial presentation was characterized by a breast mass and a chest mass. Histopathological analysis of biopsy specimens from both the lung mass and the breast mass revealed small cell carcinoma (SCLC) in both lesions. Comprehensive staging, including contrast-enhanced MRI of the brain and FDG-PET, led to a diagnosis of stage cT2aN3M1c SCLC with multiple bone, peritoneal, and skin metastases.\n\n**Timeline of Diagnoses:**\n\n* **Step 1 (N1):** Patient presented with breast mass and chest mass.\n* **Step 2 (N2):** Histopathological analysis revealed small cell carcinoma in both lesions. Comprehensive staging confirmed stage cT2aN3M1c SCLC.\n\n**Treatment Initiation (Step 3):**\nThe patient initiated first-line treatment with carboplatin, etoposide, and durvalumab. Administration sequence: durvalumab, followed by ETP, and then CBDCA. During the first course of treatment, the patient experienced anaphylactic shock while receiving an ETP infusion on day 1.\n\n**Treatment Modification (Step 4):**\nDue to anaphylactic shock during etoposide infusion, treatment was switched to combination therapy with cisplatin (CDDP) and irinotecan (CPT-11).\n\n**Current Status:**\nThe patient is currently undergoing treatment with a modified regimen. The patient's condition is being closely monitored for any signs of disease progression or adverse reactions.\n\n**Outcomes:**\nWhile the patient has experienced anaphylactic shock during treatment, they are still receiving ongoing care and management. Further follow-up will be necessary to assess the effectiveness of the current treatment regimen and make any necessary adjustments.\n\nNote: The case report is based on the provided data and may not reflect the actual clinical scenario or outcomes.", + "bertscore": { + "precision": [ + 0.33418387174606323 + ], + "recall": [ + 0.4088182747364044 + ], + "f1": [ + 0.3677525520324707 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.15035732090473175, + 0.08811881393194199, + -0.19972163438796997, + 0.14578032493591309, + 0.23200318217277527, + 0.13004496693611145, + 0.015617452561855316, + 0.2698851525783539, + 0.4273703098297119, + -0.5097478032112122, + -0.08371931314468384, + 0.2273850440979004, + -0.7754285931587219, + 0.03681084141135216, + -0.3211135268211365, + 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Report**\n\n**Patient Demographics:**\nThe patient is a 44-year-old man with a significant smoking history of 24 years. He has no other notable medical history.\n\n**Initial Presentation (Step 1):**\nThe patient presented to the emergency department due to cough, dyspnea, and throat pain. This was his first visit to the hospital in two weeks, during which he had undergone noncontrast CT scans that showed a 5.0 x 5.0 cm tumor in the superior-to-anterior mediastinum.\n\n**Imaging Findings (Step 2):**\nFollow-up imaging revealed an enlarged shadow in the right upper mediastinum on chest radiography, which was later confirmed by CT scan to be a mediastinal mass.\n\n**Progression of Disease (Steps 3-5):**\nOver two weeks, the tumor grew from 5.0 x 5.0 cm to 9.0 x 7.0 cm in size, causing compression and narrowing of the right brachiocephalic vein and superior vena cava, as well as left deviation of the trachea.\n\n**Symptom Onset (Step 4):**\nThe patient developed respiratory symptoms, including cough, dyspnea, and throat pain, which prompted further imaging to evaluate the cause of these symptoms.\n\n**Imaging Evaluation (Steps 5-6):**\nNoncontrast CT scans two weeks prior to admission showed a tumor in the superior-to-anterior mediastinum. Dynamic CT scans at admission revealed a weakly enhanced tumor in the superior-to-middle mediastinum, which had grown to 9.0 x 7.0 cm over two weeks.\n\n**Laboratory Findings (Step 6):**\nLaboratory tests revealed slightly elevated levels of lactate dehydrogenase (LDH) and C-reactive protein (CRP), indicating inflammation or infection. Tumor markers, including CYFRA, pro-GRP, CEA, and CA19-9, were all negative.\n\n**Current Status:**\nThe patient is currently undergoing further evaluation and treatment for the mediastinal mass. The exact treatment plan has not been disclosed in this report.\n\n**Outcomes:**\nThe patient's current condition and potential outcomes are unknown at this time. Further follow-up will be necessary to determine the effectiveness of any treatments and to monitor for any changes in the patient's condition.", + "bertscore": { + "precision": [ + 0.32771092653274536 + ], + "recall": [ + 0.4161722660064697 + ], + "f1": [ + 0.3666817843914032 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.3709355294704437, + 0.02028684876859188, + -0.037475328892469406, + 0.05414177477359772, + 0.11516084522008896, + 0.028672976419329643, + 0.002444108249619603, + 0.26623213291168213, + 0.3955191671848297, + -0.28058165311813354, + -0.18973876535892487, + 0.09418404847383499, + -0.6652488708496094, + -0.08837980031967163, + -0.3189680576324463, + 0.20539359748363495, + 0.10319840908050537, + 0.2507036030292511, + 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However, based on the clinical data, it appears that the patient has a history of lung cancer.\n\n**Timeline of Diagnoses:**\n\n1. **September 2021:** The patient presented to The First Affiliated Hospital of Dalian Medical University with complaints of chest pain and fatigue for half a year. A CT scan revealed partial solid nodules in the posterior segment of the upper lobe of the right lung, which were later diagnosed as malignant neoplasm of bronchus and lung (C34).\n2. **Multiple small lung nodules in both lungs:** Following the initial diagnosis, the patient developed multiple small lung nodules in both lungs, accompanied by abnormal blood test results (lymphocytopenia and neutrophilia). This led to a decision to proceed with surgical resection of lung tissue.\n3. **November 2022:** The patient underwent surgical resection of lung tissue, which revealed invasive adenocarcinoma in the upper lobe of the right lung. The cancer was diagnosed as C2330808 (Adenocarcinoma, Invasive).\n4. **January 2024:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm.\n\n**Timeline of Treatments:**\n\n1. **Surgical resection of lung tissue:** The patient underwent surgical resection of lung tissue in November 2022.\n2. **No second surgical treatment:** The patient refused a second surgical treatment for the recurrence of primary cancer, which presented as ground glass nodules in the left lung.\n\n**Timeline of Outcomes:**\n\n1. **Pathological diagnosis:** The pathological diagnosis of invasive adenocarcinoma was confirmed post-surgery in November 2022.\n2. **Recurrence of primary cancer:** The patient developed recurrence of primary cancer with ground glass nodules in the left lung and new symptoms (fatigue, pale tongue, white fur, and weak pulse) in November 2022.\n3. **Recurrent tumor shrinkage:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm in January 2024.\n\n**Clinical Findings:**\n\nThroughout the patient's treatment, various clinical findings were reported, including:\n\n* Chest pain and fatigue\n* Multiple small lung nodules in both lungs\n* Abnormal blood test results (lymphocytopenia and neutrophilia)\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Laboratory Results:**\n\nThe patient's laboratory results showed:\n\n* Normal blood work (January 2024)\n* Elevated carcinoembryonic antigen level (November 2022)\n\n**Imaging Results:**\n\nThe patient underwent various imaging studies, including CT scans and pathology reports, which revealed:\n\n* Partial solid nodules in the posterior segment of the upper lobe of the right lung (September 2021)\n* Multiple small lung nodules in both lungs\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Prognosis:**\nThe patient's prognosis remains uncertain, as the cancer has recurred and treatment options are limited. Further evaluation and management are necessary to determine the best course of action.\n\n**Conclusion:**\nThis clinical case report highlights the complexities of managing lung cancer, particularly in cases where recurrence occurs. 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Report**\n\n**Patient Demographics:**\nThe patient is a 56-year-old non-smoking male with pulmonary carcinosarcoma.\n\n**Initial Presentation (Step 1):**\nOn January 28, 2023, the patient presented at The Third People\u2019s Hospital of Yunnan Province with a progressively enlarging mass in the right neck. Imaging findings revealed multiple nodular shadows of various sizes within the right cervical region posterior to the sternocleidomastoid muscle and adjacent to the carotid artery sheath, which partially fused.\n\n**Diagnosis (Step 2):**\nCT scans confirmed the presence of a pulmonary malignancy with cervical and mediastinal lymph node metastasis. The largest mass measured approximately 3.8 cm x 2.6 cm with indistinct margins and uneven ring-shaped enhancement.\n\n**Biopsy and Pathological Diagnosis (Step 3):**\nA CT-guided puncture biopsy of the mass in the left inferior lobe of the lung was performed, which led to a pathological diagnosis of lung carcinosarcoma.\n\n**Immunohistochemistry and NGS Testing (Step 4):**\nImmunohistochemistry revealed a Ki-67 index of 80%, while Next-Generation Sequencing (NGS) detected mutations in the TMB gene. These results further supported the presence of pulmonary carcinomas.\n\n**Timeline:**\n\n* January 28, 2023: Patient presents with progressively enlarging neck mass and imaging findings consistent with pulmonary malignancy.\n* January 28, 2023: CT-guided puncture biopsy is performed to confirm diagnosis.\n* (Date not specified): Immunohistochemistry and NGS testing are performed.\n\n**Outcomes:**\nThe patient's condition remains active, with ongoing management of the pulmonary carcinosarcoma. The results of immunohistochemistry and NGS testing have provided valuable information for further treatment planning.\n\nNote: The timeline is incomplete as some dates were not specified in the original data.", + "bertscore": { + "precision": [ + 0.3337828814983368 + ], + "recall": [ + 0.4093906879425049 + ], + "f1": [ + 0.3677407205104828 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.26591718196868896, + -0.01149221882224083, + -0.05490458011627197, + 0.09002448618412018, + 0.12090761959552765, + -0.02566247433423996, + 0.06007498502731323, + 0.25383898615837097, + 0.2421899437904358, + -0.4905059337615967, + -0.13693289458751678, + 0.12649738788604736, + -0.6974141597747803, + 0.05220205709338188, + -0.4585632383823395, + 0.09128075838088989, + 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file diff --git a/src/benchmark/setup_env.sh b/src/benchmark/setup_env.sh index 095f3c2..5360a9e 100755 --- a/src/benchmark/setup_env.sh +++ b/src/benchmark/setup_env.sh @@ -18,5 +18,8 @@ else echo "No requirements.txt found. Skipping dependency installation." fi -echo "Running main..." -python3 main.py \ No newline at end of file +# echo "Running main..." +# python3 batch_run.py + +echo "Generating plots..." +python3 generate_visuals.py \ No newline at end of file diff --git a/webapp/static/graphs/graph_metadata.csv b/webapp/static/graphs/mapping/graph_metadata.csv similarity index 100% rename from webapp/static/graphs/graph_metadata.csv rename to webapp/static/graphs/mapping/graph_metadata.csv diff --git a/webapp/static/graphs/graph_metadata.json b/webapp/static/graphs/mapping/graph_metadata.json similarity index 100% rename from webapp/static/graphs/graph_metadata.json rename to webapp/static/graphs/mapping/graph_metadata.json diff --git a/webapp/static/graphs/graph_metadata_true.json b/webapp/static/graphs/mapping/graph_metadata_true.json similarity index 100% rename from webapp/static/graphs/graph_metadata_true.json rename to webapp/static/graphs/mapping/graph_metadata_true.json From bec50feb499fbbfbc5c55e3515318aec15b33265 Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Sat, 10 May 2025 13:35:15 -0700 Subject: [PATCH 03/11] Run benchmark on test set of 88 cases in --- src/benchmark/batch_run.py | 57 +- src/benchmark/modules/io_utils.py | 97 ++- .../output/plots/bertscore_f1_barplot.png | Bin 16630 -> 30199 bytes .../output/plots/topology_distributions.png | Bin 32789 -> 45771 bytes .../output/plots/trajectory_tsne.png | Bin 19219 -> 43188 bytes src/benchmark/output/results/results0.json | 795 ------------------ .../output/results/results_graph_001.json | 795 ++++++++++++++++++ .../output/results/results_graph_003.json | 795 ++++++++++++++++++ .../output/results/results_graph_004.json | 795 ++++++++++++++++++ .../output/results/results_graph_005.json | 795 ++++++++++++++++++ .../output/results/results_graph_006.json | 795 ++++++++++++++++++ .../output/results/results_graph_007.json | 795 ++++++++++++++++++ .../output/results/results_graph_008.json | 795 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special}/Case_Report__Subacute_cutaneous_lupus_erythematosus_induced_by_the_anti_PD_1_ant_PMC11985835.html (100%) rename webapp/static/pmc_htmls/{ => special}/Successful_Management_of_Acquired_von_Willebrand_Syndrome_Associated_with_Monocl_PMC12027059.html (100%) diff --git a/src/benchmark/batch_run.py b/src/benchmark/batch_run.py index fc18995..1427c51 100644 --- a/src/benchmark/batch_run.py +++ b/src/benchmark/batch_run.py @@ -11,41 +11,21 @@ and trajectory representation. """ -import sys from pathlib import Path -sys.path.append(str(Path(__file__).resolve().parents[1])) # Adds 'src' to sys.path # Local application imports -from benchmark.modules.io_utils import ( +from modules.run_benchmark import run_pipeline +from modules.logging_utils import setup_logger +from modules.io_utils import ( load_graph_from_file, save_results, build_graph_to_text_mapping, - extract_original_text_from_html + extract_case_presentation_from_file, ) -from benchmark.modules.run_benchmark import run_pipeline -from benchmark.modules.logging_utils import setup_logger logger = setup_logger(__name__) -# Replace this with your actual text used as reference -ORIGINAL_TEXT = ( - "Starry starry night, " - "Paint your palette blue and grey, " - "Look out on a summer's day, " - "With eyes that know the darkness in my soul. " - "Shadows on the hills, " - "Sketch the trees and daffodils, " - "Catch the breeze and winter chills, " - "In colors on the snowy linen land. " - "Now I understand, " - "What you tried to say to me, " - "And how you suffered for your sanity, " - "And how you tried to set them free. " - "They would not listen, they did not know how, " - "Perhaps they'll listen now. " -) - # Input directory: All graph files GRAPH_INPUT_DIR = Path(__file__).resolve().parents[2] / "webapp/static/graphs" @@ -54,10 +34,10 @@ RESULTS_OUTPUT_DIR.mkdir(parents=True, exist_ok=True) # Paths -metadata_csv = "webapp/static/graphs/mapping/graph_metadata.csv" -html_root_dir = "webapp/static/pmhc_html" +METADATA_CSV_PATH = Path(__file__).resolve().parents[2] / "webapp/static/graphs/mapping/graph_metadata.csv" +HTML_ROOT_DIR = Path(__file__).resolve().parents[2] / "webapp/static/pmc_htmls" -# graph_to_html = build_graph_to_text_mapping(metadata_csv, html_root_dir) +graph_to_html = build_graph_to_text_mapping(METADATA_CSV_PATH, HTML_ROOT_DIR) if __name__ == "__main__": graph_files = list(GRAPH_INPUT_DIR.glob("*.json")) @@ -65,22 +45,21 @@ if not graph_files: logger.warning("No JSON files found in input directory.") else: - for fpath in graph_files[:5]: # Limit to first 5 files for demonstration + for fpath in graph_files: #[:5]: Limit to first 5 files for demonstration graph_id = fpath.stem - # html_path = graph_to_html.get(graph_id) + html_path = graph_to_html.get(graph_id) + + if not html_path: + logger.warning("No HTML path found for %s", graph_id) + continue - # if not html_path: - # logger.warning(f"No HTML path found for {graph_id}") - # continue - - # reference_case_text = extract_original_text_from_html(html_path) - reference_case_text = ORIGINAL_TEXT + reference_case_text = extract_case_presentation_from_file(str(html_path)) - logger.info(f"Running pipeline on: {fpath.name}") + logger.info("Running pipeline on: %s",fpath.name) graph, ok = load_graph_from_file(fpath) if not ok: - logger.error(f"Skipping {fpath.name} due to load error.") + logger.error("Skipping %s due to load error.", fpath.name) continue cfg = { @@ -91,7 +70,7 @@ } results = run_pipeline(graph, reference_case_text, cfg) - output_path = RESULTS_OUTPUT_DIR / f"{graph_id}.json" + output_path = RESULTS_OUTPUT_DIR / f"results_{graph_id}.json" save_results(results, output_path) - logger.info("Batch benchmarking completed.") \ No newline at end of file + logger.info("Batch benchmarking completed.") diff --git a/src/benchmark/modules/io_utils.py b/src/benchmark/modules/io_utils.py index cf6e7ba..822a876 100644 --- a/src/benchmark/modules/io_utils.py +++ b/src/benchmark/modules/io_utils.py @@ -14,14 +14,34 @@ import json import os from typing import Any +import warnings +import re + +# Third-party imports import networkx as nx from networkx.readwrite import json_graph +from bs4 import BeautifulSoup +from bs4 import MarkupResemblesLocatorWarning # Local application imports from .logging_utils import setup_logger logger = setup_logger(__name__) + +warnings.filterwarnings("ignore", category=MarkupResemblesLocatorWarning) + UTF_8 = "utf-8" +# Extended to match parts like: +# - 2.1. Case Summary +# - 3.2.1 Case Report +# - Case presentation and technical note +# - Case Description +CASE_SECTION_PATTERNS = [ + r"^\d+(\.\d+)*\.?\s*case (presentation|summary|report|description|history)\b", + r"^case presentation and technical note\b", + r"^case\b", +] + def load_graph_from_file(path: str) -> tuple[nx.DiGraph, bool]: """ @@ -34,13 +54,14 @@ def load_graph_from_file(path: str) -> tuple[nx.DiGraph, bool]: try: with open(path, encoding=UTF_8) as f: data = json.load(f) - converted_data = convert_to_node_link_format(data) + converted_data = convert_to_node_link_format(data) normalized_data = normalize_graph_for_networkx(converted_data) return json_graph.node_link_graph(normalized_data, directed=True), True except Exception as e: logger.error("Error loading graph: %s", e) return nx.DiGraph(), False + def save_results(results: dict, path: str) -> None: """ Save the pipeline results to a JSON file. @@ -52,6 +73,7 @@ def save_results(results: dict, path: str) -> None: with open(path, "w", encoding=UTF_8) as f: json.dump(results, f, indent=2) + def data_display(results: dict[str, Any]) -> None: """ Pretty-print the pipeline results as structured tables for easy terminal viewing. @@ -107,8 +129,10 @@ def data_display(results: dict[str, Any]) -> None: # 6) Any other top-level keys other_keys = { - k: v for k, v in results.items() - if k not in {"status", "bertscore", "topology", "regex", "reconstructed_narrative"} + k: v + for k, v in results.items() + if k + not in {"status", "bertscore", "topology", "regex", "reconstructed_narrative"} } if other_keys: print("Additional Data:") @@ -116,6 +140,7 @@ def data_display(results: dict[str, Any]) -> None: print(f"{key}: {val}") print() + def convert_to_node_link_format(original_json: dict) -> dict: """ Convert a JSON object to the node-link format used by networkx. @@ -124,12 +149,7 @@ def convert_to_node_link_format(original_json: dict) -> dict: Returns: dict: The converted JSON object in node-link format. """ - converted = { - "directed": True, - "graph": {}, - "nodes": [], - "links": [] - } + converted = {"directed": True, "graph": {}, "nodes": [], "links": []} for node in original_json.get("nodes", []): new_node = dict(node) # copy @@ -156,7 +176,7 @@ def normalize_graph_for_networkx(raw_graph: dict) -> dict: raw_graph (dict): The raw graph data. Returns: dict: The normalized graph data. - """ + """ for node in raw_graph["nodes"]: # Promote content and timestamp from customData if "customData" in node: @@ -176,6 +196,7 @@ def normalize_graph_for_networkx(raw_graph: dict) -> dict: return raw_graph + def save_embedding_vector(vec: list[float], out_path: str, metadata: dict = None): """ Save an embedding vector to a JSON file, appending it to the file if it already exists. @@ -191,7 +212,10 @@ def save_embedding_vector(vec: list[float], out_path: str, metadata: dict = None json.dump(row, f) f.write("\n") -def build_graph_to_text_mapping(metadata_csv_path: str, html_root_dir: str) -> dict[str, str]: + +def build_graph_to_text_mapping( + metadata_csv_path: str, html_root_dir: str +) -> dict[str, str]: """ Build a mapping from graph ID (e.g., 'graph_006') to full HTML file path. @@ -204,29 +228,50 @@ def build_graph_to_text_mapping(metadata_csv_path: str, html_root_dir: str) -> d """ graph_to_html = {} - with open(metadata_csv_path, newline='', encoding='utf-8') as csvfile: + with open(metadata_csv_path, newline="", encoding="utf-8") as csvfile: reader = csv.reader(csvfile) for row in reader: graph_id = row[0].strip() - html_rel_path = row[2].strip().replace("./pmc_htmls", html_root_dir) + html_rel_path = row[2].strip().replace("./pmc_htmls", str(html_root_dir)) graph_to_html[graph_id] = html_rel_path return graph_to_html -def extract_original_text_from_html(html_path: str) -> str: - """ - Placeholder function to extract original case report text from HTML. +def extract_case_presentation(html: str) -> str: + """ + Extract the case presentation section from an HTML string. Args: - html_path (str): Path to the HTML file. - + html (str): The HTML content as a string. Returns: - str: Raw text extracted (currently placeholder). + str: The extracted case presentation text. """ - try: - with open(html_path, encoding='utf-8') as f: - html = f.read() - # TODO: replace with BeautifulSoup parsing - return f"[PLACEHOLDER] Text extracted from: {Path(html_path).name}" - except Exception as e: - return f"[ERROR] Failed to extract from {html_path}: {e}" \ No newline at end of file + soup = BeautifulSoup(html, "html.parser") + sections = soup.find_all("section") + + for sec in sections: + # Find section title tag: prefers class='pmc_sec_title', otherwise any h2/h3 + title_tag = sec.find(["h2", "h3"], class_="pmc_sec_title") or sec.find( + ["h2", "h3"] + ) + if not title_tag: + continue + + title = title_tag.get_text(strip=True).lower() + for pattern in CASE_SECTION_PATTERNS: + if re.search(pattern, title): + return sec.get_text(separator="\n", strip=True) + + return "" + + +def extract_case_presentation_from_file(filepath: str) -> str: + """ + Extract the case presentation section from an HTML file. + Args: + filepath (str): Path to the HTML file. + Returns: + str: The extracted case presentation text.""" + with open(filepath, "r", encoding="utf-8") as file: + html = file.read() + return extract_case_presentation(html) diff --git a/src/benchmark/output/plots/bertscore_f1_barplot.png b/src/benchmark/output/plots/bertscore_f1_barplot.png index e3d768e081339e2faddc7f7bed715fb4515c10c1..c194c133afac9576af13bb0dc420338ef915d387 100644 GIT binary patch literal 30199 zcmeFZbySsa*DeYuh=eqVbV+x&(v65BAl-;`hoI8k(x9aL=#cJQw1jkb$D(Vo?}hL8 zz27-wfBTH{#~I`7G4>zESgiG|`?;SvuX)XDUN^z7RAe#Ho}nQiAYjVNNxeouK>Cb; zfVhZ?0$$-Ao?Qk12sue>I;q>5Ik_4-m?9_}I@x`+b^2&&MCoGc;Am-U!_CIY!N$!( zY2oB#=P1O^ZvCI{V6$~FXE&q!6#}mE*iKH%5di_q5dH`8r+A(v0)n%#ywuA#ZmD}| zj~m{OUf;bt7Wu7{`7)V6Ifg4IOrLo4yI+h}tO-LfS1z{v1F9S;ubfw01o{1ODEOAR z1CG~s9wiH|X?IN<>5g@C`*vq@8Rt9Bb!m-*+C$0b73sWdP>~^S2~;XSY-*m>!F^Qt z|0IG6rP01)gIA>>QAiBn1ymfaYy>p;kNhwgKi|KdO7j1Mw@~*9u7q(bHF}(u3qORpN+ z;~uXMgr>|F6xT69>;2J*l2dHzdU!sJL00<`hUy+gi+Y|V=4E(Kr@BmAuK&!6;JQ5C 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z-*VUl0|~8B%L?!v94C;yUt!RAA%77Fpq5RL_SC|)Y<=tbu1N(Hw2JPV_iaMFXz-8N zhhodV|IR_7nSAW+fi<6f8yv61M0{fLw8VjFd;K|3y?*a$GY5T{{uSkV0|gpp!^69N{ESP-&KgMFz?T~ zqmrfNJh<;L+J*|2a0%gP&a>2BECX1g+BRESCZ=wRNtGlK4!-Q%ONV;=mRw%2b} z*p(+H&t|){thL=d=~XK+D;IPZRnf%N^v==(W&i)odzf;=kBROM;i)bpqxN|Ok(N}D K$h!OV<^KgHcu*Vw diff --git a/src/benchmark/output/results/results0.json b/src/benchmark/output/results/results0.json deleted file mode 100644 index 37ec246..0000000 --- a/src/benchmark/output/results/results0.json +++ /dev/null @@ -1,795 +0,0 @@ -{ - "status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 37-year-old male with bilateral painless testicular masses. His age and gender are noted in the initial diagnosis (node A).\n\n**Initial Diagnosis (2015-12-01T00:00:00Z):**\nThe patient presented with bilateral macro-orchitis and multifocal hyperechoic lesions on ultrasound, followed by intense contrast enhancement on MRI. The initial presentation was characterized as \"bilateral testicular masses.\" The patient's laboratory results showed normal levels of AFP, b-hCG, and LDH.\n\n**Surgical Intervention (2015-12-01T00:00:00Z):**\nThe patient underwent testis-sparing surgery, which revealed a benign large-cell calcifying Sertoli cell tumor. The histological diagnosis confirmed the presence of a benign tumor with no atypia.\n\n**Metastatic Disease (2021-06-01T00:00:00Z):**\nApproximately 6 years after the initial diagnosis, the patient's condition worsened, and lymph node metastases were detected. A bilateral radical orchiectomy and lymphadenectomy were performed to manage the disease. The histological examination revealed malignant LCCSCT with vascular permeation and spermatic cord invasion.\n\n**Progression to Terminal Stage (2021-11-01T00:00:00Z):**\nDespite chemotherapy, the patient's disease progressed further, with the development of pleural metastases, pulmonary nodules, and spine lesions. The patient received multiple rounds of chemotherapy, including vinblastine, cisplatin, ifosfamide, and paclitaxel.\n\n**Clinical Trial (2022-12-01T00:00:00Z):**\nIn an attempt to manage the disease, a clinical trial was initiated with axitinib and pazopanib. However, this treatment approach proved ineffective.\n\n**Terminal Stage (2023-07-01T00:00:00Z):**\nThe patient's condition continued to deteriorate, and he progressed to a terminal stage. The patient received palliative care, and unfortunately, passed away.\n\nIn summary, the patient presented with bilateral testicular masses in 2015 and underwent successful surgical intervention. However, the disease eventually progressed to metastatic disease, which was managed with chemotherapy and clinical trials. Despite these efforts, the patient's condition continued to worsen, ultimately leading to a terminal stage and death.", - "bertscore": { - "precision": [ - 0.31829699873924255 - ], - "recall": [ - 0.5213518738746643 - ], - "f1": [ - 0.39527177810668945 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.20442374050617218, - 0.08089178055524826, - -0.024914061650633812, - -0.03979193791747093, - 0.0259078536182642, - 0.2874663174152374, - 0.0590699277818203, - 0.1804632693529129, - 0.678746223449707, - -0.3412137031555176, - 0.09028627723455429, - -0.126709446310997, - -0.49773454666137695, - -0.3380317687988281, - -0.11197445541620255, - 0.31535783410072327, - -0.4333740174770355, - 0.27163252234458923, - -0.03901287913322449, - -0.3344475328922272, - 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He has been a tobacco chewer for over 20 years.\n\n**Initial Presentation:**\nThe patient presented to the clinic with right-sided chest pain, dry cough, on-off fever, and hematuria for 2 months. Physical examination revealed decreased air entry on the right side of the lung.\n\n**Imaging and Diagnosis (Step 1-3):**\n\n* Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within.\n* Bronchoscopy with bronchoscopic-guided biopsy and BAL was performed, which showed negative results for malignant cells. Biopsy results were suggestive of squamous cell carcinoma.\n\n**Symptoms and Imaging (Step 4-5):**\n\n* The patient reported decreased and blurring of vision.\n* An 18F-FDG PET/CT scan revealed a FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm with spiculated margins in the upper lobe of the right lung, along with multiple sub-centimetric to centimetric-sized bilateral lung nodules and metastases to mediastinal, abdominopelvic lymph nodes.\n\n**Progression and Diagnosis (Step 6-7):**\n\n* The patient presented with severe headaches and blurring of vision for 15 days.\n* Biopsy results confirmed metastatic involvement.\n\n**Treatment Plan:**\nUnfortunately, the provided data does not include a treatment plan or outcomes. However, based on the diagnosis of squamous cell carcinoma and metastases, further treatment options would likely involve chemotherapy, radiation therapy, or a combination of both, depending on the patient's overall health and specific tumor characteristics.\n\n**Outcomes:**\nThe patient's current status is unknown, as the provided data only includes the timeline of diagnoses and treatments. Further follow-up and monitoring are necessary to assess the patient's response to treatment and any potential complications or side effects.\n\nIn conclusion, this patient presented with a complex clinical scenario involving a heterogeneous lesion in the mediastinal region, squamous cell carcinoma, and metastases. The patient's symptoms and imaging results suggest an aggressive disease course, and further treatment options would be necessary to manage the patient's condition effectively.", + "bertscore": { + "precision": [ + 0.7080437541007996 + ], + "recall": [ + 0.7307168245315552 + ], + "f1": [ + 0.7192016243934631 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.22544555366039276, + -0.021888595074415207, + -0.0058143287897109985, + 0.03279201313853264, + 0.012158679775893688, + 0.124949149787426, + 0.055165503174066544, + 0.12983736395835876, + 0.3739190995693207, + -0.2663968503475189, + -0.19686637818813324, + 0.07701147347688675, + -0.5400644540786743, + -0.07584770768880844, + -0.26406726241111755, + -0.02046271786093712, + 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Demographics**\n\nThe patient is an adult male with a history of Small Cell Lung Cancer (SCLC). Unfortunately, the exact age and other demographic details are not provided in the data.\n\n**Timeline of Diagnoses**\n\nThe patient's diagnosis timeline begins with the onset of symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. This marked the progression from symptom onset to diagnosis.\n\n**Timeline of Treatments**\n\nThe patient's treatment timeline began with endovascular intervention to address IVC stenosis due to compression caused by the tumor. The procedure involved thrombectomy and stent placement. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered.\n\n**Timeline of Outcomes**\n\nThe patient's outcome timeline began with significant alleviation of IVCS symptoms (trunk and lower limb edema) following the intervention. However, unfortunately, the patient died 8 days later from his primary disease (SCLC).\n\n**Narrative Summary**\n\nA male patient with Small Cell Lung Cancer presented with symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. Endovascular intervention was performed to address IVC stenosis caused by compression from the tumor. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered. However, despite these interventions, the patient's primary disease ultimately led to his death 8 days later.\n\n**Key Takeaways**\n\n* The patient had a poor performance status and significant tumor burden at diagnosis.\n* Endovascular intervention was effective in alleviating IVCS symptoms but did not address the underlying cause of death.\n* Low-molecular-weight heparin was administered post-intervention, but its effectiveness is unclear given the patient's rapid decline.\n\n**Limitations**\n\nThe narrative summary is limited by the lack of detailed information on patient demographics, treatment outcomes, and long-term follow-up. Further investigation would be necessary to fully understand the patient's clinical course and the effectiveness of interventions.", + "bertscore": { + "precision": [ + 0.5732179880142212 + ], + "recall": [ + 0.5156488418579102 + ], + "f1": [ + 0.5429115891456604 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.2569149434566498, + 0.23160001635551453, + -0.23048092424869537, + 0.06365886330604553, + 0.06271032989025116, + -0.032205305993556976, + -0.0353657603263855, + 0.14690855145454407, + 0.3527328073978424, + -0.24249935150146484, + -0.23033425211906433, + 0.13146138191223145, + -0.44394129514694214, + -0.1020270437002182, + -0.1855921894311905, + 0.17859384417533875, + 0.08802724629640579, + 0.2158854901790619, + -0.10283444821834564, + -0.29911351203918457, + 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over a 10-day period. She has no history of smoking or malignancy.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (Day 0-9):** The patient initially presents with progressive chest tightness, dyspnea, cough, and back pain. Chest CT imaging reveals a large left-sided pleural effusion.\n2. **Step 2 (Day 10):** Thoracentesis is performed, and the drained pleural fluid is sent to the Department of Pathology for further evaluation.\n3. **Step 3 (Day 11-12):** Post-thoracic drainage chest CT reveals a 6.7 cm x 2.8 cm heterogeneous mass in the left inferior lobe with irregular contrast enhancement, suggestive of a left lung tumor.\n4. **Step 4 (Day 13-14):** Pulmonary window analysis shows multiple nodular high-density foci scattered across both lungs, concerning for bilateral pulmonary metastases. Mediastinal window assessment reveals bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis.\n5. **Step 5 (Day 15-16):** Abdominal CT scan detects multiple low-density hepatic nodules of varying sizes, with the largest lesion located in the right hepatic lobe. Enhanced brain CT identifies an irregular heterogeneously enhancing mass within the right frontal lobe, consistent with brain metastasis.\n6. **Step 6 (Day 17-18):** Cell block analysis of the pleural effusion demonstrates poorly cohesive round-to-oval cells with a dispersed distribution exhibiting eccentrically located nuclei with dense chromatin.\n\n**Treatments:**\n\n1. Thoracentesis and post-thoracic drainage chest CT\n2. Abdominal CT scan and enhanced brain CT\n\n**Outcomes:**\nThe patient's diagnosis is confirmed as lung cancer with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The cell block analysis of the pleural effusion reveals poorly cohesive round-to-oval cells consistent with adenocarcinoma.\n\n**Conclusion:**\nThis 81-year-old female patient presents with progressive chest tightness and dyspnea due to a large left-sided pleural effusion, which is later confirmed as a left lung tumor with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The diagnosis is made after thoracentesis, post-thoracic drainage chest CT, abdominal CT scan, enhanced brain CT, and cell block analysis of the pleural effusion.", + "bertscore": { + "precision": [ + 0.7519660592079163 + ], + "recall": [ + 0.7654501795768738 + ], + "f1": [ + 0.7586482167243958 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.2583933174610138, + -0.1034068688750267, + 0.02750878781080246, + 0.12225138396024704, + 0.07123710960149765, + 0.08420076966285706, + -0.025338614359498024, + 0.20714537799358368, + 0.42998072504997253, + -0.2773303687572479, + -0.23241369426250458, + 0.0849342942237854, + -0.532634437084198, + 0.050035249441862106, + -0.25669047236442566, + 0.11723083257675171, + 0.17126429080963135, + 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He presented with worsening cough for 3 months, which led to further investigation via CT imaging.\n\n**Timeline of Diagnoses:**\n\n1. **April 2023:** Enhanced CT revealed a 22 mm \u00d7 12 mm \u00d7 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal. PET-CT scan confirmed the CT findings.\n2. **Biopsy (Upper Right Lobe):** Biopsy of the lung lesion showed positive immunohistochemistry (IHC) for TTF-1, NpA, CK7, CD5/6, and Ki67 (60%); and negative for p40, p63, and CD56. Diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0).\n3. **May 2023:** Targeted NGS analysis identified an EGFRG719X mutation with a mutant allele frequency (MAF) of 3.8%.\n\n**Timeline of Treatments:**\n\n1. **May 2023:** The patient received two cycles of PC chemotherapy (pemetrexed 0.9g d1 and carboplatin 600mg d1) and dacomitinib (30mg).\n2. **Initial Treatment Evaluation:** Initial tumor was considered unresectable due to metastasis in the right hilum and mediastinum.\n\n**Timeline of Outcomes:**\n\n1. **May 2023:** Chest CT showed obvious shrinkage in the lesions in the right upper lung lobe and the lymph nodes of the mediastinum, contributing to partial response (PR).\n2. **Current Status:** The patient is currently receiving treatment for stage IIIA lung adenocarcinoma with EGFRG719X mutation.\n\n**Clinical Summary:**\nThe patient presented with worsening cough and a significant smoking history, leading to further investigation via CT imaging. Biopsy of the lung lesion confirmed the diagnosis of stage IIIA lung adenocarcinoma (cT1cN2M0) with an EGFRG719X mutation. The patient received two cycles of PC chemotherapy and dacomitinib, resulting in a partial response (PR). Further treatment is ongoing to manage this complex case.\n\n**Key Findings:**\n\n* Stage IIIA lung adenocarcinoma with EGFRG719X mutation\n* Partial response (PR) after initial treatment evaluation\n* Significant smoking history of 30 years\n* Worsening cough for 3 months\n\n**Recommendations:**\nFurther evaluation and management are necessary to optimize the patient's care. This may include additional imaging, laboratory tests, or other treatments to manage this complex case.\n\nNote: The above narrative is based on the provided data and may not be a comprehensive clinical case report.", + "bertscore": { + "precision": [ + 0.7573888301849365 + ], + "recall": [ + 0.7618044018745422 + ], + "f1": [ + 0.759590208530426 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.26444298028945923, + 0.15941788256168365, + -0.1746055781841278, + 0.1967768669128418, + 0.13093367218971252, + 0.108800008893013, + 0.047415077686309814, + 0.3190433979034424, + 0.4498003125190735, + -0.4936943054199219, + -0.028453731909394264, + 0.19775180518627167, + -0.6453556418418884, + -0.2056516706943512, + -0.17296206951141357, + 0.10433705896139145, + 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"**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 54-year-old man with a history of colitis. He is an ex-smoker with 60 pack-years of smoking experience.\n\n**Timeline of Diagnoses:**\n\n1. **June 2014:** The patient presents to the clinic with right hip pain for two months.\n2. **June 2014 (CT scan):** A CT scan reveals a ~25-mm nodule in the right upper lobe of the lung and a 50-mm mass in the right pelvic region.\n3. **June 2014 (18F-fluorodeoxyglucose positron emission tomography-CT):** The patient undergoes further imaging, which shows intense accumulation in the right S2 nodule of the lung.\n4. **June 2014 (18F-fluorodeoxyglucose positron emission tomography-CT):** The patient receives additional imaging, which reveals standardized uptake value (SUV) max: 15.2 in the right adrenal gland and a pelvic mass from the right sciatic/pubic bone to the right internal obturator muscle (SUV max: 10.81).\n5. **Biopsy:** A transbronchial biopsy (TBB) specimen from the nodule in the right lung is performed, which identifies carcinoma with neuroendocrine features.\n6. **June 2014 (staging and mutation status):** The patient's cancer is staged, and his mutation status is determined.\n\n**Timeline of Treatments:**\n\n1. **June 2014:** The patient undergoes a CT scan to evaluate the right hip pain.\n2. **June 2014:** The patient receives further imaging using 18F-fluorodeoxyglucose positron emission tomography-CT.\n3. **June 2014:** The patient undergoes additional imaging using 18F-fluorodeoxyglucose positron emission tomography-CT.\n4. **June 2014:** The patient receives a transbronchial biopsy (TBB) of the nodule in the right lung.\n\n**Outcomes:**\n\n1. **Diagnosis:** The patient is diagnosed with carcinoma with neuroendocrine features, which is confirmed by histopathological examination of the TBB specimen.\n2. **Staging and Mutation Status:** The patient's cancer is staged as stage IV lung cancer (T1bN0M1b), and his mutation status is negative for epidermal growth factor receptor and anaplastic lymphoma kinase gene, with a programmed death-ligand 1 (PD-L1) tumor proportion score of less than 1%.\n3. **Treatment:** The patient's treatment plan is not specified in the provided data.\n\n**Conclusion:**\nThe patient presents with right hip pain and is diagnosed with carcinoma with neuroendocrine features after undergoing imaging studies and a transbronchial biopsy (TBB). His cancer is staged as stage IV lung cancer, and his mutation status is negative. The patient's treatment plan is not specified in the provided data.", + "bertscore": { + "precision": [ + 0.704978883266449 + ], + "recall": [ + 0.6731678247451782 + ], + "f1": [ + 0.6887062788009644 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.22079414129257202, + 0.0068036518059670925, + -0.10039127618074417, + 0.16631634533405304, + 0.10629185289144516, + 0.08402007818222046, + 0.24246330559253693, + 0.2994869649410248, + 0.36667490005493164, + -0.5220186710357666, + -0.11857226490974426, + 0.10266987234354019, + -0.7685451507568359, + 0.058542799204587936, + -0.482259601354599, + 0.13929423689842224, + 0.1318996697664261, + 0.4940612316131592, + 0.04252505302429199, + -0.15624141693115234, + -0.44017040729522705, + 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examination on April 20, 2020. He has a smoking history of over 7 years, with an average of 20-30 cigarettes per day, and had abstained from smoking for nearly 30 years.\n\n**Timeline of Diagnoses:**\n\n1. **April 20, 2020:** The patient presented asymptomatic, with no cough, sputum, hemoptysis, chest pain, or dyspnea. A chest CT revealed a 4.0 cm x 3.4 cm mass in the inferior lobe of the right lung, with swollen and fused lymph nodes in the hilum and mediastinum.\n2. **May 2, 2020:** The diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma was confirmed.\n3. **May 20, 2020:** Alectinib therapy was initiated at 600 mg twice daily following a multidisciplinary team discussion for potentially resectable NSCLC with ALK rearrangement.\n\n**Timeline of Treatments:**\n\n1. **May 20, 2020:** Initiation of alectinib therapy.\n2. **Unknown date (after 4 months):** A chest CT scan was performed after 4 months of alectinib therapy, showing shrinkage of the primary tumor and a 1.1 cm x 0.6 cm nodule in the inferior lobe of the right lung.\n\n**Outcomes:**\n\nThe patient's treatment with alectinib has resulted in partial response, as evidenced by the shrinkage of the primary tumor and the development of a new nodule. The patient remains on treatment, and further follow-up is required to assess the efficacy of the therapy and monitor for any signs of disease progression.\n\n**Additional Notes:**\n\nThe patient's NGS results revealed ELMOD3-ALK (E8: A20) fusion at 41.23% abundance and EML4-ALK (E13: A20) double-ALK fusion at 68.21% abundance, confirming the presence of ALK rearrangement in the tumor tissue. The patient's CEA levels are not reported.\n\nIn conclusion, this patient has been diagnosed with stage IIIA lung adenocarcinoma and is currently undergoing treatment with alectinib. While the partial response to therapy is encouraging, further follow-up is necessary to assess the long-term efficacy of the treatment and monitor for any signs of disease progression.", + "bertscore": { + "precision": [ + 0.6810472011566162 + ], + "recall": [ + 0.7104792594909668 + ], + "f1": [ + 0.6954519748687744 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.34632283449172974, + 0.13255642354488373, + -0.16146747767925262, + 0.06857442855834961, + -0.053984127938747406, + -0.0689462199807167, + 0.14064376056194305, + 0.2152150720357895, + 0.37596216797828674, + -0.42233654856681824, + -0.13927848637104034, + 0.08689076453447342, + -0.6545354127883911, + 0.01794014871120453, + -0.3974427878856659, + 0.21673455834388733, + 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Demographics:**\nThe patient is a 37-year-old female. Her medical history includes untreated congenital heart disease (patent ductus arteriosus) for 20 years and hypertension for half a year, with irregular use of valsartan.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient reported intermittent cough and slight chest discomfort for 3 months and painless cervical mass for 1 month.\n2. **Step 2:** A left cervical lymph node puncture was performed one week ago, which showed granulomatous inflammation with caseous necrosis and Langhans' giant cells observed.\n3. **Step 3:** The patient's past medical history of untreated congenital heart disease and hypertension became relevant.\n4. **Step 4:** Physical examination revealed a well-defined, poorly mobile, non-tender mass on the left clavicle without surface ulceration or redness.\n5. **Step 5:** Laboratory tests showed normal blood CEA, squamous cell carcinoma antigen, cytokeratin 19 fragment, and NSE levels, with no evidence of cancer in sputum AFB and GeneXpert MTB/RIF.\n6. **Step 6:** EB virus blood test results indicated increased antibody titers for capsid antigen IgG antibody, early antigen IgM antibody, and core antigen IgG antibody.\n7. **Step 7:** Ultrasound-guided left supraclavicular lymph node puncture was performed, showing focal distribution of epithelioid cells and multinucleated giant cells suggestive of granulomatous inflammation.\n8. **Step 8:** Histopathology confirmed the presence of granuloma.\n\n**Timeline of Treatments:**\n\n1. **Step 2:** Left cervical lymph node puncture was performed due to intermittent cough, slight chest discomfort, and painless cervical mass.\n2. **Step 7:** Ultrasound-guided left supraclavicular lymph node puncture was performed as part of the diagnostic workup.\n\n**Outcomes:**\n\n1. The patient's diagnosis of granuloma was confirmed through histopathology.\n2. No evidence of cancer was found in sputum AFB and GeneXpert MTB/RIF, ruling out tuberculosis or other infections.\n3. EB virus blood test results indicated increased antibody titers, suggesting a possible infection or autoimmune response.\n\n**Conclusion:**\nThe patient's diagnosis of granuloma is likely related to her underlying medical history of untreated congenital heart disease and hypertension. Further investigation into the cause of granulomatous inflammation is necessary to determine the best course of treatment.", + "bertscore": { + "precision": [ + 0.6920709609985352 + ], + "recall": [ + 0.6939922571182251 + ], + "f1": [ + 0.6930302977561951 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 9, + "edge_count": 7, + "avg_in_degree": 0.7777777777777778, + "density": 0.09722222222222222 + }, + "trajectory_embedding": [ + 0.32178184390068054, + 0.0587812140583992, + -0.04031328856945038, + 0.1223248541355133, + 0.1420980840921402, + 0.1322871595621109, + 0.09575825184583664, + 0.21854537725448608, + 0.3668004274368286, + -0.415396511554718, + -0.23321908712387085, + 0.043559107929468155, + -0.6951784491539001, + -0.018354633823037148, + -0.3261258900165558, + 0.10526271909475327, + 0.0806720182299614, + 0.30150094628334045, + 0.05325983837246895, + 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exertional breathlessness, and chronic fatigue in March 2025.\n\n**Timeline of Diagnoses:**\n\n1. **March 2025:** The patient's symptoms began, including bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue.\n2. **April 2025 (Step 2):** Chest radiograph showed a left lung opacification, indicating the presence of an abnormality in the lung tissue.\n3. **May 2025 (Step 3):** CT and PET-CT scan confirmed a 53 mm avid left upper lobe mass with associated hilar and mediastinal lymphadenopathy (T3N2M0), which is indicative of cancerous cells.\n4. **June 2025 (Step 4):** Endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis, a type of non-small cell lung cancer.\n5. **July 2025 (Step 5):** Molecular testing showed 60% PD-L1 positivity, indicating the presence of a protein that can help the immune system recognize and attack cancer cells.\n6. **August 2025 (Step 6):** The patient consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy.\n7. **September 2025 (Step 7):** Initial scan post radiotherapy showed a limited response to treatment, indicating that the cancer had not fully responded to the treatment.\n8. **October 2025 (Step 8):** Subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base.\n9. **November 2025 (Step 9):** Post radiotherapy imaging showed complete response to treatment, with two small bullae seen in the post aspect of the lower lobe.\n10. **December 2025 (Step 10):** Follow-up scan showed upward curving of the lower segmental bronchi and pulmonary vessels.\n11. **January 2026 (Step 11):** Imaging showed two small bullae initially seen in the post aspect of the lower lobe relocated to the upper zone anteriorly, with lung torsion with 180-degree rotation diagnosed.\n12. **February 2026 (Step 12):** Follow-up imaging 12 months after previous imaging demonstrated migration of the emphysematous bullae anteriorly and superiorly towards the apex of the lung.\n13. **March 2026 (Step 13):** CT imaging showed left lung base collapse and tapering/curved orientation of the lower lobe segmental bronchi and pulmonary vessels of the right lung, indicating twisting of the lobe.\n\n**Treatments:**\n\n* Radiotherapy with concurrent chemotherapy\n* Surgery to remove the tumor\n\n**Outcomes:**\n\n* The patient's cancer was diagnosed and treated, but unfortunately, the treatment did not completely eliminate the cancer.\n* The patient developed lung torsion with 180-degree rotation, which is a complication of radiotherapy.\n* Despite this complication, the patient remains asymptomatic and managed conservatively.\n\nThis case highlights the complexities of treating non-small cell lung cancer, particularly in older adults. While the patient's cancer was diagnosed and treated, the treatment did not completely eliminate the cancer, and the patient developed a significant complication. Further research is needed to improve treatment outcomes for patients with this type of cancer.", + "bertscore": { + "precision": [ + 0.6804789304733276 + ], + "recall": [ + 0.7055283188819885 + ], + "f1": [ + 0.6927772164344788 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 13, + "edge_count": 12, + "avg_in_degree": 0.9230769230769231, + "density": 0.07692307692307693 + }, + "trajectory_embedding": [ + 0.30061694979667664, + 0.13679052889347076, + -0.03965549170970917, + 0.1295793503522873, + 0.008763031102716923, + 0.07028906792402267, + 0.014980574138462543, + 0.28833457827568054, + 0.4558904469013214, + -0.27837973833084106, + -0.10914869606494904, + 0.01314648985862732, + -0.4926709830760956, + -0.17142295837402344, + -0.19755218923091888, + 0.20304308831691742, + 0.08181775361299515, + 0.25292664766311646, + -0.10463114827871323, + -0.2849089205265045, + 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with squamous cell carcinoma (SCC) of the esophagus. She underwent various treatments, including surgery, chemotherapy, radiation therapy, and immunotherapy, before being diagnosed with another type of cancer.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient was diagnosed with SCC of the esophagus (cT3N2M0, stage IIIB) at an unknown date.\n2. **Step 2:** Six months later, she underwent esophagectomy with gastric pull-up reconstruction.\n3. **Step 3:** Two years after her surgery, she received neo-adjuvant concurrent chemoradiation therapy (ypT2N1 stage IIB disease).\n4. **Step 4:** Six weeks after completing her chemotherapy and radiation therapy, she received a total of 50 Gray of radiation over 6 weeks, along with Carboplatin and Paclitaxel for 6 weeks.\n5. **Step 5:** Six years later, a CT scan revealed stage IA TTF-1 positive adenocarcinoma in the left upper lobe.\n6. **Step 6:** Two years after her diagnosis of adenocarcinoma, she underwent treatment with stereotactic radiotherapy.\n7. **Step 7:** Two years after her radiotherapy, squamous cell carcinoma of the right upper lobe was discovered.\n8. **Step 8:** The patient initiated Pembrolizumab with curative intent due to high PD-L1 expression.\n9. **Step 9:** A follow-up CT scan showed no biological response and a tumor diameter of 54 mm.\n10. **Step 10:** Salvage lobectomy including complete mediastinal lymph node dissection was performed.\n11. **Step 11:** Pre-operative positron emission tomography CT scan demonstrated the exact localization of the tumor in the right upper lobe.\n\n**Timeline of Treatments:**\n\n1. **Esophagectomy with gastric pull-up reconstruction (Step 2):**\n - Date: Unknown\n - Treatment: Surgery\n\n2. **Neo-adjuvant concurrent chemoradiation therapy (Step 3):**\n - Date: Two years after esophagectomy\n - Treatment: Chemotherapy and radiation therapy\n\n3. **Radiation therapy with Carboplatin and Paclitaxel (Step 4):**\n - Date: Six weeks after completing chemotherapy and radiation therapy\n - Treatment: Radiation therapy, chemotherapy, and medication\n\n4. **Stereotactic radiotherapy (Step 6):**\n - Date: Two years after diagnosis of adenocarcinoma\n - Treatment: Radiotherapy\n\n5. **Pembrolizumab (Step 8):**\n - Date: After diagnosis of squamous cell carcinoma of the right upper lobe\n - Treatment: Immunotherapy\n\n**Outcomes:**\n\n1. **Esophagectomy with gastric pull-up reconstruction:** The patient underwent successful surgery.\n2. **Neo-adjuvant concurrent chemoradiation therapy:** The patient received treatment for her cancer, but no further information is available on the effectiveness of this treatment.\n3. **Radiation therapy with Carboplatin and Paclitaxel:** No biological response was observed after completing this treatment.\n4. **Stereotactic radiotherapy:** No biological response was observed after completing this treatment.\n5. **Pembrolizumab:** The patient did not respond to Pembrolizumab, as indicated by a follow-up CT scan showing no biological response and a tumor diameter of 54 mm.\n\n**Conclusion:**\nThe patient underwent various treatments for her esophageal cancer before being diagnosed with another type of cancer. Despite receiving multiple treatments, she did not achieve a complete response to any treatment. Salvage lobectomy including complete mediastinal lymph node dissection was performed, but the outcome is unknown.", + "bertscore": { + "precision": [ + 0.6025055050849915 + ], + "recall": [ + 0.7357915043830872 + ], + "f1": [ + 0.6625112891197205 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 11, + "edge_count": 10, + "avg_in_degree": 0.9090909090909091, + "density": 0.09090909090909091 + }, + "trajectory_embedding": [ + 0.21590237319469452, + 0.1823497712612152, + -0.11964480578899384, + 0.07587544620037079, + 0.18606476485729218, + 0.21188677847385406, + -0.11044882982969284, + 0.41281792521476746, + 0.48045822978019714, + -0.37073710560798645, + -0.20201373100280762, + -0.17259280383586884, + -0.5821730494499207, + -0.11790329962968826, + -0.2575705647468567, + 0.43589040637016296, + -0.25557705760002136, + 0.2976360023021698, + -0.1255851835012436, + 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The patient's demographic information includes:\n\n* Name: [insert name]\n* Date of Birth: [insert date of birth]\n* Sex: [insert sex]\n\n**Diagnosis Timeline**\n\nThe patient's diagnosis timeline began on [insert date], when they presented to the clinic with [insert initial symptoms or concerns]. Following a series of diagnostic tests, including imaging studies and biopsies, the patient was diagnosed with [insert primary diagnosis].\n\nOver the next several months, the patient underwent various treatments, including:\n\n* First-line systemic therapy: The patient received treatment with [insert medication] from [insert start date] to [insert end date].\n* Maintenance therapy: Following completion of first-line therapy, the patient transitioned to maintenance therapy with pemetrexed from [insert start date] to [insert end date].\n* Second-line treatment: In response to disease progression, the patient received treatment with cabozantinib from [insert start date] to [insert end date], which was discontinued due to adverse effects.\n* Third-line treatment: The patient then transitioned to pembrolizumab, initiating treatment on [insert start date].\n\n**Treatment Timeline**\n\nThe patient's treatment timeline is as follows:\n\n| Treatment | Start Date | End Date |\n| --- | --- | --- |\n| First-line therapy | [insert start date] | [insert end date] |\n| Maintenance therapy | [insert start date] | [insert end date] |\n| Cabozantinib | [insert start date] | [insert end date] (discontinued) |\n| Pembrolizumab | [insert start date] | Ongoing |\n\n**Outcomes**\n\nThe patient's treatment outcomes have been as follows:\n\n* Partial tumor response: The patient experienced a partial tumor response to first-line therapy, which was observed on imaging studies.\n* Disease progression: Following completion of first-line therapy, the patient experienced disease progression, leading to the initiation of second-line treatment.\n* Adverse effects: The patient experienced adverse effects while receiving cabozantinib, leading to discontinuation of treatment.\n* Symptomatic improvement: The patient has experienced significant symptomatic improvement since initiating pembrolizumab, including complete hearing recovery and a substantial reduction in dizziness and headache complaints.\n\n**Current Status**\n\nThe patient is currently undergoing treatment with pembrolizumab, which was initiated on [insert start date]. The patient's current status includes:\n\n* Ongoing treatment with pembrolizumab\n* Continued monitoring for disease progression or adverse effects\n* Regular follow-up appointments to assess treatment outcomes and adjust treatment as needed\n\nOverall, the patient has undergone a complex treatment journey, involving multiple treatments and transitions. 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He has a significant smoking history, having consumed two packs per day for 55 years, which is reflected in his Brinkman Index score of 1100. Additionally, he has a history of total thyroidectomy five years prior due to papillary thyroid carcinoma (PTC).\n\n**Timeline of Diagnoses:**\n\n1. **Six years ago:** The patient was found to have left cervical lymphadenopathy of unknown origin, suspected to be cervical lymph node metastasis of PTC.\n2. **Five years ago:** The patient underwent total thyroidectomy and left cervical lymph node dissection, with histopathology revealing multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins.\n3. **Two years prior to current encounter:** A nodule in the right upper lobe of the lung was identified and monitored with chest CT scans. Increase in nodule density observed compared to two years prior, prompting a transbronchial biopsy; however, no definitive diagnosis was made.\n\n**Timeline of Treatments:**\n\n1. **Five years ago:** The patient underwent total thyroidectomy and left cervical lymph node dissection.\n2. **Current encounter:** The patient was treated with radioiodine therapy (Iodine-131).\n\n**Timeline of Outcomes:**\n\n1. **Six years ago:** Left cervical lymphadenopathy of unknown origin, suspected to be cervical lymph node metastasis of PTC.\n2. **Five years ago:** Multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins.\n3. **Current encounter:** Serum thyroglobulin levels showed a gradual increase over time, indicating progression of disease.\n\n**Clinical Findings:**\n\n* The patient's serum thyroglobulin levels have shown a gradual increase over time, indicating progression of disease.\n* Chest X-rays and CT scans revealed an irregular nodule measuring 15\u00d714 mm in the S1 segment of the right upper lobe.\n* Pulmonary function and electrocardiogram tests showed no abnormalities.\n\n**Surgical Plan:**\nA surgical plan was made to perform intraoperative rapid diagnosis, followed by right upper lobectomy.", + "bertscore": { + "precision": [ + 0.7508742809295654 + ], + "recall": [ + 0.7241371870040894 + ], + "f1": [ + 0.7372633814811707 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.34912702441215515, + -0.02949952892959118, + -0.1141456887125969, + 0.04978491738438606, + 0.08703146129846573, + 0.0669483095407486, + 0.02256781794130802, + 0.284852534532547, + 0.38056764006614685, + -0.44284701347351074, + -0.2560020983219147, + -0.03550972789525986, + 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d9ea34d..d436e7d 100644 --- a/src/benchmark/output/results/graph_013.json +++ b/src/benchmark/output/results/results_graph_013.json @@ -3,13 +3,13 @@ "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an adult with a diagnosis of stage III Non-Small Cell Lung Carcinoma (NSCLC) accompanied by an upper esophageal stricture. The patient's demographic information is not explicitly provided in the data, but based on the clinical presentation and treatment plan, it can be inferred that the patient is likely an older adult.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient was diagnosed with stage III NSCLC and upper esophageal stricture around the same time.\n2. **Step 2 (Two months later):** An initial MRI performed revealed no abnormalities, but the patient's diagnosis of NSCLC remained active.\n3. **Step 3 (One year after Step 1):** Follow-up CT scans showed metastatic spread throughout the brain after presentation to the ED with neurological weakness.\n4. **Step 4:** The patient was admitted to hospital and started on dexamethasone, continued treatment for hypokalemia, and placed on neutropenic precautions. Pantoprazole and enoxaparin sodium were initiated due to possible hemorrhages and deep vein thrombosis prophylaxis.\n5. **Step 5:** MRI confirmed multiple new brain metastases with vasogenic edema and possible hemorrhagic components. The patient's oncologist confirmed metastasis to the brain and bone, and dexamethasone was increased to 6 mg every eight hours. Enoxaparin sodium was discontinued due to possible hemorrhages; mechanical prophylaxis started with thromboembolic deterrent stockings and sequential compression devices.\n6. **Step 6:** The patient tolerated radiation therapy well and docetaxel was re-initiated.\n7. **Step 7 (Refractory disease):** CT scans revealed new developments in the liver and possibly pancreas, indicating refractory disease to second-line docetaxel.\n8. **Step 8 (Hospice care recommendation):** The oncologist discussed a third-line option and recommended hospice care.\n\n**Timeline of Treatments:**\n\n1. **Dexamethasone:** Initially started at 4 mg twice daily, increased to 6 mg every eight hours due to metastasis.\n2. **Docetaxel:** Re-initiated after radiation therapy, with no specified dosage or frequency.\n3. **Pantoprazole and Enoxaparin Sodium:** Initiated for possible hemorrhages and deep vein thrombosis prophylaxis.\n\n**Outcomes:**\n\n1. **Radiation Therapy:** The patient tolerated the treatment well, indicating a positive response to radiation therapy.\n2. **Hospice Care Recommendation:** The oncologist recommended hospice care due to refractory disease, indicating a poor prognosis for the patient's overall health and quality of life.\n\nIn conclusion, this patient was diagnosed with stage III NSCLC accompanied by an upper esophageal stricture and underwent multiple treatments, including radiation therapy, dexamethasone, docetaxel, pantoprazole, and enoxaparin sodium. Despite initial positive responses to treatment, the patient's disease progressed, leading to a recommendation for hospice care due to refractory disease.", "bertscore": { "precision": [ - 0.3270224332809448 + 0.5511878728866577 ], "recall": [ - 0.4040271043777466 + 0.5822768211364746 ], "f1": [ - 0.3614691495895386 + 0.5663059949874878 ] }, "topology": { diff --git a/src/benchmark/output/results/results_graph_014.json b/src/benchmark/output/results/results_graph_014.json new file mode 100644 index 0000000..de6b176 --- /dev/null +++ b/src/benchmark/output/results/results_graph_014.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient's demographic information is not explicitly provided in the data. However, based on the content of the clinical notes, it appears that the patient has been diagnosed with a malignancy affecting the right upper lobe of the lung.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Initial Diagnosis:** The patient underwent an enhanced chest CT scan on March 3, 2023 (Node N2), which revealed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32\u00d727 mm. Enlarged and moderately enhanced lymph nodes were also detected in the 10R, 4R, and 2R regions.\n2. **Treatment Initiation:** Vancomycin was administered for anti-infection and anti-viral treatment (Node N1) on an unspecified date prior to March 3, 2023.\n3. **Repeat Imaging:** A repeat enhanced chest CT scan was performed on May 29, 2023 (Node N2), which showed a significant reduction in the size of the solid component of the right upper lobe mass and similar-sized mediastinal lymph nodes compared to the previous CT scan.\n4. **Immunotherapy and Chemotherapy:** A second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023 (Node N3).\n\n**Outcomes:**\n\n1. **Partial Remission:** The patient's response assessment indicated partial remission following the repeat imaging study on May 29, 2023.\n2. **Treatment Tolerability:** The patient tolerated the immunotherapy and chemotherapy treatment well, as evidenced by the administration of a second cycle of these treatments.\n\n**Clinical Implications:**\n\nThe patient's clinical course suggests that the malignancy affecting the right upper lobe of the lung is responsive to immunotherapy and chemotherapy. However, further monitoring and follow-up are necessary to assess the durability of the partial remission and to identify potential side effects or toxicities associated with these treatments.\n\n**Future Directions:**\n\n1. **Regular Imaging:** Regular imaging studies should be performed to monitor the patient's response to treatment and to detect any signs of disease progression.\n2. **Dose Escalation:** The dose of immunotherapy and chemotherapy may need to be escalated in subsequent cycles to maintain efficacy and tolerability.\n3. **Combination Therapy:** Further investigation into combination therapies involving immunotherapy, chemotherapy, and targeted therapies may be warranted to optimize treatment outcomes.\n\nIn conclusion, the patient's clinical case report highlights the importance of regular imaging studies, effective treatment strategies, and careful monitoring to manage malignancies affecting the lung.", + "bertscore": { + "precision": [ + 0.5968338847160339 + ], + 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non-small cell carcinoma of the lung: The patient's cancer was diagnosed, which led to further complications.\n* Coronary artery disease: The patient had a history of coronary artery disease, which required CABG surgery.\n* Intracardiac metastasis: The patient developed intracardiac metastasis, indicating that the cancer had spread to the heart.\n* Transient ischemic attack (TIA): The patient experienced a TIA, which is a temporary interruption in blood flow to part of the brain.\n\n**Timeline of Treatments:**\n\n* Coronary artery bypass grafting (CABG): The patient underwent CABG surgery as part of his treatment for coronary artery disease.\n* No specific treatments are mentioned for the metastatic non-small cell carcinoma or intracardiac metastasis in this case report.\n\n**Clinical Findings and Outcomes:**\n\nThe patient's clinical findings include:\n- Metastatic non-small cell carcinoma of the lung (diagnosis code C34.9)\n- Atherosclerotic heart disease of native coronary artery without angina pectoris (diagnosis code I25.10)\n- Chronic total occlusion of coronary artery (diagnosis code I25.82)\n- Cerebral infarction, unspecified (diagnosis code I63.9)\n\nThe patient's treatment for coronary artery disease involved CABG surgery.\n\n**Current Status:**\n\nThe patient is currently under the care of [insert name] and has a diagnosis of malignant neoplasm of unspecified part of bronchus or lung (C34.9) and cerebral infarction, unspecified (I63.9). The patient's history of coronary artery disease is noted as historical.\n\n**Prognosis:**\n\nThe prognosis for this patient is uncertain due to the presence of metastatic non-small cell carcinoma of the lung and intracardiac metastasis. Further treatment options should be discussed with a healthcare provider.\n\nNote: This narrative is based on the provided data and may not reflect the actual clinical case report or patient's current status.", + "bertscore": { + "precision": [ + 0.5106064677238464 + ], + "recall": [ + 0.5770247578620911 + ], + "f1": [ + 0.5417876243591309 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 1, + "edge_count": 0, + "avg_in_degree": 0.0, + "density": 0 + }, + "trajectory_embedding": [ + 0.2389703392982483, + 0.3098335266113281, + -0.3165978193283081, + -9.601563215255737e-05, + 0.38989344239234924, + 0.5903520584106445, + -0.588888943195343, + -0.03018897771835327, + -0.08889243006706238, + -0.6207064390182495, + -0.0009037437266670167, + 0.39261308312416077, + -0.7441316843032837, + -0.2979073226451874, + 0.16640852391719818, + 0.43679654598236084, + 0.048064105212688446, 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She presented with a subsolid pulmonary lesion incidentally detected during a routine follow-up for malignant melanoma.\n\n**Timeline of Diagnoses:**\n\n1. **April 2013:** The patient was diagnosed with malignant melanoma and underwent resection videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent.\n2. **Late April 2013:** Left axillary dissection revealed metastasis in one of 19 lymph nodes, and molecular genetic testing confirmed a BRAF mutation at codon 600.\n3. **November 2017:** A routine CT scan detected a new asymptomatic 7 mm lesion in segment S10 of the right lower lobe with a density consistent with a pure ground glass nodule.\n4. **June 2020:** Follow-up CT scans showed the lesion changed character to a subsolid lesion with the presence of a solid component.\n5. **July 2020:** PET/CT scans confirmed the persistence of the lesion without increased metabolic activity.\n6. **April 2021:** Follow-up confirmed persistence and slight size progression of the solid component of the lesion, leading to indication for surgical resection.\n\n**Timeline of Treatments:**\n\n1. **April 2013:** Resection videothoracoscopically\n2. **Late April 2013:** Left axillary dissection and initiation of targeted therapy with BRAF inhibitors\n3. **November 2017:** No treatment mentioned\n4. **June 2020:** No treatment mentioned\n5. **July 2020:** No treatment mentioned\n6. **April 2021:** Surgical resection\n\n**Timeline of Outcomes:**\n\n1. **Late April 2013:** Metastasis in one of 19 lymph nodes confirmed, and targeted therapy with BRAF inhibitors initiated.\n2. **November 2017:** New asymptomatic lesion detected during routine CT scan\n3. **June 2020:** Lesion changed character to a subsolid lesion with the presence of a solid component.\n4. **July 2020:** Persistence of lesion without increased metabolic activity confirmed by PET/CT scans\n5. **April 2021:** Surgical resection performed, and follow-up confirmed persistence and slight size progression of the solid component of the lesion.\n\n**Conclusion:**\nThe patient was diagnosed with malignant melanoma in April 2013 and underwent resection videothoracoscopically. Following this, she developed metastasis in one of 19 lymph nodes and was treated with targeted therapy with BRAF inhibitors. In November 2017, a new asymptomatic lesion was detected during routine CT scan, which changed character to a subsolid lesion with the presence of a solid component by June 2020. The persistence of this lesion without increased metabolic activity was confirmed by PET/CT scans in July 2020. Finally, surgical resection was performed in April 2021, and follow-up confirmed persistence and slight size progression of the solid component of the lesion.", + "bertscore": { + "precision": [ + 0.4778168499469757 + ], + "recall": [ + 0.7119154334068298 + ], + "f1": [ + 0.5718348622322083 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.149007648229599, + 0.05697751045227051, + -0.07104989141225815, + 0.04486839473247528, + -0.15542572736740112, + -0.011686301790177822, + 0.04617166519165039, + 0.17946068942546844, + 0.2943315804004669, + -0.3095993399620056, + -0.16567997634410858, + 0.13099738955497742, + -0.5008986592292786, + -0.13083820044994354, + -0.32352951169013977, + 0.1127810999751091, + 0.0062797837890684605, + 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with primary lung adenocarcinoma in 2023. He presented with severe, debilitating shoulder pain (VAS 9) in the low dorsal area, which prompted further investigation and diagnosis.\n\n**Timeline of Diagnoses:**\n\n1. **Primary Lung Adenocarcinoma Diagnosis:** The patient was diagnosed with primary lung adenocarcinoma in 2023.\n2. **Shoulder Pain Presentation:** The patient presented with severe, debilitating shoulder pain (VAS 9) in the low dorsal area, which prompted further investigation and diagnosis.\n3. **Compression Fracture Diagnosis:** A CT scan revealed a compression fracture of the T8 vertebral body with multiple fracture lines and a mixed lytic-sclerotic tumor component.\n4. **Pathological Fracture Diagnosis:** The patient was diagnosed with pathological fracture due to metastasis from lung adenocarcinoma.\n5. **Treatment of Pathological Fracture:** The patient underwent treatment for the pathological fracture, including microwave ablation and SpineJack system.\n\n**Timeline of Treatments:**\n\n1. **Microwave Ablation and SpineJack System Treatment:** The patient received treatment with microwave ablation and SpineJack system to manage the pathological fracture.\n2. **Initial CT Scan:** An initial CT scan was performed to assess the lesion's size, location, and radiological characteristics.\n3. **Conscious Sedation Administration:** Patient was positioned prone, and conscious sedation was administered using continuous intravenous infusion of fentanyl citrate.\n\n**Timeline of Outcomes:**\n\n1. **Pathological Fracture Management:** The patient's pathological fracture was successfully managed with microwave ablation and SpineJack system treatment.\n2. **Lesion Assessment:** The initial CT scan provided valuable information on the lesion's size, location, and radiological characteristics.\n3. **Patient Recovery:** The patient recovered from the procedure without any significant complications.\n\n**Conclusion:**\nThe patient underwent a comprehensive evaluation for severe shoulder pain, which led to the diagnosis of compression fracture due to metastasis from lung adenocarcinoma. Treatment with microwave ablation and SpineJack system was effective in managing the pathological fracture, and the initial CT scan provided valuable information on the lesion's characteristics. The patient recovered without any significant complications.\n\n**Recommendations:**\n\n1. **Regular Follow-up:** Regular follow-up appointments are recommended to monitor the patient's condition and adjust treatment as needed.\n2. **Imaging Studies:** Imaging studies should be performed regularly to assess the progression of the disease and the effectiveness of treatment.\n3. **Pain Management:** Pain management strategies should be implemented to ensure optimal pain control for the patient.\n\n**Limitations:**\nThis case report is limited by its retrospective nature, which may not capture all relevant information or outcomes. Further follow-up studies are necessary to fully evaluate the effectiveness of treatment and monitor long-term outcomes.", + "bertscore": { + "precision": [ + 0.6227207183837891 + ], + "recall": [ + 0.6329694986343384 + ], + "f1": [ + 0.6278032660484314 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.18080228567123413, + -0.01176790613681078, + 0.10657219588756561, + 0.21200677752494812, + 0.1496204435825348, + 0.09226961433887482, + -0.08451242744922638, + 0.22056791186332703, + 0.5967764258384705, + -0.16920879483222961, + -0.2202618569135666, + -0.1208207830786705, + -0.3906412720680237, + -0.08555690199136734, + -0.24673983454704285, + 0.1816776692867279, + 0.06529556214809418, + 0.02827569469809532, + -0.09853260964155197, + -0.2589186131954193, + 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He was diagnosed with small-cell lung cancer (SCLC) with hilar, mediastinal lymph node, and pleural metastases (cT1N3M1a, extensive stage) and a Performance Status (PS) score of 1.\n\n**Timeline of Diagnoses:**\n\n* July 2023: The patient presented with facial and dorsal hand edema, leading to the diagnosis of small-cell lung cancer.\n* September 9, 2024: The patient was admitted to the gastroenterology department due to a 5-day period of no bowel movement, resulting in a diagnosis of constipation.\n\n**Timeline of Treatments:**\n\n* July 2023: The patient started chemotherapy with four cycles of intravenous etoposide 160 mg (days 1-3), carboplatin (400 mg) on day 1, and serplulimab 300 mg on day 1 (Q3W).\n* After 18 cycles of chemotherapy and serplulimab maintenance: The patient experienced a partial response (PR).\n\n**Timeline of Outcomes:**\n\n* After two cycles of serplulimab treatment: The patient intermittently experienced hard stools and occasional constipation, relieved with glycerin suppositories.\n* September 9, 2024: The patient was admitted to the gastroenterology department due to a 5-day period of no bowel movement, resulting in a diagnosis of constipation.\n* Abdominal CT revealed diffuse dilatation and gas accumulation in the bowel, particularly the colon, suggesting incomplete intestinal obstruction.\n* Gastroscopy showed chronic atrophic gastritis (C2) with bile reflux.\n* Colonoscopy revealed a subpedunculated polyp approximately 1.5 cm in size, 20 cm from the anus, with smooth mucosa in the sigmoid colon.\n\n**Clinical Course:**\n\nThe patient's clinical course was marked by a series of diagnostic and therapeutic challenges. Initially, the patient presented with symptoms suggestive of small-cell lung cancer, which led to the initiation of chemotherapy and serplulimab maintenance. However, despite this treatment, the patient experienced worsening constipation, prompting further evaluation.\n\nFurther investigation revealed chronic atrophic gastritis (C2) with bile reflux, as well as a subpedunculated polyp in the sigmoid colon. These findings suggested incomplete intestinal obstruction and gastrointestinal distress, which were exacerbated by the patient's underlying small-cell lung cancer.\n\nThe patient's clinical course was ultimately marked by a series of diagnostic and therapeutic challenges, including worsening constipation, chronic atrophic gastritis, and gastrointestinal distress. Despite these challenges, the patient received treatment for their underlying small-cell lung cancer, as well as management for their gastrointestinal symptoms.\n\n**Conclusion:**\n\nThis case highlights the complexities of managing patients with multiple comorbidities, particularly those with small-cell lung cancer. The patient's clinical course was marked by a series of diagnostic and therapeutic challenges, including worsening constipation, chronic atrophic gastritis, and gastrointestinal distress. Despite these challenges, the patient received treatment for their underlying small-cell lung cancer, as well as management for their gastrointestinal symptoms.", + "bertscore": { + "precision": [ + 0.7377782464027405 + ], + "recall": [ + 0.7519990801811218 + ], + "f1": [ + 0.744820773601532 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.19909723103046417, + 0.12390078604221344, + -0.27012550830841064, + 0.19638073444366455, + 0.11007723957300186, + 0.15321364998817444, + -0.10099908709526062, + 0.23281972110271454, + 0.6538661122322083, + -0.3013831377029419, + -0.03854934498667717, + -0.08443812280893326, + -0.5399647355079651, + -0.23934105038642883, + -0.10716229677200317, + 0.29621395468711853, + -0.2592211961746216, + 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with symptoms of toe redness and pain. This condition had been present for several weeks prior to his current encounter. The patient's vital signs were stable during this initial visit, but as time progressed, he began to experience coughing, expectoration, fever, and left lumbar/groin erythema/pain.\n\nFollowing a hospital admission, the patient underwent various tests, including cultures and CT scans, which initially suggested a possible bacterial infection. Despite treatment with piperacillin-tazobactam, the patient's condition worsened, leading to further hospitalization.\n\nDuring this period, the patient experienced significant changes in his vital signs and mental status, including stupor and hypoxia. His electrocardiogram revealed atrial fibrillation, and antimicrobial susceptibility testing indicated sensitivity to meropenem.\n\nThe patient's lab values continued to show abnormal results, with elevated white blood cell count, neutrophil percentage, albumin levels, C-reactive protein, procalcitonin, N-terminal pro b-type natriuretic peptide, alanine aminotransferase, aspartate aminotransferase, and creatinine.\n\nThroughout the patient's hospital stay, he received treatment with meropenem, which was found to be sensitive in antimicrobial susceptibility testing. Despite this, the patient continued to experience persistent symptoms and abnormal lab values.\n\nThe timeline of diagnoses and treatments for this patient can be summarized as follows:\n\n* Initial visit: Toe redness/pain (weeks prior)\n* Hospital admission: Coughing, expectoration, fever, left lumbar/groin erythema/pain\n* Treatment with piperacillin-tazobactam\n* Further hospitalization due to worsening condition\n* Development of stupor, hypoxia, and atrial fibrillation\n* Treatment with meropenem\n\nThe patient's outcomes are currently uncertain, as the narrative does not provide information on his current status or any subsequent treatments. However, it is clear that this patient has experienced a significant decline in his health status over time, requiring multiple hospitalizations and various treatments to manage his symptoms and lab values.", + "bertscore": { + "precision": [ + 0.510433554649353 + ], + "recall": [ + 0.565669059753418 + ], + "f1": [ + 0.5366336703300476 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2106419950723648, + 0.10880613327026367, + -0.019303588196635246, + 0.17433996498584747, + 0.13737574219703674, + 0.09073399007320404, + 0.057045288383960724, + 0.16380244493484497, + 0.42614296078681946, + -0.31337109208106995, + -0.12151220440864563, + 0.03720476105809212, + -0.6054100394248962, + -0.16327770054340363, + -0.23895896971225739, + 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"success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 77-year-old man with a history of hypertension, hyperlipidemia, and right-sided hearing loss due to chronic otitis media. He is a heavy smoker with no medical history of malignancy.\n\n**Initial Presentation (Step 1):**\nThe patient presented with left-sided hearing loss, otalgia, and a red mass in the left external auditory canal (EAC) that persisted for several weeks. Physical examination revealed a red, soft mass measuring approximately 20 mm occupying the left EAC.\n\n**Diagnostic Workup:**\nImaging studies, including CT scans and MRI, were performed to evaluate the extent of the mass. Laboratory tests showed normal Span-1 and DUPAN2 levels, elevated ProGRP (698 pg/mL) and NSE (31.1 ng/mL). Pure-tone audiometry revealed bilateral mixed hearing loss.\n\n**Diagnosis:**\nThe diagnosis was initially suspected to be carcinoma of the EAC based on imaging findings and laboratory results. However, further testing, including biopsies from the EAC mass, lung, and pancreas, confirmed the presence of small cell lung cancer (SCLC).\n\n**Treatment:**\nChemotherapy with carboplatin, etoposide, and zoledronic acid was initiated to treat bone metastases. The treatment resulted in a reduction in size of metastatic lesions in the EAC and middle ear, improvement in hearing impairment and otalgia, and a decrease in ProGRP levels.\n\n**Outcome:**\nThe patient experienced severe hearing loss but regained the ability to understand conversations as the tumor shrank. Otalgia resolved, and opioid therapy was discontinued. Unfortunately, the patient died 15 months later due to complications from SCLC.\n\n**Autopsy Findings:**\nAt autopsy, resolution of EAC lesions was observed grossly. CT imaging revealed mastoid destruction and tumor invasion into the EAC.\n\n**Conclusion:**\nThis case highlights the importance of comprehensive diagnostic workup and multidisciplinary treatment approaches for patients with suspected carcinoma of the EAC. Early detection and treatment can improve outcomes, but the disease is often aggressive, leading to poor prognosis in some cases.", + "bertscore": { + "precision": [ + 0.6627601981163025 + ], + "recall": [ + 0.6721744537353516 + ], + "f1": [ + 0.6674340963363647 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.14263400435447693, + -0.013967558741569519, + -0.2280512899160385, + 0.02719009481370449, + -0.11668924242258072, + -0.14093691110610962, + 0.10111647099256516, + 0.0954238548874855, + 0.22714979946613312, + -0.2350296974182129, + -0.3323439657688141, + 0.36267557740211487, + -0.6519513130187988, + 0.014573529362678528, + -0.52058345079422, + -0.19109226763248444, + 0.09013906866312027, + 0.25849395990371704, + 0.0019105846295133233, 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adult male with no specified age or background information. However, it can be inferred that he has been diagnosed with multiple conditions over the years, including melanoma and choroidal neoplasms.\n\n**Timeline of Diagnoses**\n\nThe patient's journey began with a diagnosis of melanoma in 2015 (N1). He underwent lymph node scintigraphy and removal of four sentinel lymph nodes as part of his treatment plan. This was followed by yearly follow-up visits at the dermato-oncologist, which helped monitor his condition for any signs of recurrence or metastasis.\n\nIn 2018, the patient presented with worsening eyesight in one eye due to a pigmented choroidal tumor (N4). He underwent brachytherapy for this condition, which involved the placement of a ruthenium-106 plaque in the affected area. This treatment helped stabilize his visual function and reduce the size of the tumor.\n\nOver the next few years, the patient's oncologist conducted regular follow-up appointments to monitor his condition. In 2020, it was discovered that the patient had metastatic disease throughout his body, with a pattern characteristic of primary cutaneous melanoma (N6). As a result, he began systemic cancer treatment with ipilimumab and nivolumab.\n\n**Timeline of Treatments**\n\n* 2015: Melanoma diagnosis and lymph node scintigraphy\n* 2018: Brachytherapy for pigmented choroidal tumor\n* 2020: Systemic cancer treatment with ipilimumab and nivolumab\n\n**Outcomes**\n\nThe patient's treatment plan has been successful in managing his conditions. His melanoma was successfully treated, and he has not experienced any significant recurrence or metastasis.\n\nRegarding the pigmented choroidal tumor, brachytherapy helped stabilize his visual function and reduce the size of the tumor. However, a new lesion developed in 2022 (N13), which required further treatment with brachytherapy.\n\nThe patient's PET/CT scan in 2023 showed no pathological processes, indicating that his cancer is currently under control (N9).\n\n**Current Status**\n\nThe patient continues to receive regular follow-up appointments with his oncologist and dermato-oncologist. He is being monitored for any signs of recurrence or metastasis, and his treatment plan will be adjusted as needed.\n\nOverall, the patient's journey has been marked by a series of diagnoses, treatments, and outcomes that have helped manage his conditions. While there are still challenges ahead, his current status suggests that he is in good hands with his healthcare team.", + "bertscore": { + "precision": [ + 0.6081898808479309 + ], + "recall": [ + 0.6577727794647217 + ], + "f1": [ + 0.6320104002952576 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 6, + "node_count": 15, + "edge_count": 9, + "avg_in_degree": 0.6, + "density": 0.04285714285714286 + }, + "trajectory_embedding": [ + 0.10540588945150375, + 0.12294507771730423, + -0.10281980782747269, + 0.1525949388742447, + 0.008018000051379204, + 0.2466597855091095, + 0.03886903077363968, + 0.2453383058309555, + 0.4833277463912964, + -0.4130333662033081, + -0.19181455671787262, + -0.0784992128610611, + -0.5563032031059265, + -0.12875708937644958, + -0.3123818039894104, + 0.17844067513942719, + -0.15840710699558258, + 0.31354740262031555, + -0.14745765924453735, + -0.240568146109581, + 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physical examination.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (June 2022):** The patient presented with initial symptoms, which led to further evaluation.\n2. **Step 2 (June 2022):** PET-CT findings revealed right upper lung cancer and multiple tiny nodules in both lungs, as well as thyroid isthmus occupancy.\n3. **Step 3 (June 2022):** Diagnosis of the right upper lung nodule via CT-guided puncture confirmed lung adenocarcinoma with a PD-L1 TPS of 2%. Diagnosis of the thyroid gland via fine-needle aspiration revealed papillary carcinoma.\n4. **Step 4 (July 2022):** Chest CT scans showed stable disease following treatments.\n5. **Step 5 (August 2022):** Post-surgery chest CT examination revealed no signs of tumor recurrence.\n6. **Step 6 (September 2022):** Thyroid color ultrasonography suggested isthmic thyroid nodules.\n7. **Step 7 (October 2022):** Postoperative thyroid ultrasound showed no signs of tumor recurrence.\n8. **Step 8 (November 2022):** PET-CT scans revealed a primary tumor mass in the right neck subcutaneous at the time of diagnosis.\n9. **Step 9 (December 2022):** Ultrasound results suggested a hypoechoic mass in the V region of the right neck.\n10. **Step 10 (January 2023):** Puncture biopsies revealed adenocarcinoma of lung, papillary carcinoma of thyroid, and a spindle cell.\n\n**Timeline of Treatments:**\n\n1. **CT-guided puncture (June 2022):** Used to diagnose the right upper lung nodule.\n2. **Fine-needle aspiration (June 2022):** Used to diagnose the thyroid gland.\n3. **Treatments (July 2022):** Administered following PET-CT findings.\n4. **Surgery (August 2022):** Performed to remove the tumor.\n5. **Postoperative care (September 2022):** Provided to monitor for tumor recurrence.\n\n**Outcomes:**\n\n1. **Lung adenocarcinoma:** Stable disease was observed following treatments, and no signs of tumor recurrence were seen on post-surgery chest CT examination.\n2. **Papillary carcinoma of thyroid:** No signs of tumor recurrence were seen on postoperative thyroid ultrasound.\n3. **Primary tumor mass in the right neck subcutaneous:** PET-CT scans revealed a primary tumor mass at the time of diagnosis, but no further treatment was mentioned.\n\n**Conclusion:**\nThe patient underwent a series of diagnostic tests and treatments for lung cancer and papillary carcinoma of the thyroid. Following these interventions, stable disease was observed in both conditions, with no signs of tumor recurrence seen on post-surgery chest CT examination and postoperative thyroid ultrasound. However, PET-CT scans revealed a primary tumor mass in the right neck subcutaneous at the time of diagnosis, which warrants further evaluation and treatment.", + "bertscore": { + "precision": [ + 0.6954405307769775 + ], + "recall": [ + 0.7023525238037109 + ], + "f1": [ + 0.6988794207572937 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.34409192204475403, + 0.07935971021652222, + 0.046093933284282684, + 0.01933947391808033, + -0.0402722992002964, + 0.1429879069328308, + 0.05653051286935806, + 0.2529970109462738, + 0.3755955100059509, + -0.32734960317611694, + -0.2119436264038086, + -0.10174901783466339, + -0.4879678785800934, + -0.0025561749935150146, + -0.42852139472961426, + 0.38021185994148254, + 0.006385275162756443, + 0.34415745735168457, + 0.034441545605659485, 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in November 2022 for evaluation of an abnormal chest CT scan. She has a medical history of hypertension but no smoking or family history of cancer.\n\n**Initial Presentation (Step 1):**\nThe patient presented with an abnormal chest CT scan, which led to further investigation. The initial presentation was characterized by the absence of respiratory symptoms such as cough or dyspnea.\n\n**Diagnostic Findings (Step 2):**\nChest CT revealed a 1.1-cm spiculated nodule in the right middle lobe (RML), multiple pleural nodules with mild pleural thickening, and fibrotic lesions in the right upper lobe (RUL). These findings prompted further investigation.\n\n**Biopsy and Diagnosis (Step 3):**\nLinear endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) of enlarged lymph node 7 revealed metastatic adenocarcinoma with ALK rearrangement, wild type EGFR mutation, and echinoderm microtubule-associated protein-like 4 (EML 4)-ALK fusion. The first biopsy of the mediastinal 7th lymph node was positive for ALK stain.\n\n**Diagnosis Confirmation (Step 4):**\nPET-CT revealed pleural, multiple enhancing nodules with lymph nodes metastasis, leading to a diagnosis of stage IV lung cancer (T2N2M1a).\n\n**Treatment Initiation (Step 5):**\nTargeted mutation chemotherapy with alectinib was initiated and continued for a period of one and a half years. Follow-up chest CT scans during treatment with alectinib demonstrated a reduction in the lung mass and pleural metastatic lesions.\n\n**Follow-Up and Recurrence (Step 6):**\nIn July 2024, Chest CT showed the previously observed main mass in the RML, indicating recurrence of the disease.\n\n**Timeline:**\n\n* November 2022: Patient admitted to Pulmonology Department for evaluation of abnormal chest CT scan.\n* Step 2: Chest CT reveals abnormalities.\n* Step 3: EBUS-TBNA and biopsy confirm diagnosis of metastatic adenocarcinoma.\n* Step 4: Diagnosis confirmed with PET-CT.\n* Step 5: Targeted mutation chemotherapy with alectinib initiated.\n* July 2024: Follow-up chest CT shows recurrence of the disease.\n\n**Outcomes:**\nThe patient received targeted mutation chemotherapy with alectinib, which led to a reduction in lung mass and pleural metastatic lesions. However, the disease recurred in July 2024, indicating the need for further treatment options.", + "bertscore": { + "precision": [ + 0.5603240728378296 + ], + "recall": [ + 0.662941038608551 + ], + "f1": [ + 0.6073283553123474 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.4501422345638275, + 0.09562578797340393, + -0.1269008368253708, + 0.16001977026462555, + -0.027514860033988953, + 0.06566961854696274, + 0.10955768078565598, + 0.3071059286594391, + 0.3549204170703888, + -0.3344673812389374, + -0.10898244380950928, + 0.05722176656126976, + -0.6175083518028259, + -0.03839653357863426, + -0.21359169483184814, + 0.22728413343429565, + 0.024842113256454468, + 0.2667379677295685, + 0.009542305953800678, + -0.11258780211210251, + 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history of hypertension, carotid artery stenosis, cerebral artery stenosis, and primary malignant neoplasm of the lung. The patient's demographic information includes a 30-year history of hypertension, a 7-year history of carotid stenosis on the left side, and a 4-year history of right lung cancer surgery.\n\nThe patient's timeline of diagnoses began with the discovery of black stool on January 9, 2024. Upon presentation to the emergency department, the patient was found to have a hemoglobin level of 58 g/L. This marked the beginning of an acute upper gastrointestinal hemorrhage, which required immediate attention.\n\nFollowing stabilization, the patient's medical history and current medications were reviewed (N11). The patient had been managed with compound reserpine, nifedipine extended-release tablets, and captopril for their hypertension, as well as a 30-year history of hypertension. Additionally, the patient had undergone right lung cancer surgery 4 years prior and thermal ablation of a right lung tumor 5 months prior.\n\nThe patient's symptoms and laboratory results led to the diagnosis of gastrointestinal hemorrhage, unspecified (K92.2). The patient was subsequently admitted for further evaluation and management.\n\nIn the course of their treatment, the patient underwent several procedures, including CT-guided percutaneous lung nodule aspiration biopsy (N7), thermal ablation of a right lung tumor (N8), and regular follow-up with surveillance imaging (N9).\n\nThe patient's hemoglobin level was found to be 58 g/L upon presentation, indicating severe anemia. The patient's symptoms and laboratory results led to the diagnosis of gastrointestinal hemorrhage, unspecified (K92.2). The patient was subsequently admitted for further evaluation and management.\n\nIn the course of their treatment, the patient underwent several procedures, including CT-guided percutaneous lung nodule aspiration biopsy (N7), thermal ablation of a right lung tumor (N8), and regular follow-up with surveillance imaging (N9).\n\nThe patient's timeline of diagnoses is as follows:\n\n* January 9, 2024: Patient presents with black stool and is found to have a hemoglobin level of 58 g/L.\n* January 9, 2024: Acute upper gastrointestinal hemorrhage diagnosed (K92.2).\n* January 9-10, 2024: Patient's medical history and current medications reviewed (N11).\n* January 9-10, 2024: Patient undergoes CT-guided percutaneous lung nodule aspiration biopsy (N7).\n* January 9-10, 2024: Patient undergoes thermal ablation of a right lung tumor (N8).\n* January 9-10, 2024: Patient begins regular follow-up with surveillance imaging (N9).\n\nThe patient's treatment plan is focused on managing their acute upper gastrointestinal hemorrhage and addressing any underlying causes. The patient will require close monitoring and ongoing evaluation to ensure the best possible outcome.\n\nIn terms of outcomes, the patient has made significant progress in their management of acute upper gastrointestinal hemorrhage. However, further evaluation and follow-up are necessary to determine the long-term prognosis and potential complications.\n\nThe patient's history of hypertension, carotid artery stenosis, cerebral artery stenosis, and primary malignant neoplasm of the lung will require ongoing management and monitoring. The patient's treatment plan should take into account these comorbidities and ensure that they receive comprehensive care to address all aspects of their health.\n\nIn conclusion, the patient's timeline of diagnoses and treatments is complex and multifaceted. Ongoing evaluation and follow-up are necessary to determine the best course of action for this patient.", + "bertscore": { + "precision": [ + 0.4498176574707031 + ], + "recall": [ + 0.5712114572525024 + ], + "f1": [ + 0.5032980442047119 + ] + }, + "trajectory_embedding": [ + 0.1456865519285202, + 0.1314917504787445, + -0.0931175947189331, + 0.04623199999332428, + 0.059770286083221436, + 0.0806192085146904, + 0.04538099840283394, + 0.17417706549167633, + 0.28361740708351135, + -0.24916689097881317, + -0.11881931871175766, + 0.03163249418139458, + -0.5529548525810242, + -0.09358691424131393, + -0.20111314952373505, + 0.28860440850257874, + 0.023606710135936737, + 0.25683730840682983, + 0.03913749381899834, + -0.2733571231365204, + -0.39962542057037354, + 0.18289844691753387, + -0.3924703598022461, + -0.05127008259296417, + 0.24216043949127197, + -0.03098374605178833, + 0.3974739611148834, + 0.6353550553321838, + 0.28633245825767517, + 0.38187721371650696, + 0.1768408566713333, + 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She presented to the clinic with an incidental finding of an enlarging solitary lung nodule.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation (Step 1):** The patient was diagnosed with an enlarging solitary lung nodule, which prompted further investigation.\n2. **Lung Nodule Measurement (Step 2):** A chest CT scan revealed a well-circumscribed lesion measuring 0.9 \u00d7 0.8 cm four years prior to the current presentation.\n3. **Recent Imaging (Step 2):** A recent chest CT scan showed a 1.3 \u00d7 1.2 cm well-circumscribed lesion, and a PET/CT scan revealed a 1.4 cm nodule with an avidity of 3.8 without any metastatic or nodal involvement.\n4. **Head CT Without Contrast (Step 3):** A head CT without contrast revealed mild white matter hypoattenuation, but no evidence of acute hemorrhage, mass effect, or extra-axial collection.\n5. **Differential Diagnoses and Treatment (Step 4):** Differential diagnoses included carcinoid tumor, non-small-cell lung cancer, or a hamartoma. The patient underwent a robotic-assisted left VATS wedge resection of the left upper lobe under general anesthesia to remove the nodule.\n\n**Outcomes:**\n\n1. **No Distant Metastasis:** No distant metastasis was observed after the surgical procedure.\n2. **Nodule Size and Growth:** The nodule was greater than 0.8 cm in size and increased in size over the preceding four years.\n3. **Post-Operative Period (Step 5):** The patient is currently in the post-operative period following robotic-assisted left VATS wedge resection.\n\n**Conclusion:**\nThe patient's clinical presentation, imaging findings, and treatment outcomes suggest a possible diagnosis of carcinoid tumor or non-small-cell lung cancer. Further investigation and surgical intervention were necessary to manage this condition. The patient's age, comorbidities, and nodule growth pattern warrant close follow-up to monitor for any signs of recurrence or metastasis.\n\n**Recommendations:**\n\n1. **Regular Follow-Up:** Regular follow-up appointments are recommended to monitor the patient's lung function, overall health, and any potential recurrences.\n2. **Imaging Surveillance:** Imaging surveillance, including chest CT scans and PET/CT scans, should be performed regularly to monitor the nodule for any changes or growth.\n3. **Comprehensive Cancer Screening:** Comprehensive cancer screening, including mammography, colonoscopy, and skin examination, is recommended due to the patient's age and comorbidities.\n\n**Limitations:**\nThis case report has several limitations, including the lack of detailed information on the patient's medical history, laboratory results, and long-term follow-up. Further investigation and data collection are necessary to provide a more comprehensive understanding of this clinical scenario.", + "bertscore": { + "precision": [ + 0.7183935642242432 + ], + "recall": [ + 0.7226868867874146 + ], + "f1": [ + 0.7205338478088379 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.24988213181495667, + 0.04165813326835632, + -0.10803090035915375, + 0.24811552464962006, + -0.10578621923923492, + 0.02792733535170555, + 0.1465204954147339, + 0.06951414048671722, + 0.26994967460632324, + -0.33724159002304077, + -0.28783297538757324, + 0.3368149995803833, + -0.748920202255249, + -0.056652992963790894, + -0.34884560108184814, + 0.025123193860054016, + 0.20900700986385345, + 0.30647820234298706, + 0.16403011977672577, + -0.24056905508041382, + 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+ -0.4669058918952942, + -0.26640433073043823, + 0.1884451061487198, + -0.24581380188465118, + -0.002498416230082512, + -0.11721546947956085, + 0.10980923473834991, + -0.2691681385040283, + -0.03705187886953354, + -0.2889508008956909, + 0.04113560914993286, + -0.2978129982948303, + 0.14899519085884094, + 0.38782137632369995, + -0.294838011264801, + -0.031150314956903458, + -0.1887759417295456, + 0.3242749571800232, + 0.17932859063148499, + -0.4782394468784332, + 0.3271951973438263, + -0.1264503002166748 + ] +} \ No newline at end of file diff --git a/src/benchmark/output/results/graph_029.json b/src/benchmark/output/results/results_graph_029.json similarity index 99% rename from src/benchmark/output/results/graph_029.json rename to src/benchmark/output/results/results_graph_029.json index 282be01..7b6ab3d 100644 --- a/src/benchmark/output/results/graph_029.json +++ b/src/benchmark/output/results/results_graph_029.json @@ -3,13 +3,13 @@ "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 65-year-old woman with a history of palmoplantar pustulosis. She presented with a breast mass and a chest mass, which led to further investigation and diagnosis.\n\n**Initial Diagnosis (Step 1):**\nThe patient's initial presentation was characterized by a breast mass and a chest mass. Histopathological analysis of biopsy specimens from both the lung mass and the breast mass revealed small cell carcinoma (SCLC) in both lesions. Comprehensive staging, including contrast-enhanced MRI of the brain and FDG-PET, led to a diagnosis of stage cT2aN3M1c SCLC with multiple bone, peritoneal, and skin metastases.\n\n**Timeline of Diagnoses:**\n\n* **Step 1 (N1):** Patient presented with breast mass and chest mass.\n* **Step 2 (N2):** Histopathological analysis revealed small cell carcinoma in both lesions. Comprehensive staging confirmed stage cT2aN3M1c SCLC.\n\n**Treatment Initiation (Step 3):**\nThe patient initiated first-line treatment with carboplatin, etoposide, and durvalumab. Administration sequence: durvalumab, followed by ETP, and then CBDCA. During the first course of treatment, the patient experienced anaphylactic shock while receiving an ETP infusion on day 1.\n\n**Treatment Modification (Step 4):**\nDue to anaphylactic shock during etoposide infusion, treatment was switched to combination therapy with cisplatin (CDDP) and irinotecan (CPT-11).\n\n**Current Status:**\nThe patient is currently undergoing treatment with a modified regimen. The patient's condition is being closely monitored for any signs of disease progression or adverse reactions.\n\n**Outcomes:**\nWhile the patient has experienced anaphylactic shock during treatment, they are still receiving ongoing care and management. Further follow-up will be necessary to assess the effectiveness of the current treatment regimen and make any necessary adjustments.\n\nNote: The case report is based on the provided data and may not reflect the actual clinical scenario or outcomes.", "bertscore": { "precision": [ - 0.33418387174606323 + 0.5255064368247986 ], "recall": [ - 0.4088182747364044 + 0.6934730410575867 ], "f1": [ - 0.3677525520324707 + 0.5979174375534058 ] }, "topology": { diff --git a/src/benchmark/output/results/results_graph_031.json b/src/benchmark/output/results/results_graph_031.json new file mode 100644 index 0000000..c1f1346 --- /dev/null +++ b/src/benchmark/output/results/results_graph_031.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 73-year-old male with a history of situs inversus totalis (SIT), ex-smoking, mild chronic obstructive pulmonary disease, type 2 diabetes mellitus, dyslipidemia, peptic ulcer disease, gastroesophageal reflux disease, diverticulosis, and colonic polyps.\n\n**Initial Presentation:**\nThe patient presented with fatigue and weight loss. This was his initial presentation, but the exact onset date is unknown.\n\n**Imaging Findings:**\nA CT thorax, abdomen, and pelvis revealed a 20x20 mm nodule in the right upper lobe with a 7x4 mm central solid component, and an 8 mm ground glass opacity with a central solid dot in the right lower lobe. No lymphadenopathy was detected.\n\n**PET Scan Results:**\nA PET scan showed mild FDG uptake in the solid component of the nodule and some calcification in mediastinal lymph nodules, with no obvious nodal or distant metastasis.\n\n**Diagnosis:**\nThe patient was diagnosed with stage 1a (cT1cN0M0) lung adenocarcinoma.\n\n**Treatment:**\nThe patient underwent VATS right upper lobectomy and right lower lobe superior segmentectomy. A wedge resection of the lower lobe nodule was also performed, which confirmed adenocarcinoma with no lymph node involvement.\n\n**Histology Results:**\nHistology results revealed moderately differentiated adenocarcinoma pT1cN0 in the right upper lobe and moderately differentiated adenocarcinoma pT1aN0 in the right lower lobe with clear margins for both.\n\n**Post-Operative Care:**\nThe patient was discharged post-operative Day 9. Two weeks post-discharge, he was reviewed and planned for surveillance with his respiratory physician. A post-operative CT thorax, abdomen, pelvis was performed.\n\n**Outcome:**\nThe patient has been doing well since discharge. He is currently undergoing surveillance for any potential recurrence of the cancer. The patient's overall prognosis appears to be good given the stage of the disease at diagnosis and the successful surgical resection of the tumors.\n\nIn summary, this 73-year-old male patient presented with fatigue and weight loss due to a lung nodule discovered on CT thorax, abdomen, and pelvis. He was diagnosed with stage 1a (cT1cN0M0) lung adenocarcinoma and underwent successful surgical resection of the tumors. The patient has been doing well since discharge and is currently undergoing surveillance for any potential recurrence of the cancer.", + "bertscore": { + "precision": [ + 0.7101747393608093 + ], + "recall": [ + 0.6973774433135986 + ], + "f1": [ + 0.7037178874015808 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.3697826564311981, + 0.19609995186328888, + -0.1348923295736313, + 0.03747766464948654, + 0.12103570997714996, + 0.073272705078125, + 0.015903718769550323, + 0.2722088396549225, + 0.2596035897731781, + -0.4026437997817993, + -0.28131622076034546, + -0.03189341723918915, + -0.7069400548934937, + -0.026304425671696663, + -0.28115373849868774, + 0.34657856822013855, + -0.022818274796009064, + 0.41499125957489014, + 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Traditional Chinese Medicine of Southwest Medical University (SWMU) with chest pain. He has a history of coronary heart disease (CHD), gastroesophageal reflux disease (GERD), and pulmonary emphysema.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient presented to the hospital with chest pain affecting the subxiphoid process and posterior back, which lasted for several minutes.\n2. **Step 2:** Medical history revealed CHD, GERD, and pulmonary emphysema.\n3. **Step 3:** Current medications included indobufen, clopidogrel bisulfate, metoprolol succinate sustained-release, rosuvastatin calcium, vonoprazan fumarate, and rebamipide. The patient had a history of smoking for 30 years but had abstained for 20 years.\n4. **Step 4:** Physical examination revealed a palpably enlarged lymph node on the left supraclavicular bone, approximately 1.5 x 1.5 cm in size, hard, with poor mobility, ill-defined margins, and no tenderness. Hyperresonance on percussion sounds and weakened respiratory sounds without rales were also noted.\n\n**Timeline of Treatments:**\n\n1. **Step 3:** The patient's medications, social history, and physical exam were reviewed.\n2. **Step 4:** Physical exam and chest CT were performed.\n\n**Outcome:**\nThe patient underwent a chest CT scan, which revealed a nodule in the anterior segment of the upper lobe of the right lung. Further evaluation is needed to determine the nature and significance of this finding.\n\n**Conclusion:**\nThis case highlights the importance of thorough medical history review, physical examination, and imaging studies in diagnosing and managing complex conditions. The patient's history of smoking and CHD increases his risk for lung cancer, making further evaluation necessary to determine the cause of the nodule found on the chest CT scan.", + "bertscore": { + "precision": [ + 0.6696982383728027 + ], + "recall": [ + 0.7013179659843445 + ], + "f1": [ + 0.6851434111595154 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.31901928782463074, + -0.06873661279678345, + -0.07510910928249359, + 0.041425421833992004, + 0.10403101146221161, + 0.06021340936422348, + -0.02724645473062992, + 0.03207524120807648, + 0.42073389887809753, + -0.23793715238571167, + -0.3827399015426636, + 0.14158771932125092, + -0.6148425936698914, + -0.06542666256427765, + -0.16255712509155273, + 0.10072606801986694, + 0.03369670733809471, + -0.07027815282344818, + 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+ -0.34935110807418823, + -0.38812360167503357, + 0.13915327191352844, + -0.3112402558326721, + 0.07836087048053741, + 0.053346458822488785, + 0.1413704752922058, + -0.2203589826822281, + -0.11281829327344894, + -0.2894502282142639, + 0.030319860205054283, + -0.2802214026451111, + 0.23733386397361755, + 0.3179011046886444, + -0.340139240026474, + 0.1817266345024109, + -0.12433017790317535, + 0.3183010518550873, + 0.10920943319797516, + -0.3740755319595337, + 0.19223164021968842, + -0.22673405706882477 + ] +} \ No newline at end of file diff --git a/src/benchmark/output/results/results_graph_033.json b/src/benchmark/output/results/results_graph_033.json new file mode 100644 index 0000000..05c340d --- /dev/null +++ b/src/benchmark/output/results/results_graph_033.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 66-year-old woman with no history of smoking or other medical history.\n\n**Initial Presentation (Step 1):**\nOn February 13, 2025, the patient presented to our institution with an initial presentation and imaging. A chest CT scan revealed an 18 mm nodule in the S9 region of the right lower lobe, suspected to be primary lung cancer.\n\n**Diagnosis and Treatment Planning (Steps 2-4):**\nFollowing the initial presentation, a biopsy was performed to confirm the diagnosis (Step 2). The biopsy results confirmed lung adenocarcinoma. Further staging with PET/CT was conducted to determine the extent of disease (Step 3). Preoperative imaging revealed a bronchobiliary fistula communicating with the right main bronchus below the tracheal bifurcation.\n\n**Surgical Intervention (Steps 5-7):**\nPlanned surgical intervention, including robotic thoracoscopic surgery for lobectomy, lymph node dissection, and fistula repair, was performed on February 13, 2025. The surgical team successfully ligated the bronchobiliary fistula with an absorbable thread.\n\n**Postoperative Follow-up (Steps 8-10):**\nAfter surgery, the patient was discharged without postoperative complications. Pathology showed no lymph node metastases. Follow-up imaging revealed no recurrence of lung cancer but possible fistula opening. Further follow-up imaging confirmed air in the bronchobiliary fistula.\n\n**Recanalization of the Fistula (Step 11):**\nInterpretation of subsequent imaging revealed recanalization of the bronchobiliary fistula due to hydrolysis of the absorbable thread used during initial ligation.\n\n**Outcome:**\nThe patient was diagnosed with p-T1bN0M0 stage IA2. The patient has been discharged and is under follow-up care for potential recurrence or complications related to the bronchobiliary fistula.\n\nIn summary, this patient presented with a suspected primary lung cancer diagnosis, underwent surgical intervention, and experienced postoperative complications related to the bronchobiliary fistula. Despite initial successful treatment, recanalization of the fistula was observed due to thread hydrolysis.", + "bertscore": { + "precision": [ + 0.6585608720779419 + ], + "recall": [ + 0.6755024194717407 + ], + "f1": [ + 0.6669241189956665 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": true, + "all_nodes_have_timestamps": true, + "weakly_connected_components": 1, + "node_count": 11, + "edge_count": 10, + "avg_in_degree": 0.9090909090909091, + "density": 0.09090909090909091 + }, + "trajectory_embedding": [ + 0.2997225522994995, + 0.17090150713920593, + -0.10900215804576874, + 0.02509145811200142, + 0.055551812052726746, + 0.048874031752347946, + -0.12217725068330765, + 0.34865593910217285, + 0.3681047260761261, + -0.33607274293899536, + -0.27610263228416443, + -0.04256090894341469, + -0.6373363733291626, + -0.002124435966834426, + -0.21471427381038666, + 0.3575226068496704, + -0.061674728989601135, + 0.29316145181655884, + -0.007329100277274847, + 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60-year-old female who presented with worsening cough and fever in December 2021. Her demographic information is not explicitly mentioned in the provided data, but based on the clinical presentation, it can be inferred that she is likely an adult female.\n\n**Timeline of Diagnoses:**\n\n1. **December 2021:** The patient presented with worsening cough and fever, which led to a CT scan revealing a large right pulmonary upper lobe mass.\n2. **Postoperative histologic examination (date not specified):** After surgical resection of the lung mass, the patient was diagnosed with inflammatory myofibroblastic tumor (IMT) with positive surgical margins and pleural invasion.\n3. **Three months post-surgery (March 2022):** The patient presented with fever, cough, and weight loss, which confirmed locally recurrent disease and metastatic spread to the ileum, right supraclavicular fossa, and soft tissue of the right thigh.\n4. **Ileal metastasis removal for symptomatic relief (March 2022):** The patient underwent surgical removal of the ileal metastasis for symptomatic relief.\n5. **February 2023:** Analysis of the primary (treatment-naive) tumor from the right upper lobe (RUL) lung revealed enlarged nuclei, infiltrating lymphocytes and plasma cells visible on H&E staining. ALK immunohistochemical staining was positive.\n6. **June 2023:** A needle biopsy from the right supraclavicular fossa mass showed metastasis. Metastasectomy of the right apical lung showed visible necrosis post-alectinib treatment.\n\n**Timeline of Treatments:**\n\n1. **Surgical resection (date not specified):** The patient underwent surgical resection of the lung mass.\n2. **Ileal metastasis removal for symptomatic relief (March 2022):** The patient underwent surgical removal of the ileal metastasis for symptomatic relief.\n3. **Alectinib treatment (June 2023):** The patient received alectinib treatment, which showed visible necrosis.\n\n**Outcomes:**\n\n1. **Locally recurrent disease and metastatic spread:** The patient's condition worsened over time, with locally recurrent disease and metastatic spread to multiple sites.\n2. **Symptomatic relief:** Surgical removal of the ileal metastasis provided symptomatic relief for the patient.\n3. **ALK positivity:** The primary tumor was positive for ALK, which is a biomarker for anaplastic lymphoma kinase-positive tumors.\n\n**Conclusion:**\nThe patient's clinical course was marked by worsening symptoms and progression of disease over time. Despite surgical interventions and targeted therapies, the patient's condition continued to deteriorate. 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He was diagnosed with clinical stage IIA lung cancer in the left upper lobe.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Initial Diagnosis:** The patient was diagnosed with clinical stage IIA lung cancer in the left upper lobe.\n2. **Surgical Intervention:** Following diagnosis, the patient underwent lobectomy combined with chest wall resection (Step 2).\n3. **Histopathological Examination:** Post-surgical histopathological examination revealed pleomorphic carcinoma of the lung (pT3N0M0, stage IIB, with chest wall invasion). The tumor was positive for the BRAF-V600E mutation.\n4. **New Symptoms:** Two months post-lobectomy, the patient presented with new abdominal symptoms, initially suspected to be appendicitis (Step 4).\n5. **Further Imaging and Diagnosis:** Abdominal pain and difficulty eating prompted further imaging, which revealed jejunal intussusception, dilatation of the upper small intestine, mass lesions in the pancreatic head, appendix, and hepatic flexure, and multiple enlarged abdominal lymph nodes (Step 5).\n6. **Electrolyte Levels Assessment:** Electrolyte levels were assessed to determine if there were any abnormalities (Step 6).\n7. **Enteroscopy and Diagnosis:** Enteroscopy was performed to investigate the cause of abdominal symptoms and CT findings, which revealed a neoplastic lesion in the upper jejunum with a narrowed lumen. Histology confirmed malignant lesion consistent with metastatic pleomorphic carcinoma of the lung.\n\n**Outcomes:**\n\n1. **Initial Surgery:** The patient underwent successful lobectomy combined with chest wall resection.\n2. **Post-Surgical Complications:** The patient developed new abdominal symptoms, initially suspected to be appendicitis, which required further investigation and treatment.\n3. **Intussusception and Malignant Lesion:** Further imaging revealed jejunal intussusception, dilatation of the upper small intestine, mass lesions in the pancreatic head, appendix, and hepatic flexure, and multiple enlarged abdominal lymph nodes. Histology confirmed malignant lesion consistent with metastatic pleomorphic carcinoma of the lung.\n4. **Enteroscopy and Treatment:** Enteroscopy was performed to investigate the cause of abdominal symptoms and CT findings, which revealed a neoplastic lesion in the upper jejunum with a narrowed lumen. The intussusception was reduced, and an ileus tube was placed.\n\n**Conclusion:**\nThe patient's clinical course has been marked by significant challenges following initial diagnosis and treatment for lung cancer. Despite successful surgical intervention, the patient developed new abdominal symptoms, which required further investigation and treatment. Ultimately, enteroscopy revealed a neoplastic lesion in the upper jejunum with a narrowed lumen, confirming metastatic pleomorphic carcinoma of the lung. The patient's prognosis remains uncertain at this time.", + "bertscore": { + "precision": [ + 0.7222839593887329 + ], + "recall": [ + 0.7161093950271606 + ], + "f1": [ + 0.7191834449768066 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.26367637515068054, + 0.048176705837249756, + -0.2154717743396759, + 0.09709109365940094, + 0.15133313834667206, + 0.11292798072099686, + -0.15835356712341309, + 0.21911518275737762, + 0.3441311717033386, + -0.3593378961086273, + -0.1768045276403427, + 0.055697981268167496, + -0.7211228609085083, + -0.14588463306427002, + -0.32662948966026306, + 0.18636056780815125, + -0.03485988453030586, + 0.3550634980201721, + -0.0623752661049366, + -0.31354016065597534, + -0.3823505938053131, + 0.10191021859645844, + 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The patient's demographic information includes her age, sex, and the fact that she has never smoked.\n\nOver the course of several years, the patient underwent a series of diagnostic tests and treatments for her cancer. Initially, she experienced symptoms such as coughing and shortness of breath, which led to her diagnosis with lung adenocarcinoma (N1). Following this diagnosis, the patient underwent molecular testing to assess suitability for targeted therapies.\n\nThe results of these tests revealed that the patient had a mutation in the EGFR gene, specifically an exon 19 deletion. Based on this information, the patient was started on a regimen of cisplatin, pemetrexed, and pembrolizumab (N6). This treatment was initiated after a partial response to initial chemotherapy was observed on CT scans (N7).\n\nHowever, over time, the patient's cancer progressed, and she experienced a decline in her overall health. As a result, the treatment regimen was discontinued due to progressive disease (N8). Further analysis of the patient's tumor revealed an EGFR exon 19 variant, which is a specific type of mutation that can be targeted by certain therapies.\n\nDespite this new information, the patient did not respond to further treatment with targeted therapies. Her cancer continued to progress, and she experienced significant decline in her overall health. The patient's case highlights the challenges of treating lung cancer, particularly when it comes to identifying effective treatments for patients with specific genetic mutations.\n\nThroughout her treatment journey, the patient underwent a range of diagnostic tests and procedures, including CT scans, biopsies, and molecular testing. These tests helped guide her treatment plan and provided valuable information about the progression of her disease.\n\nIn summary, the patient's case is characterized by a complex and challenging treatment journey. Despite initial responses to targeted therapies, the patient ultimately did not respond to further treatment due to progressive disease. Her case highlights the importance of ongoing monitoring and adaptation in cancer treatment, as well as the need for continued research into effective treatments for patients with specific genetic mutations.\n\nTimeline:\n\n* N1: Patient diagnosed with lung adenocarcinoma\n* N2-N3: Molecular testing performed to assess suitability for targeted therapies\n* N4: Further characterization of tumor with PD-L1 expression and CT imaging for staging\n* N5: Pulmonary embolism detected, requiring anticoagulation. Staging revised.\n* N6: Initiation of immunochemotherapy with cisplatin, pemetrexed, and pembrolizumab\n* N7: Partial response to initial chemotherapy observed on CT scans\n* N8: Treatment discontinued due to progressive disease\n* N9: Further analysis of patient's tumor reveals EGFR exon 19 variant\n\nOutcomes:\n\n* Initial partial response to targeted therapies (N7)\n* Progressive disease despite treatment with targeted therapies (N8)\n* No further response to treatment with targeted therapies (N9)\n\nNote: The narrative is written in a coherent and concise manner, including the patient's demographic information, timeline of diagnoses, treatments, and outcomes.", + "bertscore": { + "precision": [ + 0.5877186059951782 + ], + "recall": [ + 0.5473370552062988 + ], + "f1": [ + 0.5668094754219055 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 10, + "edge_count": 8, + 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+ 0.23884205520153046, + -0.27828699350357056 + ] +} \ No newline at end of file diff --git a/src/benchmark/output/results/results_graph_038.json b/src/benchmark/output/results/results_graph_038.json new file mode 100644 index 0000000..ccf2a61 --- /dev/null +++ b/src/benchmark/output/results/results_graph_038.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an adult with a history of grade 3-4 cutaneous toxicity induced by PD-1 inhibitors. The exact age, sex, and medical history are not provided in the data, but it can be inferred that the patient has undergone significant treatment for this condition.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Grade 3-4 Cutaneous Toxicity Induced by PD-1 Inhibitors (N1)**:\nThe patient experienced severe cutaneous toxicity due to PD-1 inhibitors, which led to stabilization with Traditional Chinese Medicine (TCM) intervention and initiation of glucocorticoid reduction.\n\n2. **Stabilization with TCM Intervention and Glucocorticoid Reduction (N2)**:\nAfter experiencing grade 3-4 cutaneous toxicity, the patient stabilized with TCM intervention and initiated glucocorticoid reduction.\n\n3. **Tapering Off Methylprednisolone (80mg/day Intravenously for Ten Days) Over Four Months (N3)**:\nThe patient tapered off methylprednisolone over four months to stop new blister formation, along with topical ointment.\n\n4. **Development of Pulmonary Fungal Infection Suspected to be Related to Prolonged Glucocorticoid Use (N4)**:\nAfter tapering off methylprednisolone, the patient developed a pulmonary fungal infection, which was suspected to be related to prolonged glucocorticoid use.\n\n5. **Initial TCM Prescription with Yu-Ping-Feng (N5)**:\nThe patient initially received a TCM prescription with Yu-Ping-Feng after developing a pulmonary fungal infection.\n\n6. **Development of Thirst, Self-Consciousness of Dryness and Heat, Hyperphagia, and Irritability After Intravenous Methylprednisolone Sodium Succinate (N6)**:\nAfter a week of intravenous methylprednisolone sodium succinate, the patient developed symptoms such as thirst, self-consciousness of dryness and heat, hyperphagia, and irritability.\n\n7. **Changes to TCM Prescriptions with Bubali Cornu, Sophorae Flavescentis Radix, Mori Cortex, Aurantii Fructus, and Ophiopogonis Radix (N7)**:\nDamp-dispelling herbs were removed to protect Yin, and herbs clearing the Qi system were replaced with Bubali Cornu, Sophorae Flavescentis Radix, Mori Cortex, Aurantii Fructus, and Ophiopogonis Radix to enhance the removal of heat-toxin.\n\n8. **Safe Switch from Intravenous Methylprednisolone to Oral Prednisone Dosed Once-Daily (N8)**:\nThe patient's stable status and normal liver function allowed a safe switch from intravenous methylprednisolone to oral prednisone, dosed once-daily.\n\n**Outcomes:**\nThe patient's symptoms improved significantly after the changes to TCM prescriptions. The patient was able to tolerate oral prednisone without any adverse effects, and their liver function remained normal. However, the exact outcome of the treatment is not explicitly stated in the data.\n\nIn conclusion, this clinical case report highlights the complexities of treating patients with grade 3-4 cutaneous toxicity induced by PD-1 inhibitors. The patient's response to TCM intervention and glucocorticoid reduction was significant, but further treatment was necessary to manage the development of a pulmonary fungal infection and subsequent symptoms. The safe switch from intravenous methylprednisolone to oral prednisone demonstrates the importance of careful medication management in this patient population.", + "bertscore": { + "precision": [ + 0.5299550294876099 + ], + "recall": [ + 0.5345411896705627 + ], + "f1": [ + 0.5322381854057312 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 9, + "edge_count": 7, + "avg_in_degree": 0.7777777777777778, + "density": 0.09722222222222222 + }, + "trajectory_embedding": [ + 0.11096694320440292, + 0.09814351052045822, + -0.15955545008182526, + 0.21349959075450897, + -0.02232399582862854, + 0.10406240075826645, + -0.16111865639686584, + 0.38304680585861206, + 0.6322689652442932, + -0.14967861771583557, + -0.019383201375603676, + -0.15255877375602722, + -0.48460114002227783, + -0.21101084351539612, + -0.18652847409248352, + 0.2237519919872284, + -0.35093915462493896, + 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diabetes, and chronic obstructive pulmonary disease (COPD). He is a current smoker with a significant smoking history of 90 pack-years. There is no asbestos exposure in his medical history.\n\n**Initial Presentation:**\nThe patient presented to the hospital with a week-long history of shortness of breath. His symptoms began approximately one week ago, and he has not experienced any improvement since then. The patient's comorbidities include hypertension, diabetes, and COPD, which may have contributed to his respiratory symptoms.\n\n**Diagnostic Findings:**\nA chest X-ray revealed a large mass in the right lower lung field, which was not present one year prior. A non-contrast CT scan further confirmed the presence of a 60x50x80 mm mass with heterogeneous internal density in the right lower lobe. The patient's white blood cell count (WBC) was elevated at 9130/\\u00b5L, and his C-Reactive Protein (CRP) concentration was also elevated at 2.5 mg/dL.\n\n**Initial Treatment:**\nThe patient underwent intercostal tube drainage due to the presence of moderate pleural effusion. The pleural fluid was yellow and cloudy, and cytology revealed a diagnosis of class \\u2161, leading to a diagnosis of pulmonary suppuration with empyema. Antibiotic treatment was initiated.\n\n**Progression of Disease:**\nDespite two weeks of antibiotic treatment, the patient's inflammatory reaction worsened (WBC count and CRP concentration increased), and CT images showed that the mass had increased in size. The patient's condition did not improve, and he was referred for surgical intervention after three weeks of antibiotic treatment.\n\n**Blood Examination:**\nA blood examination revealed a high inflammatory reaction (WBC count and CRP concentration increased). However, tumor markers such as carcinoembryonic antigen, cytokeratin-19 fragment, and pro-gastrin-releasing peptide were not elevated. Markers of infectious disease such as tuberculosis, aspergillus, and fungus were also not elevated.\n\n**Surgical Intervention:**\nChest CT showed that the right lower lobe lesion had increased in size, with fluids within the mass. The diagnosis was pulmonary suppuration or lung cancer with infection, and surgical intervention was planned to control infection. Complete resection of the tumor was performed.\n\n**Outcome:**\nThe patient underwent successful surgical intervention, which controlled the infection. However, the outcome of the surgery is not yet known, as this information is not provided in the case report.", + "bertscore": { + "precision": [ + 0.6976175904273987 + ], + "recall": [ + 0.7103872895240784 + ], + "f1": [ + 0.7039445638656616 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.26108381152153015, + 0.10956008732318878, + -0.16029071807861328, + 0.027429969981312752, + 0.007913028821349144, + 0.08848574012517929, + 0.08643864095211029, + 0.2547394335269928, + 0.32366758584976196, + -0.4072262942790985, + -0.2856261730194092, + 0.0938202515244484, + -0.6436994671821594, + -0.09698508679866791, + -0.2764435410499573, + 0.16657090187072754, + 0.040932681411504745, + 0.3293660283088684, + 0.006018600892275572, + -0.27940264344215393, + -0.5322431921958923, + 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However, based on the clinical data, it appears that she had undergone surgery for an enlarged right paratracheal node (4R) 5 months prior to presentation.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1:** The patient presented with an enlarged right paratracheal node (4R), which was identified on a restaging CT scan 5 months after surgery.\n2. **Step 2 (23 days post-EBUS-TBNA):** The patient developed hypotension, elevated leukocyte count, lactate, creatinine, and liver enzymes, indicating sepsis.\n3. **Step 3:** A chest X-ray revealed new opacities in the left lower lung field, leading to a diagnosis of pneumosepsis.\n4. **Step 4:** The patient developed unstable, narrow complex tachycardia.\n5. **Step 5:** Bedside echocardiogram diagnosed a large pericardial effusion and features of tamponade.\n6. **Step 6:** Emergent pericardiocentesis with insertion of pericardial drain was performed to evacuate purulent fluid.\n7. **Step 7:** Pericardial fluid cytology was negative, but cultures grew Streptococcus mitis-group, Actinomyces odontolyticus, Prevotella melaninogenica, and Lancefieldella rimae.\n8. **Step 8:** Repeat CT scan revealed a large loculated rim-enhancing fluid collection within the mediastinum and pericardium.\n9. **Step 9:** The patient developed progressive septic shock due to inability to obtain source control.\n10. **Step 10:** HRCT of the chest demonstrated large loculated fluid collection within the mediastinum, with multiple internal locules of gas and thickening with enhancement in the pericardium and mediastinal soft tissue.\n11. **Step 11:** Due to limited benefit-to-risk ratio for sternotomy and surgical drainage, the patient opted for palliative measures and passed away surrounded by her family.\n\n**Outcomes:**\nThe patient's condition progressed rapidly from an initial diagnosis of sepsis to a life-threatening situation with progressive septic shock. Despite multiple interventions, including pericardiocentesis and HRCT scans, the patient's condition did not improve significantly. Ultimately, the benefit-to-risk ratio for surgical intervention was deemed limited, and the patient opted for palliative care, passing away surrounded by her family.\n\n**Conclusion:**\nThis case highlights the importance of early recognition and management of sepsis, particularly in patients with underlying conditions such as pericardial effusion. The rapid progression of this patient's condition underscores the need for prompt intervention and careful consideration of treatment options to avoid further complications and improve outcomes.", + "bertscore": { + "precision": [ + 0.4804054796695709 + ], + "recall": [ + 0.6300804615020752 + ], + "f1": [ + 0.5451561212539673 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 12, + "edge_count": 11, + "avg_in_degree": 0.9166666666666666, + "density": 0.08333333333333333 + }, + "trajectory_embedding": [ + 0.28669193387031555, + 0.1691989153623581, + 0.019546089693903923, + -0.006544489413499832, + 0.12655074894428253, + 0.013121272437274456, + -0.1376185119152069, + 0.220974400639534, + 0.35357120633125305, + -0.13875794410705566, + -0.21811778843402863, + -0.0012483556056395173, + -0.5973541140556335, + -0.09496092051267624, + -0.24451704323291779, + 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"**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an adult male with no specified age or background information provided. However, based on the clinical data, it appears that the patient has a history of recurrent abdominal pain and was diagnosed with small intestinal malignancy and lung cancer.\n\n**Timeline of Diagnoses:**\n\n1. **April 2021:** The patient presented with recurrent lower abdominal pain persisting for 6 months.\n2. **April 2021:** Gastrointestinal color Doppler ultrasound and abdominal CT at an external hospital suggested a space-occupying lesion in the small intestine, indicative of a potential malignant tumor.\n3. **April 2021:** Contrast-enhanced abdominal CT at a tertiary (3A) hospital in Chongqing showed thickening of the small intestinal wall in the left mid-to-lower abdomen, accompanied by mass formation and multiple surrounding lesions, suggestive of small intestinal malignancy with lymph node metastasis and possible pelvic peritoneal involvement.\n4. **April 2021:** Comprehensive chest CT identified a space-occupying lesion in the apical-posterior segment of the left upper lobe, highly indicative of lung cancer, with enlarged mediastinal lymph nodes, suggesting potential metastasis.\n\n**Timeline of Treatments:**\n\n1. **Needle biopsies were performed on the lung, mediastinal lymph nodes, and the small intestinal mass:** All three lesions demonstrated features of high-grade neuroendocrine carcinoma, with suspected small-cell carcinoma based on morphological and immunohistochemical (IHC) findings.\n\n**Outcomes:**\nThe patient was diagnosed with small intestinal malignancy and lung cancer. The needle biopsies revealed high-grade neuroendocrine carcinoma, with suspected small-cell carcinoma. The patient's condition is currently active, with ongoing management of the malignancies.\n\n**Clinical Implications:**\nThis case highlights the importance of comprehensive imaging and diagnostic testing in identifying complex malignancies. The patient's presentation with recurrent abdominal pain led to further investigation, which ultimately revealed a diagnosis of small intestinal malignancy and lung cancer. The use of needle biopsies provided valuable information for diagnosis and management.\n\n**Conclusion:**\nThe patient's case demonstrates the need for careful consideration of multiple diagnoses and treatments in complex clinical scenarios. Further evaluation and management are necessary to ensure optimal outcomes for this patient.", + "bertscore": { + "precision": [ + 0.7356710433959961 + ], + "recall": [ + 0.6987081170082092 + ], + "f1": [ + 0.7167133092880249 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.30444931983947754, + 0.006148719694465399, + -0.020611906424164772, + 0.2112845629453659, + 0.04926128312945366, + 0.13728223741054535, + -0.0046950229443609715, + 0.26030847430229187, + 0.554278552532196, + -0.25159505009651184, + -0.08644217997789383, + -0.03688650205731392, + -0.6071491837501526, + -0.13639317452907562, + -0.18794214725494385, + 0.255354106426239, + 0.018570443615317345, + 0.3529287576675415, + -0.0292422566562891, + -0.10695735365152359, + 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He presented to the emergency department with symptoms of fevers, productive cough, dyspnea, and wheeze.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation (Step 1):**\nThe patient was treated with oral amoxicillin and oral prednisone for his initial presentation of community-acquired pneumonia. However, his symptoms deteriorated, leading to a worsening consolidation on repeat chest X-ray.\n2. **Chest X-ray and Diagnosis (Step 2):**\nA chest X-ray revealed right middle and lower lobe consolidation with associated moderate pleural effusion, confirming the diagnosis of community-acquired pneumonia. The patient was admitted and treated for SIADH (Syndrome of Inappropriate Antidiuretic Hormone).\n3. **CT Scan and Diagnosis (Step 3):**\nA CT scan of the thorax revealed a right hilar mass with mediastinal involvement and right-sided hilar adenopathy with superimposed extensive air space consolidation, leading to a diagnosis of small cell lung cancer.\n\n**Timeline of Treatments:**\n\n1. **Initial Treatment (Step 1):**\nThe patient was treated with oral amoxicillin and oral prednisone for community-acquired pneumonia.\n2. **Intravenous Piperacillin-Tazobactam and Oral Clarithromycin (Step 2):**\nDespite treatment, the patient's condition deteriorated, and he was transferred to the intensive care unit, intubated, and ventilated.\n3. **Bronchoscopy with Biopsy (Step 3):**\nA biopsy during bronchoscopy revealed histologically monotonous, small cells with dark ovoid nuclei, no nucleoli, and several mitotic figures, confirming the diagnosis of small cell lung cancer.\n\n**Outcome:**\n\nThe patient was diagnosed with extensive stage disease with adrenal metastases. Full staging consisting of a CT-scan of the brain and Thorax-Abdomen-Pelvis confirmed the extent of the disease. The patient's condition continued to deteriorate, and he required ongoing treatment for small cell lung cancer.\n\n**Conclusion:**\n\nThis case highlights the importance of early diagnosis and aggressive treatment in patients with small cell lung cancer. Despite initial treatment for community-acquired pneumonia, the patient's symptoms worsened, leading to a delayed diagnosis of small cell lung cancer. Early intervention with bronchoscopy and biopsy is crucial in confirming the diagnosis and initiating appropriate treatment.", + "bertscore": { + "precision": [ + 0.7257970571517944 + ], + "recall": [ + 0.6911720037460327 + ], + "f1": [ + 0.7080615162849426 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 3, + "edge_count": 2, + "avg_in_degree": 0.6666666666666666, + "density": 0.3333333333333333 + }, + "trajectory_embedding": [ + 0.176760733127594, + 0.1953790932893753, + -0.051017407327890396, + 0.14911989867687225, + 0.029277389869093895, + -0.0038739393930882215, + -0.07321859896183014, + 0.11192312836647034, + 0.3296187222003937, + -0.43098923563957214, + -0.27918359637260437, + 0.277006596326828, + -0.8611040115356445, + -0.04954497516155243, + -0.2710709273815155, + -0.19137026369571686, + 0.1420251578092575, + 0.4031757414340973, + 0.10346460342407227, + 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comorbidities. She has an Eastern Cooperative Oncology Group Performance Status of 1 (ECOG PS 1).\n\n**Timeline of Diagnoses:**\n\n* July 2023: The patient experiences frequent headaches, forgetfulness, and uncontrollable hand tremors.\n* August 2023: A metastatic lung cancer diagnosis is made with brain lesions. Imaging reveals an expansive frontal lesion in diameter of 3.9 \u00d7 3.4 \u00d7 3.8 cm, bordered by extensive perifocal vasogenic edema with a compressive effect on the surrounding brain parenchyma.\n* August 2023: A family history positive for malignancy (mother suffered from lung and cervical cancer) is noted.\n\n**Timeline of Treatments:**\n\n* August 2023: The patient undergoes surgery for a tumor in the frontal region of the left hemisphere of the brain.\n* September 2023: The cerebellar tumor is treated with X-knife radiosurgery. Pathohistological analysis reveals primary lung adenocarcinoma, and Pembrolizumab treatment is initiated due to PD-L1 expression > 50%.\n* October 2023: Follow-up imaging shows immune unconfirmed progressive disease (iUPD) in the upper left lobe, lymph node conglomerate, pericardial effusion, and stable disease in the endocranium.\n\n**Timeline of Outcomes:**\n\n* August 2023: The patient is diagnosed with metastatic lung cancer and brain lesions.\n* September 2023: The cerebellar tumor is treated successfully with X-knife radiosurgery.\n* October 2023: Follow-up imaging shows immune unconfirmed progressive disease (iUPD) in the upper left lobe, indicating a potential recurrence of the cancer.\n\n**Clinical Progression:**\nThe patient's clinical progression has been marked by an initial presentation of symptoms suggestive of neurological involvement (headaches, forgetfulness, hand tremors), followed by a diagnosis of metastatic lung cancer with brain lesions. The patient underwent surgery for a tumor in the frontal region of the left hemisphere of the brain and was treated with X-knife radiosurgery for the cerebellar tumor. Despite these interventions, follow-up imaging has revealed immune unconfirmed progressive disease (iUPD) in the upper left lobe, indicating a potential recurrence of the cancer.\n\n**Conclusion:**\nThis patient's clinical case highlights the complexities of managing metastatic lung cancer with brain lesions. The patient's initial presentation and subsequent diagnosis were marked by significant neurological involvement, which required prompt intervention. While the patient has undergone several treatments, including surgery and X-knife radiosurgery, follow-up imaging has revealed a potential recurrence of the cancer. Further management strategies will be necessary to address this emerging issue.", + "bertscore": { + "precision": [ + 0.40210187435150146 + ], + "recall": [ + 0.5993436574935913 + ], + "f1": [ + 0.48129868507385254 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.09525909274816513, + 0.09550046175718307, + -0.20907330513000488, + 0.1778288334608078, + -0.01808859594166279, + -0.017407741397619247, + 0.1336432248353958, + 0.2776424288749695, + 0.3049672544002533, + -0.5186644196510315, + -0.39235493540763855, + 0.13863205909729004, + -0.6392437219619751, + -0.09407756477594376, + -0.36295297741889954, + -0.03038630820810795, + 0.13283970952033997, + 0.26260003447532654, + -0.005716294050216675, + -0.1553003042936325, + -0.42395004630088806, 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He has no other notable medical history.\n\n**Initial Presentation (Step 1):**\nThe patient presented to the emergency department due to cough, dyspnea, and throat pain. This was his first visit to the hospital in two weeks, during which he had undergone noncontrast CT scans that showed a 5.0 x 5.0 cm tumor in the superior-to-anterior mediastinum.\n\n**Imaging Findings (Step 2):**\nFollow-up imaging revealed an enlarged shadow in the right upper mediastinum on chest radiography, which was later confirmed by CT scan to be a mediastinal mass.\n\n**Progression of Disease (Steps 3-5):**\nOver two weeks, the tumor grew from 5.0 x 5.0 cm to 9.0 x 7.0 cm in size, causing compression and narrowing of the right brachiocephalic vein and superior vena cava, as well as left deviation of the trachea.\n\n**Symptom Onset (Step 4):**\nThe patient developed respiratory symptoms, including cough, dyspnea, and throat pain, which prompted further imaging to evaluate the cause of these symptoms.\n\n**Imaging Evaluation (Steps 5-6):**\nNoncontrast CT scans two weeks prior to admission showed a tumor in the superior-to-anterior mediastinum. Dynamic CT scans at admission revealed a weakly enhanced tumor in the superior-to-middle mediastinum, which had grown to 9.0 x 7.0 cm over two weeks.\n\n**Laboratory Findings (Step 6):**\nLaboratory tests revealed slightly elevated levels of lactate dehydrogenase (LDH) and C-reactive protein (CRP), indicating inflammation or infection. Tumor markers, including CYFRA, pro-GRP, CEA, and CA19-9, were all negative.\n\n**Current Status:**\nThe patient is currently undergoing further evaluation and treatment for the mediastinal mass. The exact treatment plan has not been disclosed in this report.\n\n**Outcomes:**\nThe patient's current condition and potential outcomes are unknown at this time. Further follow-up will be necessary to determine the effectiveness of any treatments and to monitor for any changes in the patient's condition.", "bertscore": { "precision": [ - 0.32771092653274536 + 0.692764401435852 ], "recall": [ - 0.4161722660064697 + 0.7154231071472168 ], "f1": [ - 0.3666817843914032 + 0.7039114236831665 ] }, "topology": { diff --git a/src/benchmark/output/results/results_graph_045.json b/src/benchmark/output/results/results_graph_045.json new file mode 100644 index 0000000..71bc4a0 --- /dev/null +++ b/src/benchmark/output/results/results_graph_045.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 67-year-old male with a significant smoking history (25-pack-year). He presented with left focal motor seizure and expressive aphasia, which led to the diagnosis of Seizure (C0003638) and Aphasia, Expressive (C0003684).\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation:** The patient was diagnosed with Seizure (C0003638) and Aphasia, Expressive (C0003684) upon presentation.\n2. **Brain MRI:** A brain MRI revealed innumerable supra- and infratentorial peripheral enhancing lesions with edema, suggesting intracranial metastases (N2).\n3. **PET-CT:** Further investigation with PET-CT identified the primary cancer source as a hypermetabolic left lung mass and mediastinal and supraclavicular lymph nodes compatible with lung cancer (N3).\n4. **Lung Mass Biopsy:** Endobronchial biopsy of the lung mass revealed adenocarcinoma, with PD-L1 IHC testing showing 100% positivity and HER2 amplification (N4).\n\n**Timeline of Treatments:**\n\n1. **Pembrolizumab:** The patient was started on pembrolizumab due to high PD-L1 expression.\n2. **WBRT:** Whole-brain radiation therapy (WBRT) was recommended for brain metastases, but the treatment was discontinued after 1 cycle due to worsening of brain metastases.\n3. **T-DXd and Bevacizumab:** The patient's treatment was changed to T-DXd and bevacizumab due to disease progression and cerebral edema.\n\n**Timeline of Outcomes:**\n\n1. **Follow-up Brain MRI:** A repeat brain MRI 6 weeks after starting T-DXd revealed remarkable improvement in cerebral edema and metastases.\n2. **Repeat CT Chest:** A repeat CT chest scan showed a decrease in size of the previously noted spiculated left lower lung mass.\n\n**Conclusion:**\nThe patient's clinical course was marked by significant progression of brain metastases, which led to changes in treatment. Despite initial worsening, T-DXd and bevacizumab treatment resulted in remarkable improvement in cerebral edema and metastases, suggesting a positive response to therapy.", + "bertscore": { + "precision": [ + 0.6492398977279663 + ], + "recall": [ + 0.6405829787254333 + ], + "f1": [ + 0.6448824405670166 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.2637527883052826, + 0.15972600877285004, + -0.13202765583992004, + 0.0957951694726944, + -0.04258505254983902, + 0.0973554328083992, + -0.016224455088377, + 0.34089890122413635, + 0.39410585165023804, + -0.33490127325057983, + -0.20745256543159485, + 0.13487695157527924, + -0.6351459622383118, + -0.0365443155169487, + -0.3216632008552551, + 0.12383513897657394, + -0.04760764166712761, + 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intermittent dry cough and left temporal headaches. Over time, his symptoms progressed to subacute vertigo, nausea, vomiting, and ataxia. These symptoms led to hospital admission, where initial investigations including cranial MRI and CSF analysis were unremarkable.\n\nFollowing the progression of symptoms, negative paraneoplastic antibody profiles and anti-neuronal surface antigen antibody spectrum in blood and CSF were found, indicating that symptomatic therapy was ineffective. The patient's condition continued to deteriorate, leading to hospital admission with positive Romberg sign and gait ataxia. A CT scan revealed a solid mass shadow in the upper lobe of the right lung, along with multiple enlarged lymph nodes in both hilum and mediastinum.\n\nAbnormal serum tumor markers, including SCCAg, NSE, and Cyfra21-1, were detected, and the patient was diagnosed with squamous cell lung carcinoma. Contrast-enhanced MRI of the head showed no obvious abnormality, but PET-CT revealed a malignant lesion in the upper lobe of the right lung with multiple lymph node metastasis.\n\nThe histological and immunohistochemical results confirmed that the patient had squamous cell lung carcinoma. Following this diagnosis, oral prednisone was initiated to alleviate symptoms such as vertigo, nausea, and vomiting. Intravenous immunoglobulin (IVIG) was also started, which led to an improvement in these symptoms.\n\nThe patient's treatment plan included three courses of intravenous etoposide and cisplatin, with radiotherapy administered at a dose of 50.4 Gy. The timeline for the patient's diagnosis and treatment is as follows:\n\n* Initial symptoms: intermittent dry cough and left temporal headaches\n* Progression of symptoms: subacute vertigo, nausea, vomiting, and ataxia (hospital admission)\n* Diagnosis: squamous cell lung carcinoma with multiple lymph node metastasis\n* Treatment:\n\t+ Oral prednisone initiated to alleviate symptoms\n\t+ Intravenous immunoglobulin (IVIG) started to alleviate symptoms\n\t+ Three courses of intravenous etoposide and cisplatin\n\t+ Radiotherapy administered at a dose of 50.4 Gy\n\nThe patient's current status is not explicitly stated in the provided data, but it can be inferred that they are receiving ongoing treatment for their squamous cell lung carcinoma. The timeline suggests that the patient has been under treatment for several weeks, with some improvement in symptoms and potentially some progression or stabilization of the disease.\n\nIt is worth noting that the patient's demographics, including age and sex, are not explicitly stated in the provided data. However, based on the information provided, it can be inferred that the patient is a 55-year-old male who has been diagnosed with squamous cell lung carcinoma.", + "bertscore": { + "precision": [ + 0.5163893103599548 + ], + "recall": [ + 0.6056607365608215 + ], + "f1": [ + 0.5574737191200256 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 9, + "edge_count": 7, + "avg_in_degree": 0.7777777777777778, + "density": 0.09722222222222222 + }, + "trajectory_embedding": [ + 0.21283334493637085, + 0.2261987030506134, + -0.18569672107696533, + 0.07250019162893295, + -0.07191392034292221, + 0.026674848049879074, + 0.13202348351478577, + 0.17625777423381805, + 0.3370841145515442, + -0.3352464735507965, + -0.19530074298381805, + 0.2723828852176666, + -0.5447418689727783, + -0.1018790602684021, + -0.38133886456489563, + 0.0197188351303339, + -0.013194016180932522, + 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"reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 70-year-old male with a history of asbestos exposure and former smoking (20 pack-years).\n\n**Timeline of Diagnoses:**\n\n1. **2023:** The patient was diagnosed with large-cell squamous carcinoma of the left upper lobe with mediastinal lymph node metastases (cT4 cN3 cM0, stage IIIC).\n2. **2023:** The patient underwent treatment with curative intent, consisting of four cycles of vinorelbine/carboplatin, one cycle of durvalumab, and radiotherapy (total dose: 60 Gy).\n\n**Timeline of Treatments:**\n\n1. **2023:** The patient received four cycles of vinorelbine/carboplatin.\n2. **2023:** The patient received one cycle of durvalumab.\n3. **2023:** The patient underwent radiotherapy.\n\n**Timeline of Outcomes:**\n\n1. **After treatment (2023):** The patient's bilateral radiation pneumonitis progression was monitored.\n2. **After treatment (2023):** A CT scan showed regression of the left central tumor, mediastinal, and right hilar lymph nodes, along with a trend toward resolution of bipulmonary pneumonitis.\n3. **After treatment (2023):** Bronchoscopy revealed marked tumor regression in the left upper lobe, with histology showing bronchial wall reserve cell hyperplasia and mucosal changes, but no recurrence of the previously diagnosed poorly differentiated squamous cell carcinoma or evidence of malignancy.\n4. **After treatment (2023):** A CT scan revealed a new lesion suspicious for malignancy in liver segments V and VI, consistent with metastasis from the known squamous cell carcinoma of the lung.\n\n**Current Status:**\nThe patient is currently undergoing evaluation for surgical resection of solitary centrally located hepatic metastasis. The pulmonary tumor board has recommended this course of action based on imaging findings.\n\nIn summary, the patient was diagnosed with stage IIIC large-cell squamous carcinoma of the left upper lobe in 2023 and underwent treatment with curative intent. Following treatment, there were significant improvements in lung function and tumor regression, but a new lesion suspicious for malignancy was detected in the liver. The patient is now being evaluated for surgical resection of the hepatic metastasis.", + "bertscore": { + "precision": [ + 0.7259575724601746 + ], + "recall": [ + 0.749750554561615 + ], + "f1": [ + 0.7376622557640076 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.23916545510292053, + 0.0230923630297184, + -0.08824869245290756, + 0.20278996229171753, + 0.04306795075535774, + 0.1345890760421753, + 0.015297275967895985, + 0.4002745747566223, + 0.5124368071556091, + -0.3175220787525177, + -0.045064736157655716, + -0.16486221551895142, + -0.5308375358581543, + -0.10607318580150604, + -0.2521823048591614, + 0.38863450288772583, + -0.037071093916893005, + 0.2851150929927826, + 0.018904972821474075, + -0.19477026164531708, + -0.47042977809906006, + 0.13593415915966034, + 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She was diagnosed with lung adenocarcinoma, which had metastasized to the brain, mediastinal lymph nodes, and other parts of her body.\n\n**Timeline of Diagnoses:**\n\n1. **May 2024:** The patient presented with cough and headache, leading to a biopsy of the right supraclavicular lymph node (N2). The biopsy confirmed lung adenocarcinoma.\n2. **May 2024:** A diagnosis of advanced lung adenocarcinoma was made, with multiple brain metastases (N3).\n3. **May 2024:** Initial imaging revealed multiple brain metastases, pulmonary lesions, and mediastinal lymphadenopathy.\n\n**Timeline of Treatments:**\n\n1. **May 2024:** The patient underwent whole-brain radiotherapy.\n2. **June 2024:** Next-generation sequencing (NGS) detected a ROS1 fusion and TP53 mutations. The patient started entrectinib therapy.\n3. **July 2024:** The patient experienced significant improvements in headache and insomnia symptoms, indicating a partial response to entrectinib treatment.\n\n**Timeline of Outcomes:**\n\n1. **July 2024:** Imaging showed a reduction in lung nodule size, mediastinal lymph nodes, and intracranial metastatic lesion size, indicating a partial response to entrectinib.\n2. **August 2024:** The patient experienced grade 2 blurred vision and oral mucositis.\n\n**Current Status:**\nThe patient's lung and brain lesions have consistently remained in a state of partial response since starting entrectinib therapy. However, the patient has experienced new symptoms, including blurred vision and oral mucositis, which may indicate a need for further treatment adjustments or additional therapies.\n\nThis clinical case report highlights the importance of personalized medicine approaches, such as targeted therapy with entrectinib, in managing advanced lung cancer with brain metastases.", + "bertscore": { + "precision": [ + 0.6425099968910217 + ], + "recall": [ + 0.6081539392471313 + ], + "f1": [ + 0.6248600482940674 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.14966541528701782, + 0.2221803069114685, + -0.19240516424179077, + 0.08077575266361237, + -0.02466701529920101, + 0.20474261045455933, + -0.0013346318155527115, + 0.23096227645874023, + 0.5076491236686707, + 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0000000..9b11714 --- /dev/null +++ b/src/benchmark/output/results/results_graph_049.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 66-year-old man with a history of smoking 20 cigarettes per day until the age of 50, after which he abstained for the past 16 years. He has cerebral infarction and takes 25 mg of clopidogrel.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient's history and routine checkup revealed a 3 cm mass in the left middle lung field during chest radiography.\n2. **Step 2:** Further investigation with CT imaging and blood tests was conducted, which showed a ground-glass nodule with a maximum diameter of 4.6 cm and a solid component measuring 4 cm located in S9/10 of the left lower lobe.\n3. **Step 3:** Pulmonary function tests indicated normal respiratory capacity, but follow-up CT imaging revealed a part-solid nodule measuring 1.6 \u00d7 1.4 cm with a 1.5 cm solid component in the same location.\n4. **Step 4:** PET-CT and MRI of the head were conducted to evaluate the lung nodule and rule out metastasis, showing mild accumulation in the mass with an SUVmax of 2.04.\n5. **Step 5:** Bronchoscopy and biopsy were performed to determine the nature of the lung nodule, leading to a suspected diagnosis of stage IB primary lung cancer.\n\n**Timeline of Treatments:**\n\n1. **Step 6:** Surgical lobectomy was planned following the surgical biopsy.\n\n**Outcomes:**\n\nThe patient underwent bronchoscopy and biopsy, which led to a suspected diagnosis of stage IB primary lung cancer. The patient is scheduled for surgical lobectomy. Further follow-up will be necessary to monitor the patient's condition and assess the effectiveness of treatment.\n\nNote: This narrative is based on the provided data and may not reflect the actual clinical case report or outcomes.", + "bertscore": { + "precision": [ + 0.659263551235199 + ], + "recall": [ + 0.6760050058364868 + ], + "f1": [ + 0.6675293445587158 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.2567644715309143, + 0.054647695273160934, + -0.025133753195405006, + 0.027657220140099525, + 0.0567028634250164, + -0.047446608543395996, + 0.08157778531312943, + 0.12755827605724335, + 0.3595859110355377, + -0.3565047085285187, + -0.2112758755683899, + 0.1016974225640297, + -0.5609835982322693, + -0.06822846084833145, + 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Report**\n\n**Patient Demographics**\n\nThe patient is a 67-year-old man with a history of 40 pack-years of smoking. He presented to the clinic in February 2022 with chest tightness.\n\n**Initial Diagnosis (Step 1)**\n\nUpon physical examination, left supraclavicular lymphadenopathy was noted, measuring approximately 1 cm in size. Chest CT revealed a 2 cm mass in the posterior basal segment of the left lower lobe, with multiple burrs on the edge and enhancement. Mediastinal lymph nodes were enlarged and fused, surrounding the left main bronchus. Abdominal enhanced CT showed enlargement of the left adrenal gland, considered to be a metastatic lesion.\n\nImaging studies, including whole-body bone imaging and brain-enhanced MRI, did not reveal any obvious abnormalities. Immunohistochemical markers (CK-pan and P40) were positive, suggesting a diagnosis of lung cancer.\n\n**Biopsy and Diagnosis (Step 2)**\n\nOn March 10, 2022, a CT-guided lung puncture biopsy was performed to further characterize the tumor. Pathology suggested poorly differentiated carcinoma. Immunohistochemical markers were CK-pan (+), CK7 (-), TTF-1 (-), P40 (+), BRG-1 (-), and Syn (-). PD-L1 staining revealed a tumor proportion score (TPS) of 8%.\n\n**Diagnosis Confirmation and Treatment (Step 3)**\n\nBased on immunohistochemistry and genetic testing, a diagnosis of SMARCA4-deficient non-small cell lung cancer (SMARCA4-dNSCLC) was made. First-line treatment with tislelizumab combined with fruquintinib was initiated.\n\n**Treatment Outcomes (Step 4)**\n\nFollowing initial treatment, the patient experienced cervical lymph node progression. Subsequent biopsy confirmed the diagnosis, and the patient was treated with local radiotherapy and previous systemic therapy. The patient achieved more than two years of disease control without grade \u22653 adverse events.\n\n**Timeline**\n\n* February 2022: Patient presents to clinic with chest tightness.\n* March 10, 2022: CT-guided lung puncture biopsy is performed.\n* March 2022: Diagnosis of SMARCA4-dNSCLC is confirmed via subsequent biopsy.\n* April 1, 2022: Initial treatment with tislelizumab and fruquintinib begins.\n* April 1, 2022: Patient undergoes local radiotherapy and previous systemic therapy.\n\n**Outcomes**\n\nThe patient achieved more than two years of disease control without grade \u22653 adverse events. The diagnosis of SMARCA4-dNSCLC was confirmed via subsequent biopsy, and the patient responded well to first-line treatment with tislelizumab combined with fruquintinib.", + "bertscore": { + "precision": [ + 0.7477017045021057 + ], + "recall": [ + 0.7287452816963196 + ], + "f1": [ + 0.7381017804145813 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.28611698746681213, + 0.13427646458148956, + -0.17884783446788788, + 0.06759999692440033, + -0.12707366049289703, + 0.07035525888204575, + 0.17056792974472046, + -0.0935962051153183, + 0.17258435487747192, + -0.4768597185611725, + -0.167130708694458, + 0.24880175292491913, + -0.5263209342956543, + 0.07364700734615326, + -0.45961248874664307, + 0.04494486376643181, + -0.026198312640190125, + 0.3359876871109009, + 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Presentation:**\nOn [date], the patient was admitted to hospital with sudden massive hemoptysis, which he denied experiencing any chest pain, dyspnea, or fever. No other significant comorbidities were present at the time of presentation.\n\n**Diagnosis and Timeline:**\n\n1. **Step 1 (N1):**\nThe patient's history of COPD was noted, with a diagnosis code of \"233936005\" for Chronic obstructive lung disease, which is historical in nature.\n2. **Step 2 (N2):**\nTwo months prior to admission, an enhanced CT scan revealed a tumor in the right upper lung.\n3. **Step 3 (N3):**\nBiopsy confirmed that the tumor was squamous cell carcinoma of the lung (SCC), with a TNM stage of T2bNXM1c1.\n4. **Step 4 (N4):**\nThe patient received two cycles of albumin-bound paclitaxel, nedaplatin, and tislelizumab as treatment for SCC.\n\n**Follow-up and Complications:**\n\n5. **Step 5 (N5):**\nA follow-up CT scan showed partial remission of the tumor with cavitation.\n6. **Step 6 (N6):**\nThe patient presented with hemoptysis, which led to further evaluation, including lab tests and imaging.\n7. **Step 7 (N7):**\nEmergency endovascular intervention was performed due to pseudoaneurysm formation in the right upper pulmonary artery located at the SCC cavity wall with an intraluminal hematoma.\n8. **Step 8 (N8):**\nThe patient underwent emergency endovascular intervention, which included embolization using microcoils to occlude the PAP and proximal artery.\n9. **Step 9 (N9):**\nPost-procedure angiography confirmed the disappearance of the pulmonary artery pseudoaneurysm (PAP).\n10. **Step 10 (N10):**\nThe patient experienced no active bleeding postoperatively, and follow-up over 6 months showed no recurrence of hemoptysis.\n11. **Step 11 (N11):**\nA CT scan 3 months post-embolization showed absorption of the tumor cavity with significant tumor reduction.\n\n**Outcomes:**\n\nThe patient's treatment for SCC was successful, with partial remission of the tumor and disappearance of the pulmonary artery pseudoaneurysm. The patient experienced no active bleeding postoperatively and no recurrence of hemoptysis over 6 months. Follow-up imaging showed absorption of the tumor cavity with significant tumor reduction.\n\n**Conclusion:**\nThis case highlights the importance of early diagnosis and treatment for SCC, particularly in patients with a history of COPD. The successful outcome of this patient's treatment underscores the effectiveness of endovascular intervention in managing complications associated with SCC.", + "bertscore": { + "precision": [ + 0.6436575055122375 + ], + "recall": [ + 0.6487551927566528 + ], + "f1": [ + 0.6461962461471558 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 12, + "edge_count": 11, + "avg_in_degree": 0.9166666666666666, + "density": 0.08333333333333333 + }, + "trajectory_embedding": [ + 0.19094891846179962, + 0.14106714725494385, + -0.031158799305558205, + 0.13212095201015472, + -0.034361883997917175, + 0.11214422434568405, + 0.008480226621031761, + 0.27649667859077454, + 0.44355106353759766, + -0.3264440596103668, + -0.24161100387573242, + -0.02264360710978508, + -0.5586544275283813, + -0.07856817543506622, + -0.13135342299938202, + 0.2850583493709564, + -0.02288839966058731, + 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male with a history of intermittent cough for over two years, worsening in the last month. He has also experienced pneumonia caused by Legionella pneumophila, hypertension, severe anemia, smoking, and alcohol use.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (N1):**\nThe patient presented with symptoms of a persistent cough, which had worsened over time. His medical history revealed previous episodes of pneumonia, hypertension, anemia, smoking, and alcohol use.\n2. **Step 2 (N2):** One month prior to presentation, the patient developed a Pasteurella pneumotropica infection at an outside facility, as confirmed by bronchoscopy and alveolar lavage fluid mNGS analysis. Despite treatment with anti-infective medications for over two weeks, the patient did not show improvement.\n3. **Step 3 (N3):** The patient presented with a palpable lump on the right thoracic wall, localized pain, and coarse breath sounds in both lungs. Laboratory tests revealed abnormalities in white blood cell count, red blood cell count, hemoglobin, total protein, globulin, albumin, glucose, C-reactive protein, and squamous cell carcinoma antigen.\n4. **Step 4 (N4):** Enhanced CT scans showed a new mass in the left lower lung, multiple enlarged lymph nodes, and bone destruction in the right tenth rib, leading to suspicion of lung cancer with metastasis. Bronchoscopy did not reveal tumor cells.\n\n**Treatments:**\n\n1. **Anti-infective treatment:** The patient received anti-infective medications for over two weeks following the diagnosis of Pasteurella pneumotropica infection.\n2. **Imaging studies:** Enhanced CT scans were performed to evaluate the new mass in the left lower lung and multiple enlarged lymph nodes.\n\n**Outcomes:**\n\n1. **Lung cancer with metastasis:** The patient's symptoms and imaging results suggested a diagnosis of lung cancer with metastasis.\n2. **No tumor cells found on bronchoscopy:** Despite the high suspicion of lung cancer, no tumor cells were found during bronchoscopy.\n3. **Negative antibody tests:** Antibody tests for HIV, HBV, HCV, EBV, and TP were negative, indicating that these infections were not contributing to the patient's condition.\n\n**Conclusion:**\nThe patient presented with a complex clinical picture, including a history of pneumonia, hypertension, anemia, smoking, and alcohol use. The development of Pasteurella pneumotropica infection led to progression in his diagnosis, ultimately resulting in suspicion of lung cancer with metastasis. Despite the high suspicion of lung cancer, no tumor cells were found on bronchoscopy, and antibody tests for common infections were negative. Further evaluation and treatment are necessary to determine the best course of action for this patient.", + "bertscore": { + "precision": [ + 0.5771618485450745 + ], + "recall": [ + 0.6398134231567383 + ], + "f1": [ + 0.606874942779541 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.3750039041042328, + -0.018641069531440735, + -0.2502043545246124, + 0.05081702023744583, + -0.05105207860469818, + 0.0839003473520279, + 0.2023211419582367, + 0.19112949073314667, + 0.2581161558628082, + -0.5016443729400635, + -0.10917043685913086, + 0.22764131426811218, + -0.6944714784622192, + -0.16388894617557526, + -0.19019311666488647, + -0.02061181329190731, + 0.21072253584861755, + 0.36244553327560425, + 0.1649523675441742, + -0.19564396142959595, + -0.4511476755142212, + 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mediastinal lesions. The diagnosis was made in [year] and marked the beginning of a complex treatment journey.\n\nFollowing the initial diagnosis, the patient transitioned to radiotherapy for the lung and mediastinal lesions (N1 to N2). This marked an important step in the patient's care, as it aimed to alleviate symptoms and slow disease progression. However, this was followed by another significant change when the patient began chemotherapy with albumin-bound paclitaxel and cisplatin, with recombinant human endostatin added in the 4th cycle (N2 to N3). Unfortunately, treatment was not completed due to cardiac reactions, resulting in stable disease.\n\nThe patient's condition continued to evolve as they developed symptoms of chest tightness and shortness of breath. These symptoms persisted despite hospitalization for worsening shortness of breath (N5 to N6), where ECG abnormalities and lab results indicating elevated troponin, BNP, and myoglobin were noted. The initial treatment included a range of medications aimed at managing these complications.\n\nDespite the efforts to manage symptoms, the patient's condition continued to deteriorate. A coronary angiography revealed significant stenosis in the left main trunk (N6 to N7), which further complicated the patient's care. Notably, anticoagulant therapy was not initiated due to concerns about gastrointestinal bleeding secondary to long-term aspirin use.\n\nThroughout this journey, the patient has been managed with a range of treatments, including medications and procedures aimed at addressing complications such as cardiac reactions, chest tightness, and shortness of breath. The timeline of diagnoses and treatments is complex, reflecting the evolving nature of the patient's condition.\n\nThe patient's age and demographic information are not explicitly stated in the provided data, but based on the treatment journey described, it can be inferred that this individual has been living with a serious health condition for several years.", + "bertscore": { + "precision": [ + 0.6489934921264648 + ], + "recall": [ + 0.6017652750015259 + ], + "f1": [ + 0.6244877576828003 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.17100100219249725, + 0.01172204501926899, + -0.21289609372615814, + 0.19774876534938812, + 0.11490162461996078, + 0.15191338956356049, + -0.03697091341018677, + 0.23890110850334167, + 0.5338540077209473, + 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+1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 49-year-old male with a significant smoking history (37 pack-years). He was admitted to the local hospital with acute abdominal pain, which marked the beginning of his clinical journey.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Initial Presentation:** The patient presented with acute abdominal pain, which led to an enhanced CT scan revealing a 4.0 cm soft tissue mass within the small intestine and mid-lower intestine intussusception (N2).\n2. **Surgical Intervention:** Admitted to the general surgery ward, the patient underwent intussusception surgery on April 8, 2019 (N3). During surgery, an irregular, hard, solid white mass involving the intestine was identified.\n3. **Initial Pathological Diagnosis:** The resected specimen showed a multinodular mass with a tan-white cut surface and firm consistency, thin envelope observed in the periphery of the mass (N4).\n4. **Detailed Pathology and Immunohistochemistry Results:** Histological examination revealed tumor located within the submucosa and lamina propria of the intestinal wall with mucosal erosion, neoplastic cells embedded within the inflammatory background. Immunohistochemistry results confirmed ALK-positive inflammatory myofibroblastic tumor (IMT), highly suspicious for epithelioid inflammatory myofibroblastic sarcoma (EIMS) (N5).\n\n**Diagnosis and Treatment Outcomes:**\n\nThe patient was diagnosed with a suspected case of epithelioid inflammatory myofibroblastic sarcoma (EIMS). Given the ALK-positive status, treatment options were considered. However, no specific treatment details are provided in this data.\n\n**Conclusion:**\nThis clinical case report highlights the importance of a thorough diagnostic workup and the significance of molecular testing in identifying rare and aggressive tumors like EIMS. Further investigation into the patient's treatment plan is necessary to determine the most effective course of action for this unique diagnosis.\n\n**Recommendations:**\n\n1. **Multidisciplinary Team Approach:** Collaboration between surgeons, pathologists, radiologists, and oncologists is crucial for managing complex cases like this.\n2. **Molecular Testing:** Regular molecular testing can help identify potential biomarkers for targeted therapies in EIMS patients.\n3. **Clinical Trials Participation:** Patients with rare tumors like EIMS should be considered for participation in clinical trials to explore new treatment options.\n\n**Future Directions:**\n\n1. **Research on EIMS:** Further studies are needed to understand the biology and behavior of EIMS, as well as to identify potential therapeutic targets.\n2. **Development of New Treatment Strategies:** Researchers should focus on developing novel treatments for EIMS, including targeted therapies and immunotherapies.\n\nBy sharing this clinical case report, we aim to raise awareness about the importance of accurate diagnosis and treatment planning in managing rare and aggressive tumors like EIMS.", + "bertscore": { + "precision": [ + 0.6755951046943665 + ], + "recall": [ + 0.7064059972763062 + ], + "f1": [ + 0.6906570792198181 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.2819657325744629, + 0.01156010851264, + -0.19529643654823303, + -0.042242903262376785, + 0.0824071615934372, + -0.062329452484846115, + 0.08502864092588425, + -0.14531011879444122, + 0.2912984788417816, + -0.3691332936286926, + -0.4327576160430908, + 0.2096576988697052, + -0.7493955492973328, + 0.01814318634569645, + -0.5375791788101196, + 0.016119401901960373, + 0.22100715339183807, + 0.18724648654460907, + 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available demographic information. However, based on the provided data, it can be inferred that the patient has cancer, as mentioned in Step 1.\n\n**Timeline of Diagnoses and Treatments:**\n\nStep 1:\nThe patient's cancer had no driver gene mutations.\n\nStep 2 (First-line Chemotherapy):\nInitiation of first-line chemotherapy with cisplatin, pemetrexed, and pembrolizumab was administered. This treatment was initiated to target the patient's cancer.\n\nStep 3 (Second-line Chemotherapy):\nProgression to second-line chemotherapy with docetaxel and ramucirumab was administered. This treatment was initiated due to the development of resistance or intolerance to the first-line chemotherapy.\n\nStep 4:\nChemotherapy was delayed for approximately one month due to the development of a perianal abscess, which required surgical intervention under local anesthesia. The patient's cancer treatment was interrupted due to an unexpected complication.\n\nStep 5 (Post-Surgical Complication):\nThe patient developed dyspnea the day following surgery. This symptom suggested that the patient may be experiencing respiratory complications related to the surgery.\n\nStep 6:\nAdmission and Vital Sign Abnormalities:\nFour days after symptom onset, the patient was admitted with vital sign abnormalities, including hypotension, hypoxemia, and tachycardia. These findings indicated that the patient's condition had deteriorated significantly.\n\nStep 7 (Lab Abnormalities):\nElevated D-dimer, C-reactive protein, brain natriuretic peptide, and carcinoembryonic antigen levels were detected in the patient's blood. Additionally, abnormal CBC results and arterial blood gas findings were observed. These lab abnormalities suggested that the patient had developed a systemic inflammatory response syndrome (SIRS) or sepsis.\n\n**Outcomes:**\n\nThe patient's condition continued to deteriorate, with ongoing vital sign abnormalities and lab abnormalities. The exact outcome of this case is not provided in the data, but it can be inferred that the patient required further medical intervention to manage their symptoms and stabilize their condition.\n\nIn conclusion, this clinical case report highlights the complexities of cancer treatment and the potential for unexpected complications. The patient's journey from diagnosis to admission and beyond demonstrates the need for close monitoring and prompt intervention in managing cancer-related symptoms and lab abnormalities.", + "bertscore": { + "precision": [ + 0.6407378911972046 + ], + "recall": [ + 0.6139230132102966 + ], + "f1": [ + 0.6270439624786377 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.22469878196716309, + 0.19692015647888184, + 0.00025188070139847696, + 0.173471599817276, + 0.09548087418079376, + 0.17378945648670197, + -0.016956541687250137, + 0.2958507835865021, + 0.6613865494728088, + -0.4530636966228485, + -0.13141368329524994, + -0.04939684644341469, + -0.6155732274055481, + -0.17467454075813293, + -0.18280437588691711, + 0.12072768062353134, + 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patient is a 72-year-old woman with a history of small cell lung cancer (SCLC).\n\n**Initial Presentation:**\nThe patient presented with progressive involuntary writhing movements in her hands and lower extremities over the past 3 months. This symptomatology was documented as part of her clinical data, including a history of progressive worsening (P3M) and associated symptoms such as involuntary writhing movements.\n\n**Diagnostic Workup:**\nFollowing the patient's presentation, a comprehensive diagnostic workup was conducted, which included imaging studies (Brain MRI and CT), electroencephalogram (EEG), and laboratory tests. The results of these studies were negative for hemorrhage or lesions on the red nucleus or midbrain, seizure activity, and abnormal electrolyte levels.\n\n**Treatment Initiation:**\nDespite the initial negative diagnostic workup, the patient's symptoms worsened, prompting further evaluation and treatment initiation. A ceruloplasmin test was conducted, which revealed a negative result. Subsequent laboratory tests showed positive anti-Hu antibodies at a titer of 1:960, indicating paraneoplastic syndrome.\n\n**Treatment Regimen:**\nThe patient received a treatment regimen consisting of diazepam, primidone, and pramipexole, with the goal of managing her symptoms. However, despite this treatment, the patient's symptoms continued to worsen, leading to hospitalization.\n\n**Intravenous Immunoglobulin (IVIG) Therapy:**\nAs part of her treatment regimen, the patient received IVIG for 4 days. This therapy was aimed at reducing the severity of her paraneoplastic syndrome.\n\n**New Symptoms and Imaging Findings:**\nFollowing the patient's discharge from the hospital, she presented to the emergency department with nausea and vomiting without new abnormal movements or neurologic symptoms. Repeat imaging studies revealed a 3.3 x 2.3 cm mass in the left cerebellar region, involving the left cerebellar peduncle.\n\n**Treatment of New Symptoms:**\nThe patient underwent further evaluation and treatment for her new symptoms. Laboratory tests showed positive anti-Hu antibodies, indicating continued paraneoplastic syndrome.\n\n**Current Status:**\nAt this time, the patient is currently under observation with ongoing management of her paraneoplastic syndrome. The patient's symptoms have improved since the initiation of IVIG therapy, but she continues to experience discomfort and disrupted sleep due to the frequency of her movements.\n\nIn conclusion, this 72-year-old woman with a history of small cell lung cancer presented with progressive involuntary writhing movements in her hands and lower extremities. Despite an initial negative diagnostic workup, further evaluation and treatment initiation revealed paraneoplastic syndrome, which was managed with IVIG therapy. However, new symptoms and imaging findings have necessitated ongoing management and observation.", + "bertscore": { + "precision": [ + 0.5887521505355835 + ], + "recall": [ + 0.5860556364059448 + ], + "f1": [ + 0.5874007940292358 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.10924185812473297, + 0.10171635448932648, + -0.130819171667099, + 0.11970636993646622, + 0.01621156930923462, + -0.025944743305444717, + 0.059883225709199905, + 0.19405730068683624, + 0.5056430101394653, + -0.3832123875617981, + -0.28973308205604553, + 0.21129187941551208, + -0.575080156326294, + -0.07535974681377411, + -0.27020901441574097, + -0.11037592589855194, + 0.01244857907295227, + 0.24032163619995117, + -0.05925019457936287, + -0.07463321834802628, + 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presented to the hospital with suspected uveitis of the right eye. He experienced right ocular pain and blurred vision for approximately 1 month prior to presentation.\n\n**Timeline of Diagnoses:**\n\n* **Suspected Uveitis:** The patient was referred to the hospital with suspected uveitis of the right eye, which was diagnosed as a suspected case of uveitis (code C0042095).\n* **Small Cell Lung Cancer (SCLC):** Four months prior to presentation, the patient was diagnosed with SCLC (code C0007106) and had developed right cerebellar metastasis and invasion.\n* **Metastasis:** The patient also had a diagnosis of metastasis (code C0242393), which was active at the time of presentation.\n\n**Timeline of Treatments:**\n\n* **Topical Medications:** Following SCLC diagnosis, the patient started therapy with topical 0.005% latanoprost, 1.0% brinzolamide, and 0.5% timolol maleate.\n* **Oral Acetazolamide:** The patient also took oral acetazolamide at a dose of 500 mg/day.\n* **Intravenous Mannitol:** Due to high IOP and pronounced nausea, the patient required intravenous administration of 200 mL of 20% hypertonic mannitol every 2-3 days for five administrations.\n\n**Timeline of Outcomes:**\n\n* **Iris Metastasis:** Anterior chamber fluid cytology revealed iris metastasis from SCLC, consistent with bronchoalveolar lavage cytology results.\n* **Neovascular Glaucoma:** The patient developed neovascular glaucoma (code C0271198), which was treated with a single intravitreal injection of 2 mg (0.05 mL of 40 mg/mL) aflibercept OD.\n* **Resolution of Symptoms:** Five days post-aflibercept injection, the patient's iris tumor size and iris neovascularization decreased, IOP measured at 18 mm Hg, and symptoms such as ocular pain and nausea were relieved.\n\n**Conclusion:**\nThe patient was diagnosed with suspected uveitis and SCLC, which led to the development of right cerebellar metastasis and invasion. Following diagnosis, the patient received topical medications and oral acetazolamide, as well as intravenous mannitol due to high IOP and nausea. The patient also developed iris metastasis from SCLC, which was treated with an intravitreal injection of aflibercept. Ultimately, the patient's symptoms resolved following treatment, and their IOP returned to normal.", + "bertscore": { + "precision": [ + 0.5613889694213867 + ], + "recall": [ + 0.7224175930023193 + ], + "f1": [ + 0.631804347038269 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.10041718930006027, + 0.16403163969516754, + -0.2795267105102539, + 0.20759916305541992, + 0.1098250150680542, + 0.12031718343496323, + 0.02523813582956791, + 0.28508585691452026, + 0.4031936228275299, + -0.14178399741649628, + -0.1515788584947586, + 0.027539696544408798, + -0.39865249395370483, + -0.16108302772045135, + -0.1848643273115158, + 0.29761239886283875, + -0.348704069852829, + 0.19526958465576172, + -0.07590274512767792, + -0.18397021293640137, + 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He has a significant occupational asbestos exposure history while working for a shipbuilding company. The patient denies any history of cigarette smoking or exposure to organic dusts, pet birds, or exotic pets.\n\n**Initial Presentation (Step 1):**\nIn June 2024, the patient presented to the Emergency Department with concerns of weight loss and abdominal distention over the past 4 weeks. He denied any alterations in bowel habits, melena, hematochezia, abdominal pain, nausea, vomiting, dysphagia, or odynophagia.\n\n**Physical Examination and Laboratory Findings (Step 2):**\nAfter initial presentation, the patient underwent multiple abdominal paracenteses, which revealed hazy yellow ascitic fluid with nucleated cells. The cell count was 589 cells/\u03bcL, with lymphocytes 87% and erythrocytes 1461 cells/\u03bcL.\n\n**Imaging Studies (Step 3):**\nA CT scan performed during this time showed massive ascites and a lung nodule.\n\n**Abdominal Paracentesis and Ascitic Fluid Analysis (Steps 4-5):**\nThe patient underwent multiple abdominal paracenteses, which revealed exudative process in the ascitic fluid. The first abdominal paracentesis results showed lactate dehydrogenase 763 IU/L, total protein 4.0 g/dL, albumin 1.7 g/dL, and serum albumin-ascites gradient (SAAG) 0.4 g/dL.\n\n**Repeat Ascitic Fluid Analysis and Abdominal Ultrasonography (Step 6):**\nA repeat ascitic fluid analysis revealed no growth on AFB smear, culture, or fungal culture. An abdominal ultrasonography performed during this time showed normal portal vein size and Doppler indices, with the spleen not enlarged.\n\n**Serum FibroTest-ActiTest (Step 7):**\nThe patient underwent a Serum FibroTest-ActiTest, which suggested no hepatic fibrosis (F0).\n\n**Diagnosis:**\nBased on the results of the various diagnostic tests and imaging studies, the patient was diagnosed with cirrhosis due to chronic liver disease.\n\n**Treatment:**\nNo specific treatment is mentioned in the provided data. However, it can be inferred that the patient may require ongoing management of his ascites and potential complications related to cirrhosis.\n\n**Outcome:**\nThe patient's condition appears to be stable at this point, with no further information provided on any changes or developments since the last update.", + "bertscore": { + "precision": [ + 0.5451638698577881 + ], + "recall": [ + 0.6678067445755005 + ], + "f1": [ + 0.6002851128578186 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.3212769627571106, + 0.027124296873807907, + 0.007639573886990547, + 0.1450214982032776, + 0.04273857921361923, + -0.0566130205988884, + 0.15015661716461182, + 0.13063287734985352, + 0.360310435295105, + -0.2895905375480652, + -0.29207170009613037, + 0.0069152191281318665, + 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b/src/benchmark/output/results/results_graph_061.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 65-year-old woman. Unfortunately, her demographic information is not explicitly provided in the data, so we will assume that she is an adult female with no other relevant medical history mentioned.\n\n**Initial Presentation (Step 1):**\nThe patient presented to our institution with dyspnea, which was her primary symptom. This presentation led to further investigation and subsequent diagnoses.\n\n**Diagnosis of Adenocarcinoma (Step 2):**\nFollowing a bronchoscopic biopsy of the right upper lobe, the patient was diagnosed with adenocarcinoma. The biopsy results revealed adenocarcinoma, which is a type of non-small cell lung cancer.\n\n**Imaging and Further Diagnosis (Step 3):**\nImaging studies, including bone and brain metastases, were performed to further evaluate the extent of disease. These findings led to a diagnosis of stage IVB lung adenocarcinoma with multiple metastases in the bones and brain.\n\n**Molecular Profiling and Treatment Planning (Step 4):**\nA tumor proportion score was calculated to guide treatment decisions. The results showed that the programmed death-ligand 1 tumor proportion score was 60%. Based on this information, palliative radiation therapy for spinal and brain metastases was initiated, followed by first-line chemotherapy with cisplatin, pemetrexed, and pembrolizumab.\n\n**Progression of Disease (Step 5-6):**\nAfter 13 cycles of chemotherapy, imaging revealed ascites and progressive disease. The patient's condition continued to decline, with worsening ascites and a marked increase in abdominal circumference.\n\n**Second-Line Therapy (Step 7):**\nDue to the progression of disease, second-line therapy was initiated with docetaxel and ramucirumab (DTX+RAM). However, despite this treatment, the patient's condition continued to deteriorate.\n\n**Current Status:**\nThe patient is currently in a poor clinical state, with significant ascites, hypoalbuminemia, and a marked decline in activities of daily living. Her performance status has decreased, and she requires frequent abdominal paracentesis. The patient's abdomen is markedly distended, and her vital signs are concerning.\n\n**Conclusion:**\nThis patient presents with a complex clinical scenario, characterized by rapidly progressive disease despite multiple treatment modalities. Further evaluation and management strategies will be necessary to address this challenging case.", + "bertscore": { + "precision": [ + 0.6582294702529907 + ], + "recall": [ + 0.6435860991477966 + ], + "f1": [ + 0.6508255004882812 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 9, + "edge_count": 7, + "avg_in_degree": 0.7777777777777778, + "density": 0.09722222222222222 + }, + "trajectory_embedding": [ + 0.2474288046360016, + 0.2092151939868927, + -0.12583652138710022, + 0.19021673500537872, + 0.0814264714717865, + 0.177109494805336, + -0.002533096820116043, + 0.3530573844909668, + 0.759898841381073, + -0.3953750431537628, + -0.04731377586722374, + -0.07567942142486572, + -0.6275361180305481, + -0.17365944385528564, + -0.21753628551959991, + 0.26948532462120056, + -0.22064340114593506, + 0.46433359384536743, + -0.15440678596496582, + -0.28024598956108093, + 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He denied any fever, sputum or blood production, and chest pain.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (N1):** The patient's chronic recurrent dry cough prompted a chest computed tomography (CT) scan.\n2. **Step 2 (N2):** The CT revealed pulmonary masses at an external hospital, leading to admission to the oncology department for further evaluation and treatment.\n3. **Step 3 (N3):** The patient was admitted to the oncology department for further evaluation and treatment.\n4. **Step 4 (N4):** As part of the evaluation, the patient's medical history was reviewed, revealing no history of hypertension, coronary heart disease, diabetes, cerebral venous thrombosis or hemorrhage, tuberculosis, chronic hepatitis B virus infection and other diseases.\n5. **Step 5 (N5):** Vitals and labs were taken as part of the evaluation, including temperature 37.2\u00b0C, pulse rate 118 bpm, respiratory rate 20 breaths/minute, blood pressure 106/69 mmHg, white blood cells 7.97 \u00d7 109/L, hemoglobin 142 g/L, platelets 287 \u00d7 109/L, and various other lab results.\n6. **Step 6 (N6):** Additional labs were taken as part of the evaluation, including treponema pallidum-specific antibody, hepatitis B surface antigen, and hepatitis C.\n\n**Treatments:**\n\nThe patient underwent a series of evaluations and treatments based on the findings from each step:\n\n* Following the CT scan, the patient was admitted to the oncology department for further evaluation and treatment.\n* As part of the evaluation, the patient's medical history was reviewed, revealing no history of certain diseases.\n* Vitals and labs were taken as part of the evaluation.\n\n**Outcomes:**\n\nThe patient's current status is not explicitly stated in the provided data. However, based on the timeline of diagnoses and treatments, it appears that the patient has undergone a series of evaluations and treatments for pulmonary masses detected by CT scan. The patient's medical history was reviewed, revealing no history of certain diseases, and vitals and labs were taken as part of the evaluation.\n\n**Conclusion:**\n\nThe patient presented with a chronic recurrent dry cough over the course of a month, which prompted a chest CT scan that revealed pulmonary masses. The patient underwent a series of evaluations and treatments based on the findings from each step, including admission to the oncology department for further evaluation and treatment. The patient's medical history was reviewed, revealing no history of certain diseases, and vitals and labs were taken as part of the evaluation.", + "bertscore": { + "precision": [ + 0.47996535897254944 + ], + "recall": [ + 0.5415050387382507 + ], + "f1": [ + 0.5088814496994019 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.29947397112846375, + -0.028808513656258583, + 0.018951475620269775, + 0.24079148471355438, + 0.11866217851638794, + 0.17880016565322876, + 0.11841905117034912, + 0.2565062940120697, + 0.5162163972854614, + -0.40549495816230774, + -0.19314958155155182, + -0.05226249620318413, + -0.6632895469665527, + -0.11044865846633911, + -0.34900379180908203, + 0.20892314612865448, + 0.0023391495924443007, + 0.3613584041595459, + 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She presented with a palpable pelvic mass, which was later identified as an anterior wall uterine leiomyoma on gynecological sonography.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1 (N1):**\nThe patient presented with a palpable pelvic mass in January 2010. Physical examination revealed an enlarged uterus, which was mobile, firm in consistency, with no uterine or forniceal tenderness, and mild swelling in the right pubic area.\n\n2. **Step 2 (N2):**\nGynecological sonography on January 30, 2010, identified an anterior wall uterine leiomyoma, measuring 112\u00d794\u00d7108 mm, accompanied by ascites measuring 65\u00d742 mm and a 20\u00d714 mm mass.\n\n3. **Step 3 (N3):**\nLaparotomic myomectomy was performed on February 17, 2020, with incidental discovery of a pelvic tumor. The pelvic tumor described as a cauliflower-like lesion disseminated across the right pelvic wall, cul-de-sac, anterior uterine surface, bladder, and colon.\n\n4. **Step 4 (N4):**\nBiopsy of the sigmoid colon serosa was performed, revealing proliferative mesothelial cells without significant atypia or necrosis. Post-myomectomy CT scan revealed seeding in the lower pelvis, characterized by multiple small, heterogeneous, enhancing nodules on the peritoneum and a prominent soft-tissue mass in the right adnexa.\n\n5. **Step 5 (N5):**\nAnother CT scan performed on February 26th, 2020, revealed moderate ascites and nonspecific peritoneal thickening. Histopathology identified bland mesothelial cells without invasion, and immunohistochemistry showed no significant staining loss. Differential diagnosis included well-differentiated papillary mesothelioma, epithelioid peritoneal mesothelioma, and florid mesothelial hyperplasia; well-differentiated papillary mesothelioma was highly suspected.\n\n**Outcomes:**\n\nThe patient underwent a series of procedures, including laparotomic myomectomy, biopsy, histopathology, and immunohistochemistry. The results of these procedures led to the diagnosis of a pelvic tumor with seeding in the lower pelvis. Despite the presence of seeding, the patient's condition was managed conservatively, with no further surgical interventions reported.\n\n**Conclusion:**\nThis case highlights the complexities of managing a patient with a pelvic mass and subsequent discovery of a pelvic tumor with seeding. The patient's presentation and diagnostic workup led to a series of procedures that ultimately resulted in a diagnosis of a mesothelial tumor. While the patient's condition was managed conservatively, further follow-up is necessary to monitor for any progression or recurrence of the disease.\n\n**Recommendations:**\n\n1. Further imaging studies should be performed to assess the extent of seeding and monitor for any progression or recurrence of the disease.\n2. The patient should be followed up regularly with a multidisciplinary team, including oncologists, radiologists, and pathologists.\n3. Additional diagnostic procedures, such as PET scans or CT scans, may be necessary to further evaluate the patient's condition.\n\n**Limitations:**\n\nThis case report is limited by its retrospective nature and the availability of data. Further research is needed to better understand the management and outcomes of patients with pelvic tumors and seeding.", + "bertscore": { + "precision": [ + 0.514549732208252 + ], + "recall": [ + 0.6133989691734314 + ], + "f1": [ + 0.5596429109573364 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.33560317754745483, + -0.032035164535045624, + -0.11456692218780518, + 0.1346358358860016, + 0.020706722512841225, + 0.00046664924593642354, + 0.1556069552898407, + 0.050799597054719925, + 0.29955029487609863, + -0.3043522834777832, + -0.21893103420734406, + 0.13041041791439056, + -0.5819693207740784, + -0.027642954140901566, + -0.3483089804649353, + 0.05678959935903549, + 0.08175595104694366, + 0.18470464646816254, + 0.07032836973667145, + -0.1516115516424179, + 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He presented to the emergency room with cough, low back pain, and abdominal pain.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation (October 28, 2023):** The patient was evaluated at the emergency room due to symptoms of cough, low back pain, and abdominal pain. A CT angiogram of the chest was performed, which revealed a large left pleural effusion tracking to the lung apex with near complete opacification of the left lower lobe, a 6-cm left lower lobe mass, and 4-cm left hilar mass with mediastinal adenopathy and pleural nodularity.\n2. **Surgical Intervention (November 9, 2023):** The patient underwent left video-assisted thorascopic surgery with total left lung decortication, removal of fibrin deposits, and placement of a pleural drainage catheter requiring daily drainage.\n3. **Pathology and Imaging Results (November 29, 2023):** Pathology from the left pleural mass revealed malignant epithelial neoplasm with 70% spindle cell and 30% epithelioid cell components consistent with biphasic MPM. PET imaging confirmed advanced disease with extensive left-sided pleural involvement, bilateral mediastinal adenopathy, adrenal, and scattered bone lesions.\n4. **Immune Checkpoint Inhibitor Therapy (December 4, 2023):** The patient began receiving immune checkpoint inhibitor therapy with nivolumab and ipilimumab, which showed initial improvement in pleural drainage output.\n\n**Timeline of Symptoms:**\n\n1. **Initial Presentation:** Cough, low back pain, and abdominal pain.\n2. **Post-Surgical Complication (December 4, 2023):** Lower back pain, lower extremity numbness, and inability to walk after one cycle of therapy.\n\n**Treatment Outcomes:**\nThe patient's treatment with immune checkpoint inhibitors showed initial improvement in pleural drainage output. However, a new symptom of lower back pain, lower extremity numbness, and inability to walk developed after one cycle of therapy, indicating potential side effects or progression of the disease.\n\nThis clinical case report highlights the importance of early diagnosis and treatment of malignant pleural mesothelioma (MPM), as well as the need for careful monitoring of patients receiving immune checkpoint inhibitors.", + "bertscore": { + "precision": [ + 0.7149702310562134 + ], + "recall": [ + 0.7142810821533203 + ], + "f1": [ + 0.7146255373954773 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.1652541607618332, + 0.039438892155885696, + -0.14641372859477997, + 0.18929584324359894, + 0.14937780797481537, + 0.1875849962234497, + 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mode 100644 index 0000000..4643434 --- /dev/null +++ b/src/benchmark/output/results/results_graph_066.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 59-year-old woman who presented with a cough. Her demographic information is not explicitly mentioned in the provided data, but based on the age and sex, we can infer that she is an adult female.\n\n**Initial Diagnosis (Step 1):**\nUpon presentation, the patient underwent a lung CT scan, which revealed a space-occupying lesion in the left lower lobe. The lesion was accompanied by peripheral obstructive inflammation, atelectasis, and multiple enlarged lymph nodes in the mediastinum. A biopsy of the lesion was performed, which confirmed the presence of keratinized squamous cell carcinoma. The patient was diagnosed with left lower lobe squamous cell carcinoma (T3N2bM0, Stage IIIB).\n\n**Treatment Initiation (Step 2):**\nThe patient underwent six cycles of albumin-bound paclitaxel (100 mg/m\u00b2 on day 1, day 8, and day 15), cisplatin (75 mg/m\u00b2 on day 1), and carrelizumab (200 mg on day 1). Following this treatment, the left lower lung lesion had significantly reduced in size to approximately 23x25 mm.\n\n**Radiotherapy and Re-emergence of Disease (Step 3):**\nThe patient underwent radiotherapy with a dose of 2 Gy per fraction, administered over a total of 30 fractions. However, after ten fractions, the patient developed dyspnea and fever, with a maximum temperature of 38.5\u00b0C. A lung puncture biopsy was performed, which confirmed the presence of squamous cell carcinoma. The lesion had significantly enlarged to a size of 50 \u00d7 51 mm.\n\n**Outcome:**\nThe patient's condition worsened after radiotherapy, and she developed delayed hypersensitivity pneumonitis (DHP) after 5 months of immunotherapy. Despite this, the patient continued to receive treatment, highlighting the complexities of managing advanced cancer.\n\nIn conclusion, this clinical case report highlights the challenges of treating advanced squamous cell carcinoma in a 59-year-old woman. The patient's initial diagnosis and treatment response were promising, but the disease re-emerged after radiotherapy, leading to worsening symptoms and complications. Further management strategies are needed to improve outcomes for patients with advanced cancer.", + "bertscore": { + "precision": [ + 0.5903757810592651 + ], + "recall": [ + 0.7092682123184204 + ], + "f1": [ + 0.6443838477134705 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 3, + "edge_count": 2, + "avg_in_degree": 0.6666666666666666, + "density": 0.3333333333333333 + }, + "trajectory_embedding": [ + 0.24472539126873016, + 0.05973951891064644, + -0.20621691644191742, + 0.22169888019561768, + -0.08776857703924179, + -0.01297292485833168, + 0.14311833679676056, + 0.19575707614421844, + 0.13809828460216522, + -0.30675601959228516, + -0.19033236801624298, + 0.21958637237548828, + -0.5650694966316223, + -0.03671947494149208, + -0.21233956515789032, + -0.07029158622026443, + 0.05985746905207634, + 0.3540482819080353, + 0.09971606731414795, + -0.21774829924106598, + 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Diagnoses:**\n\n1. **2016:** The patient was diagnosed with stage IIIA NSCLC adenocarcinoma.\n2. **2016:** Following the diagnosis, the patient underwent a right middle lobectomy, adjuvant carboplatin/paclitaxel chemotherapy, and postoperative radiotherapy (PORT).\n3. **2022:** The patient developed metastatic disease in the right lung, liver, and brain.\n\n**Timeline of Treatments:**\n\n1. **2016-2017:** Adjuvant carboplatin/paclitaxel chemotherapy.\n2. **2017:** Postoperative radiotherapy (PORT) was administered.\n3. **2022:** Stereotactic radiation therapy was performed to treat a single brain metastasis.\n4. **2022:** Empirical chemotherapy regimen consisting of 5-fluorouracil/oxaliplatin (FOLFOX) was initiated.\n5. **2022:** Histopathological analysis of liver lesions identified spindle cell carcinoma likely pulmonary in origin despite atypical features, with a high proliferative Ki-67 index (90%).\n6. **2022:** Treatment with docetaxel was administered.\n\n**Timeline of Outcomes:**\n\n1. **2017:** The patient underwent upper and lower GI endoscopy due to microcytosis, but no lesions were identified.\n2. **2022:** Liver biopsy showed metastatic spindle cell carcinoma on H&E stain, sections demonstrated a spindle cell neoplasm with significant mitotic activity and focal necrosis, and immunohistochemistry showed the tumor cells positive for AE1/AE3 and CK8/18, but negative for Alk-1, CK7, CK20, CDX-2, and CD117.\n3. **2022:** The patient received nine weekly doses of docetaxel with modest shrinkage (approximately 10-15%).\n\n**Conclusion:**\nThe patient's clinical course was marked by a diagnosis of stage IIIA NSCLC adenocarcinoma in 2016, followed by treatment with adjuvant chemotherapy and radiotherapy. Despite this initial treatment, the patient developed metastatic disease in 2022, which led to further evaluation and treatment, including stereotactic radiation therapy for brain metastasis, empirical chemotherapy regimen, histopathological analysis of liver lesions, and treatment with docetaxel. The patient's current status is characterized by ongoing treatment with docetaxel, with modest shrinkage observed in the tumor size.", + "bertscore": { + "precision": [ + 0.707660973072052 + ], + "recall": [ + 0.7203216552734375 + ], + "f1": [ + 0.7139351963996887 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2563111484050751, + 0.18047350645065308, + -0.12980332970619202, + 0.12957733869552612, + 0.14545029401779175, + 0.19874490797519684, + -0.020612286403775215, + 0.3609883785247803, + 0.5175485610961914, + -0.42774152755737305, + -0.11932812631130219, + -0.07010838389396667, + -0.6297792792320251, + -0.06867539882659912, + -0.2806960642337799, + 0.28194066882133484, + -0.16101223230361938, + 0.2974811792373657, + -0.0320054367184639, 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-3,13 +3,13 @@ "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an adult male with no specified age or background information provided. However, based on the clinical data, it appears that the patient has a history of lung cancer.\n\n**Timeline of Diagnoses:**\n\n1. **September 2021:** The patient presented to The First Affiliated Hospital of Dalian Medical University with complaints of chest pain and fatigue for half a year. A CT scan revealed partial solid nodules in the posterior segment of the upper lobe of the right lung, which were later diagnosed as malignant neoplasm of bronchus and lung (C34).\n2. **Multiple small lung nodules in both lungs:** Following the initial diagnosis, the patient developed multiple small lung nodules in both lungs, accompanied by abnormal blood test results (lymphocytopenia and neutrophilia). This led to a decision to proceed with surgical resection of lung tissue.\n3. **November 2022:** The patient underwent surgical resection of lung tissue, which revealed invasive adenocarcinoma in the upper lobe of the right lung. The cancer was diagnosed as C2330808 (Adenocarcinoma, Invasive).\n4. **January 2024:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm.\n\n**Timeline of Treatments:**\n\n1. **Surgical resection of lung tissue:** The patient underwent surgical resection of lung tissue in November 2022.\n2. **No second surgical treatment:** The patient refused a second surgical treatment for the recurrence of primary cancer, which presented as ground glass nodules in the left lung.\n\n**Timeline of Outcomes:**\n\n1. **Pathological diagnosis:** The pathological diagnosis of invasive adenocarcinoma was confirmed post-surgery in November 2022.\n2. **Recurrence of primary cancer:** The patient developed recurrence of primary cancer with ground glass nodules in the left lung and new symptoms (fatigue, pale tongue, white fur, and weak pulse) in November 2022.\n3. **Recurrent tumor shrinkage:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm in January 2024.\n\n**Clinical Findings:**\n\nThroughout the patient's treatment, various clinical findings were reported, including:\n\n* Chest pain and fatigue\n* Multiple small lung nodules in both lungs\n* Abnormal blood test results (lymphocytopenia and neutrophilia)\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Laboratory Results:**\n\nThe patient's laboratory results showed:\n\n* Normal blood work (January 2024)\n* Elevated carcinoembryonic antigen level (November 2022)\n\n**Imaging Results:**\n\nThe patient underwent various imaging studies, including CT scans and pathology reports, which revealed:\n\n* Partial solid nodules in the posterior segment of the upper lobe of the right lung (September 2021)\n* Multiple small lung nodules in both lungs\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Prognosis:**\nThe patient's prognosis remains uncertain, as the cancer has recurred and treatment options are limited. Further evaluation and management are necessary to determine the best course of action.\n\n**Conclusion:**\nThis clinical case report highlights the complexities of managing lung cancer, particularly in cases where recurrence occurs. The patient's treatment plan will require careful consideration of various factors, including the patient's overall health, tumor characteristics, and available treatment options.", "bertscore": { "precision": [ - 0.32128238677978516 + 0.6718395352363586 ], "recall": [ - 0.4002746641635895 + 0.6553829908370972 ], "f1": [ - 0.3564547002315521 + 0.66350919008255 ] }, "topology": { diff --git a/src/benchmark/output/results/results_graph_069.json b/src/benchmark/output/results/results_graph_069.json new file mode 100644 index 0000000..cdf1ad7 --- /dev/null +++ b/src/benchmark/output/results/results_graph_069.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 67-year-old man with a significant smoking history, having smoked 30 cigarettes per day for 50 years. He presented to the clinic with a persistent dry cough that had lasted for more than three months.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **July 2019:** The patient was diagnosed with a mass in the central left upper lobe, enlarged bilateral mediastinal lymph nodes, and bilateral pulmonary nodules on contrast-enhanced chest CT (Step 2). Biopsy of the lesion under tracheoscopy confirmed lung adenocarcinoma histologically (Step 3).\n2. **July-September 2019:** The patient underwent whole-body scanning, which revealed macroscopic metastases in the bone. He was clinically classified as stage IVB (T4N0M1c) Non-Small Cell Lung Carcinoma (NSCLC). Zoledronic acid was administered to control bone destruction (Step 4).\n3. **September-October 2019:** The patient underwent tissue biopsy, which detected an acquired T790M mutation in exon 20 (c.2369C>T, frequency as 61.9%) via droplet digital polymerase chain reaction (ddPCR) (Step 7).\n4. **October-November 2019:** Due to the detection of the T790M mutation, the patient was switched to osimertinib 80mg once daily, achieving stable disease with shrinkage of hepatic lesions (Step 8).\n\n**Outcomes:**\n\n1. The patient experienced a rapid clinical benefit lasting 11 months after starting treatment with gefitinib (250 mg once daily) in response to the detection of EGFR exon 19 deletion (Step 6).\n2. After 11 months on gefitinib, tissue biopsy was performed to investigate resistance mechanisms, detecting an acquired T790M mutation in exon 20 (c.2369C>T, frequency as 61.9%) via droplet digital polymerase chain reaction (ddPCR) (Step 7).\n\n**Conclusion:**\nThe patient's clinical course highlights the importance of molecular testing and targeted therapy in the management of NSCLC. The detection of EGFR exon 19 deletion led to treatment with gefitinib, resulting in a rapid clinical benefit. However, the subsequent development of T790M mutation necessitated a switch to osimertinib, achieving stable disease with shrinkage of hepatic lesions.\n\n**Recommendations:**\n\n1. Regular molecular testing for EGFR mutations and T790M status should be performed in patients with NSCLC.\n2. Targeted therapy with gefitinib or osimertinib should be considered based on molecular test results.\n3. Close monitoring of disease progression and response to treatment is essential in managing NSCLC.\n\n**Limitations:**\n\n1. The patient's clinical course was limited by the availability of targeted therapies at the time of diagnosis.\n2. Further research is needed to explore the optimal timing and sequence of molecular testing and targeted therapy in NSCLC.\n\nThis case highlights the importance of personalized medicine in the management of NSCLC, emphasizing the need for regular molecular testing and targeted therapy based on test results.", + "bertscore": { + "precision": [ + 0.7394998073577881 + ], + "recall": [ + 0.7590272426605225 + ], + "f1": [ + 0.7491363286972046 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.25666746497154236, + 0.09836211800575256, + -0.10564713180065155, + 0.11217941343784332, + 0.015587031841278076, + 0.07877800613641739, + -0.006527600809931755, + 0.30493852496147156, + 0.5536767244338989, + -0.33620452880859375, + -0.018288739025592804, + -0.09518112242221832, + 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"status": "success", + "reconstructed_narrative": "**Patient Demographics**\n\nThe patient is a 35-year-old female who was diagnosed with breast cancer. Unfortunately, the demographic information provided does not include her name, address, or any other identifying details.\n\n**Timeline of Diagnoses**\n\nThe patient's journey began in [month/year] when she developed memory problems following a COVID-19 infection. Two days later, she underwent lumpectomy due to the worsening symptoms. The pathology report revealed infiltrative breast carcinoma of mixed type (80% non-specific, 20% lobular), histoprognostic grade I (2-2-1), and histological tumor size of 30 mm along the long axis.\n\n**Timeline of Treatments**\n\nFollowing the lumpectomy, the patient was diagnosed with anti-LGI1 limbic encephalitis associated with early-stage breast cancer. MRI, EEG, and positive anti-LGI1 antibodies supported this diagnosis. As a result, she underwent PET scans to further investigate the breast cancer diagnosis.\n\nThe PET scan identified a moderately hypermetabolic lesion in the right breast, leading to resection of the breast tumor with immunohistopathological analysis. The pathological stage was determined as pT2 N0 (sn) G1 R. Following resection, immunosuppressive treatment was started within 24 hours of admission.\n\n**Timeline of Outcomes**\n\nThe patient's condition improved gradually over time. She recovered from the initial symptoms and no longer experienced headaches or focal epileptic seizures since hospitalization. However, partial retrograde and anterograde amnesia persisted during the initial week, followed by a slow and steady improvement.\n\nAfter 12 months of recovery, the patient returned to work with 80% of her previous productivity. Neuropsychological evaluations at baseline showed impairment in verbal episodic memory (Free and Cued Selective Reminding Test) and visual episodic memory (recall of the Rey-Osterrieth complex figure). However, after six months of treatment, objective cognitive improvement was observed.\n\n**Current Status**\n\nThe patient's current status is one of ongoing management and monitoring. She continues to receive immunosuppressive treatment to manage her anti-LGI1 limbic encephalitis. Regular follow-up appointments with her healthcare team are necessary to monitor her condition and adjust treatment as needed.\n\nDespite the challenges she has faced, the patient has demonstrated remarkable resilience and determination in her pursuit of recovery. Her progress is a testament to the importance of comprehensive care and ongoing support for individuals with complex medical conditions.", + "bertscore": { + "precision": [ + 0.5682033896446228 + ], + "recall": [ + 0.5968579053878784 + ], + "f1": [ + 0.5821782946586609 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 12, + "edge_count": 11, + "avg_in_degree": 0.9166666666666666, + "density": 0.08333333333333333 + }, + "trajectory_embedding": [ + 0.13369283080101013, + 0.14433510601520538, + -0.22548367083072662, + 0.060306016355752945, + -0.08639272302389145, + 0.002943794010207057, + 0.23735707998275757, + 0.16482573747634888, + 0.5013976693153381, + -0.3400944769382477, + -0.0792926773428917, + 0.0980411171913147, + -0.5940414071083069, + -0.14733976125717163, + -0.22831867635250092, + 0.1983317881822586, + -0.00968053936958313, + 0.277439147233963, + 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Unfortunately, the provided data does not include the patient's demographic information such as age, address, or contact details.\n\nHowever, based on the timeline of diagnoses and treatments provided, we can reconstruct a coherent narrative:\n\nThe patient was first diagnosed with lung cancer, which led to the start of gyroknife radiotherapy for left and right lung malignancies 12 times. This treatment was likely aimed at reducing the size of the tumors in the lungs.\n\nAfter completing this treatment, the patient experienced tumor progression, leading to the start of anlotinib 8mg orally once daily for 14 days every 3 weeks. This medication was intended to slow down the growth of the cancer cells.\n\nHowever, after 14 cycles of anlotinib treatment, the patient presented with hyperglycemia (fasting plasma glucose of 26.1 mmol/L) and urine ketone (+++), leading to a diagnosis of type 1 diabetes. As a result, the patient was discharged with a hypoglycemic regimen of insulin degludec 5 units in the morning and insulin aspartate 4 units three times a day.\n\nOne week after discharge, the patient's blood glucose levels significantly increased after re-starting anlotinib (highest recorded level was 30.1 mmol/L), and the insulin dose was increased. Despite this escalation, the patient continued to experience significant improvements in their laboratory parameters, including GADA, ICA, IAA, Fasting blood glucose, Hemoglobin A1c, Hemoglobin, and Serum albumin.\n\nAfter two cycles of anlotinib treatment, the medication was discontinued due to tumor progression and its significant negative impact on glucose metabolism. However, by the 16th cycle, laboratory parameters showed a marked improvement in these areas.\n\nThe patient's current status is unclear from the provided data, but it appears that they have undergone various treatments for their lung cancer and diabetes. The exact outcome of these treatments is not specified, but the narrative suggests that the patient has experienced significant improvements in their laboratory parameters over time.", + "bertscore": { + "precision": [ + 0.6911485195159912 + ], + "recall": [ + 0.6727587580680847 + ], + "f1": [ + 0.6818296313285828 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.1467558592557907, + 0.21578022837638855, + -0.22472743690013885, + 0.1429169625043869, + -0.0391475111246109, + 0.10741577297449112, + 0.24607594311237335, + 0.2464669942855835, + 0.3772128224372864, + -0.3546753525733948, + -0.1136227399110794, + 0.030413171276450157, + -0.4117017686367035, + -0.1751895248889923, + -0.3702186644077301, + 0.24298548698425293, + -0.22810597717761993, + 0.43166160583496094, + 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with a history of immunocompromised status due to HIV/AIDS. He was admitted to the hospital on day 1 (N1) with symptoms of pneumonia and acute hypoxic respiratory failure requiring intubation. His vital signs were unstable, and he required close monitoring in the intensive care unit.\n\n**Timeline of Diagnoses**\n\n* Day 1 (N1): Admitted with pneumonia and acute hypoxic respiratory failure.\n* Day 14 (N2): Developed septic shock and PICC-line-associated MSSA bacteremia. He was treated with IV cefazolin.\n* Day 28 (N3): Developed SVC syndrome and left upper extremity DVT. He was treated with therapeutic enoxaparin.\n* Day 42 (N4): Recurrent fevers and transfer back to the ICU for septic shock management. Blood cultures grew MSSA, and a transesophageal echocardiogram showed no endocarditis.\n* Day 54 (N5): Repeat blood cultures grew A. fumigatus in addition to MSSA. The infectious disease team recommended continuing IV cefazolin for MSSA bacteremia and adding caspofungin for fungal coverage.\n* Day 56 (N6): Atovaquone continued for pneumocystis jirovecii prophylaxis, and tenofovir discontinued due to concern for contributing to acute kidney injury. The antiretroviral regimen was changed to dolutegravir/rilpivirine plus emtricitabine pending further evaluation of hepatitis B status.\n* Day 62 (N9): Patient died of his illness.\n\n**Timeline of Treatments**\n\n* Day 1-14 (N2): IV cefazolin for MSSA bacteremia\n* Day 28-42 (N3): Therapeutic enoxaparin for SVC syndrome and DVT\n* Day 54 (N5): IV cefazolin continued, caspofungin added for fungal coverage\n* Day 56 (N6): Atovaquone continued, tenofovir discontinued, dolutegravir/rilpivirine plus emtricitabine started\n\n**Outcome**\n\nThe patient's condition worsened over time, and he eventually died on day 62 due to his illness. Despite multiple treatments, including IV cefazolin, therapeutic enoxaparin, and caspofungin, the patient's immune system was unable to overcome the infections.\n\nNote: The narrative is based on the provided data and may not be a comprehensive or entirely accurate representation of the patient's medical history.", + "bertscore": { + "precision": [ + 0.7339485883712769 + ], + "recall": [ + 0.7237894535064697 + ], + "f1": [ + 0.7288336157798767 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.18157726526260376, + 0.24173596501350403, + -0.15064290165901184, + 0.07789953052997589, + 0.15454770624637604, + 0.16961298882961273, + -0.11799095571041107, + 0.21222464740276337, + 0.46130186319351196, + -0.346190482378006, + -0.21522000432014465, + 0.06953564286231995, + 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b/src/benchmark/output/results/results_graph_074.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an unknown female with no specified age or background information provided in the data. However, based on the clinical presentation and imaging findings, it can be inferred that she is likely a young adult.\n\n**Initial Presentation (Step 1):**\nThe patient presented with a fluid collection adjacent to the spleen, which was identified through abdominal ultrasound. The fluid collection had septations, and no malignant cells were found in the aspirated fluid.\n\n**Progression of Disease (Steps 2-5):**\nOver time, the cystic lesion in the left upper quadrant of the abdomen grew in size, with a notable increase from 7.6 x 11.7 cm to 11 x 22 cm. The patient reported feeling pressure and a pulling sensation on the left side of her abdomen, rated as 4/10 for pain. Ultrasound-guided aspiration revealed 33 mL of clear yellow fluid, which was sent to pathology and showed no evidence of malignant cells.\n\n**Imaging Findings:**\nThroughout the course of the disease, various imaging modalities were used, including ultrasound, CT scans, and MRI. These studies consistently demonstrated a large cystic mass extending from the spleen on the left to the left hemipelvis, with enhancing septations.\n\n**Treatment (Step 7):**\nThe patient received doxycycline sclerotherapy over eight months as part of her treatment plan. Post-sclerotherapy ultrasound showed no significant changes in the size or appearance of the cystic mass.\n\n**Outcome:**\nDespite the growth of the cystic lesion, the patient did not experience any symptoms that would suggest malignancy. The sclerotherapy treatment appears to have been effective in stabilizing the lesion, and further imaging studies are scheduled for follow-up.\n\nIn summary, this patient presented with a fluid collection adjacent to the spleen, which progressed over time into a large cystic mass extending from the spleen on the left to the left hemipelvis. The patient received doxycycline sclerotherapy as part of her treatment plan, and post-treatment imaging studies showed no significant changes in the size or appearance of the lesion.", + "bertscore": { + "precision": [ + 0.7009899616241455 + ], + "recall": [ + 0.6653150320053101 + ], + "f1": [ + 0.6826867461204529 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.37995657324790955, + 0.09801924228668213, + 0.029700586572289467, + 0.12594357132911682, + 0.10155230760574341, + 0.09751962870359421, + -0.09553129225969315, + 0.2206941395998001, + 0.4248223304748535, + -0.16399696469306946, + -0.31089702248573303, + -0.05961534380912781, + -0.545925498008728, + 0.12594513595104218, + -0.3283112645149231, + 0.15797248482704163, + 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Demographics:**\nThe patient is a 77-year-old man with a history of smoking, hypertension, benign prostatic hyperplasia, and hyperuricemia. He was admitted for his first cycle of chemotherapy for stage IV small cell lung cancer without cerebral metastases.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Diagnosis:** The patient's diagnosis of stage IV small cell lung cancer was confirmed upon admission.\n2. **Somnolence and Right-Sided Weakness:** 30 minutes after chemotherapy premedication, the patient experienced a sudden change in mental status, progressing to somnolence. Physical examination revealed altered mental status and right-sided weakness (N2).\n3. **Neurological Examination:** The patient's neurological examination showed signs of reduced mobility on the right side, accompanied by right facial paresis (N3).\n4. **Blood Gas Analysis and Brain CT Angiography:** Blood gas analysis showed no respiratory, metabolic, or electrolyte abnormalities, while brain CT angiography did not reveal any vascular lesions or thrombi in major vessels (N4).\n\n**Timeline of Treatments:**\n\n1. **Chemotherapy Premedication:** The patient received 4 mg intravenous ondansetron and 8 mg intravenous dexamethasone as premedication for chemotherapy.\n2. **Aspirin Administration:** Due to the suspicion of a transient ischemic event, a loading dose of 300 mg of aspirin was administered, followed by a daily dose of 100 mg of aspirin (N6).\n\n**Outcome:**\n\nThe patient gradually became more alert approximately one hour after the onset of symptoms and returned to his baseline mental status without any neurological deficits by one hour and thirty minutes after onset. The suspicion of a transient ischemic event as the primary cause of the symptoms was confirmed, and the patient's condition improved with the administration of aspirin.\n\n**Conclusion:**\n\nThis case highlights the importance of prompt recognition and management of acute neurological events in patients undergoing chemotherapy for cancer. Early intervention with aspirin may have contributed to the patient's rapid recovery from a suspected transient ischemic event. Further evaluation and monitoring are necessary to ensure that this patient does not experience any further complications related to his cancer treatment or underlying medical conditions.", + "bertscore": { + "precision": [ + 0.7189599275588989 + ], + "recall": [ + 0.7112793326377869 + ], + "f1": [ + 0.715099036693573 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.045807287096977234, + 0.11770268529653549, + -0.03572636470198631, + 0.021092357113957405, + 0.07645720988512039, + 0.007500001695007086, + 0.008010799996554852, + 0.14289645850658417, + 0.3722045123577118, + -0.33858588337898254, + -0.3850763738155365, + 0.18912379443645477, + -0.6559848189353943, + -0.16191299259662628, + -0.20137447118759155, + 0.0759354755282402, + 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"**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 37-year-old woman diagnosed with left lung adenocarcinoma in November 2019. She has extensive bone metastases (cT4N3M1c, stage IVB).\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **November 2019:** The patient was diagnosed with left lung adenocarcinoma and had a baseline chest CT scan and head MRI performed.\n2. **December 2019:** Tumor tissue NGS revealed EGFR exon 18 p.G719S mutation and EGFR exon 20 p.S768I mutation, which led to the initiation of first-line afatinib treatment (40 mg daily po).\n3. **January 2020 - October 2020:** The patient experienced therapeutic failure after 10 months of afatinib treatment, as indicated by time to failure.\n4. **October 2020:** The patient developed new brain lesions and had a partial response on afatinib treatment (lung lesion stable disease, head lesions partial response).\n5. **February 2021:** The patient's brain lesions continued to deteriorate, leading to the reversion of third-line afatinib treatment.\n6. **February 2021:** The patient was switched to second-line osimertinib treatment (80 mg daily po).\n\n**Outcomes:**\n\n* Lung lesion stable disease (SD) at October 2020 and February 2021.\n* Head lesions partial response (PR) on afatinib treatment at October 2020 and February 2021.\n* Brain lesions deteriorated over time, with a new onset of symptoms in February 2021.\n\n**Medications:**\n\n* Afatinib (40 mg daily po): initiated in December 2019, experienced therapeutic failure after 10 months, and partially responsive to treatment at October 2020.\n* Osimertinib (80 mg daily po): started in February 2021 as a second-line treatment.\n\n**Imaging:**\n\n* Baseline chest CT scan and head MRI performed in November 2019.\n* Follow-up imaging not specified for each time point, but mentioned to be performed at October 2020 and February 2021.\n\nNote: The patient's timeline is based on the provided data, which may not be comprehensive or up-to-date.", + "bertscore": { + "precision": [ + 0.6782082915306091 + ], + "recall": [ + 0.6782101988792419 + ], + "f1": [ + 0.6782092452049255 + ] + 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He received cefaclor and azithromycin at a local clinic without significant alleviation of his symptoms.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (September 2023):**\nThe patient was initially evaluated in an outpatient setting with persistent respiratory symptoms. A chest X-ray revealed a space-occupying mass in the left lung, prompting hospitalization on September 10, 2023.\n2. **Step 2 (September 10, 2023):**\nUpon admission, laboratory investigations were normal, and CT imaging demonstrated irregularly shaped soft tissue masses in both the upper and lower lobes of the left lung.\n3. **Step 3 (September 11-12, 2023):**\nFurther characterization of the lung mass was performed through additional CT imaging, which showed an oval mass in the lower lobe of the lung measuring approximately 2.3 cm x 1.7 cm with lobulated and spiculated margins.\n4. **Step 4 (September 13-14, 2023):**\nPET-CT imaging revealed high-density lesions in both the upper and lower lobes of the left lung, with increased glucose metabolism. Multiple enlarged lymph nodes were detected in the mediastinum and interlobular spaces.\n\n**Treatments:**\n\n1. **Step 1 (September 2023):**\nThe patient received cefaclor and azithromycin at a local clinic.\n2. **Step 2-4 (September 10-14, 2023):**\nNo specific treatments were mentioned in the provided data.\n\n**Outcomes:**\n\n1. **Imaging:** The initial chest X-ray revealed a space-occupying mass in the left lung, which was later characterized through additional imaging studies.\n2. **Laboratory Investigations:** Normal laboratory results were reported during hospitalization.\n3. **PET-CT Imaging:** High-density lesions with increased glucose metabolism were detected in both the upper and lower lobes of the left lung.\n\n**Conclusion:**\nThe patient's clinical presentation and diagnostic timeline suggest a complex respiratory condition, potentially related to malignancy or other pathologies. Further investigation and characterization are necessary to determine the underlying cause and develop an effective treatment plan.", + "bertscore": { + "precision": [ + 0.5229495763778687 + ], + "recall": [ + 0.6768455505371094 + ], + "f1": [ + 0.5900275707244873 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.28606685996055603, + 0.19629862904548645, + -0.1704561412334442, + 0.05046887323260307, + 0.02108978107571602, + -0.05829715356230736, + -0.002245333045721054, + 0.13291165232658386, + 0.2349492609500885, + -0.29417815804481506, + -0.1785058230161667, + 0.17046767473220825, + -0.6892815232276917, + -0.1641303449869156, + -0.12110166251659393, + -0.009564938955008984, + 0.20506024360656738, + 0.19735971093177795, + -0.06371694803237915, + -0.168881356716156, + 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She was diagnosed with stage IVa epidermal growth factor receptor (EGFR)L858R-mutated non-small cell lung cancer (NSCLC).\n\n**Timeline of Diagnoses:**\n\n* September 2019: The patient presented with symptoms of shortness of breath, cough, and hemoptysis, leading to a diagnosis of stage IVa (cT4N2M1a) lung adenocarcinoma in the right upper lobe, with multiple ipsilateral lung metastases, and involvement of the pleura and mediastinal lymph nodes.\n* September 2019: A bronchoscopic lung biopsy revealed the presence of EGFR p.L858R and TP53 p.R248L mutations.\n\n**Timeline of Treatments:**\n\n1. **First-Line Treatment (October 11, 2019 - February 2020)**:\nThe patient received first-line treatment with icotinib (125 mg orally, three times daily) and pemetrexed. After two months, the patient experienced partial response.\n2. **Second-Line Treatment (April 28, 2020 - July 2020)**:\nThe patient commenced second-line treatment with amonertinib (110 mg orally, once daily) in combination with anlotinib (12 mg orally, once daily for 2 weeks, followed by a 1-week drug-free period). The treatment resulted in stable disease initially but progressed after 3 months.\n3. **Third-Line Treatment (August 3, 2020 - November 2020)**:\nThe patient initiated treatment with osimertinib (80 mg orally, once daily) and bevacizumab (350 mg IV, on day 1 of a 21-day cycle). The treatment resulted in partial response after two cycles and significant reduction in tumor lesions after four cycles.\n4. **Fourth-Line Treatment (October 10, 2020 - present)**:\nThe patient received pembrolizumab (200 mg IV on day 1 of every 3 weeks), pemetrexed, and carboplatin. The treatment resulted in partial response after two cycles and significant reduction in tumor lesions after four cycles.\n\n**Outcomes:**\n\n* **Pathological Complete Response (pCR)**:\nThe patient achieved a pathological complete response (pCR) and prolonged survival.\n* **High PD-L1 Expression**:\nTumor microenvironment analysis showed high programmed cell death 1 ligand 1 (PD-L1) expression on tumor cells, indicating potential for immune checkpoint therapy.\n* **Increased Immune Cell Infiltration**:\nThe patient had increased infiltration of immune cells, particularly PD-1+CD8+T cells and PD-L1+macrophages, in the tumor microenvironment.\n\nIn conclusion, this patient's case highlights the importance of personalized medicine approaches in treating advanced NSCLC. The use of targeted therapies, such as EGFR inhibitors and immunotherapies, has led to significant improvements in treatment outcomes and quality of life for patients with this disease.", + "bertscore": { + "precision": [ + 0.5608479976654053 + ], + "recall": [ + 0.6207950711250305 + ], + "f1": [ + 0.5893009901046753 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.28967222571372986, + 0.13287165760993958, + -0.27321428060531616, + 0.1138295978307724, + -0.09009366482496262, + 0.025592172518372536, + 0.09159565716981888, + 0.1864396333694458, + 0.445202499628067, + -0.5484539866447449, + -0.1185631975531578, + 0.20055018365383148, + -0.6732085347175598, + -0.10172402113676071, + -0.23370732367038727, + 0.013881613500416279, + 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medical history of tobacco use, who quit more than 24 years ago. He presented with a newly diagnosed lung cancer and a progressively increasing lump in the right axilla over 2 months.\n\n**Initial Diagnosis (Step 1):**\nUpon presentation, the patient underwent an ultrasound examination, which revealed a 3.7 cm enlarged lymph node (LN) in the right axilla with effacement and hypervascularity. A biopsy of the LN showed carcinoma with cytokeratin 7 (CK-7) and thyroid transcription factor-1 (TTF-1) positivity, consistent with lung adenocarcinoma, with a possibility of squamous component. Further imaging studies, including a PET scan, revealed multiple F-fluorodeoxyglucose (FDG) avid nodes in the right hilum, thoracic inlet, mediastinum, and right axilla, concerning for metastatic disease.\n\n**Treatment Initiation (Step 2):**\nThe patient was started on single-agent pembrolizumab, a checkpoint inhibitor, with good treatment response. However, after 17 months of treatment, the patient presented to the clinic with worsening shortness of breath (SOB), which he noted a few months ago, was mild in the beginning, and has progressively gotten worse in the last few weeks.\n\n**Progression and Complications (Step 3):**\nA recent PET scan did not show any evidence of disease progression or signs of inflammation in lungs. However, echocardiography revealed severe pulmonary arterial hypertension (PAH), with elevated right ventricular systolic pressure (RVSP) at 86 mm Hg. The patient also had mild regurgitation noted at the pulmonary valve with no structural abnormalities.\n\n**Current Status:**\nThe patient is currently under close observation for worsening symptoms and potential disease progression. Further management strategies, including additional immunotherapies or PAH-specific treatments, are being considered based on ongoing clinical evaluation.\n\n**Timeline of Diagnoses and Treatments:**\n\n* Month 0-2: Patient presents with newly diagnosed lung cancer and progressively increasing lump in the right axilla.\n* Month 2-17: Patient undergoes treatment with pembrolizumab, showing good initial response.\n* Month 17-present: Patient experiences worsening shortness of breath, prompting further evaluation.\n\n**Outcomes:**\n\n* The patient's current disease status is concerning for metastatic lung cancer with PAH.\n* Further management strategies are being considered to address the patient's worsening symptoms and potential disease progression.", + "bertscore": { + "precision": [ + 0.7466033101081848 + ], + "recall": [ + 0.7676594853401184 + ], + "f1": [ + 0.7569850087165833 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + 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No symptoms were reported, and she had no significant medical history, including no history of tuberculosis or lung infections.\n\n**Initial Diagnosis (Step 1):**\nA chest radiograph revealed a solitary pulmonary nodule in the left lower lung field. The patient was diagnosed with a pulmonary nodule (code: 7225005) and underwent further evaluation.\n\n**Biopsy and Initial Treatment (Steps 2-3):**\nA peripheral pulmonary nodule was identified on a chest CT scan, which led to the performance of an endobronchial ultrasound transbronchial lung biopsy. The procedure was successful, but minor bleeding occurred. Biopsy specimens revealed granulomatous inflammation. Following this, a transbronchial lung cryobiopsy was performed four times through the same guide sheath, also with minor bleeding.\n\n**Post-Biopsy Complications and Treatment Initiation (Step 3):**\nAfter the cryobiopsy, increased density in the lower zone of the left lung was observed on chest radiograph. Tissue sample PCR tests were negative for Mycobacterium tuberculosis and NTM. However, one week post-biopsy, follow-up outpatient chest radiographs revealed an enlarged shadow at the location of the original lesion. The patient reported discharge of a purulent and intermittent blood-tinged sputum, which led to the initiation of antibiotic therapy with moxifloxacin (400 mg daily).\n\n**Response to Antibiotics and Follow-Up (Step 4):**\nTwo weeks after starting antibiotics, chest radiographs indicated a slight increase in the size of the lesion. However, there was an improvement in her symptoms, with no other abnormal findings such as fever. The antibiotic therapy continued with regular outpatient follow-ups.\n\n**Lesion Improvement and Acid-Fast Bacilli Growth (Step 5):**\nThree weeks after tissue biopsy, chest radiographs showed improvement in the lesion size. Notably, growth of acid-fast bacilli was reported in the bronchoalveolar lavage fluid obtained during examination.\n\n**Outcome:**\nThe patient's symptoms improved significantly with antibiotic therapy and follow-up care. The growth of acid-fast bacilli in the bronchoalveolar lavage fluid suggested that the patient had a Mycobacterium tuberculosis infection, which was confirmed by PCR tests. However, due to the presence of granulomatous inflammation in biopsy specimens, it is possible that the patient had an NTM infection as well.\n\n**Conclusion:**\nThe patient's case highlights the importance of prompt evaluation and treatment for pulmonary nodules, particularly those with granulomatous inflammation or acid-fast bacilli growth. Early detection and management can significantly improve outcomes and prevent complications.", + "bertscore": { + "precision": [ + 0.6428266167640686 + ], + "recall": [ + 0.7402181625366211 + ], + "f1": [ + 0.6880933046340942 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 6, + "edge_count": 4, + "avg_in_degree": 0.6666666666666666, + "density": 0.13333333333333333 + }, + "trajectory_embedding": [ + 0.1967584788799286, + 0.11755304038524628, + -0.10197411477565765, + -0.01451544463634491, + -0.10492626577615738, + -0.16041645407676697, + 0.15277233719825745, + 0.07490139454603195, + 0.196526437997818, + -0.2453027218580246, + -0.23723392188549042, + 0.15686118602752686, + -0.45318803191185, + -0.14287793636322021, + -0.1919034719467163, + -0.01922443136572838, + 0.09047435224056244, + 0.2307237833738327, + 0.06612925231456757, + -0.30490654706954956, + 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The patient's demographic information is not provided in the data.\n\n**Initial Presentation:**\nThe patient presented with symptoms of intracranial hypertension, including nausea and vomiting (Step 1). This was the initial presentation that led to further investigation.\n\n**Diagnosis:**\nFurther investigation revealed brain MRI suggesting leptomeningeal metastases (Step 2). Lumbar puncture was performed, and cerebrospinal fluid cytology confirmed leptomeningeal metastases (Step 3).\n\n**Treatment:**\nThe patient received treatment for the diagnosed condition. The treatment sequence included initial monotherapy with Olaparib, followed by combination therapy with intrathecal chemotherapy, and eventually a triple combination of Olaparib, Furmonertinib, and intrathecal chemotherapy (Step 5). Intrathecal pemetrexed was administered since October 2021 (Step 8).\n\n**Progression:**\nSymptoms of leptomeningeal metastases worsened dramatically, including lethargy, unresponsiveness, difficulty in eating and swallowing, necessitating intravenous nutritional support. The patient's ECOG performance status declined to 4 (Step 9). This marked a significant progression of the disease.\n\n**Outcome:**\nThe patient experienced a durable response to Olaparib lasting approximately 21 months (Step 6). However, the worsening of leptomeningeal metastases symptoms and decline in functional status necessitated further treatment adjustments.\n\n**Timeline:**\n\n* Step 1: Initial presentation with intracranial hypertension symptoms\n* Step 2: Diagnosis of leptomeningeal metastases confirmed by brain MRI\n* Step 3: Lumbar puncture performed, and cerebrospinal fluid cytology confirmed leptomeningeal metastases\n* Step 4: Placement of Ommaya reservoir for treatment delivery\n* Step 5: Identification of EGFR and BRCA2 mutations\n* Step 6: Initiation of Olaparib therapy with durable response lasting approximately 21 months\n* Step 7: Treatment escalation to combination therapy with intrathecal chemotherapy\n* Step 8: Administration of intrathecal pemetrexed since October 2021\n* Step 9: Worsening of leptomeningeal metastases symptoms and decline in functional status\n\n**Conclusion:**\nThe patient was diagnosed with leptomeningeal metastases and received treatment with Olaparib, Furmonertinib, and intrathecal chemotherapy. The patient experienced a durable response to Olaparib but ultimately required further treatment adjustments due to worsening of symptoms and decline in functional status.", + "bertscore": { + "precision": [ + 0.5512253046035767 + ], + "recall": [ + 0.5020527839660645 + ], + "f1": [ + 0.5254911780357361 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2321387678384781, + 0.21690434217453003, + -0.13298587501049042, + 0.17195039987564087, + 0.08285973221063614, + 0.15777303278446198, + 0.1095961406826973, + 0.3161073923110962, + 0.6317851543426514, + -0.3226621448993683, + -0.16632980108261108, + -0.09433408826589584, + -0.4814378321170807, + -0.1313047707080841, + -0.1984696239233017, + 0.20387743413448334, + -0.17162606120109558, + 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question is a female who was diagnosed with pulmonary adenocarcinoma, a type of lung cancer. Unfortunately, the patient also had bilateral scattered breast metastases, which made her diagnosis even more complex.\n\nThe patient's journey began when she experienced persistent coughing for one month, which led to a chest CT scan that revealed a 3.1 cm right lower lobe tumor, lymphadenopathy, right pleural effusion, pericardial effusion, and scattered nodules in both breasts. Her CA19-9 level was also elevated at 282 U/mL.\n\nFollowing this initial diagnosis, the patient underwent further testing, including molecular analysis that detected an EML4-ALK fusion gene. This led to a biopsy of her bilateral breast tumors, which revealed adenocarcinoma derived from the lungs or breasts.\n\nThe patient's treatment plan began with oral medication, specifically alectinib (600 mg once daily), which was initiated in response to changes in her lab results and imaging findings. The goal of this treatment was to target the ALK rearrangement present in her cancer cells.\n\nOver time, the patient experienced significant reductions in tumor size, particularly in her breast metastases, which nearly disappeared after a maximum size of 4 mm. Her pleural effusion also resolved, and her CA19-9 level decreased from 282 U/mL to 3.7 U/mL.\n\nSix months after starting treatment with alectinib, the patient underwent another CT scan that showed further tumor shrinkage in her lower right lobe and resolution of her pleural effusion. This marked a significant milestone in her treatment journey, indicating that the medication was effective in controlling her cancer.\n\nThe patient's ongoing treatment with alectinib has been accompanied by regular monitoring of her lab results and imaging findings. Her CA19-9 level remains decreased, and she continues to experience no evidence of recurrence. The resolution of shadows in both breasts on CT scans also suggests that the medication is effective in controlling her breast metastases.\n\nThroughout this journey, the patient's treatment plan has been tailored to address changes in her lab results and imaging findings. Her care team has closely monitored her response to treatment and made adjustments as needed to ensure she receives the most effective therapy possible.\n\nThe patient's story highlights the importance of early detection and targeted therapies in managing complex cancers like pulmonary adenocarcinoma with bilateral breast metastases. With ongoing treatment and close monitoring, this patient is able to manage her disease effectively and maintain a good quality of life.", + "bertscore": { + "precision": [ + 0.6228880882263184 + ], + "recall": [ + 0.5976125597953796 + ], + "f1": [ + 0.6099885702133179 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2193172574043274, + 0.17341764271259308, + -0.28511232137680054, + 0.06250262260437012, + -0.2072673738002777, + -0.09170977771282196, + 0.21316777169704437, + 0.09700273722410202, + 0.22861331701278687, + -0.39751580357551575, + -0.20688259601593018, + 0.24647818505764008, + -0.7876354455947876, + -0.08496146649122238, + -0.4245613217353821, + 0.042675264179706573, + 0.13037434220314026, + 0.3195406198501587, + 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adult male with a history of respiratory symptoms. Unfortunately, the demographic information is not provided in the given data.\n\n**Initial Presentation (Step 1):**\nThe patient presented with right locus coeruleus, visceral inversion, sinusitis, and bronchial dilatation. These symptoms led to further cardiac evaluation.\n\n**Diagnostic Journey:**\n\n1. **Electrocardiography (ECG) and Initial Diagnosis (Step 2):**\nAn ECG showed a right-sided heart, prompting further imaging with chest CT and 3D reconstruction of the ribs to evaluate lung and organ positioning.\n\n2. **Chest CT Findings (Step 3):**\nThe chest CT revealed chronic inflammation of both lungs, multiple bronchiectasis in both lungs, nodules in the upper lobe of the right lung, a flaky high-density shadow in the right main bronchus, bilateral pleural thickening, localized calcification of the right pleura, and a right-sided heart with transposition of thoracic and abdominal organs.\n\n3. **Paranasal Sinus CT Findings (Step 4):**\nA paranasal sinus CT showed right maxillary sinusitis, ethmoid sinus, nasal soft tissue shadow, polyps, deviated nasal septum, and bilateral middle and lower turbinate hypertrophy.\n\n4. **Bronchoscopy Evaluation (Steps 5-6):**\nNormal bronchial tubes in the right lung led to further bronchoscopic evaluation of the left lung, where a polypoid neoplasm was found in the opening of the upper lobe of the left lung.\n\n5. **Cancer Diagnosis and Treatment Planning (Step 7):**\nBronchoalveolar lavage fluid cytology showed cancer cells, prompting immunohistochemistry to determine the type of cancer. The diagnosis confirmed small cell lung cancer.\n\n6. **Bone Metastasis Evaluation (Step 8):**\nExtrapulmonary auxiliary examination suggested bone metastasis.\n\n7. **Final Diagnosis and Treatment (Step 10):**\nThe patient was diagnosed with extensive stage small cell lung cancer of the left lung, accompanied by Kartagener Syndrome. The ECOG performance status score was 1.\n\n**Outcomes:**\n\n- The patient has been diagnosed with small cell lung cancer.\n- Bone metastasis is suspected but not confirmed.\n- Treatment plans are pending further evaluation and consultation.\n\nThis clinical case report highlights the importance of a comprehensive diagnostic journey, from initial presentation to final diagnosis. Each step in the diagnostic process builds upon previous findings, ultimately leading to an accurate diagnosis and treatment plan for this patient with small cell lung cancer.", + "bertscore": { + "precision": [ + 0.6484930515289307 + ], + "recall": [ + 0.6397433876991272 + ], + "f1": [ + 0.6440885066986084 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.3022826015949249, + -0.0002478778478689492, + 0.07108965516090393, + 0.18501682579517365, + 0.12881651520729065, + 0.13057772815227509, + 0.010211390443146229, + 0.27111274003982544, + 0.48087310791015625, + -0.30358201265335083, + -0.15933957695960999, + -0.05752738192677498, + -0.5778652429580688, + -0.08748479187488556, + -0.32486921548843384, + 0.2844110131263733, + 0.11371511220932007, + 0.32671236991882324, + 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presented to Anhui Chest Hospital with cough and chest pain for 2 months. She had no history of smoking.\n\n**Timeline of Diagnoses:**\n\n1. **March 2022:** The patient initially presented to the hospital with symptoms of cough and chest pain, which led to a chest computed tomography (CT) scan.\n2. **March 21, 2022:** The CT scan revealed left pleural thickening and pleural effusion, prompting further investigation.\n3. **Thoracoscopic left pleural biopsy** was performed on the same day, followed by plasma DNA analysis via next-generation sequencing (NGS), which identified EGFR exon L858R mutation.\n4. **April 2022:** The diagnosis of stage IV lung adenocarcinoma with EGFR exon L858R mutation was confirmed.\n\n**Timeline of Treatments:**\n\n1. **March 2022:** The patient received osimertinib as the first-line treatment for her lung cancer.\n2. **May 22, 2022:** A follow-up chest CT scan revealed a partial response (PR) to osimertinib treatment.\n3. **April 4, 2024:** Due to progressive disease, the patient's treatment regimen was changed to dabrafenib, trametinib, and aumolertinib concurrently.\n4. **June 3, 2024:** A follow-up chest CT scan revealed a complete response (CR) to the new treatment regimen.\n\n**Timeline of Outcomes:**\n\n1. **May 22, 2022:** The patient experienced a partial response to osimertinib treatment.\n2. **April 4, 2024:** The patient's disease progressed, and she was diagnosed with progressive disease (PD).\n3. **June 3, 2024:** The patient achieved a complete response (CR) to the new treatment regimen.\n\n**Notable Events:**\n\n* During treatment with dabrafenib, trametinib, and aumolertinib, the patient experienced a transient fever.\n* The patient's disease was diagnosed as stage IV lung adenocarcinoma with EGFR exon L858R mutation.\n\n**Conclusion:**\nThe patient's clinical course was marked by an initial presentation of cough and chest pain, followed by a diagnosis of stage IV lung adenocarcinoma with EGFR exon L858R mutation. The patient received osimertinib as the first-line treatment and experienced a partial response. Due to progressive disease, the treatment regimen was changed to dabrafenib, trametinib, and aumolertinib concurrently, resulting in a complete response.", + "bertscore": { + "precision": [ + 0.6942758560180664 + ], + "recall": [ + 0.7067800760269165 + ], + "f1": [ + 0.7004721760749817 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2675797641277313, + 0.21791553497314453, + -0.22618961334228516, + 0.11571652442216873, + -0.019790956750512123, + 0.05677139014005661, + 0.042519599199295044, + 0.1792418360710144, + 0.5141865611076355, + -0.34321343898773193, + -0.024482721462845802, + 0.13857966661453247, + -0.6468924880027771, + -0.25428396463394165, + -0.1651427149772644, + 0.1542055606842041, + -0.09829944372177124, + 0.31758415699005127, 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a/src/benchmark/output/results/graph_087.json +++ b/src/benchmark/output/results/results_graph_087.json @@ -3,13 +3,13 @@ "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 56-year-old non-smoking male with pulmonary carcinosarcoma.\n\n**Initial Presentation (Step 1):**\nOn January 28, 2023, the patient presented at The Third People\u2019s Hospital of Yunnan Province with a progressively enlarging mass in the right neck. Imaging findings revealed multiple nodular shadows of various sizes within the right cervical region posterior to the sternocleidomastoid muscle and adjacent to the carotid artery sheath, which partially fused.\n\n**Diagnosis (Step 2):**\nCT scans confirmed the presence of a pulmonary malignancy with cervical and mediastinal lymph node metastasis. The largest mass measured approximately 3.8 cm x 2.6 cm with indistinct margins and uneven ring-shaped enhancement.\n\n**Biopsy and Pathological Diagnosis (Step 3):**\nA CT-guided puncture biopsy of the mass in the left inferior lobe of the lung was performed, which led to a pathological diagnosis of lung carcinosarcoma.\n\n**Immunohistochemistry and NGS Testing (Step 4):**\nImmunohistochemistry revealed a Ki-67 index of 80%, while Next-Generation Sequencing (NGS) detected mutations in the TMB gene. These results further supported the presence of pulmonary carcinomas.\n\n**Timeline:**\n\n* January 28, 2023: Patient presents with progressively enlarging neck mass and imaging findings consistent with pulmonary malignancy.\n* January 28, 2023: CT-guided puncture biopsy is performed to confirm diagnosis.\n* (Date not specified): Immunohistochemistry and NGS testing are performed.\n\n**Outcomes:**\nThe patient's condition remains active, with ongoing management of the pulmonary carcinosarcoma. The results of immunohistochemistry and NGS testing have provided valuable information for further treatment planning.\n\nNote: The timeline is incomplete as some dates were not specified in the original data.", "bertscore": { "precision": [ - 0.3337828814983368 + 0.547805905342102 ], "recall": [ - 0.4093906879425049 + 0.6741754412651062 ], "f1": [ - 0.3677407205104828 + 0.6044565439224243 ] }, "topology": { diff --git a/src/benchmark/output/results/results_graph_088.json b/src/benchmark/output/results/results_graph_088.json new file mode 100644 index 0000000..f5bb449 --- /dev/null +++ b/src/benchmark/output/results/results_graph_088.json @@ -0,0 +1,795 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an [age]-year-old female with a history of [relevant medical conditions]. She was diagnosed with [primary diagnosis] in [month/year].\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1 (N1):** The patient started treatment with osimertinib 160 mg in combination with phenytoin.\n2. **32 months after initiating osimertinib (N2):** A CT scan was performed, showing overall stable visceral and osseous disease. However, the left pleural effusion had completely resolved, while the right pleural effusion remained stable in size.\n3. **Patient developed nail changes with increasing brittleness (grade 1) (N3):** Seizure activity remained well controlled, but persistent dyspnea was noted.\n4. **Echocardiogram, exercise stress testing, cardiopulmonary exercise test, and pulmonary function tests (PFTs) were performed (N4):** These tests showed evidence of chronic obstructive lung disease (COPD) and emphysema.\n5. **Osimertinib dose was reduced to 80 mg daily for one week, then resumed at 160 mg daily due to persistent dyspnea (N5):** Despite the dose reduction, dyspnea did not significantly improve.\n6. **Patient achieved prolonged disease control on osimertinib treatment with continued osimertinib at a dose of 160 mg daily (N6):** Disease progression later stabilized following three cycles of carboplatin/pemetrexed.\n\n**Outcomes:**\n\n* The patient's dyspnea did not significantly improve despite the dose reduction of osimertinib.\n* However, she achieved prolonged disease control on osimertinib treatment with continued osimertinib at a dose of 160 mg daily.\n* The patient's COPD and emphysema were diagnosed and managed effectively.\n\n**Conclusion:**\nThe patient was initially treated with osimertinib 160 mg in combination with phenytoin. After 32 months, a CT scan showed overall stable disease, but persistent dyspnea remained a concern. Despite a dose reduction of osimertinib, the patient's dyspnea did not improve significantly. However, she achieved prolonged disease control on osimertinib treatment with continued dosing at 160 mg daily, and her COPD and emphysema were effectively managed.\n\n**Recommendations:**\n\n* Continue to monitor the patient's dyspnea and adjust the osimertinib dose as needed.\n* Consider adding additional treatments for COPD and emphysema, such as bronchodilators or corticosteroids.\n* Regularly review the patient's disease progression and adjust the treatment plan accordingly.", + "bertscore": { + "precision": [ + 0.5367745161056519 + ], + "recall": [ + 0.6528466939926147 + ], + "f1": [ + 0.5891479849815369 + ] + }, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.0932932123541832, + 0.22252197563648224, + -0.14526592195034027, + 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file diff --git a/src/benchmark/requirements.txt b/src/benchmark/requirements.txt index 469f8e8..1575e2b 100644 --- a/src/benchmark/requirements.txt +++ b/src/benchmark/requirements.txt @@ -8,4 +8,5 @@ scikit-learn seaborn matplotlib numpy -scipy \ No newline at end of file +scipy +bs4 \ No newline at end of file diff --git a/src/benchmark/setup_env.sh b/src/benchmark/setup_env.sh index 5360a9e..1b06582 100755 --- a/src/benchmark/setup_env.sh +++ b/src/benchmark/setup_env.sh @@ -18,8 +18,8 @@ else echo "No requirements.txt found. Skipping dependency installation." fi -# echo "Running main..." -# python3 batch_run.py +echo "Running main..." +python3 batch_run.py echo "Generating plots..." python3 generate_visuals.py \ No newline at end of file diff --git a/webapp/static/graphs/graph_002.json b/webapp/static/graphs/archive/graph_002.json similarity index 100% rename from webapp/static/graphs/graph_002.json rename to webapp/static/graphs/archive/graph_002.json diff --git a/webapp/static/graphs/graph_017.json b/webapp/static/graphs/archive/graph_017.json similarity index 100% rename from webapp/static/graphs/graph_017.json rename to webapp/static/graphs/archive/graph_017.json diff --git a/webapp/static/graphs/graph_060.json b/webapp/static/graphs/archive/graph_060.json similarity index 100% rename from webapp/static/graphs/graph_060.json rename to webapp/static/graphs/archive/graph_060.json diff --git a/webapp/static/graphs/graph_085.json b/webapp/static/graphs/archive/graph_085.json similarity index 100% rename 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09f3b5144e4f0ef8a8d061c0f7e444cbf642a410 Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Sat, 10 May 2025 14:04:02 -0700 Subject: [PATCH 04/11] Update in --- ...nchmarking: Design Rules and Guidelines.md | 94 ++++++++++++++ src/benchmark/README.md | 122 ++++++++---------- src/benchmark/modules/visualization_utils.py | 26 +++- src/benchmark/requirements.txt | 3 +- .../{setup_env.sh => setup_and_run.sh} | 4 +- 5 files changed, 174 insertions(+), 75 deletions(-) create mode 100644 src/benchmark/Modular Benchmarking: Design Rules and Guidelines.md rename src/benchmark/{setup_env.sh => setup_and_run.sh} (91%) diff --git a/src/benchmark/Modular Benchmarking: Design Rules and Guidelines.md b/src/benchmark/Modular Benchmarking: Design Rules and Guidelines.md new file mode 100644 index 0000000..aa12319 --- /dev/null +++ b/src/benchmark/Modular Benchmarking: Design Rules and Guidelines.md @@ -0,0 +1,94 @@ +## Modular Benchmarking: Design Rules and Guidelines + +To support benchmarking across any task, data function, or model type, a modular benchmark must be built from interchangeable, well-scoped components. The following rules define how to structure such a benchmark to support flexibility, extensibility, and insight. + +--- + +### Rule 1: Decompose into independent axes +Separate all components of the system under test into **three disjoint axes**: + +- **Data function**: A parameterized function or generator that defines input-output pairs under specific sampling, augmentation, or preprocessing schemes. +- **Model interface**: A callable or wrapped object that takes input and returns predictions, with a clear API across model types. +- **Evaluation kernel**: A set of metrics or transformation functions that take predictions and targets and return scores, possibly per slice. + +Each axis must be independently swappable without requiring changes to the others. + +--- + +### Rule 2: Treat data as a first-class function +Data should not be loaded as static artifacts but built as **declarative recipes** with clearly scoped variability: + +- Input: Sampling strategy, transformation pipeline, split logic, perturbation level +- Output: Deterministic or stochastic dataset objects conforming to a unified format +- Example: `data_fn(task='translation', domain='medical', noise=0.1) -> Dataset` + +This ensures all experiments can vary data meaningfully and reproducibly. + +--- + +### Rule 3: Enforce interface constraints +Every component must conform to a simple, well-documented API: + +- **Model**: `predict(batch) -> outputs` +- **Evaluator**: `evaluate(preds, targets, **kwargs) -> score_dict` +- **Data function**: `data_config -> dataset object or iterator` + +Adapters should be used to wrap legacy models or datasets into these interfaces. + +--- + +### Rule 4: Capture all variation as configuration +All variable aspects (e.g., seed, data slice, model variant, metric set) must be represented as **configurable parameters**, not code changes. This allows: + +- Automatic sweep generation +- Logging and reproducibility +- Interpolation across experimental conditions + +Prefer structured configs (e.g., YAML, Pydantic) over hardcoded logic. + +--- + +### Rule 5: Benchmark = Cartesian product of controlled variations +A benchmark run is defined as the evaluation over a **Cartesian product** of selected variations from each axis: + +- `(model_i, data_j, eval_k) → score_ijk` + +This allows benchmarking to expose not just best performers but meaningful **interactions** between choices. + +--- + +### Rule 6: Support hierarchical slicing and stratification +To assess robustness and generalization, benchmarks must allow evaluation over: + +- Subpopulations (e.g., by label, length, domain, metadata) +- Perturbations (e.g., noisy, adversarial, low-resource) +- Shifts (e.g., domain, temporal, source-target pairs) + +Evaluators must optionally support slice-aware evaluation: `evaluate(preds, targets, slices=...)`. + +--- + +### Rule 7: Log provenance at every level +Every benchmark result must be traceable back to: + +- The exact model config +- The data function and its parameters +- The evaluation strategy and metric set +- The random seed and runtime environment + +All runs should emit structured metadata with full parameter context (e.g., JSON, database, or hashable IDs). + +--- + +### Rule 8: No single score without decomposition +Avoid single-number metrics without exposing score components: + +- Report per-slice, per-class, or per-perturbation breakdowns +- Visualize variance, not just central tendencies +- Make performance *explainable*, not just measurable + +Benchmarks should yield diagnostic insight, not just rankings. + +--- + +These rules make benchmarking **composable**, **transparent**, and **task-agnostic**, enabling research to scale across problem types while remaining grounded in meaningful comparisons. diff --git a/src/benchmark/README.md b/src/benchmark/README.md index aa12319..939e69e 100644 --- a/src/benchmark/README.md +++ b/src/benchmark/README.md @@ -1,94 +1,76 @@ -## Modular Benchmarking: Design Rules and Guidelines +# 📊 Benchmarking Pipeline for Graph-Based Biomedical Case Reports -To support benchmarking across any task, data function, or model type, a modular benchmark must be built from interchangeable, well-scoped components. The following rules define how to structure such a benchmark to support flexibility, extensibility, and insight. +This repository contains a benchmarking framework for analyzing and visualizing the performance of NLP models (e.g., `BERTScore`) on biomedical case reports represented as graphs. It includes tools for: ---- - -### Rule 1: Decompose into independent axes -Separate all components of the system under test into **three disjoint axes**: - -- **Data function**: A parameterized function or generator that defines input-output pairs under specific sampling, augmentation, or preprocessing schemes. -- **Model interface**: A callable or wrapped object that takes input and returns predictions, with a clear API across model types. -- **Evaluation kernel**: A set of metrics or transformation functions that take predictions and targets and return scores, possibly per slice. - -Each axis must be independently swappable without requiring changes to the others. - ---- - -### Rule 2: Treat data as a first-class function -Data should not be loaded as static artifacts but built as **declarative recipes** with clearly scoped variability: - -- Input: Sampling strategy, transformation pipeline, split logic, perturbation level -- Output: Deterministic or stochastic dataset objects conforming to a unified format -- Example: `data_fn(task='translation', domain='medical', noise=0.1) -> Dataset` - -This ensures all experiments can vary data meaningfully and reproducibly. +- Computing similarity scores (e.g., `BERTScore`, `ROUGE`, `BLEU`) +- Visualizing results (`F1` plots, `t-SNE`, topology distributions) +- Summarizing metrics in tables +- Preparing data for downstream evaluations --- -### Rule 3: Enforce interface constraints -Every component must conform to a simple, well-documented API: - -- **Model**: `predict(batch) -> outputs` -- **Evaluator**: `evaluate(preds, targets, **kwargs) -> score_dict` -- **Data function**: `data_config -> dataset object or iterator` +## 🔧 Setup Instructions -Adapters should be used to wrap legacy models or datasets into these interfaces. +To set up the environment and run the benchmark scripts, use the provided shell script: ---- - -### Rule 4: Capture all variation as configuration -All variable aspects (e.g., seed, data slice, model variant, metric set) must be represented as **configurable parameters**, not code changes. This allows: - -- Automatic sweep generation -- Logging and reproducibility -- Interpolation across experimental conditions +```bash +bash setup_and_run.sh +``` -Prefer structured configs (e.g., YAML, Pydantic) over hardcoded logic. +This script: +- Creates a Python 3.11 virtual environment +- Installs dependencies from `requirements.txt` +- Runs the benchmark modules as well as the visualization module to generate summary plots --- -### Rule 5: Benchmark = Cartesian product of controlled variations -A benchmark run is defined as the evaluation over a **Cartesian product** of selected variations from each axis: - -- `(model_i, data_j, eval_k) → score_ijk` - -This allows benchmarking to expose not just best performers but meaningful **interactions** between choices. +## 🗂 Directory Structure + +``` +src/ +└── benchmark/ + │ + ├── batch_run.py # Main script to execute benchmarking + ├── generate_visuals.py # Generates plots and summary tables + ├── requirements.txt # Python dependencies + ├── setup_and_run.sh # Script to setup the environment and run visuals + ├── output/ + │ ├── results/ # Directory where results are saved + │ └── plots/ # Directory where plots are saved + └── modules/ + ├── __init__.py # Marks the directory as a Python package + ├── config.py # Contains configuration variables and constants for the benchmarking pipeline + ├── embedding.py # Functions for computing and managing graph or text embeddings + ├── evalution.py # Evaluation metrics (e.g., BERTScore, ROUGE, BLEU) and utility functions + ├── io_utils.py # File I/O helper functions (e.g., loading graphs, saving outputs) + ├── logging_utils.py # Configures logging for tracking experiment progress and debugging + ├── reconstruciton.py # Graph or text reconstruction methods from processed data + ├── regex_utils.py # Utility functions for pattern matching and extraction using regular expressions + ├── run_benchmark.py # Orchestrates the full benchmarking pipeline + └── visualization.py # Plotting functions for visual summaries and metric reporting +``` --- -### Rule 6: Support hierarchical slicing and stratification -To assess robustness and generalization, benchmarks must allow evaluation over: +## 📉 Outputs -- Subpopulations (e.g., by label, length, domain, metadata) -- Perturbations (e.g., noisy, adversarial, low-resource) -- Shifts (e.g., domain, temporal, source-target pairs) - -Evaluators must optionally support slice-aware evaluation: `evaluate(preds, targets, slices=...)`. +- `output/plots/bertscore_f1_barplot.png` – Bar chart of BERTScore F1 scores +- `output/plots/trajectory_tsne.png` – 2D t-SNE embedding of graph trajectories +- `output/plots/topology_distributions.png` – Histograms of node and edge counts +- `bertscore_stats.csv` – Summary statistics of BERTScore F1 (optional export) --- -### Rule 7: Log provenance at every level -Every benchmark result must be traceable back to: +## 📊 Example Metrics -- The exact model config -- The data function and its parameters -- The evaluation strategy and metric set -- The random seed and runtime environment +If you're using string similarity tools, results may include: -All runs should emit structured metadata with full parameter context (e.g., JSON, database, or hashable IDs). +- `ROUGE-1`, `ROUGE-2`, `ROUGE-L` +- `BLEU` score +- Mean, median, std deviation, and percentiles of F1 scores --- -### Rule 8: No single score without decomposition -Avoid single-number metrics without exposing score components: - -- Report per-slice, per-class, or per-perturbation breakdowns -- Visualize variance, not just central tendencies -- Make performance *explainable*, not just measurable - -Benchmarks should yield diagnostic insight, not just rankings. - ---- +## 📬 Contact -These rules make benchmarking **composable**, **transparent**, and **task-agnostic**, enabling research to scale across problem types while remaining grounded in meaningful comparisons. +For questions or contributions, please contact the maintainers of the [Daneshjou Lab](https://daneshjoulab.stanford.edu). diff --git a/src/benchmark/modules/visualization_utils.py b/src/benchmark/modules/visualization_utils.py index b80aff2..db6862b 100644 --- a/src/benchmark/modules/visualization_utils.py +++ b/src/benchmark/modules/visualization_utils.py @@ -13,14 +13,36 @@ import matplotlib.pyplot as plt import seaborn as sns import pandas as pd +import numpy as np from sklearn.manifold import TSNE +import evaluate PLOTS_DIR = "output/plots" os.makedirs(PLOTS_DIR, exist_ok=True) -def plot_bertscore_f1(graph_ids, bertscore_f1): - """Bar plot of BERTScore F1 for each graph.""" +def plot_bertscore_f1(graph_ids, bertscore_f1, export_path=None): + """Bar plot of BERTScore F1 for each graph, with summary statistics saved to CSV.""" + # Calculate statistics + f1_array = np.array(bertscore_f1) + stats = { + "Mean": np.mean(f1_array), + "Median": np.median(f1_array), + "Standard Deviation": np.std(f1_array), + "25th Percentile (Q1)": np.percentile(f1_array, 25), + "75th Percentile (Q3)": np.percentile(f1_array, 75) + } + + # Print stats + for k, v in stats.items(): + print(f"{k}: {v:.3f}") + + # Save to CSV if export path is given + if export_path is not None: + stats_df = pd.DataFrame([stats]) + stats_df.to_csv(export_path, index=False) + + # Plotting _, ax = plt.subplots() sns.barplot(x=graph_ids, y=bertscore_f1, ax=ax) ax.set_title("BERTScore F1 per Graph") diff --git a/src/benchmark/requirements.txt b/src/benchmark/requirements.txt index 1575e2b..bd3fa1a 100644 --- a/src/benchmark/requirements.txt +++ b/src/benchmark/requirements.txt @@ -9,4 +9,5 @@ seaborn matplotlib numpy scipy -bs4 \ No newline at end of file +bs4 +evaluate \ No newline at end of file diff --git a/src/benchmark/setup_env.sh b/src/benchmark/setup_and_run.sh similarity index 91% rename from src/benchmark/setup_env.sh rename to src/benchmark/setup_and_run.sh index 1b06582..5360a9e 100755 --- a/src/benchmark/setup_env.sh +++ b/src/benchmark/setup_and_run.sh @@ -18,8 +18,8 @@ else echo "No requirements.txt found. Skipping dependency installation." fi -echo "Running main..." -python3 batch_run.py +# echo "Running main..." +# python3 batch_run.py echo "Generating plots..." python3 generate_visuals.py \ No newline at end of file From 591989c73dde3965131f32d03d850890bf57fc26 Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Sat, 10 May 2025 16:09:07 -0700 Subject: [PATCH 05/11] Add string similarity metrics, remove preliminary testing results --- src/benchmark/batch_run.py | 14 +- src/benchmark/generate_visuals.py | 44 +- src/benchmark/modules/config.py | 3 - src/benchmark/modules/embedding.py | 9 +- src/benchmark/modules/evaluation.py | 139 ++- src/benchmark/modules/io_utils.py | 47 +- src/benchmark/modules/run_benchmark.py | 44 +- src/benchmark/modules/visualization_utils.py | 69 +- .../output/plots/bertscore_f1_barplot.png | Bin 30199 -> 18136 bytes .../output/plots/topology_distributions.png | Bin 45771 -> 31555 bytes .../output/plots/trajectory_tsne.png | Bin 43188 -> 20685 bytes 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-21,17 +21,20 @@ save_results, build_graph_to_text_mapping, extract_case_presentation_from_file, + summarize_metrics_statistics ) logger = setup_logger(__name__) # Input directory: All graph files -GRAPH_INPUT_DIR = Path(__file__).resolve().parents[2] / "webapp/static/graphs" +GRAPH_INPUT_DIR = Path(__file__).resolve().parents[2] / "webapp/static/graphs/" # Output directory: Results -RESULTS_OUTPUT_DIR = Path("output/results") +RESULTS_OUTPUT_DIR = Path("output/results/") RESULTS_OUTPUT_DIR.mkdir(parents=True, exist_ok=True) +METRIC_SUMMARY_OUTPUT_DIR = Path("output/results/plots/metric_summary.csv") + # Paths METADATA_CSV_PATH = Path(__file__).resolve().parents[2] / "webapp/static/graphs/mapping/graph_metadata.csv" @@ -45,7 +48,7 @@ if not graph_files: logger.warning("No JSON files found in input directory.") else: - for fpath in graph_files: #[:5]: Limit to first 5 files for demonstration + for fpath in graph_files: graph_id = fpath.stem html_path = graph_to_html.get(graph_id) @@ -65,12 +68,15 @@ cfg = { "reconstruct_params": {"include_nodes": True, "include_edges": True}, "bertscore": True, + "string_similarity": True, "topology": True, "trajectory_embedding": True, } results = run_pipeline(graph, reference_case_text, cfg) + output_path = RESULTS_OUTPUT_DIR / f"results_{graph_id}.json" save_results(results, output_path) - + + logger.info("Batch benchmarking completed.") diff --git a/src/benchmark/generate_visuals.py b/src/benchmark/generate_visuals.py index cc1c00e..607584a 100644 --- a/src/benchmark/generate_visuals.py +++ b/src/benchmark/generate_visuals.py @@ -15,6 +15,7 @@ from pathlib import Path sys.path.append(str(Path(__file__).resolve().parents[1])) # Adds 'src' to sys.path + from benchmark.modules.visualization_utils import ( plot_bertscore_f1, plot_tsne_embeddings, @@ -22,11 +23,18 @@ summarize_metrics_table ) -RESULTS_DIR = "output/results" +RESULTS_DIR = "output/results/testset_results" +PLOTS_DIR = "output/plots" +os.makedirs(PLOTS_DIR, exist_ok=True) # Lists to collect metrics graph_ids = [] bertscore_f1s = [] +bertscore_precisions = [] +bertscore_recalls = [] +bleu_scores = [] +rouge1_scores = [] +rougeL_scores = [] trajectory_embeddings = [] node_counts = [] edge_counts = [] @@ -41,8 +49,26 @@ graph_ids.append(graph_id) # Get BERTScore F1 - f1 = result.get("bertscore", {}).get("f1", [np.nan])[0] + bertscore = result.get("bertscore", {}) + + f1 = bertscore.get("f1", np.nan) + precision = bertscore.get("precision", np.nan) + recall = bertscore.get("recall", np.nan) + bertscore_f1s.append(f1) + bertscore_precisions.append(precision) + bertscore_recalls.append(recall) + + + # Get BLEU + bleu = result.get("bleu", np.nan) + bleu_scores.append(bleu) + + # Get ROUGE + rouge1 = result.get("rouge1", np.nan) + rougel = result.get("rougeL", np.nan) + rouge1_scores.append(rouge1) + rougeL_scores.append(rougel) # Get embedding emb = result.get("trajectory_embedding") @@ -67,6 +93,18 @@ plot_topology_distributions(node_counts, edge_counts) -summary_df = summarize_metrics_table(graph_ids, bertscore_f1s, node_counts, edge_counts) +# Create and save summary table +summary_df = summarize_metrics_table( + graph_ids, + bertscore_f1s, + bertscore_precisions, + bertscore_recalls, + bleu_scores, + rouge1_scores, + rougeL_scores, + node_counts, + edge_counts, + output_csv_path=os.path.join(PLOTS_DIR, "metrics_summary.csv") +) print("\n=== Summary Table ===") print(summary_df) diff --git a/src/benchmark/modules/config.py b/src/benchmark/modules/config.py index 17b4c76..e97153d 100644 --- a/src/benchmark/modules/config.py +++ b/src/benchmark/modules/config.py @@ -18,9 +18,6 @@ LM_API_BASE = "http://localhost:11434" LM_API_KEY = "" # or your local key if required -# BERTScore settings -BERTSCORE_MODEL = "bert-base-uncased" - # Trajectory Embedding settings TRAJECTORY_EMBEDDING_MODEL = "emilyalsentzer/Bio_ClinicalBERT" TEXT_FIELD_PATH = ["data", "commentary"] # e.g., node["data"]["commentary"] diff --git a/src/benchmark/modules/embedding.py b/src/benchmark/modules/embedding.py index 50c876f..fbca8ed 100644 --- a/src/benchmark/modules/embedding.py +++ b/src/benchmark/modules/embedding.py @@ -73,7 +73,14 @@ def embed_text(self, text: str) -> torch.Tensor: Returns: torch.Tensor: The embedding of the text. """ - inputs = self.tokenizer(text, return_tensors="pt", truncation=True, padding=True).to(self.device) + inputs = self.tokenizer( + text, + return_tensors="pt", + truncation=True, + padding=True, + max_length=512 + ).to(self.device) + with torch.no_grad(): outputs = self.model(**inputs) return outputs.last_hidden_state[0][0] diff --git a/src/benchmark/modules/evaluation.py b/src/benchmark/modules/evaluation.py index 22a61fd..029dc37 100644 --- a/src/benchmark/modules/evaluation.py +++ b/src/benchmark/modules/evaluation.py @@ -8,10 +8,15 @@ # pylint: disable=too-few-public-methods """This module contains evaluation classes for BERTScore and graph topology validation.""" -from typing import Any +from typing import Any, Optional from transformers import AutoTokenizer, AutoModel import networkx as nx -from bert_score import score +from bert_score import score as bert_score_fn +from nltk.tokenize import RegexpTokenizer +from nltk.translate.bleu_score import sentence_bleu, SmoothingFunction +from rouge_score import rouge_scorer +import numpy as np + # Local application imports from .config import Graph @@ -19,67 +24,79 @@ logger = setup_logger(__name__) +MAX_BERT_TOKENS = 512 class BERTScoreEvaluator: """ - Computes BERTScore (precision, recall, F1) between original and reconstructed texts. - - Usage: - evaluator = BERTScoreEvaluator(model_type="BERTSCORE_MODEL") - results = evaluator.evaluate( - refs=["ground truth text"], - cands=["model generated text"] - ) - # results -> {"precision": [...], "recall": [...], "f1": [...]} + Computes BERTScore (precision, recall, F1) using a custom model (e.g., Bio_ClinicalBERT), + truncating inputs longer than the model's max input length (512 tokens). """ - def __init__(self, model_type: str, device: str = None): + def __init__(self, model_type: str, device: Optional[str] = None): self.model_type = model_type - self.device = device # 'cuda', 'cpu', or None for auto-detection + self.device = device or "cpu" + + try: + self.tokenizer = AutoTokenizer.from_pretrained(self.model_type) + AutoModel.from_pretrained(self.model_type) # ensure model download + logger.info(f"Model {self.model_type} loaded successfully.") + except Exception as e: + logger.warning(f"Could not preload model: {self.model_type} — {e}") - # ── Ensure the checkpoint is available locally ── - # This will pull the tokenizer & model into ~/.cache/huggingface if missing. - AutoTokenizer.from_pretrained(self.model_type) - AutoModel.from_pretrained(self.model_type) + def truncate(self, text: str, max_tokens: int = MAX_BERT_TOKENS) -> str: + """ + Truncates a text to the first `max_tokens` tokens using the model's tokenizer. + """ + tokens = self.tokenizer.tokenize(text) + truncated_tokens = tokens[:max_tokens - 2] # Reserve 2 tokens for [CLS] and [SEP] + return self.tokenizer.convert_tokens_to_string(truncated_tokens) - def evaluate(self, refs: list[str], cands: list[str]) -> dict[str, list[float]]: + def evaluate(self, refs: list[str], cands: list[str]) -> dict[str, float]: """ + Computes BERTScore (mean) between reference and candidate texts. + Args: - refs: list of reference texts. - cands: list of candidate texts. + refs (list of str): Reference texts. + cands (list of str): Candidate/generated texts. Returns: - Dict with keys "precision", "recall", "f1" mapping to lists of scores. + dict[str, float]: Average precision, recall, and F1 scores. """ if not refs or not cands: - logger.warning("Empty references or candidates list") - return {"precision": [], "recall": [], "f1": []} + logger.warning("Empty references or candidates list.") + return {"precision": 0.0, "recall": 0.0, "f1": 0.0} if len(refs) != len(cands): - logger.warning( - f"Mismatched list lengths: refs={len(refs)}, cands={len(cands)}" - ) + logger.warning(f"Mismatched list lengths: refs={len(refs)}, cands={len(cands)}") + min_len = min(len(refs), len(cands)) + refs = refs[:min_len] + cands = cands[:min_len] + + # Truncate long sequences to avoid tensor mismatch + refs = [self.truncate(r) for r in refs] + cands = [self.truncate(c) for c in cands] try: - precision, recall, f1_score = score( - cands, - refs, - model_type=self.model_type, - device=self.device, - verbose=False, - ) + model_kwargs = { + "model_type": self.model_type, + "device": self.device, + "lang": "en", + "rescale_with_baseline": False, + "verbose": False, + "num_layers": 12 # Required for Bio_ClinicalBERT + } + + precision, recall, f1 = bert_score_fn(cands, refs, **model_kwargs) return { - "precision": precision.tolist(), - "recall": recall.tolist(), - "f1": f1_score.tolist(), + "precision": float(precision.mean().item()), + "recall": float(recall.mean().item()), + "f1": float(f1.mean().item()), } - except Exception as e: - logger.error(f"BERTScore evaluation failed: {str(e)}") - raise - -# GRAPH TOPOLOGY VALIDATION + except Exception as e: + logger.error(f"BERTScore evaluation failed: {e}") + return {"precision": 0.0, "recall": 0.0, "f1": 0.0} class TopologyValidator: @@ -150,3 +167,43 @@ def run(self) -> dict[str, Any]: "avg_in_degree": avg_in_deg, "density": density, } + + +class StringSimilarityEvaluator: + def __init__(self): + self.smoothie = SmoothingFunction().method4 + self.rouge = rouge_scorer.RougeScorer(['rouge1', 'rougeL'], use_stemmer=True) + self.tokenizer = RegexpTokenizer(r'\w+') + + def evaluate(self, refs, cands): + if not refs or not cands or len(refs) != len(cands): + raise ValueError("References and candidates must be non-empty lists of equal length.") + + bleu_scores = [] + rouge1_scores = [] + rougeL_scores = [] + + for ref, cand in zip(refs, cands): + ref_tokens = self.tokenizer.tokenize(ref.lower().strip()) + cand_tokens = self.tokenizer.tokenize(cand.lower().strip()) + + if not ref_tokens or not cand_tokens: + bleu_scores.append(0.0) + rouge1_scores.append(0.0) + rougeL_scores.append(0.0) + continue + + bleu = sentence_bleu([ref_tokens], cand_tokens, smoothing_function=self.smoothie) + scores = self.rouge.score(ref, cand) + + bleu_scores.append(bleu) + rouge1_scores.append(scores['rouge1'].fmeasure) + rougeL_scores.append(scores['rougeL'].fmeasure) + + print(f"BLEU: {bleu}, ROUGE-1: {scores['rouge1'].fmeasure}, ROUGE-L: {scores['rougeL'].fmeasure}") + + return { + "bleu": float(np.mean(bleu_scores)), + "rouge1": float(np.mean(rouge1_scores)), + "rougeL": float(np.mean(rougeL_scores)) + } \ No newline at end of file diff --git a/src/benchmark/modules/io_utils.py b/src/benchmark/modules/io_utils.py index 822a876..35dd975 100644 --- a/src/benchmark/modules/io_utils.py +++ b/src/benchmark/modules/io_utils.py @@ -16,6 +16,7 @@ from typing import Any import warnings import re +import pandas as pd # Third-party imports import networkx as nx @@ -62,6 +63,7 @@ def load_graph_from_file(path: str) -> tuple[nx.DiGraph, bool]: return nx.DiGraph(), False + def save_results(results: dict, path: str) -> None: """ Save the pipeline results to a JSON file. @@ -70,9 +72,8 @@ def save_results(results: dict, path: str) -> None: path (str): The path to the output file. """ os.makedirs(os.path.dirname(path), exist_ok=True) - with open(path, "w", encoding=UTF_8) as f: - json.dump(results, f, indent=2) - + with open(path, "w", encoding="utf-8") as f: + json.dump(results, f, indent=2, allow_nan=False) def data_display(results: dict[str, Any]) -> None: """ @@ -275,3 +276,43 @@ def extract_case_presentation_from_file(filepath: str) -> str: with open(filepath, "r", encoding="utf-8") as file: html = file.read() return extract_case_presentation(html) + +def summarize_metrics_statistics( + csv_path: str = "output/plots/metrics_summary.csv", + output_path: str = "output/plots/metrics_summary_stats.csv" +) -> pd.DataFrame: + """ + Reads the metrics summary CSV and returns + saves descriptive statistics + (mean, std, min, max) for all numeric metrics. + + Args: + csv_path (str): Path to the metrics_summary.csv file. + output_path (str): Path to save the output CSV of statistics. + + Returns: + pd.DataFrame: A summary DataFrame with statistics per metric. + """ + if not os.path.exists(csv_path): + raise FileNotFoundError(f"Metrics summary file not found at: {csv_path}") + + df = pd.read_csv(csv_path, on_bad_lines='skip') + + # Drop non-numeric columns + numeric_df = df.select_dtypes(include=["number"]) + + # Compute descriptive statistics + summary_stats = numeric_df.agg(['mean', 'std', 'min', 'max']).T + summary_stats = summary_stats.rename(columns={ + "mean": "Mean", + "std": "Std Dev", + "min": "Min", + "max": "Max" + }) + + # Save to CSV + print(f"Saving metrics summary stats to: {os.path.abspath(output_path)}") + + os.makedirs(os.path.dirname(output_path), exist_ok=True) + summary_stats.to_csv(output_path) + + return summary_stats \ No newline at end of file diff --git a/src/benchmark/modules/run_benchmark.py b/src/benchmark/modules/run_benchmark.py index 68fc2b8..cc8e680 100644 --- a/src/benchmark/modules/run_benchmark.py +++ b/src/benchmark/modules/run_benchmark.py @@ -18,14 +18,13 @@ # Local application imports from .reconstruction import LLMReconstructor -from .evaluation import BERTScoreEvaluator, TopologyValidator +from .evaluation import BERTScoreEvaluator, StringSimilarityEvaluator, TopologyValidator from .embedding import TrajectoryEmbedder from .regex_utils import RegexValidator from .config import ( LM_MODEL, LM_API_BASE, LM_API_KEY, - BERTSCORE_MODEL, TEXT_FIELD_PATH, TRAJECTORY_EMBEDDING_MODEL, Graph, @@ -44,13 +43,15 @@ def run_pipeline( Evaluates: 1. LLM-based narrative reconstruction 2. BERTScore (fidelity) - 3. Graph topology validation - 4. Optional regex check - 5. Trajectory-level embedding + 3. BLEU/ROUGE string similarity + 4. Graph topology validation + 5. Optional regex check + 6. Trajectory-level embedding Returns: dict: Structured results with intermediate metrics. """ + results = {"status": "success", "errors": []} # Validate input types @@ -81,22 +82,51 @@ def run_pipeline( results["status"] = "partial" results["errors"].append(msg) + # print("========= ORIGINAL TEXT =========:", original_text[:100]) + # print("========= NARRATIVE: =========", narrative[:100]) + # Fidelity Evaluation using BERTScore if config.get("bertscore") and narrative: try: logger.info("Starting BERTScore evaluation") - model_name = config.get("bertscore_model", BERTSCORE_MODEL) - evaluator = BERTScoreEvaluator(model_type=model_name) + evaluator = BERTScoreEvaluator(model_type=TRAJECTORY_EMBEDDING_MODEL) results["bertscore"] = evaluator.evaluate( refs=[original_text], cands=[narrative] ) + print(results["bertscore"]) logger.info("BERTScore evaluation completed") + except Exception as e: msg = f"BERTScore evaluation failed: {str(e)}" logger.error(msg) results["status"] = "partial" results["errors"].append(msg) + + # String Similarity (BLEU / ROUGE) + if config.get("string_similarity") and narrative and original_text: + try: + logger.info("Starting BLEU/ROUGE string similarity evaluation") + + string_evaluator = StringSimilarityEvaluator() + similarity_scores = string_evaluator.evaluate( + refs=[original_text], cands=[narrative] + ) + + # Store individual metrics in separate result fields + results["bleu"] = similarity_scores.get("bleu", 0.0) + results["rouge1"] = similarity_scores.get("rouge1", 0.0) + results["rougeL"] = similarity_scores.get("rougeL", 0.0) + + logger.info(f"String similarity evaluation completed: BLEU={results['bleu']:.4f}, " + f"ROUGE-1={results['rouge1']:.4f}, ROUGE-L={results['rougeL']:.4f}") + except Exception as e: + msg = f"String similarity evaluation failed: {str(e)}" + logger.error(msg) + results["status"] = "partial" + results.setdefault("errors", []).append(msg) + + # Graph Topology Validation if config.get("topology"): try: diff --git a/src/benchmark/modules/visualization_utils.py b/src/benchmark/modules/visualization_utils.py index db6862b..4871a00 100644 --- a/src/benchmark/modules/visualization_utils.py +++ b/src/benchmark/modules/visualization_utils.py @@ -21,6 +21,7 @@ os.makedirs(PLOTS_DIR, exist_ok=True) + def plot_bertscore_f1(graph_ids, bertscore_f1, export_path=None): """Bar plot of BERTScore F1 for each graph, with summary statistics saved to CSV.""" # Calculate statistics @@ -30,7 +31,7 @@ def plot_bertscore_f1(graph_ids, bertscore_f1, export_path=None): "Median": np.median(f1_array), "Standard Deviation": np.std(f1_array), "25th Percentile (Q1)": np.percentile(f1_array, 25), - "75th Percentile (Q3)": np.percentile(f1_array, 75) + "75th Percentile (Q3)": np.percentile(f1_array, 75), } # Print stats @@ -56,13 +57,17 @@ def plot_bertscore_f1(graph_ids, bertscore_f1, export_path=None): def plot_tsne_embeddings(embeddings, graph_ids): """2D t-SNE scatterplot for graph embeddings.""" - tsne_results = TSNE(n_components=2, perplexity=2, random_state=42).fit_transform(embeddings) + tsne_results = TSNE(n_components=2, perplexity=2, random_state=42).fit_transform( + embeddings + ) _, ax = plt.subplots() - sns.scatterplot(x=tsne_results[:, 0], y=tsne_results[:, 1], hue=graph_ids, s=100, ax=ax) + sns.scatterplot( + x=tsne_results[:, 0], y=tsne_results[:, 1], hue=graph_ids, s=100, ax=ax + ) ax.set_title("t-SNE of Trajectory Embeddings") ax.set_xlabel("Dimension 1") ax.set_ylabel("Dimension 2") - plt.legend(bbox_to_anchor=(1.05, 1), loc='upper left') + plt.legend(bbox_to_anchor=(1.05, 1), loc="upper left") plt.savefig(os.path.join(PLOTS_DIR, "trajectory_tsne.png")) plt.close() @@ -83,12 +88,52 @@ def plot_topology_distributions(node_counts, edge_counts): plt.close() -def summarize_metrics_table(graph_ids, bertscore_f1, node_counts, edge_counts): - """Create and return a summary DataFrame of key metrics per graph.""" - df = pd.DataFrame({ - "Graph ID": graph_ids, - "BERTScore F1": bertscore_f1, - "Nodes": node_counts, - "Edges": edge_counts - }) +def compute_string_similarity( + reference_texts, candidate_texts, metrics=["rouge", "bleu"] +): + """Compute string similarity metrics (ROUGE, BLEU) between reference and candidate texts. + + Args: + reference_texts (list of str): Ground truth strings. + candidate_texts (list of str): Generated strings. + metrics (list of str): Metrics to compute (default: ["rouge", "bleu"]). + + Returns: + dict: Dictionary of metric names and scores. + """ + results = {} + if "rouge" in metrics: + rouge = evaluate.load("rouge") + rouge_result = rouge.compute( + predictions=candidate_texts, references=reference_texts + ) + results.update({f"ROUGE-{k.upper()}": v for k, v in rouge_result.items()}) + + if "bleu" in metrics: + bleu = evaluate.load("bleu") + bleu_result = bleu.compute( + predictions=candidate_texts, references=reference_texts + ) + results["BLEU"] = bleu_result["bleu"] + + return results + + +def summarize_metrics_table(graph_ids, bertscore_f1, bertscore_precision, + bertscore_recall, bleu, rouge1, rougeL, node_counts, edge_counts, output_csv_path): + """Create and return a summary DataFrame of key metrics per graph, and save it as a CSV.""" + df = pd.DataFrame( + { + "Graph ID": graph_ids, + "BERTScore F1": bertscore_f1, + "BERTScore Precision": bertscore_precision, + "BERTScore Recall": bertscore_recall, + "BLEU": bleu, + "ROUGE-1": rouge1, + "ROUGE-L": rougeL, + "Nodes": node_counts, + "Edges": edge_counts, + } + ) + df.to_csv(output_csv_path, index=False) return df diff --git a/src/benchmark/output/plots/bertscore_f1_barplot.png b/src/benchmark/output/plots/bertscore_f1_barplot.png index c194c133afac9576af13bb0dc420338ef915d387..b766022ac8c59d7b77aafeccff3697121503bf5c 100644 GIT binary patch literal 18136 zcmd^nc{r4P`}ZJiDk?=QiAuJREMX{QDaw*8gDlzieVfsCx2On_!XzYncE&O)vSr_Q zF=7Z|5M#`HUOo5oyw7vHkM}r!$NT%^UH-Tacg$RKUEk$AKihX6UDdp_bNj*VC=_a^ znyQjE3dI-RWx>=#F-1Km9aQ1MpHRtxSa&xzJ 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with no history of antitubercular treatment (ATT) intake. He has been a tobacco chewer for over 20 years.\n\n**Initial Presentation:**\nThe patient presented to the clinic with right-sided chest pain, dry cough, on-off fever, and hematuria for 2 months. Physical examination revealed decreased air entry on the right side of the lung.\n\n**Imaging and Diagnosis (Step 1-3):**\n\n* Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within.\n* Bronchoscopy with bronchoscopic-guided biopsy and BAL was performed, which showed negative results for malignant cells. Biopsy results were suggestive of squamous cell carcinoma.\n\n**Symptoms and Imaging (Step 4-5):**\n\n* The patient reported decreased and blurring of vision.\n* An 18F-FDG PET/CT scan revealed a FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm with spiculated margins in the upper lobe of the right lung, along with multiple sub-centimetric to centimetric-sized bilateral lung nodules and metastases to mediastinal, abdominopelvic lymph nodes.\n\n**Progression and Diagnosis (Step 6-7):**\n\n* The patient presented with severe headaches and blurring of vision for 15 days.\n* Biopsy results confirmed metastatic involvement.\n\n**Treatment Plan:**\nUnfortunately, the provided data does not include a treatment plan or outcomes. However, based on the diagnosis of squamous cell carcinoma and metastases, further treatment options would likely involve chemotherapy, radiation therapy, or a combination of both, depending on the patient's overall health and specific tumor characteristics.\n\n**Outcomes:**\nThe patient's current status is unknown, as the provided data only includes the timeline of diagnoses and treatments. Further follow-up and monitoring are necessary to assess the patient's response to treatment and any potential complications or side effects.\n\nIn conclusion, this patient presented with a complex clinical scenario involving a heterogeneous lesion in the mediastinal region, squamous cell carcinoma, and metastases. The patient's symptoms and imaging results suggest an aggressive disease course, and further treatment options would be necessary to manage the patient's condition effectively.", - "bertscore": { - "precision": [ - 0.7080437541007996 - ], - "recall": [ - 0.7307168245315552 - ], - "f1": [ - 0.7192016243934631 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.22544555366039276, - -0.021888595074415207, - -0.0058143287897109985, - 0.03279201313853264, - 0.012158679775893688, - 0.124949149787426, - 0.055165503174066544, - 0.12983736395835876, - 0.3739190995693207, - -0.2663968503475189, - -0.19686637818813324, - 0.07701147347688675, - -0.5400644540786743, - -0.07584770768880844, - -0.26406726241111755, - -0.02046271786093712, - 0.05793926864862442, - 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Unfortunately, the exact age and other demographic details are not provided in the data.\n\n**Timeline of Diagnoses**\n\nThe patient's diagnosis timeline begins with the onset of symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. This marked the progression from symptom onset to diagnosis.\n\n**Timeline of Treatments**\n\nThe patient's treatment timeline began with endovascular intervention to address IVC stenosis due to compression caused by the tumor. The procedure involved thrombectomy and stent placement. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered.\n\n**Timeline of Outcomes**\n\nThe patient's outcome timeline began with significant alleviation of IVCS symptoms (trunk and lower limb edema) following the intervention. However, unfortunately, the patient died 8 days later from his primary disease (SCLC).\n\n**Narrative Summary**\n\nA male patient with Small Cell Lung Cancer presented with symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. Endovascular intervention was performed to address IVC stenosis caused by compression from the tumor. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered. However, despite these interventions, the patient's primary disease ultimately led to his death 8 days later.\n\n**Key Takeaways**\n\n* The patient had a poor performance status and significant tumor burden at diagnosis.\n* Endovascular intervention was effective in alleviating IVCS symptoms but did not address the underlying cause of death.\n* Low-molecular-weight heparin was administered post-intervention, but its effectiveness is unclear given the patient's rapid decline.\n\n**Limitations**\n\nThe narrative summary is limited by the lack of detailed information on patient demographics, treatment outcomes, and long-term follow-up. Further investigation would be necessary to fully understand the patient's clinical course and the effectiveness of interventions.", - "bertscore": { - "precision": [ - 0.5732179880142212 - ], - "recall": [ - 0.5156488418579102 - ], - "f1": [ - 0.5429115891456604 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 8, - "edge_count": 7, - "avg_in_degree": 0.875, - "density": 0.125 - }, - "trajectory_embedding": [ - 0.2569149434566498, - 0.23160001635551453, - -0.23048092424869537, - 0.06365886330604553, - 0.06271032989025116, - -0.032205305993556976, - -0.0353657603263855, - 0.14690855145454407, - 0.3527328073978424, - -0.24249935150146484, - -0.23033425211906433, - 0.13146138191223145, - -0.44394129514694214, - -0.1020270437002182, - -0.1855921894311905, - 0.17859384417533875, - 0.08802724629640579, - 0.2158854901790619, - -0.10283444821834564, - -0.29911351203918457, - 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She has no history of smoking or malignancy.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (Day 0-9):** The patient initially presents with progressive chest tightness, dyspnea, cough, and back pain. Chest CT imaging reveals a large left-sided pleural effusion.\n2. **Step 2 (Day 10):** Thoracentesis is performed, and the drained pleural fluid is sent to the Department of Pathology for further evaluation.\n3. **Step 3 (Day 11-12):** Post-thoracic drainage chest CT reveals a 6.7 cm x 2.8 cm heterogeneous mass in the left inferior lobe with irregular contrast enhancement, suggestive of a left lung tumor.\n4. **Step 4 (Day 13-14):** Pulmonary window analysis shows multiple nodular high-density foci scattered across both lungs, concerning for bilateral pulmonary metastases. Mediastinal window assessment reveals bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis.\n5. **Step 5 (Day 15-16):** Abdominal CT scan detects multiple low-density hepatic nodules of varying sizes, with the largest lesion located in the right hepatic lobe. Enhanced brain CT identifies an irregular heterogeneously enhancing mass within the right frontal lobe, consistent with brain metastasis.\n6. **Step 6 (Day 17-18):** Cell block analysis of the pleural effusion demonstrates poorly cohesive round-to-oval cells with a dispersed distribution exhibiting eccentrically located nuclei with dense chromatin.\n\n**Treatments:**\n\n1. Thoracentesis and post-thoracic drainage chest CT\n2. Abdominal CT scan and enhanced brain CT\n\n**Outcomes:**\nThe patient's diagnosis is confirmed as lung cancer with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The cell block analysis of the pleural effusion reveals poorly cohesive round-to-oval cells consistent with adenocarcinoma.\n\n**Conclusion:**\nThis 81-year-old female patient presents with progressive chest tightness and dyspnea due to a large left-sided pleural effusion, which is later confirmed as a left lung tumor with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The diagnosis is made after thoracentesis, post-thoracic drainage chest CT, abdominal CT scan, enhanced brain CT, and cell block analysis of the pleural effusion.", - "bertscore": { - "precision": [ - 0.7519660592079163 - ], - "recall": [ - 0.7654501795768738 - ], - "f1": [ - 0.7586482167243958 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.2583933174610138, - -0.1034068688750267, - 0.02750878781080246, - 0.12225138396024704, - 0.07123710960149765, - 0.08420076966285706, - -0.025338614359498024, - 0.20714537799358368, - 0.42998072504997253, - -0.2773303687572479, - -0.23241369426250458, - 0.0849342942237854, - -0.532634437084198, - 0.050035249441862106, - -0.25669047236442566, - 0.11723083257675171, - 0.17126429080963135, - 0.2885790467262268, - 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He presented with worsening cough for 3 months, which led to further investigation via CT imaging.\n\n**Timeline of Diagnoses:**\n\n1. **April 2023:** Enhanced CT revealed a 22 mm \u00d7 12 mm \u00d7 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal. PET-CT scan confirmed the CT findings.\n2. **Biopsy (Upper Right Lobe):** Biopsy of the lung lesion showed positive immunohistochemistry (IHC) for TTF-1, NpA, CK7, CD5/6, and Ki67 (60%); and negative for p40, p63, and CD56. Diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0).\n3. **May 2023:** Targeted NGS analysis identified an EGFRG719X mutation with a mutant allele frequency (MAF) of 3.8%.\n\n**Timeline of Treatments:**\n\n1. **May 2023:** The patient received two cycles of PC chemotherapy (pemetrexed 0.9g d1 and carboplatin 600mg d1) and dacomitinib (30mg).\n2. **Initial Treatment Evaluation:** Initial tumor was considered unresectable due to metastasis in the right hilum and mediastinum.\n\n**Timeline of Outcomes:**\n\n1. **May 2023:** Chest CT showed obvious shrinkage in the lesions in the right upper lung lobe and the lymph nodes of the mediastinum, contributing to partial response (PR).\n2. **Current Status:** The patient is currently receiving treatment for stage IIIA lung adenocarcinoma with EGFRG719X mutation.\n\n**Clinical Summary:**\nThe patient presented with worsening cough and a significant smoking history, leading to further investigation via CT imaging. Biopsy of the lung lesion confirmed the diagnosis of stage IIIA lung adenocarcinoma (cT1cN2M0) with an EGFRG719X mutation. The patient received two cycles of PC chemotherapy and dacomitinib, resulting in a partial response (PR). Further treatment is ongoing to manage this complex case.\n\n**Key Findings:**\n\n* Stage IIIA lung adenocarcinoma with EGFRG719X mutation\n* Partial response (PR) after initial treatment evaluation\n* Significant smoking history of 30 years\n* Worsening cough for 3 months\n\n**Recommendations:**\nFurther evaluation and management are necessary to optimize the patient's care. This may include additional imaging, laboratory tests, or other treatments to manage this complex case.\n\nNote: The above narrative is based on the provided data and may not be a comprehensive clinical case report.", - "bertscore": { - "precision": [ - 0.7573888301849365 - ], - "recall": [ - 0.7618044018745422 - ], - "f1": [ - 0.759590208530426 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 5, - "edge_count": 4, - "avg_in_degree": 0.8, - "density": 0.2 - }, - "trajectory_embedding": [ - 0.26444298028945923, - 0.15941788256168365, - -0.1746055781841278, - 0.1967768669128418, - 0.13093367218971252, - 0.108800008893013, - 0.047415077686309814, - 0.3190433979034424, - 0.4498003125190735, - -0.4936943054199219, - -0.028453731909394264, - 0.19775180518627167, - -0.6453556418418884, - -0.2056516706943512, - -0.17296206951141357, - 0.10433705896139145, - -0.08722388744354248, - 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He is an ex-smoker with 60 pack-years of smoking experience.\n\n**Timeline of Diagnoses:**\n\n1. **June 2014:** The patient presents to the clinic with right hip pain for two months.\n2. **June 2014 (CT scan):** A CT scan reveals a ~25-mm nodule in the right upper lobe of the lung and a 50-mm mass in the right pelvic region.\n3. **June 2014 (18F-fluorodeoxyglucose positron emission tomography-CT):** The patient undergoes further imaging, which shows intense accumulation in the right S2 nodule of the lung.\n4. **June 2014 (18F-fluorodeoxyglucose positron emission tomography-CT):** The patient receives additional imaging, which reveals standardized uptake value (SUV) max: 15.2 in the right adrenal gland and a pelvic mass from the right sciatic/pubic bone to the right internal obturator muscle (SUV max: 10.81).\n5. **Biopsy:** A transbronchial biopsy (TBB) specimen from the nodule in the right lung is performed, which identifies carcinoma with neuroendocrine features.\n6. **June 2014 (staging and mutation status):** The patient's cancer is staged, and his mutation status is determined.\n\n**Timeline of Treatments:**\n\n1. **June 2014:** The patient undergoes a CT scan to evaluate the right hip pain.\n2. **June 2014:** The patient receives further imaging using 18F-fluorodeoxyglucose positron emission tomography-CT.\n3. **June 2014:** The patient undergoes additional imaging using 18F-fluorodeoxyglucose positron emission tomography-CT.\n4. **June 2014:** The patient receives a transbronchial biopsy (TBB) of the nodule in the right lung.\n\n**Outcomes:**\n\n1. **Diagnosis:** The patient is diagnosed with carcinoma with neuroendocrine features, which is confirmed by histopathological examination of the TBB specimen.\n2. **Staging and Mutation Status:** The patient's cancer is staged as stage IV lung cancer (T1bN0M1b), and his mutation status is negative for epidermal growth factor receptor and anaplastic lymphoma kinase gene, with a programmed death-ligand 1 (PD-L1) tumor proportion score of less than 1%.\n3. **Treatment:** The patient's treatment plan is not specified in the provided data.\n\n**Conclusion:**\nThe patient presents with right hip pain and is diagnosed with carcinoma with neuroendocrine features after undergoing imaging studies and a transbronchial biopsy (TBB). His cancer is staged as stage IV lung cancer, and his mutation status is negative. The patient's treatment plan is not specified in the provided data.", - "bertscore": { - "precision": [ - 0.704978883266449 - ], - "recall": [ - 0.6731678247451782 - ], - "f1": [ - 0.6887062788009644 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.22079414129257202, - 0.0068036518059670925, - -0.10039127618074417, - 0.16631634533405304, - 0.10629185289144516, - 0.08402007818222046, - 0.24246330559253693, - 0.2994869649410248, - 0.36667490005493164, - -0.5220186710357666, - -0.11857226490974426, - 0.10266987234354019, - -0.7685451507568359, - 0.058542799204587936, - -0.482259601354599, - 0.13929423689842224, - 0.1318996697664261, - 0.4940612316131592, - 0.04252505302429199, - -0.15624141693115234, - -0.44017040729522705, - 0.15033189952373505, - 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He has a smoking history of over 7 years, with an average of 20-30 cigarettes per day, and had abstained from smoking for nearly 30 years.\n\n**Timeline of Diagnoses:**\n\n1. **April 20, 2020:** The patient presented asymptomatic, with no cough, sputum, hemoptysis, chest pain, or dyspnea. A chest CT revealed a 4.0 cm x 3.4 cm mass in the inferior lobe of the right lung, with swollen and fused lymph nodes in the hilum and mediastinum.\n2. **May 2, 2020:** The diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma was confirmed.\n3. **May 20, 2020:** Alectinib therapy was initiated at 600 mg twice daily following a multidisciplinary team discussion for potentially resectable NSCLC with ALK rearrangement.\n\n**Timeline of Treatments:**\n\n1. **May 20, 2020:** Initiation of alectinib therapy.\n2. **Unknown date (after 4 months):** A chest CT scan was performed after 4 months of alectinib therapy, showing shrinkage of the primary tumor and a 1.1 cm x 0.6 cm nodule in the inferior lobe of the right lung.\n\n**Outcomes:**\n\nThe patient's treatment with alectinib has resulted in partial response, as evidenced by the shrinkage of the primary tumor and the development of a new nodule. The patient remains on treatment, and further follow-up is required to assess the efficacy of the therapy and monitor for any signs of disease progression.\n\n**Additional Notes:**\n\nThe patient's NGS results revealed ELMOD3-ALK (E8: A20) fusion at 41.23% abundance and EML4-ALK (E13: A20) double-ALK fusion at 68.21% abundance, confirming the presence of ALK rearrangement in the tumor tissue. The patient's CEA levels are not reported.\n\nIn conclusion, this patient has been diagnosed with stage IIIA lung adenocarcinoma and is currently undergoing treatment with alectinib. While the partial response to therapy is encouraging, further follow-up is necessary to assess the long-term efficacy of the treatment and monitor for any signs of disease progression.", - "bertscore": { - "precision": [ - 0.6810472011566162 - ], - "recall": [ - 0.7104792594909668 - ], - "f1": [ - 0.6954519748687744 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.34632283449172974, - 0.13255642354488373, - -0.16146747767925262, - 0.06857442855834961, - -0.053984127938747406, - -0.0689462199807167, - 0.14064376056194305, - 0.2152150720357895, - 0.37596216797828674, - -0.42233654856681824, - -0.13927848637104034, - 0.08689076453447342, - -0.6545354127883911, - 0.01794014871120453, - -0.3974427878856659, - 0.21673455834388733, - 0.03596607223153114, - 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Her medical history includes untreated congenital heart disease (patent ductus arteriosus) for 20 years and hypertension for half a year, with irregular use of valsartan.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient reported intermittent cough and slight chest discomfort for 3 months and painless cervical mass for 1 month.\n2. **Step 2:** A left cervical lymph node puncture was performed one week ago, which showed granulomatous inflammation with caseous necrosis and Langhans' giant cells observed.\n3. **Step 3:** The patient's past medical history of untreated congenital heart disease and hypertension became relevant.\n4. **Step 4:** Physical examination revealed a well-defined, poorly mobile, non-tender mass on the left clavicle without surface ulceration or redness.\n5. **Step 5:** Laboratory tests showed normal blood CEA, squamous cell carcinoma antigen, cytokeratin 19 fragment, and NSE levels, with no evidence of cancer in sputum AFB and GeneXpert MTB/RIF.\n6. **Step 6:** EB virus blood test results indicated increased antibody titers for capsid antigen IgG antibody, early antigen IgM antibody, and core antigen IgG antibody.\n7. **Step 7:** Ultrasound-guided left supraclavicular lymph node puncture was performed, showing focal distribution of epithelioid cells and multinucleated giant cells suggestive of granulomatous inflammation.\n8. **Step 8:** Histopathology confirmed the presence of granuloma.\n\n**Timeline of Treatments:**\n\n1. **Step 2:** Left cervical lymph node puncture was performed due to intermittent cough, slight chest discomfort, and painless cervical mass.\n2. **Step 7:** Ultrasound-guided left supraclavicular lymph node puncture was performed as part of the diagnostic workup.\n\n**Outcomes:**\n\n1. The patient's diagnosis of granuloma was confirmed through histopathology.\n2. No evidence of cancer was found in sputum AFB and GeneXpert MTB/RIF, ruling out tuberculosis or other infections.\n3. EB virus blood test results indicated increased antibody titers, suggesting a possible infection or autoimmune response.\n\n**Conclusion:**\nThe patient's diagnosis of granuloma is likely related to her underlying medical history of untreated congenital heart disease and hypertension. Further investigation into the cause of granulomatous inflammation is necessary to determine the best course of treatment.", - "bertscore": { - "precision": [ - 0.6920709609985352 - ], - "recall": [ - 0.6939922571182251 - ], - "f1": [ - 0.6930302977561951 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 2, - "node_count": 9, - "edge_count": 7, - "avg_in_degree": 0.7777777777777778, - "density": 0.09722222222222222 - }, - "trajectory_embedding": [ - 0.32178184390068054, - 0.0587812140583992, - -0.04031328856945038, - 0.1223248541355133, - 0.1420980840921402, - 0.1322871595621109, - 0.09575825184583664, - 0.21854537725448608, - 0.3668004274368286, - -0.415396511554718, - -0.23321908712387085, - 0.043559107929468155, - -0.6951784491539001, - -0.018354633823037148, - -0.3261258900165558, - 0.10526271909475327, - 0.0806720182299614, - 0.30150094628334045, - 0.05325983837246895, - -0.17181721329689026, - 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While the patient's cancer was diagnosed and treated, the treatment did not completely eliminate the cancer, and the patient developed a significant complication. Further research is needed to improve treatment outcomes for patients with this type of cancer.", - "bertscore": { - "precision": [ - 0.6804789304733276 - ], - "recall": [ - 0.7055283188819885 - ], - "f1": [ - 0.6927772164344788 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 13, - "edge_count": 12, - "avg_in_degree": 0.9230769230769231, - "density": 0.07692307692307693 - }, - "trajectory_embedding": [ - 0.30061694979667664, - 0.13679052889347076, - -0.03965549170970917, - 0.1295793503522873, - 0.008763031102716923, - 0.07028906792402267, - 0.014980574138462543, - 0.28833457827568054, - 0.4558904469013214, - -0.27837973833084106, - -0.10914869606494904, - 0.01314648985862732, - -0.4926709830760956, - -0.17142295837402344, - -0.19755218923091888, - 0.20304308831691742, - 0.08181775361299515, - 0.25292664766311646, - -0.10463114827871323, - -0.2849089205265045, - -0.4398835003376007, - 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She underwent various treatments, including surgery, chemotherapy, radiation therapy, and immunotherapy, before being diagnosed with another type of cancer.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient was diagnosed with SCC of the esophagus (cT3N2M0, stage IIIB) at an unknown date.\n2. **Step 2:** Six months later, she underwent esophagectomy with gastric pull-up reconstruction.\n3. **Step 3:** Two years after her surgery, she received neo-adjuvant concurrent chemoradiation therapy (ypT2N1 stage IIB disease).\n4. **Step 4:** Six weeks after completing her chemotherapy and radiation therapy, she received a total of 50 Gray of radiation over 6 weeks, along with Carboplatin and Paclitaxel for 6 weeks.\n5. **Step 5:** Six years later, a CT scan revealed stage IA TTF-1 positive adenocarcinoma in the left upper lobe.\n6. **Step 6:** Two years after her diagnosis of adenocarcinoma, she underwent treatment with stereotactic radiotherapy.\n7. **Step 7:** Two years after her radiotherapy, squamous cell carcinoma of the right upper lobe was discovered.\n8. **Step 8:** The patient initiated Pembrolizumab with curative intent due to high PD-L1 expression.\n9. **Step 9:** A follow-up CT scan showed no biological response and a tumor diameter of 54 mm.\n10. **Step 10:** Salvage lobectomy including complete mediastinal lymph node dissection was performed.\n11. **Step 11:** Pre-operative positron emission tomography CT scan demonstrated the exact localization of the tumor in the right upper lobe.\n\n**Timeline of Treatments:**\n\n1. **Esophagectomy with gastric pull-up reconstruction (Step 2):**\n - Date: Unknown\n - Treatment: Surgery\n\n2. **Neo-adjuvant concurrent chemoradiation therapy (Step 3):**\n - Date: Two years after esophagectomy\n - Treatment: Chemotherapy and radiation therapy\n\n3. **Radiation therapy with Carboplatin and Paclitaxel (Step 4):**\n - Date: Six weeks after completing chemotherapy and radiation therapy\n - Treatment: Radiation therapy, chemotherapy, and medication\n\n4. **Stereotactic radiotherapy (Step 6):**\n - Date: Two years after diagnosis of adenocarcinoma\n - Treatment: Radiotherapy\n\n5. **Pembrolizumab (Step 8):**\n - Date: After diagnosis of squamous cell carcinoma of the right upper lobe\n - Treatment: Immunotherapy\n\n**Outcomes:**\n\n1. **Esophagectomy with gastric pull-up reconstruction:** The patient underwent successful surgery.\n2. **Neo-adjuvant concurrent chemoradiation therapy:** The patient received treatment for her cancer, but no further information is available on the effectiveness of this treatment.\n3. **Radiation therapy with Carboplatin and Paclitaxel:** No biological response was observed after completing this treatment.\n4. **Stereotactic radiotherapy:** No biological response was observed after completing this treatment.\n5. **Pembrolizumab:** The patient did not respond to Pembrolizumab, as indicated by a follow-up CT scan showing no biological response and a tumor diameter of 54 mm.\n\n**Conclusion:**\nThe patient underwent various treatments for her esophageal cancer before being diagnosed with another type of cancer. Despite receiving multiple treatments, she did not achieve a complete response to any treatment. Salvage lobectomy including complete mediastinal lymph node dissection was performed, but the outcome is unknown.", - "bertscore": { - "precision": [ - 0.6025055050849915 - ], - "recall": [ - 0.7357915043830872 - ], - "f1": [ - 0.6625112891197205 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 11, - "edge_count": 10, - "avg_in_degree": 0.9090909090909091, - "density": 0.09090909090909091 - }, - "trajectory_embedding": [ - 0.21590237319469452, - 0.1823497712612152, - -0.11964480578899384, - 0.07587544620037079, - 0.18606476485729218, - 0.21188677847385406, - -0.11044882982969284, - 0.41281792521476746, - 0.48045822978019714, - -0.37073710560798645, - -0.20201373100280762, - -0.17259280383586884, - -0.5821730494499207, - -0.11790329962968826, - -0.2575705647468567, - 0.43589040637016296, - -0.25557705760002136, - 0.2976360023021698, - -0.1255851835012436, - -0.3479345142841339, - 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The patient's demographic information includes:\n\n* Name: [insert name]\n* Date of Birth: [insert date of birth]\n* Sex: [insert sex]\n\n**Diagnosis Timeline**\n\nThe patient's diagnosis timeline began on [insert date], when they presented to the clinic with [insert initial symptoms or concerns]. Following a series of diagnostic tests, including imaging studies and biopsies, the patient was diagnosed with [insert primary diagnosis].\n\nOver the next several months, the patient underwent various treatments, including:\n\n* First-line systemic therapy: The patient received treatment with [insert medication] from [insert start date] to [insert end date].\n* Maintenance therapy: Following completion of first-line therapy, the patient transitioned to maintenance therapy with pemetrexed from [insert start date] to [insert end date].\n* Second-line treatment: In response to disease progression, the patient received treatment with cabozantinib from [insert start date] to [insert end date], which was discontinued due to adverse effects.\n* Third-line treatment: The patient then transitioned to pembrolizumab, initiating treatment on [insert start date].\n\n**Treatment Timeline**\n\nThe patient's treatment timeline is as follows:\n\n| Treatment | Start Date | End Date |\n| --- | --- | --- |\n| First-line therapy | [insert start date] | [insert end date] |\n| Maintenance therapy | [insert start date] | [insert end date] |\n| Cabozantinib | [insert start date] | [insert end date] (discontinued) |\n| Pembrolizumab | [insert start date] | Ongoing |\n\n**Outcomes**\n\nThe patient's treatment outcomes have been as follows:\n\n* Partial tumor response: The patient experienced a partial tumor response to first-line therapy, which was observed on imaging studies.\n* Disease progression: Following completion of first-line therapy, the patient experienced disease progression, leading to the initiation of second-line treatment.\n* Adverse effects: The patient experienced adverse effects while receiving cabozantinib, leading to discontinuation of treatment.\n* Symptomatic improvement: The patient has experienced significant symptomatic improvement since initiating pembrolizumab, including complete hearing recovery and a substantial reduction in dizziness and headache complaints.\n\n**Current Status**\n\nThe patient is currently undergoing treatment with pembrolizumab, which was initiated on [insert start date]. The patient's current status includes:\n\n* Ongoing treatment with pembrolizumab\n* Continued monitoring for disease progression or adverse effects\n* Regular follow-up appointments to assess treatment outcomes and adjust treatment as needed\n\nOverall, the patient has undergone a complex treatment journey, involving multiple treatments and transitions. Despite challenges, the patient has experienced significant symptomatic improvement and is currently receiving ongoing treatment with pembrolizumab.", - "bertscore": { - "precision": [ - 0.5634559392929077 - ], - "recall": [ - 0.5314140915870667 - ], - "f1": [ - 0.5469661355018616 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 6, - "node_count": 16, - "edge_count": 10, - "avg_in_degree": 0.625, - "density": 0.041666666666666664 - }, - "trajectory_embedding": [ - 0.16245156526565552, - 0.1600143313407898, - -0.07061316072940826, - 0.19158999621868134, - 0.05907982587814331, - 0.1717534214258194, - 0.06727615743875504, - 0.25085461139678955, - 0.6407455801963806, - -0.26162946224212646, - -0.03981025144457817, - -0.11866048723459244, - -0.46796175837516785, - -0.20894984900951385, - -0.15915517508983612, - 0.2649320065975189, - -0.21555562317371368, - 0.3820728063583374, - -0.021528776735067368, - 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He has a significant smoking history, having consumed two packs per day for 55 years, which is reflected in his Brinkman Index score of 1100. Additionally, he has a history of total thyroidectomy five years prior due to papillary thyroid carcinoma (PTC).\n\n**Timeline of Diagnoses:**\n\n1. **Six years ago:** The patient was found to have left cervical lymphadenopathy of unknown origin, suspected to be cervical lymph node metastasis of PTC.\n2. **Five years ago:** The patient underwent total thyroidectomy and left cervical lymph node dissection, with histopathology revealing multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins.\n3. **Two years prior to current encounter:** A nodule in the right upper lobe of the lung was identified and monitored with chest CT scans. Increase in nodule density observed compared to two years prior, prompting a transbronchial biopsy; however, no definitive diagnosis was made.\n\n**Timeline of Treatments:**\n\n1. **Five years ago:** The patient underwent total thyroidectomy and left cervical lymph node dissection.\n2. **Current encounter:** The patient was treated with radioiodine therapy (Iodine-131).\n\n**Timeline of Outcomes:**\n\n1. **Six years ago:** Left cervical lymphadenopathy of unknown origin, suspected to be cervical lymph node metastasis of PTC.\n2. **Five years ago:** Multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins.\n3. **Current encounter:** Serum thyroglobulin levels showed a gradual increase over time, indicating progression of disease.\n\n**Clinical Findings:**\n\n* The patient's serum thyroglobulin levels have shown a gradual increase over time, indicating progression of disease.\n* Chest X-rays and CT scans revealed an irregular nodule measuring 15\u00d714 mm in the S1 segment of the right upper lobe.\n* Pulmonary function and electrocardiogram tests showed no abnormalities.\n\n**Surgical Plan:**\nA surgical plan was made to perform intraoperative rapid diagnosis, followed by right upper lobectomy.", - 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The patient's demographic information is not explicitly provided in the data, but based on the clinical presentation and treatment plan, it can be inferred that the patient is likely an older adult.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient was diagnosed with stage III NSCLC and upper esophageal stricture around the same time.\n2. **Step 2 (Two months later):** An initial MRI performed revealed no abnormalities, but the patient's diagnosis of NSCLC remained active.\n3. **Step 3 (One year after Step 1):** Follow-up CT scans showed metastatic spread throughout the brain after presentation to the ED with neurological weakness.\n4. **Step 4:** The patient was admitted to hospital and started on dexamethasone, continued treatment for hypokalemia, and placed on neutropenic precautions. Pantoprazole and enoxaparin sodium were initiated due to possible hemorrhages and deep vein thrombosis prophylaxis.\n5. **Step 5:** MRI confirmed multiple new brain metastases with vasogenic edema and possible hemorrhagic components. The patient's oncologist confirmed metastasis to the brain and bone, and dexamethasone was increased to 6 mg every eight hours. Enoxaparin sodium was discontinued due to possible hemorrhages; mechanical prophylaxis started with thromboembolic deterrent stockings and sequential compression devices.\n6. **Step 6:** The patient tolerated radiation therapy well and docetaxel was re-initiated.\n7. **Step 7 (Refractory disease):** CT scans revealed new developments in the liver and possibly pancreas, indicating refractory disease to second-line docetaxel.\n8. **Step 8 (Hospice care recommendation):** The oncologist discussed a third-line option and recommended hospice care.\n\n**Timeline of Treatments:**\n\n1. **Dexamethasone:** Initially started at 4 mg twice daily, increased to 6 mg every eight hours due to metastasis.\n2. **Docetaxel:** Re-initiated after radiation therapy, with no specified dosage or frequency.\n3. **Pantoprazole and Enoxaparin Sodium:** Initiated for possible hemorrhages and deep vein thrombosis prophylaxis.\n\n**Outcomes:**\n\n1. **Radiation Therapy:** The patient tolerated the treatment well, indicating a positive response to radiation therapy.\n2. **Hospice Care Recommendation:** The oncologist recommended hospice care due to refractory disease, indicating a poor prognosis for the patient's overall health and quality of life.\n\nIn conclusion, this patient was diagnosed with stage III NSCLC accompanied by an upper esophageal stricture and underwent multiple treatments, including radiation therapy, dexamethasone, docetaxel, pantoprazole, and enoxaparin sodium. Despite initial positive responses to treatment, the patient's disease progressed, leading to a recommendation for hospice care due to refractory disease.", - "bertscore": { - "precision": [ - 0.5511878728866577 - ], - "recall": [ - 0.5822768211364746 - ], - "f1": [ - 0.5663059949874878 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.24155695736408234, - 0.21537359058856964, - -0.07995787262916565, - 0.12391994893550873, - -0.0372464694082737, - 0.15261226892471313, - -0.11476530134677887, - 0.32324033975601196, - 0.4738871157169342, - -0.23460787534713745, - -0.20247039198875427, - -0.08712716400623322, - -0.6125581860542297, - -0.031501494348049164, - -0.20453636348247528, - 0.20022889971733093, - -0.16431254148483276, - 0.29454290866851807, - 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However, based on the content of the clinical notes, it appears that the patient has been diagnosed with a malignancy affecting the right upper lobe of the lung.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Initial Diagnosis:** The patient underwent an enhanced chest CT scan on March 3, 2023 (Node N2), which revealed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32\u00d727 mm. Enlarged and moderately enhanced lymph nodes were also detected in the 10R, 4R, and 2R regions.\n2. **Treatment Initiation:** Vancomycin was administered for anti-infection and anti-viral treatment (Node N1) on an unspecified date prior to March 3, 2023.\n3. **Repeat Imaging:** A repeat enhanced chest CT scan was performed on May 29, 2023 (Node N2), which showed a significant reduction in the size of the solid component of the right upper lobe mass and similar-sized mediastinal lymph nodes compared to the previous CT scan.\n4. **Immunotherapy and Chemotherapy:** A second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023 (Node N3).\n\n**Outcomes:**\n\n1. **Partial Remission:** The patient's response assessment indicated partial remission following the repeat imaging study on May 29, 2023.\n2. **Treatment Tolerability:** The patient tolerated the immunotherapy and chemotherapy treatment well, as evidenced by the administration of a second cycle of these treatments.\n\n**Clinical Implications:**\n\nThe patient's clinical course suggests that the malignancy affecting the right upper lobe of the lung is responsive to immunotherapy and chemotherapy. However, further monitoring and follow-up are necessary to assess the durability of the partial remission and to identify potential side effects or toxicities associated with these treatments.\n\n**Future Directions:**\n\n1. **Regular Imaging:** Regular imaging studies should be performed to monitor the patient's response to treatment and to detect any signs of disease progression.\n2. **Dose Escalation:** The dose of immunotherapy and chemotherapy may need to be escalated in subsequent cycles to maintain efficacy and tolerability.\n3. **Combination Therapy:** Further investigation into combination therapies involving immunotherapy, chemotherapy, and targeted therapies may be warranted to optimize treatment outcomes.\n\nIn conclusion, the patient's clinical case report highlights the importance of regular imaging studies, effective treatment strategies, and careful monitoring to manage malignancies affecting the lung.", - "bertscore": { - "precision": [ - 0.5968338847160339 - ], - "recall": [ - 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The patient's history of coronary artery disease is noted as historical.\n\n**Prognosis:**\n\nThe prognosis for this patient is uncertain due to the presence of metastatic non-small cell carcinoma of the lung and intracardiac metastasis. Further treatment options should be discussed with a healthcare provider.\n\nNote: This narrative is based on the provided data and may not reflect the actual clinical case report or patient's current status.", - "bertscore": { - "precision": [ - 0.5106064677238464 - ], - "recall": [ - 0.5770247578620911 - ], - "f1": [ - 0.5417876243591309 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 1, - "edge_count": 0, - "avg_in_degree": 0.0, - "density": 0 - }, - "trajectory_embedding": [ - 0.2389703392982483, - 0.3098335266113281, - -0.3165978193283081, - -9.601563215255737e-05, - 0.38989344239234924, - 0.5903520584106445, - -0.588888943195343, - -0.03018897771835327, - -0.08889243006706238, - -0.6207064390182495, - -0.0009037437266670167, - 0.39261308312416077, - -0.7441316843032837, - -0.2979073226451874, - 0.16640852391719818, - 0.43679654598236084, - 0.048064105212688446, - 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She presented with a subsolid pulmonary lesion incidentally detected during a routine follow-up for malignant melanoma.\n\n**Timeline of Diagnoses:**\n\n1. **April 2013:** The patient was diagnosed with malignant melanoma and underwent resection videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent.\n2. **Late April 2013:** Left axillary dissection revealed metastasis in one of 19 lymph nodes, and molecular genetic testing confirmed a BRAF mutation at codon 600.\n3. **November 2017:** A routine CT scan detected a new asymptomatic 7 mm lesion in segment S10 of the right lower lobe with a density consistent with a pure ground glass nodule.\n4. **June 2020:** Follow-up CT scans showed the lesion changed character to a subsolid lesion with the presence of a solid component.\n5. **July 2020:** PET/CT scans confirmed the persistence of the lesion without increased metabolic activity.\n6. **April 2021:** Follow-up confirmed persistence and slight size progression of the solid component of the lesion, leading to indication for surgical resection.\n\n**Timeline of Treatments:**\n\n1. **April 2013:** Resection videothoracoscopically\n2. **Late April 2013:** Left axillary dissection and initiation of targeted therapy with BRAF inhibitors\n3. **November 2017:** No treatment mentioned\n4. **June 2020:** No treatment mentioned\n5. **July 2020:** No treatment mentioned\n6. **April 2021:** Surgical resection\n\n**Timeline of Outcomes:**\n\n1. **Late April 2013:** Metastasis in one of 19 lymph nodes confirmed, and targeted therapy with BRAF inhibitors initiated.\n2. **November 2017:** New asymptomatic lesion detected during routine CT scan\n3. **June 2020:** Lesion changed character to a subsolid lesion with the presence of a solid component.\n4. **July 2020:** Persistence of lesion without increased metabolic activity confirmed by PET/CT scans\n5. **April 2021:** Surgical resection performed, and follow-up confirmed persistence and slight size progression of the solid component of the lesion.\n\n**Conclusion:**\nThe patient was diagnosed with malignant melanoma in April 2013 and underwent resection videothoracoscopically. Following this, she developed metastasis in one of 19 lymph nodes and was treated with targeted therapy with BRAF inhibitors. In November 2017, a new asymptomatic lesion was detected during routine CT scan, which changed character to a subsolid lesion with the presence of a solid component by June 2020. The persistence of this lesion without increased metabolic activity was confirmed by PET/CT scans in July 2020. Finally, surgical resection was performed in April 2021, and follow-up confirmed persistence and slight size progression of the solid component of the lesion.", - "bertscore": { - "precision": [ - 0.4778168499469757 - ], - "recall": [ - 0.7119154334068298 - ], - "f1": [ - 0.5718348622322083 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.149007648229599, - 0.05697751045227051, - -0.07104989141225815, - 0.04486839473247528, - -0.15542572736740112, - -0.011686301790177822, - 0.04617166519165039, - 0.17946068942546844, - 0.2943315804004669, - -0.3095993399620056, - -0.16567997634410858, - 0.13099738955497742, - -0.5008986592292786, - -0.13083820044994354, - -0.32352951169013977, - 0.1127810999751091, - 0.0062797837890684605, - 0.2857533097267151, - 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He presented with severe, debilitating shoulder pain (VAS 9) in the low dorsal area, which prompted further investigation and diagnosis.\n\n**Timeline of Diagnoses:**\n\n1. **Primary Lung Adenocarcinoma Diagnosis:** The patient was diagnosed with primary lung adenocarcinoma in 2023.\n2. **Shoulder Pain Presentation:** The patient presented with severe, debilitating shoulder pain (VAS 9) in the low dorsal area, which prompted further investigation and diagnosis.\n3. **Compression Fracture Diagnosis:** A CT scan revealed a compression fracture of the T8 vertebral body with multiple fracture lines and a mixed lytic-sclerotic tumor component.\n4. **Pathological Fracture Diagnosis:** The patient was diagnosed with pathological fracture due to metastasis from lung adenocarcinoma.\n5. **Treatment of Pathological Fracture:** The patient underwent treatment for the pathological fracture, including microwave ablation and SpineJack system.\n\n**Timeline of Treatments:**\n\n1. **Microwave Ablation and SpineJack System Treatment:** The patient received treatment with microwave ablation and SpineJack system to manage the pathological fracture.\n2. **Initial CT Scan:** An initial CT scan was performed to assess the lesion's size, location, and radiological characteristics.\n3. **Conscious Sedation Administration:** Patient was positioned prone, and conscious sedation was administered using continuous intravenous infusion of fentanyl citrate.\n\n**Timeline of Outcomes:**\n\n1. **Pathological Fracture Management:** The patient's pathological fracture was successfully managed with microwave ablation and SpineJack system treatment.\n2. **Lesion Assessment:** The initial CT scan provided valuable information on the lesion's size, location, and radiological characteristics.\n3. **Patient Recovery:** The patient recovered from the procedure without any significant complications.\n\n**Conclusion:**\nThe patient underwent a comprehensive evaluation for severe shoulder pain, which led to the diagnosis of compression fracture due to metastasis from lung adenocarcinoma. Treatment with microwave ablation and SpineJack system was effective in managing the pathological fracture, and the initial CT scan provided valuable information on the lesion's characteristics. The patient recovered without any significant complications.\n\n**Recommendations:**\n\n1. **Regular Follow-up:** Regular follow-up appointments are recommended to monitor the patient's condition and adjust treatment as needed.\n2. **Imaging Studies:** Imaging studies should be performed regularly to assess the progression of the disease and the effectiveness of treatment.\n3. **Pain Management:** Pain management strategies should be implemented to ensure optimal pain control for the patient.\n\n**Limitations:**\nThis case report is limited by its retrospective nature, which may not capture all relevant information or outcomes. Further follow-up studies are necessary to fully evaluate the effectiveness of treatment and monitor long-term outcomes.", - "bertscore": { - "precision": [ - 0.6227207183837891 - ], - "recall": [ - 0.6329694986343384 - ], - "f1": [ - 0.6278032660484314 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 10, - "edge_count": 9, - "avg_in_degree": 0.9, - "density": 0.1 - }, - "trajectory_embedding": [ - 0.18080228567123413, - -0.01176790613681078, - 0.10657219588756561, - 0.21200677752494812, - 0.1496204435825348, - 0.09226961433887482, - -0.08451242744922638, - 0.22056791186332703, - 0.5967764258384705, - -0.16920879483222961, - -0.2202618569135666, - -0.1208207830786705, - -0.3906412720680237, - -0.08555690199136734, - -0.24673983454704285, - 0.1816776692867279, - 0.06529556214809418, - 0.02827569469809532, - -0.09853260964155197, - -0.2589186131954193, - -0.23060894012451172, - 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He was diagnosed with small-cell lung cancer (SCLC) with hilar, mediastinal lymph node, and pleural metastases (cT1N3M1a, extensive stage) and a Performance Status (PS) score of 1.\n\n**Timeline of Diagnoses:**\n\n* July 2023: The patient presented with facial and dorsal hand edema, leading to the diagnosis of small-cell lung cancer.\n* September 9, 2024: The patient was admitted to the gastroenterology department due to a 5-day period of no bowel movement, resulting in a diagnosis of constipation.\n\n**Timeline of Treatments:**\n\n* July 2023: The patient started chemotherapy with four cycles of intravenous etoposide 160 mg (days 1-3), carboplatin (400 mg) on day 1, and serplulimab 300 mg on day 1 (Q3W).\n* After 18 cycles of chemotherapy and serplulimab maintenance: The patient experienced a partial response (PR).\n\n**Timeline of Outcomes:**\n\n* After two cycles of serplulimab treatment: The patient intermittently experienced hard stools and occasional constipation, relieved with glycerin suppositories.\n* September 9, 2024: The patient was admitted to the gastroenterology department due to a 5-day period of no bowel movement, resulting in a diagnosis of constipation.\n* Abdominal CT revealed diffuse dilatation and gas accumulation in the bowel, particularly the colon, suggesting incomplete intestinal obstruction.\n* Gastroscopy showed chronic atrophic gastritis (C2) with bile reflux.\n* Colonoscopy revealed a subpedunculated polyp approximately 1.5 cm in size, 20 cm from the anus, with smooth mucosa in the sigmoid colon.\n\n**Clinical Course:**\n\nThe patient's clinical course was marked by a series of diagnostic and therapeutic challenges. Initially, the patient presented with symptoms suggestive of small-cell lung cancer, which led to the initiation of chemotherapy and serplulimab maintenance. However, despite this treatment, the patient experienced worsening constipation, prompting further evaluation.\n\nFurther investigation revealed chronic atrophic gastritis (C2) with bile reflux, as well as a subpedunculated polyp in the sigmoid colon. These findings suggested incomplete intestinal obstruction and gastrointestinal distress, which were exacerbated by the patient's underlying small-cell lung cancer.\n\nThe patient's clinical course was ultimately marked by a series of diagnostic and therapeutic challenges, including worsening constipation, chronic atrophic gastritis, and gastrointestinal distress. Despite these challenges, the patient received treatment for their underlying small-cell lung cancer, as well as management for their gastrointestinal symptoms.\n\n**Conclusion:**\n\nThis case highlights the complexities of managing patients with multiple comorbidities, particularly those with small-cell lung cancer. The patient's clinical course was marked by a series of diagnostic and therapeutic challenges, including worsening constipation, chronic atrophic gastritis, and gastrointestinal distress. Despite these challenges, the patient received treatment for their underlying small-cell lung cancer, as well as management for their gastrointestinal symptoms.", - "bertscore": { - "precision": [ - 0.7377782464027405 - ], - "recall": [ - 0.7519990801811218 - ], - "f1": [ - 0.744820773601532 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.19909723103046417, - 0.12390078604221344, - -0.27012550830841064, - 0.19638073444366455, - 0.11007723957300186, - 0.15321364998817444, - -0.10099908709526062, - 0.23281972110271454, - 0.6538661122322083, - -0.3013831377029419, - -0.03854934498667717, - -0.08443812280893326, - -0.5399647355079651, - -0.23934105038642883, - -0.10716229677200317, - 0.29621395468711853, - -0.2592211961746216, - 0.2792671024799347, - 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This condition had been present for several weeks prior to his current encounter. The patient's vital signs were stable during this initial visit, but as time progressed, he began to experience coughing, expectoration, fever, and left lumbar/groin erythema/pain.\n\nFollowing a hospital admission, the patient underwent various tests, including cultures and CT scans, which initially suggested a possible bacterial infection. Despite treatment with piperacillin-tazobactam, the patient's condition worsened, leading to further hospitalization.\n\nDuring this period, the patient experienced significant changes in his vital signs and mental status, including stupor and hypoxia. His electrocardiogram revealed atrial fibrillation, and antimicrobial susceptibility testing indicated sensitivity to meropenem.\n\nThe patient's lab values continued to show abnormal results, with elevated white blood cell count, neutrophil percentage, albumin levels, C-reactive protein, procalcitonin, N-terminal pro b-type natriuretic peptide, alanine aminotransferase, aspartate aminotransferase, and creatinine.\n\nThroughout the patient's hospital stay, he received treatment with meropenem, which was found to be sensitive in antimicrobial susceptibility testing. Despite this, the patient continued to experience persistent symptoms and abnormal lab values.\n\nThe timeline of diagnoses and treatments for this patient can be summarized as follows:\n\n* Initial visit: Toe redness/pain (weeks prior)\n* Hospital admission: Coughing, expectoration, fever, left lumbar/groin erythema/pain\n* Treatment with piperacillin-tazobactam\n* Further hospitalization due to worsening condition\n* Development of stupor, hypoxia, and atrial fibrillation\n* Treatment with meropenem\n\nThe patient's outcomes are currently uncertain, as the narrative does not provide information on his current status or any subsequent treatments. However, it is clear that this patient has experienced a significant decline in his health status over time, requiring multiple hospitalizations and various treatments to manage his symptoms and lab values.", - "bertscore": { - "precision": [ - 0.510433554649353 - ], - "recall": [ - 0.565669059753418 - ], - "f1": [ - 0.5366336703300476 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.2106419950723648, - 0.10880613327026367, - -0.019303588196635246, - 0.17433996498584747, - 0.13737574219703674, - 0.09073399007320404, - 0.057045288383960724, - 0.16380244493484497, - 0.42614296078681946, - -0.31337109208106995, - -0.12151220440864563, - 0.03720476105809212, - -0.6054100394248962, - -0.16327770054340363, - -0.23895896971225739, - 0.11631965637207031, - 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He is a heavy smoker with no medical history of malignancy.\n\n**Initial Presentation (Step 1):**\nThe patient presented with left-sided hearing loss, otalgia, and a red mass in the left external auditory canal (EAC) that persisted for several weeks. Physical examination revealed a red, soft mass measuring approximately 20 mm occupying the left EAC.\n\n**Diagnostic Workup:**\nImaging studies, including CT scans and MRI, were performed to evaluate the extent of the mass. Laboratory tests showed normal Span-1 and DUPAN2 levels, elevated ProGRP (698 pg/mL) and NSE (31.1 ng/mL). Pure-tone audiometry revealed bilateral mixed hearing loss.\n\n**Diagnosis:**\nThe diagnosis was initially suspected to be carcinoma of the EAC based on imaging findings and laboratory results. However, further testing, including biopsies from the EAC mass, lung, and pancreas, confirmed the presence of small cell lung cancer (SCLC).\n\n**Treatment:**\nChemotherapy with carboplatin, etoposide, and zoledronic acid was initiated to treat bone metastases. The treatment resulted in a reduction in size of metastatic lesions in the EAC and middle ear, improvement in hearing impairment and otalgia, and a decrease in ProGRP levels.\n\n**Outcome:**\nThe patient experienced severe hearing loss but regained the ability to understand conversations as the tumor shrank. Otalgia resolved, and opioid therapy was discontinued. Unfortunately, the patient died 15 months later due to complications from SCLC.\n\n**Autopsy Findings:**\nAt autopsy, resolution of EAC lesions was observed grossly. CT imaging revealed mastoid destruction and tumor invasion into the EAC.\n\n**Conclusion:**\nThis case highlights the importance of comprehensive diagnostic workup and multidisciplinary treatment approaches for patients with suspected carcinoma of the EAC. Early detection and treatment can improve outcomes, but the disease is often aggressive, leading to poor prognosis in some cases.", - "bertscore": { - "precision": [ - 0.6627601981163025 - ], - "recall": [ - 0.6721744537353516 - ], - "f1": [ - 0.6674340963363647 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.14263400435447693, - -0.013967558741569519, - -0.2280512899160385, - 0.02719009481370449, - -0.11668924242258072, - -0.14093691110610962, - 0.10111647099256516, - 0.0954238548874855, - 0.22714979946613312, - -0.2350296974182129, - -0.3323439657688141, - 0.36267557740211487, - -0.6519513130187988, - 0.014573529362678528, - -0.52058345079422, - -0.19109226763248444, - 0.09013906866312027, - 0.25849395990371704, - 0.0019105846295133233, - 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However, it can be inferred that he has been diagnosed with multiple conditions over the years, including melanoma and choroidal neoplasms.\n\n**Timeline of Diagnoses**\n\nThe patient's journey began with a diagnosis of melanoma in 2015 (N1). He underwent lymph node scintigraphy and removal of four sentinel lymph nodes as part of his treatment plan. This was followed by yearly follow-up visits at the dermato-oncologist, which helped monitor his condition for any signs of recurrence or metastasis.\n\nIn 2018, the patient presented with worsening eyesight in one eye due to a pigmented choroidal tumor (N4). He underwent brachytherapy for this condition, which involved the placement of a ruthenium-106 plaque in the affected area. This treatment helped stabilize his visual function and reduce the size of the tumor.\n\nOver the next few years, the patient's oncologist conducted regular follow-up appointments to monitor his condition. In 2020, it was discovered that the patient had metastatic disease throughout his body, with a pattern characteristic of primary cutaneous melanoma (N6). As a result, he began systemic cancer treatment with ipilimumab and nivolumab.\n\n**Timeline of Treatments**\n\n* 2015: Melanoma diagnosis and lymph node scintigraphy\n* 2018: Brachytherapy for pigmented choroidal tumor\n* 2020: Systemic cancer treatment with ipilimumab and nivolumab\n\n**Outcomes**\n\nThe patient's treatment plan has been successful in managing his conditions. His melanoma was successfully treated, and he has not experienced any significant recurrence or metastasis.\n\nRegarding the pigmented choroidal tumor, brachytherapy helped stabilize his visual function and reduce the size of the tumor. However, a new lesion developed in 2022 (N13), which required further treatment with brachytherapy.\n\nThe patient's PET/CT scan in 2023 showed no pathological processes, indicating that his cancer is currently under control (N9).\n\n**Current Status**\n\nThe patient continues to receive regular follow-up appointments with his oncologist and dermato-oncologist. He is being monitored for any signs of recurrence or metastasis, and his treatment plan will be adjusted as needed.\n\nOverall, the patient's journey has been marked by a series of diagnoses, treatments, and outcomes that have helped manage his conditions. While there are still challenges ahead, his current status suggests that he is in good hands with his healthcare team.", - "bertscore": { - "precision": [ - 0.6081898808479309 - ], - "recall": [ - 0.6577727794647217 - ], - "f1": [ - 0.6320104002952576 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 6, - "node_count": 15, - "edge_count": 9, - "avg_in_degree": 0.6, - "density": 0.04285714285714286 - }, - "trajectory_embedding": [ - 0.10540588945150375, - 0.12294507771730423, - -0.10281980782747269, - 0.1525949388742447, - 0.008018000051379204, - 0.2466597855091095, - 0.03886903077363968, - 0.2453383058309555, - 0.4833277463912964, - -0.4130333662033081, - -0.19181455671787262, - -0.0784992128610611, - -0.5563032031059265, - -0.12875708937644958, - -0.3123818039894104, - 0.17844067513942719, - -0.15840710699558258, - 0.31354740262031555, - -0.14745765924453735, - -0.240568146109581, - -0.464466392993927, - 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Diagnosis of the thyroid gland via fine-needle aspiration revealed papillary carcinoma.\n4. **Step 4 (July 2022):** Chest CT scans showed stable disease following treatments.\n5. **Step 5 (August 2022):** Post-surgery chest CT examination revealed no signs of tumor recurrence.\n6. **Step 6 (September 2022):** Thyroid color ultrasonography suggested isthmic thyroid nodules.\n7. **Step 7 (October 2022):** Postoperative thyroid ultrasound showed no signs of tumor recurrence.\n8. **Step 8 (November 2022):** PET-CT scans revealed a primary tumor mass in the right neck subcutaneous at the time of diagnosis.\n9. **Step 9 (December 2022):** Ultrasound results suggested a hypoechoic mass in the V region of the right neck.\n10. **Step 10 (January 2023):** Puncture biopsies revealed adenocarcinoma of lung, papillary carcinoma of thyroid, and a spindle cell.\n\n**Timeline of Treatments:**\n\n1. **CT-guided puncture (June 2022):** Used to diagnose the right upper lung nodule.\n2. **Fine-needle aspiration (June 2022):** Used to diagnose the thyroid gland.\n3. **Treatments (July 2022):** Administered following PET-CT findings.\n4. **Surgery (August 2022):** Performed to remove the tumor.\n5. **Postoperative care (September 2022):** Provided to monitor for tumor recurrence.\n\n**Outcomes:**\n\n1. **Lung adenocarcinoma:** Stable disease was observed following treatments, and no signs of tumor recurrence were seen on post-surgery chest CT examination.\n2. **Papillary carcinoma of thyroid:** No signs of tumor recurrence were seen on postoperative thyroid ultrasound.\n3. **Primary tumor mass in the right neck subcutaneous:** PET-CT scans revealed a primary tumor mass at the time of diagnosis, but no further treatment was mentioned.\n\n**Conclusion:**\nThe patient underwent a series of diagnostic tests and treatments for lung cancer and papillary carcinoma of the thyroid. Following these interventions, stable disease was observed in both conditions, with no signs of tumor recurrence seen on post-surgery chest CT examination and postoperative thyroid ultrasound. However, PET-CT scans revealed a primary tumor mass in the right neck subcutaneous at the time of diagnosis, which warrants further evaluation and treatment.", - "bertscore": { - "precision": [ - 0.6954405307769775 - ], - "recall": [ - 0.7023525238037109 - ], - "f1": [ - 0.6988794207572937 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 10, - "edge_count": 9, - "avg_in_degree": 0.9, - "density": 0.1 - }, - "trajectory_embedding": [ - 0.34409192204475403, - 0.07935971021652222, - 0.046093933284282684, - 0.01933947391808033, - -0.0402722992002964, - 0.1429879069328308, - 0.05653051286935806, - 0.2529970109462738, - 0.3755955100059509, - -0.32734960317611694, - -0.2119436264038086, - -0.10174901783466339, - -0.4879678785800934, - -0.0025561749935150146, - -0.42852139472961426, - 0.38021185994148254, - 0.006385275162756443, - 0.34415745735168457, - 0.034441545605659485, - 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She has a medical history of hypertension but no smoking or family history of cancer.\n\n**Initial Presentation (Step 1):**\nThe patient presented with an abnormal chest CT scan, which led to further investigation. The initial presentation was characterized by the absence of respiratory symptoms such as cough or dyspnea.\n\n**Diagnostic Findings (Step 2):**\nChest CT revealed a 1.1-cm spiculated nodule in the right middle lobe (RML), multiple pleural nodules with mild pleural thickening, and fibrotic lesions in the right upper lobe (RUL). These findings prompted further investigation.\n\n**Biopsy and Diagnosis (Step 3):**\nLinear endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) of enlarged lymph node 7 revealed metastatic adenocarcinoma with ALK rearrangement, wild type EGFR mutation, and echinoderm microtubule-associated protein-like 4 (EML 4)-ALK fusion. The first biopsy of the mediastinal 7th lymph node was positive for ALK stain.\n\n**Diagnosis Confirmation (Step 4):**\nPET-CT revealed pleural, multiple enhancing nodules with lymph nodes metastasis, leading to a diagnosis of stage IV lung cancer (T2N2M1a).\n\n**Treatment Initiation (Step 5):**\nTargeted mutation chemotherapy with alectinib was initiated and continued for a period of one and a half years. Follow-up chest CT scans during treatment with alectinib demonstrated a reduction in the lung mass and pleural metastatic lesions.\n\n**Follow-Up and Recurrence (Step 6):**\nIn July 2024, Chest CT showed the previously observed main mass in the RML, indicating recurrence of the disease.\n\n**Timeline:**\n\n* November 2022: Patient admitted to Pulmonology Department for evaluation of abnormal chest CT scan.\n* Step 2: Chest CT reveals abnormalities.\n* Step 3: EBUS-TBNA and biopsy confirm diagnosis of metastatic adenocarcinoma.\n* Step 4: Diagnosis confirmed with PET-CT.\n* Step 5: Targeted mutation chemotherapy with alectinib initiated.\n* July 2024: Follow-up chest CT shows recurrence of the disease.\n\n**Outcomes:**\nThe patient received targeted mutation chemotherapy with alectinib, which led to a reduction in lung mass and pleural metastatic lesions. However, the disease recurred in July 2024, indicating the need for further treatment options.", - "bertscore": { - "precision": [ - 0.5603240728378296 - ], - "recall": [ - 0.662941038608551 - ], - "f1": [ - 0.6073283553123474 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.4501422345638275, - 0.09562578797340393, - -0.1269008368253708, - 0.16001977026462555, - -0.027514860033988953, - 0.06566961854696274, - 0.10955768078565598, - 0.3071059286594391, - 0.3549204170703888, - -0.3344673812389374, - -0.10898244380950928, - 0.05722176656126976, - -0.6175083518028259, - -0.03839653357863426, - -0.21359169483184814, - 0.22728413343429565, - 0.024842113256454468, - 0.2667379677295685, - 0.009542305953800678, - -0.11258780211210251, - -0.5507663488388062, - 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The patient's demographic information includes a 30-year history of hypertension, a 7-year history of carotid stenosis on the left side, and a 4-year history of right lung cancer surgery.\n\nThe patient's timeline of diagnoses began with the discovery of black stool on January 9, 2024. Upon presentation to the emergency department, the patient was found to have a hemoglobin level of 58 g/L. This marked the beginning of an acute upper gastrointestinal hemorrhage, which required immediate attention.\n\nFollowing stabilization, the patient's medical history and current medications were reviewed (N11). The patient had been managed with compound reserpine, nifedipine extended-release tablets, and captopril for their hypertension, as well as a 30-year history of hypertension. Additionally, the patient had undergone right lung cancer surgery 4 years prior and thermal ablation of a right lung tumor 5 months prior.\n\nThe patient's symptoms and laboratory results led to the diagnosis of gastrointestinal hemorrhage, unspecified (K92.2). The patient was subsequently admitted for further evaluation and management.\n\nIn the course of their treatment, the patient underwent several procedures, including CT-guided percutaneous lung nodule aspiration biopsy (N7), thermal ablation of a right lung tumor (N8), and regular follow-up with surveillance imaging (N9).\n\nThe patient's hemoglobin level was found to be 58 g/L upon presentation, indicating severe anemia. The patient's symptoms and laboratory results led to the diagnosis of gastrointestinal hemorrhage, unspecified (K92.2). The patient was subsequently admitted for further evaluation and management.\n\nIn the course of their treatment, the patient underwent several procedures, including CT-guided percutaneous lung nodule aspiration biopsy (N7), thermal ablation of a right lung tumor (N8), and regular follow-up with surveillance imaging (N9).\n\nThe patient's timeline of diagnoses is as follows:\n\n* January 9, 2024: Patient presents with black stool and is found to have a hemoglobin level of 58 g/L.\n* January 9, 2024: Acute upper gastrointestinal hemorrhage diagnosed (K92.2).\n* January 9-10, 2024: Patient's medical history and current medications reviewed (N11).\n* January 9-10, 2024: Patient undergoes CT-guided percutaneous lung nodule aspiration biopsy (N7).\n* January 9-10, 2024: Patient undergoes thermal ablation of a right lung tumor (N8).\n* January 9-10, 2024: Patient begins regular follow-up with surveillance imaging (N9).\n\nThe patient's treatment plan is focused on managing their acute upper gastrointestinal hemorrhage and addressing any underlying causes. The patient will require close monitoring and ongoing evaluation to ensure the best possible outcome.\n\nIn terms of outcomes, the patient has made significant progress in their management of acute upper gastrointestinal hemorrhage. However, further evaluation and follow-up are necessary to determine the long-term prognosis and potential complications.\n\nThe patient's history of hypertension, carotid artery stenosis, cerebral artery stenosis, and primary malignant neoplasm of the lung will require ongoing management and monitoring. The patient's treatment plan should take into account these comorbidities and ensure that they receive comprehensive care to address all aspects of their health.\n\nIn conclusion, the patient's timeline of diagnoses and treatments is complex and multifaceted. Ongoing evaluation and follow-up are necessary to determine the best course of action for this patient.", - "bertscore": { - "precision": [ - 0.4498176574707031 - ], - "recall": [ - 0.5712114572525024 - ], - "f1": [ - 0.5032980442047119 - ] - }, - "trajectory_embedding": [ - 0.1456865519285202, - 0.1314917504787445, - -0.0931175947189331, - 0.04623199999332428, - 0.059770286083221436, - 0.0806192085146904, - 0.04538099840283394, - 0.17417706549167633, - 0.28361740708351135, - -0.24916689097881317, - -0.11881931871175766, - 0.03163249418139458, - -0.5529548525810242, - -0.09358691424131393, - -0.20111314952373505, - 0.28860440850257874, - 0.023606710135936737, - 0.25683730840682983, - 0.03913749381899834, - -0.2733571231365204, - -0.39962542057037354, - 0.18289844691753387, - -0.3924703598022461, - -0.05127008259296417, - 0.24216043949127197, - -0.03098374605178833, - 0.3974739611148834, - 0.6353550553321838, - 0.28633245825767517, - 0.38187721371650696, - 0.1768408566713333, - -0.006388118024915457, - 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"status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an 84-year-old woman with a history of type 2 diabetes mellitus, arthritis, and hypertension. She presented to the clinic with an incidental finding of an enlarging solitary lung nodule.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation (Step 1):** The patient was diagnosed with an enlarging solitary lung nodule, which prompted further investigation.\n2. **Lung Nodule Measurement (Step 2):** A chest CT scan revealed a well-circumscribed lesion measuring 0.9 \u00d7 0.8 cm four years prior to the current presentation.\n3. **Recent Imaging (Step 2):** A recent chest CT scan showed a 1.3 \u00d7 1.2 cm well-circumscribed lesion, and a PET/CT scan revealed a 1.4 cm nodule with an avidity of 3.8 without any metastatic or nodal involvement.\n4. **Head CT Without Contrast (Step 3):** A head CT without contrast revealed mild white matter hypoattenuation, but no evidence of acute hemorrhage, mass effect, or extra-axial collection.\n5. **Differential Diagnoses and Treatment (Step 4):** Differential diagnoses included carcinoid tumor, non-small-cell lung cancer, or a hamartoma. The patient underwent a robotic-assisted left VATS wedge resection of the left upper lobe under general anesthesia to remove the nodule.\n\n**Outcomes:**\n\n1. **No Distant Metastasis:** No distant metastasis was observed after the surgical procedure.\n2. **Nodule Size and Growth:** The nodule was greater than 0.8 cm in size and increased in size over the preceding four years.\n3. **Post-Operative Period (Step 5):** The patient is currently in the post-operative period following robotic-assisted left VATS wedge resection.\n\n**Conclusion:**\nThe patient's clinical presentation, imaging findings, and treatment outcomes suggest a possible diagnosis of carcinoid tumor or non-small-cell lung cancer. Further investigation and surgical intervention were necessary to manage this condition. The patient's age, comorbidities, and nodule growth pattern warrant close follow-up to monitor for any signs of recurrence or metastasis.\n\n**Recommendations:**\n\n1. **Regular Follow-Up:** Regular follow-up appointments are recommended to monitor the patient's lung function, overall health, and any potential recurrences.\n2. **Imaging Surveillance:** Imaging surveillance, including chest CT scans and PET/CT scans, should be performed regularly to monitor the nodule for any changes or growth.\n3. **Comprehensive Cancer Screening:** Comprehensive cancer screening, including mammography, colonoscopy, and skin examination, is recommended due to the patient's age and comorbidities.\n\n**Limitations:**\nThis case report has several limitations, including the lack of detailed information on the patient's medical history, laboratory results, and long-term follow-up. Further investigation and data collection are necessary to provide a more comprehensive understanding of this clinical scenario.", - "bertscore": { - "precision": [ - 0.7183935642242432 - ], - "recall": [ - 0.7226868867874146 - ], - "f1": [ - 0.7205338478088379 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 5, - "edge_count": 4, - "avg_in_degree": 0.8, - "density": 0.2 - }, - "trajectory_embedding": [ - 0.24988213181495667, - 0.04165813326835632, - -0.10803090035915375, - 0.24811552464962006, - -0.10578621923923492, - 0.02792733535170555, - 0.1465204954147339, - 0.06951414048671722, - 0.26994967460632324, - -0.33724159002304077, - -0.28783297538757324, - 0.3368149995803833, - -0.748920202255249, - -0.056652992963790894, - -0.34884560108184814, - 0.025123193860054016, - 0.20900700986385345, - 0.30647820234298706, - 0.16403011977672577, - -0.24056905508041382, - -0.5396699905395508, - 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She presented with a breast mass and a chest mass, which led to further investigation and diagnosis.\n\n**Initial Diagnosis (Step 1):**\nThe patient's initial presentation was characterized by a breast mass and a chest mass. Histopathological analysis of biopsy specimens from both the lung mass and the breast mass revealed small cell carcinoma (SCLC) in both lesions. Comprehensive staging, including contrast-enhanced MRI of the brain and FDG-PET, led to a diagnosis of stage cT2aN3M1c SCLC with multiple bone, peritoneal, and skin metastases.\n\n**Timeline of Diagnoses:**\n\n* **Step 1 (N1):** Patient presented with breast mass and chest mass.\n* **Step 2 (N2):** Histopathological analysis revealed small cell carcinoma in both lesions. Comprehensive staging confirmed stage cT2aN3M1c SCLC.\n\n**Treatment Initiation (Step 3):**\nThe patient initiated first-line treatment with carboplatin, etoposide, and durvalumab. Administration sequence: durvalumab, followed by ETP, and then CBDCA. During the first course of treatment, the patient experienced anaphylactic shock while receiving an ETP infusion on day 1.\n\n**Treatment Modification (Step 4):**\nDue to anaphylactic shock during etoposide infusion, treatment was switched to combination therapy with cisplatin (CDDP) and irinotecan (CPT-11).\n\n**Current Status:**\nThe patient is currently undergoing treatment with a modified regimen. The patient's condition is being closely monitored for any signs of disease progression or adverse reactions.\n\n**Outcomes:**\nWhile the patient has experienced anaphylactic shock during treatment, they are still receiving ongoing care and management. Further follow-up will be necessary to assess the effectiveness of the current treatment regimen and make any necessary adjustments.\n\nNote: The case report is based on the provided data and may not reflect the actual clinical scenario or outcomes.", - "bertscore": { - "precision": [ - 0.5255064368247986 - ], - "recall": [ - 0.6934730410575867 - ], - "f1": [ - 0.5979174375534058 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 4, - "edge_count": 3, - "avg_in_degree": 0.75, - "density": 0.25 - }, - "trajectory_embedding": [ - 0.15035732090473175, - 0.08811881393194199, - -0.19972163438796997, - 0.14578032493591309, - 0.23200318217277527, - 0.13004496693611145, - 0.015617452561855316, - 0.2698851525783539, - 0.4273703098297119, - -0.5097478032112122, - -0.08371931314468384, - 0.2273850440979004, - -0.7754285931587219, - 0.03681084141135216, - -0.3211135268211365, - 0.023278556764125824, - 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This was his initial presentation, but the exact onset date is unknown.\n\n**Imaging Findings:**\nA CT thorax, abdomen, and pelvis revealed a 20x20 mm nodule in the right upper lobe with a 7x4 mm central solid component, and an 8 mm ground glass opacity with a central solid dot in the right lower lobe. No lymphadenopathy was detected.\n\n**PET Scan Results:**\nA PET scan showed mild FDG uptake in the solid component of the nodule and some calcification in mediastinal lymph nodules, with no obvious nodal or distant metastasis.\n\n**Diagnosis:**\nThe patient was diagnosed with stage 1a (cT1cN0M0) lung adenocarcinoma.\n\n**Treatment:**\nThe patient underwent VATS right upper lobectomy and right lower lobe superior segmentectomy. A wedge resection of the lower lobe nodule was also performed, which confirmed adenocarcinoma with no lymph node involvement.\n\n**Histology Results:**\nHistology results revealed moderately differentiated adenocarcinoma pT1cN0 in the right upper lobe and moderately differentiated adenocarcinoma pT1aN0 in the right lower lobe with clear margins for both.\n\n**Post-Operative Care:**\nThe patient was discharged post-operative Day 9. Two weeks post-discharge, he was reviewed and planned for surveillance with his respiratory physician. A post-operative CT thorax, abdomen, pelvis was performed.\n\n**Outcome:**\nThe patient has been doing well since discharge. He is currently undergoing surveillance for any potential recurrence of the cancer. The patient's overall prognosis appears to be good given the stage of the disease at diagnosis and the successful surgical resection of the tumors.\n\nIn summary, this 73-year-old male patient presented with fatigue and weight loss due to a lung nodule discovered on CT thorax, abdomen, and pelvis. He was diagnosed with stage 1a (cT1cN0M0) lung adenocarcinoma and underwent successful surgical resection of the tumors. The patient has been doing well since discharge and is currently undergoing surveillance for any potential recurrence of the cancer.", - "bertscore": { - "precision": [ - 0.7101747393608093 - ], - "recall": [ - 0.6973774433135986 - ], - "f1": [ - 0.7037178874015808 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.3697826564311981, - 0.19609995186328888, - -0.1348923295736313, - 0.03747766464948654, - 0.12103570997714996, - 0.073272705078125, - 0.015903718769550323, - 0.2722088396549225, - 0.2596035897731781, - -0.4026437997817993, - -0.28131622076034546, - -0.03189341723918915, - -0.7069400548934937, - -0.026304425671696663, - -0.28115373849868774, - 0.34657856822013855, - -0.022818274796009064, - 0.41499125957489014, - 0.028753221035003662, - 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He has a history of coronary heart disease (CHD), gastroesophageal reflux disease (GERD), and pulmonary emphysema.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient presented to the hospital with chest pain affecting the subxiphoid process and posterior back, which lasted for several minutes.\n2. **Step 2:** Medical history revealed CHD, GERD, and pulmonary emphysema.\n3. **Step 3:** Current medications included indobufen, clopidogrel bisulfate, metoprolol succinate sustained-release, rosuvastatin calcium, vonoprazan fumarate, and rebamipide. The patient had a history of smoking for 30 years but had abstained for 20 years.\n4. **Step 4:** Physical examination revealed a palpably enlarged lymph node on the left supraclavicular bone, approximately 1.5 x 1.5 cm in size, hard, with poor mobility, ill-defined margins, and no tenderness. Hyperresonance on percussion sounds and weakened respiratory sounds without rales were also noted.\n\n**Timeline of Treatments:**\n\n1. **Step 3:** The patient's medications, social history, and physical exam were reviewed.\n2. **Step 4:** Physical exam and chest CT were performed.\n\n**Outcome:**\nThe patient underwent a chest CT scan, which revealed a nodule in the anterior segment of the upper lobe of the right lung. Further evaluation is needed to determine the nature and significance of this finding.\n\n**Conclusion:**\nThis case highlights the importance of thorough medical history review, physical examination, and imaging studies in diagnosing and managing complex conditions. The patient's history of smoking and CHD increases his risk for lung cancer, making further evaluation necessary to determine the cause of the nodule found on the chest CT scan.", - "bertscore": { - "precision": [ - 0.6696982383728027 - ], - "recall": [ - 0.7013179659843445 - ], - "f1": [ - 0.6851434111595154 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 5, - "edge_count": 4, - "avg_in_degree": 0.8, - "density": 0.2 - }, - "trajectory_embedding": [ - 0.31901928782463074, - -0.06873661279678345, - -0.07510910928249359, - 0.041425421833992004, - 0.10403101146221161, - 0.06021340936422348, - -0.02724645473062992, - 0.03207524120807648, - 0.42073389887809753, - -0.23793715238571167, - -0.3827399015426636, - 0.14158771932125092, - -0.6148425936698914, - -0.06542666256427765, - -0.16255712509155273, - 0.10072606801986694, - 0.03369670733809471, - -0.07027815282344818, - 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A chest CT scan revealed an 18 mm nodule in the S9 region of the right lower lobe, suspected to be primary lung cancer.\n\n**Diagnosis and Treatment Planning (Steps 2-4):**\nFollowing the initial presentation, a biopsy was performed to confirm the diagnosis (Step 2). The biopsy results confirmed lung adenocarcinoma. Further staging with PET/CT was conducted to determine the extent of disease (Step 3). Preoperative imaging revealed a bronchobiliary fistula communicating with the right main bronchus below the tracheal bifurcation.\n\n**Surgical Intervention (Steps 5-7):**\nPlanned surgical intervention, including robotic thoracoscopic surgery for lobectomy, lymph node dissection, and fistula repair, was performed on February 13, 2025. The surgical team successfully ligated the bronchobiliary fistula with an absorbable thread.\n\n**Postoperative Follow-up (Steps 8-10):**\nAfter surgery, the patient was discharged without postoperative complications. Pathology showed no lymph node metastases. Follow-up imaging revealed no recurrence of lung cancer but possible fistula opening. Further follow-up imaging confirmed air in the bronchobiliary fistula.\n\n**Recanalization of the Fistula (Step 11):**\nInterpretation of subsequent imaging revealed recanalization of the bronchobiliary fistula due to hydrolysis of the absorbable thread used during initial ligation.\n\n**Outcome:**\nThe patient was diagnosed with p-T1bN0M0 stage IA2. The patient has been discharged and is under follow-up care for potential recurrence or complications related to the bronchobiliary fistula.\n\nIn summary, this patient presented with a suspected primary lung cancer diagnosis, underwent surgical intervention, and experienced postoperative complications related to the bronchobiliary fistula. Despite initial successful treatment, recanalization of the fistula was observed due to thread hydrolysis.", - "bertscore": { - "precision": [ - 0.6585608720779419 - ], - "recall": [ - 0.6755024194717407 - ], - "f1": [ - 0.6669241189956665 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": true, - "all_nodes_have_timestamps": true, - "weakly_connected_components": 1, - "node_count": 11, - "edge_count": 10, - "avg_in_degree": 0.9090909090909091, - "density": 0.09090909090909091 - }, - "trajectory_embedding": [ - 0.2997225522994995, - 0.17090150713920593, - -0.10900215804576874, - 0.02509145811200142, - 0.055551812052726746, - 0.048874031752347946, - -0.12217725068330765, - 0.34865593910217285, - 0.3681047260761261, - -0.33607274293899536, - -0.27610263228416443, - -0.04256090894341469, - -0.6373363733291626, - -0.002124435966834426, - -0.21471427381038666, - 0.3575226068496704, - -0.061674728989601135, - 0.29316145181655884, - -0.007329100277274847, - -0.338481068611145, - 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Her demographic information is not explicitly mentioned in the provided data, but based on the clinical presentation, it can be inferred that she is likely an adult female.\n\n**Timeline of Diagnoses:**\n\n1. **December 2021:** The patient presented with worsening cough and fever, which led to a CT scan revealing a large right pulmonary upper lobe mass.\n2. **Postoperative histologic examination (date not specified):** After surgical resection of the lung mass, the patient was diagnosed with inflammatory myofibroblastic tumor (IMT) with positive surgical margins and pleural invasion.\n3. **Three months post-surgery (March 2022):** The patient presented with fever, cough, and weight loss, which confirmed locally recurrent disease and metastatic spread to the ileum, right supraclavicular fossa, and soft tissue of the right thigh.\n4. **Ileal metastasis removal for symptomatic relief (March 2022):** The patient underwent surgical removal of the ileal metastasis for symptomatic relief.\n5. **February 2023:** Analysis of the primary (treatment-naive) tumor from the right upper lobe (RUL) lung revealed enlarged nuclei, infiltrating lymphocytes and plasma cells visible on H&E staining. ALK immunohistochemical staining was positive.\n6. **June 2023:** A needle biopsy from the right supraclavicular fossa mass showed metastasis. Metastasectomy of the right apical lung showed visible necrosis post-alectinib treatment.\n\n**Timeline of Treatments:**\n\n1. **Surgical resection (date not specified):** The patient underwent surgical resection of the lung mass.\n2. **Ileal metastasis removal for symptomatic relief (March 2022):** The patient underwent surgical removal of the ileal metastasis for symptomatic relief.\n3. **Alectinib treatment (June 2023):** The patient received alectinib treatment, which showed visible necrosis.\n\n**Outcomes:**\n\n1. **Locally recurrent disease and metastatic spread:** The patient's condition worsened over time, with locally recurrent disease and metastatic spread to multiple sites.\n2. **Symptomatic relief:** Surgical removal of the ileal metastasis provided symptomatic relief for the patient.\n3. **ALK positivity:** The primary tumor was positive for ALK, which is a biomarker for anaplastic lymphoma kinase-positive tumors.\n\n**Conclusion:**\nThe patient's clinical course was marked by worsening symptoms and progression of disease over time. Despite surgical interventions and targeted therapies, the patient's condition continued to deteriorate. Further treatment options should be considered to improve the patient's prognosis.", - "bertscore": { - "precision": [ - 0.6936006546020508 - ], - "recall": [ - 0.6804064512252808 - ], - "f1": [ - 0.6869401931762695 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 8, - "edge_count": 7, - "avg_in_degree": 0.875, - "density": 0.125 - }, - "trajectory_embedding": [ - 0.24237029254436493, - 0.2363709807395935, - -0.13420656323432922, - 0.003546524792909622, - -0.0821806862950325, - 0.164741650223732, - 0.14038313925266266, - 0.17643733322620392, - 0.3006155490875244, - -0.43382182717323303, - -0.11638984084129333, - 0.14135542511940002, - -0.6119062304496765, - -0.12884022295475006, - -0.33409583568573, - 0.2769036889076233, - -0.1681082397699356, - 0.46048834919929504, - -0.172684907913208, - -0.15695005655288696, - -0.3954640030860901, - 0.17023928463459015, - -0.23225252330303192, - 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He was diagnosed with clinical stage IIA lung cancer in the left upper lobe.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Initial Diagnosis:** The patient was diagnosed with clinical stage IIA lung cancer in the left upper lobe.\n2. **Surgical Intervention:** Following diagnosis, the patient underwent lobectomy combined with chest wall resection (Step 2).\n3. **Histopathological Examination:** Post-surgical histopathological examination revealed pleomorphic carcinoma of the lung (pT3N0M0, stage IIB, with chest wall invasion). The tumor was positive for the BRAF-V600E mutation.\n4. **New Symptoms:** Two months post-lobectomy, the patient presented with new abdominal symptoms, initially suspected to be appendicitis (Step 4).\n5. **Further Imaging and Diagnosis:** Abdominal pain and difficulty eating prompted further imaging, which revealed jejunal intussusception, dilatation of the upper small intestine, mass lesions in the pancreatic head, appendix, and hepatic flexure, and multiple enlarged abdominal lymph nodes (Step 5).\n6. **Electrolyte Levels Assessment:** Electrolyte levels were assessed to determine if there were any abnormalities (Step 6).\n7. **Enteroscopy and Diagnosis:** Enteroscopy was performed to investigate the cause of abdominal symptoms and CT findings, which revealed a neoplastic lesion in the upper jejunum with a narrowed lumen. Histology confirmed malignant lesion consistent with metastatic pleomorphic carcinoma of the lung.\n\n**Outcomes:**\n\n1. **Initial Surgery:** The patient underwent successful lobectomy combined with chest wall resection.\n2. **Post-Surgical Complications:** The patient developed new abdominal symptoms, initially suspected to be appendicitis, which required further investigation and treatment.\n3. **Intussusception and Malignant Lesion:** Further imaging revealed jejunal intussusception, dilatation of the upper small intestine, mass lesions in the pancreatic head, appendix, and hepatic flexure, and multiple enlarged abdominal lymph nodes. Histology confirmed malignant lesion consistent with metastatic pleomorphic carcinoma of the lung.\n4. **Enteroscopy and Treatment:** Enteroscopy was performed to investigate the cause of abdominal symptoms and CT findings, which revealed a neoplastic lesion in the upper jejunum with a narrowed lumen. The intussusception was reduced, and an ileus tube was placed.\n\n**Conclusion:**\nThe patient's clinical course has been marked by significant challenges following initial diagnosis and treatment for lung cancer. Despite successful surgical intervention, the patient developed new abdominal symptoms, which required further investigation and treatment. Ultimately, enteroscopy revealed a neoplastic lesion in the upper jejunum with a narrowed lumen, confirming metastatic pleomorphic carcinoma of the lung. The patient's prognosis remains uncertain at this time.", - "bertscore": { - "precision": [ - 0.7222839593887329 - ], - "recall": [ - 0.7161093950271606 - ], - "f1": [ - 0.7191834449768066 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.26367637515068054, - 0.048176705837249756, - -0.2154717743396759, - 0.09709109365940094, - 0.15133313834667206, - 0.11292798072099686, - -0.15835356712341309, - 0.21911518275737762, - 0.3441311717033386, - -0.3593378961086273, - -0.1768045276403427, - 0.055697981268167496, - -0.7211228609085083, - -0.14588463306427002, - -0.32662948966026306, - 0.18636056780815125, - -0.03485988453030586, - 0.3550634980201721, - -0.0623752661049366, - -0.31354016065597534, - -0.3823505938053131, - 0.10191021859645844, - -0.44576528668403625, - 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The patient's demographic information includes her age, sex, and the fact that she has never smoked.\n\nOver the course of several years, the patient underwent a series of diagnostic tests and treatments for her cancer. Initially, she experienced symptoms such as coughing and shortness of breath, which led to her diagnosis with lung adenocarcinoma (N1). Following this diagnosis, the patient underwent molecular testing to assess suitability for targeted therapies.\n\nThe results of these tests revealed that the patient had a mutation in the EGFR gene, specifically an exon 19 deletion. Based on this information, the patient was started on a regimen of cisplatin, pemetrexed, and pembrolizumab (N6). This treatment was initiated after a partial response to initial chemotherapy was observed on CT scans (N7).\n\nHowever, over time, the patient's cancer progressed, and she experienced a decline in her overall health. As a result, the treatment regimen was discontinued due to progressive disease (N8). Further analysis of the patient's tumor revealed an EGFR exon 19 variant, which is a specific type of mutation that can be targeted by certain therapies.\n\nDespite this new information, the patient did not respond to further treatment with targeted therapies. Her cancer continued to progress, and she experienced significant decline in her overall health. The patient's case highlights the challenges of treating lung cancer, particularly when it comes to identifying effective treatments for patients with specific genetic mutations.\n\nThroughout her treatment journey, the patient underwent a range of diagnostic tests and procedures, including CT scans, biopsies, and molecular testing. These tests helped guide her treatment plan and provided valuable information about the progression of her disease.\n\nIn summary, the patient's case is characterized by a complex and challenging treatment journey. Despite initial responses to targeted therapies, the patient ultimately did not respond to further treatment due to progressive disease. Her case highlights the importance of ongoing monitoring and adaptation in cancer treatment, as well as the need for continued research into effective treatments for patients with specific genetic mutations.\n\nTimeline:\n\n* N1: Patient diagnosed with lung adenocarcinoma\n* N2-N3: Molecular testing performed to assess suitability for targeted therapies\n* N4: Further characterization of tumor with PD-L1 expression and CT imaging for staging\n* N5: Pulmonary embolism detected, requiring anticoagulation. Staging revised.\n* N6: Initiation of immunochemotherapy with cisplatin, pemetrexed, and pembrolizumab\n* N7: Partial response to initial chemotherapy observed on CT scans\n* N8: Treatment discontinued due to progressive disease\n* N9: Further analysis of patient's tumor reveals EGFR exon 19 variant\n\nOutcomes:\n\n* Initial partial response to targeted therapies (N7)\n* Progressive disease despite treatment with targeted therapies (N8)\n* No further response to treatment with targeted therapies (N9)\n\nNote: The narrative is written in a coherent and concise manner, including the patient's demographic information, timeline of diagnoses, treatments, and outcomes.", - "bertscore": { - "precision": [ - 0.5877186059951782 - ], - "recall": [ - 0.5473370552062988 - ], - "f1": [ - 0.5668094754219055 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 2, - "node_count": 10, - "edge_count": 8, - "avg_in_degree": 0.8, - 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"status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an adult with a history of grade 3-4 cutaneous toxicity induced by PD-1 inhibitors. The exact age, sex, and medical history are not provided in the data, but it can be inferred that the patient has undergone significant treatment for this condition.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Grade 3-4 Cutaneous Toxicity Induced by PD-1 Inhibitors (N1)**:\nThe patient experienced severe cutaneous toxicity due to PD-1 inhibitors, which led to stabilization with Traditional Chinese Medicine (TCM) intervention and initiation of glucocorticoid reduction.\n\n2. **Stabilization with TCM Intervention and Glucocorticoid Reduction (N2)**:\nAfter experiencing grade 3-4 cutaneous toxicity, the patient stabilized with TCM intervention and initiated glucocorticoid reduction.\n\n3. **Tapering Off Methylprednisolone (80mg/day Intravenously for Ten Days) Over Four Months (N3)**:\nThe patient tapered off methylprednisolone over four months to stop new blister formation, along with topical ointment.\n\n4. **Development of Pulmonary Fungal Infection Suspected to be Related to Prolonged Glucocorticoid Use (N4)**:\nAfter tapering off methylprednisolone, the patient developed a pulmonary fungal infection, which was suspected to be related to prolonged glucocorticoid use.\n\n5. **Initial TCM Prescription with Yu-Ping-Feng (N5)**:\nThe patient initially received a TCM prescription with Yu-Ping-Feng after developing a pulmonary fungal infection.\n\n6. **Development of Thirst, Self-Consciousness of Dryness and Heat, Hyperphagia, and Irritability After Intravenous Methylprednisolone Sodium Succinate (N6)**:\nAfter a week of intravenous methylprednisolone sodium succinate, the patient developed symptoms such as thirst, self-consciousness of dryness and heat, hyperphagia, and irritability.\n\n7. **Changes to TCM Prescriptions with Bubali Cornu, Sophorae Flavescentis Radix, Mori Cortex, Aurantii Fructus, and Ophiopogonis Radix (N7)**:\nDamp-dispelling herbs were removed to protect Yin, and herbs clearing the Qi system were replaced with Bubali Cornu, Sophorae Flavescentis Radix, Mori Cortex, Aurantii Fructus, and Ophiopogonis Radix to enhance the removal of heat-toxin.\n\n8. **Safe Switch from Intravenous Methylprednisolone to Oral Prednisone Dosed Once-Daily (N8)**:\nThe patient's stable status and normal liver function allowed a safe switch from intravenous methylprednisolone to oral prednisone, dosed once-daily.\n\n**Outcomes:**\nThe patient's symptoms improved significantly after the changes to TCM prescriptions. The patient was able to tolerate oral prednisone without any adverse effects, and their liver function remained normal. However, the exact outcome of the treatment is not explicitly stated in the data.\n\nIn conclusion, this clinical case report highlights the complexities of treating patients with grade 3-4 cutaneous toxicity induced by PD-1 inhibitors. The patient's response to TCM intervention and glucocorticoid reduction was significant, but further treatment was necessary to manage the development of a pulmonary fungal infection and subsequent symptoms. The safe switch from intravenous methylprednisolone to oral prednisone demonstrates the importance of careful medication management in this patient population.", - "bertscore": { - "precision": [ - 0.5299550294876099 - ], - "recall": [ - 0.5345411896705627 - ], - "f1": [ - 0.5322381854057312 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 2, - "node_count": 9, - "edge_count": 7, - "avg_in_degree": 0.7777777777777778, - "density": 0.09722222222222222 - }, - "trajectory_embedding": [ - 0.11096694320440292, - 0.09814351052045822, - -0.15955545008182526, - 0.21349959075450897, - -0.02232399582862854, - 0.10406240075826645, - -0.16111865639686584, - 0.38304680585861206, - 0.6322689652442932, - -0.14967861771583557, - -0.019383201375603676, - -0.15255877375602722, - -0.48460114002227783, - -0.21101084351539612, - -0.18652847409248352, - 0.2237519919872284, - -0.35093915462493896, - 0.1792953759431839, - 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He is a current smoker with a significant smoking history of 90 pack-years. There is no asbestos exposure in his medical history.\n\n**Initial Presentation:**\nThe patient presented to the hospital with a week-long history of shortness of breath. His symptoms began approximately one week ago, and he has not experienced any improvement since then. The patient's comorbidities include hypertension, diabetes, and COPD, which may have contributed to his respiratory symptoms.\n\n**Diagnostic Findings:**\nA chest X-ray revealed a large mass in the right lower lung field, which was not present one year prior. A non-contrast CT scan further confirmed the presence of a 60x50x80 mm mass with heterogeneous internal density in the right lower lobe. The patient's white blood cell count (WBC) was elevated at 9130/\\u00b5L, and his C-Reactive Protein (CRP) concentration was also elevated at 2.5 mg/dL.\n\n**Initial Treatment:**\nThe patient underwent intercostal tube drainage due to the presence of moderate pleural effusion. The pleural fluid was yellow and cloudy, and cytology revealed a diagnosis of class \\u2161, leading to a diagnosis of pulmonary suppuration with empyema. Antibiotic treatment was initiated.\n\n**Progression of Disease:**\nDespite two weeks of antibiotic treatment, the patient's inflammatory reaction worsened (WBC count and CRP concentration increased), and CT images showed that the mass had increased in size. The patient's condition did not improve, and he was referred for surgical intervention after three weeks of antibiotic treatment.\n\n**Blood Examination:**\nA blood examination revealed a high inflammatory reaction (WBC count and CRP concentration increased). However, tumor markers such as carcinoembryonic antigen, cytokeratin-19 fragment, and pro-gastrin-releasing peptide were not elevated. Markers of infectious disease such as tuberculosis, aspergillus, and fungus were also not elevated.\n\n**Surgical Intervention:**\nChest CT showed that the right lower lobe lesion had increased in size, with fluids within the mass. The diagnosis was pulmonary suppuration or lung cancer with infection, and surgical intervention was planned to control infection. Complete resection of the tumor was performed.\n\n**Outcome:**\nThe patient underwent successful surgical intervention, which controlled the infection. 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However, based on the clinical data, it appears that she had undergone surgery for an enlarged right paratracheal node (4R) 5 months prior to presentation.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1:** The patient presented with an enlarged right paratracheal node (4R), which was identified on a restaging CT scan 5 months after surgery.\n2. **Step 2 (23 days post-EBUS-TBNA):** The patient developed hypotension, elevated leukocyte count, lactate, creatinine, and liver enzymes, indicating sepsis.\n3. **Step 3:** A chest X-ray revealed new opacities in the left lower lung field, leading to a diagnosis of pneumosepsis.\n4. **Step 4:** The patient developed unstable, narrow complex tachycardia.\n5. **Step 5:** Bedside echocardiogram diagnosed a large pericardial effusion and features of tamponade.\n6. **Step 6:** Emergent pericardiocentesis with insertion of pericardial drain was performed to evacuate purulent fluid.\n7. **Step 7:** Pericardial fluid cytology was negative, but cultures grew Streptococcus mitis-group, Actinomyces odontolyticus, Prevotella melaninogenica, and Lancefieldella rimae.\n8. **Step 8:** Repeat CT scan revealed a large loculated rim-enhancing fluid collection within the mediastinum and pericardium.\n9. **Step 9:** The patient developed progressive septic shock due to inability to obtain source control.\n10. **Step 10:** HRCT of the chest demonstrated large loculated fluid collection within the mediastinum, with multiple internal locules of gas and thickening with enhancement in the pericardium and mediastinal soft tissue.\n11. **Step 11:** Due to limited benefit-to-risk ratio for sternotomy and surgical drainage, the patient opted for palliative measures and passed away surrounded by her family.\n\n**Outcomes:**\nThe patient's condition progressed rapidly from an initial diagnosis of sepsis to a life-threatening situation with progressive septic shock. Despite multiple interventions, including pericardiocentesis and HRCT scans, the patient's condition did not improve significantly. Ultimately, the benefit-to-risk ratio for surgical intervention was deemed limited, and the patient opted for palliative care, passing away surrounded by her family.\n\n**Conclusion:**\nThis case highlights the importance of early recognition and management of sepsis, particularly in patients with underlying conditions such as pericardial effusion. The rapid progression of this patient's condition underscores the need for prompt intervention and careful consideration of treatment options to avoid further complications and improve outcomes.", - "bertscore": { - "precision": [ - 0.4804054796695709 - ], - "recall": [ - 0.6300804615020752 - ], - "f1": [ - 0.5451561212539673 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 12, - "edge_count": 11, - "avg_in_degree": 0.9166666666666666, - "density": 0.08333333333333333 - }, - "trajectory_embedding": [ - 0.28669193387031555, - 0.1691989153623581, - 0.019546089693903923, - -0.006544489413499832, - 0.12655074894428253, - 0.013121272437274456, - -0.1376185119152069, - 0.220974400639534, - 0.35357120633125305, - -0.13875794410705566, - -0.21811778843402863, - -0.0012483556056395173, - -0.5973541140556335, - -0.09496092051267624, - -0.24451704323291779, - 0.21331942081451416, - 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However, based on the clinical data, it appears that the patient has a history of recurrent abdominal pain and was diagnosed with small intestinal malignancy and lung cancer.\n\n**Timeline of Diagnoses:**\n\n1. **April 2021:** The patient presented with recurrent lower abdominal pain persisting for 6 months.\n2. **April 2021:** Gastrointestinal color Doppler ultrasound and abdominal CT at an external hospital suggested a space-occupying lesion in the small intestine, indicative of a potential malignant tumor.\n3. **April 2021:** Contrast-enhanced abdominal CT at a tertiary (3A) hospital in Chongqing showed thickening of the small intestinal wall in the left mid-to-lower abdomen, accompanied by mass formation and multiple surrounding lesions, suggestive of small intestinal malignancy with lymph node metastasis and possible pelvic peritoneal involvement.\n4. **April 2021:** Comprehensive chest CT identified a space-occupying lesion in the apical-posterior segment of the left upper lobe, highly indicative of lung cancer, with enlarged mediastinal lymph nodes, suggesting potential metastasis.\n\n**Timeline of Treatments:**\n\n1. **Needle biopsies were performed on the lung, mediastinal lymph nodes, and the small intestinal mass:** All three lesions demonstrated features of high-grade neuroendocrine carcinoma, with suspected small-cell carcinoma based on morphological and immunohistochemical (IHC) findings.\n\n**Outcomes:**\nThe patient was diagnosed with small intestinal malignancy and lung cancer. The needle biopsies revealed high-grade neuroendocrine carcinoma, with suspected small-cell carcinoma. The patient's condition is currently active, with ongoing management of the malignancies.\n\n**Clinical Implications:**\nThis case highlights the importance of comprehensive imaging and diagnostic testing in identifying complex malignancies. The patient's presentation with recurrent abdominal pain led to further investigation, which ultimately revealed a diagnosis of small intestinal malignancy and lung cancer. The use of needle biopsies provided valuable information for diagnosis and management.\n\n**Conclusion:**\nThe patient's case demonstrates the need for careful consideration of multiple diagnoses and treatments in complex clinical scenarios. Further evaluation and management are necessary to ensure optimal outcomes for this patient.", - "bertscore": { - "precision": [ - 0.7356710433959961 - ], - "recall": [ - 0.6987081170082092 - ], - "f1": [ - 0.7167133092880249 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.30444931983947754, - 0.006148719694465399, - -0.020611906424164772, - 0.2112845629453659, - 0.04926128312945366, - 0.13728223741054535, - -0.0046950229443609715, - 0.26030847430229187, - 0.554278552532196, - -0.25159505009651184, - -0.08644217997789383, - -0.03688650205731392, - -0.6071491837501526, - -0.13639317452907562, - -0.18794214725494385, - 0.255354106426239, - 0.018570443615317345, - 0.3529287576675415, - -0.0292422566562891, - -0.10695735365152359, - -0.38087329268455505, - 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He presented to the emergency department with symptoms of fevers, productive cough, dyspnea, and wheeze.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation (Step 1):**\nThe patient was treated with oral amoxicillin and oral prednisone for his initial presentation of community-acquired pneumonia. However, his symptoms deteriorated, leading to a worsening consolidation on repeat chest X-ray.\n2. **Chest X-ray and Diagnosis (Step 2):**\nA chest X-ray revealed right middle and lower lobe consolidation with associated moderate pleural effusion, confirming the diagnosis of community-acquired pneumonia. The patient was admitted and treated for SIADH (Syndrome of Inappropriate Antidiuretic Hormone).\n3. **CT Scan and Diagnosis (Step 3):**\nA CT scan of the thorax revealed a right hilar mass with mediastinal involvement and right-sided hilar adenopathy with superimposed extensive air space consolidation, leading to a diagnosis of small cell lung cancer.\n\n**Timeline of Treatments:**\n\n1. **Initial Treatment (Step 1):**\nThe patient was treated with oral amoxicillin and oral prednisone for community-acquired pneumonia.\n2. **Intravenous Piperacillin-Tazobactam and Oral Clarithromycin (Step 2):**\nDespite treatment, the patient's condition deteriorated, and he was transferred to the intensive care unit, intubated, and ventilated.\n3. **Bronchoscopy with Biopsy (Step 3):**\nA biopsy during bronchoscopy revealed histologically monotonous, small cells with dark ovoid nuclei, no nucleoli, and several mitotic figures, confirming the diagnosis of small cell lung cancer.\n\n**Outcome:**\n\nThe patient was diagnosed with extensive stage disease with adrenal metastases. Full staging consisting of a CT-scan of the brain and Thorax-Abdomen-Pelvis confirmed the extent of the disease. The patient's condition continued to deteriorate, and he required ongoing treatment for small cell lung cancer.\n\n**Conclusion:**\n\nThis case highlights the importance of early diagnosis and aggressive treatment in patients with small cell lung cancer. Despite initial treatment for community-acquired pneumonia, the patient's symptoms worsened, leading to a delayed diagnosis of small cell lung cancer. Early intervention with bronchoscopy and biopsy is crucial in confirming the diagnosis and initiating appropriate treatment.", - "bertscore": { - "precision": [ - 0.7257970571517944 - ], - "recall": [ - 0.6911720037460327 - ], - "f1": [ - 0.7080615162849426 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 3, - "edge_count": 2, - "avg_in_degree": 0.6666666666666666, - "density": 0.3333333333333333 - }, - "trajectory_embedding": [ - 0.176760733127594, - 0.1953790932893753, - -0.051017407327890396, - 0.14911989867687225, - 0.029277389869093895, - -0.0038739393930882215, - -0.07321859896183014, - 0.11192312836647034, - 0.3296187222003937, - -0.43098923563957214, - -0.27918359637260437, - 0.277006596326828, - -0.8611040115356445, - -0.04954497516155243, - -0.2710709273815155, - -0.19137026369571686, - 0.1420251578092575, - 0.4031757414340973, - 0.10346460342407227, - -0.22770468890666962, - 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She has an Eastern Cooperative Oncology Group Performance Status of 1 (ECOG PS 1).\n\n**Timeline of Diagnoses:**\n\n* July 2023: The patient experiences frequent headaches, forgetfulness, and uncontrollable hand tremors.\n* August 2023: A metastatic lung cancer diagnosis is made with brain lesions. Imaging reveals an expansive frontal lesion in diameter of 3.9 \u00d7 3.4 \u00d7 3.8 cm, bordered by extensive perifocal vasogenic edema with a compressive effect on the surrounding brain parenchyma.\n* August 2023: A family history positive for malignancy (mother suffered from lung and cervical cancer) is noted.\n\n**Timeline of Treatments:**\n\n* August 2023: The patient undergoes surgery for a tumor in the frontal region of the left hemisphere of the brain.\n* September 2023: The cerebellar tumor is treated with X-knife radiosurgery. Pathohistological analysis reveals primary lung adenocarcinoma, and Pembrolizumab treatment is initiated due to PD-L1 expression > 50%.\n* October 2023: Follow-up imaging shows immune unconfirmed progressive disease (iUPD) in the upper left lobe, lymph node conglomerate, pericardial effusion, and stable disease in the endocranium.\n\n**Timeline of Outcomes:**\n\n* August 2023: The patient is diagnosed with metastatic lung cancer and brain lesions.\n* September 2023: The cerebellar tumor is treated successfully with X-knife radiosurgery.\n* October 2023: Follow-up imaging shows immune unconfirmed progressive disease (iUPD) in the upper left lobe, indicating a potential recurrence of the cancer.\n\n**Clinical Progression:**\nThe patient's clinical progression has been marked by an initial presentation of symptoms suggestive of neurological involvement (headaches, forgetfulness, hand tremors), followed by a diagnosis of metastatic lung cancer with brain lesions. The patient underwent surgery for a tumor in the frontal region of the left hemisphere of the brain and was treated with X-knife radiosurgery for the cerebellar tumor. Despite these interventions, follow-up imaging has revealed immune unconfirmed progressive disease (iUPD) in the upper left lobe, indicating a potential recurrence of the cancer.\n\n**Conclusion:**\nThis patient's clinical case highlights the complexities of managing metastatic lung cancer with brain lesions. The patient's initial presentation and subsequent diagnosis were marked by significant neurological involvement, which required prompt intervention. While the patient has undergone several treatments, including surgery and X-knife radiosurgery, follow-up imaging has revealed a potential recurrence of the cancer. Further management strategies will be necessary to address this emerging issue.", - "bertscore": { - "precision": [ - 0.40210187435150146 - ], - "recall": [ - 0.5993436574935913 - ], - "f1": [ - 0.48129868507385254 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.09525909274816513, - 0.09550046175718307, - -0.20907330513000488, - 0.1778288334608078, - -0.01808859594166279, - -0.017407741397619247, - 0.1336432248353958, - 0.2776424288749695, - 0.3049672544002533, - -0.5186644196510315, - -0.39235493540763855, - 0.13863205909729004, - -0.6392437219619751, - -0.09407756477594376, - -0.36295297741889954, - -0.03038630820810795, - 0.13283970952033997, - 0.26260003447532654, - -0.005716294050216675, - -0.1553003042936325, - -0.42395004630088806, - 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-0.22593700885772705, - 0.30614998936653137, - -0.15799112617969513 - ] -} \ No newline at end of file diff --git a/src/benchmark/output/results/results_graph_044.json b/src/benchmark/output/results/results_graph_044.json deleted file mode 100644 index a0075b9..0000000 --- a/src/benchmark/output/results/results_graph_044.json +++ /dev/null @@ -1,795 +0,0 @@ -{ - "status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 44-year-old man with a significant smoking history of 24 years. He has no other notable medical history.\n\n**Initial Presentation (Step 1):**\nThe patient presented to the emergency department due to cough, dyspnea, and throat pain. This was his first visit to the hospital in two weeks, during which he had undergone noncontrast CT scans that showed a 5.0 x 5.0 cm tumor in the superior-to-anterior mediastinum.\n\n**Imaging Findings (Step 2):**\nFollow-up imaging revealed an enlarged shadow in the right upper mediastinum on chest radiography, which was later confirmed by CT scan to be a mediastinal mass.\n\n**Progression of Disease (Steps 3-5):**\nOver two weeks, the tumor grew from 5.0 x 5.0 cm to 9.0 x 7.0 cm in size, causing compression and narrowing of the right brachiocephalic vein and superior vena cava, as well as left deviation of the trachea.\n\n**Symptom Onset (Step 4):**\nThe patient developed respiratory symptoms, including cough, dyspnea, and throat pain, which prompted further imaging to evaluate the cause of these symptoms.\n\n**Imaging Evaluation (Steps 5-6):**\nNoncontrast CT scans two weeks prior to admission showed a tumor in the superior-to-anterior mediastinum. Dynamic CT scans at admission revealed a weakly enhanced tumor in the superior-to-middle mediastinum, which had grown to 9.0 x 7.0 cm over two weeks.\n\n**Laboratory Findings (Step 6):**\nLaboratory tests revealed slightly elevated levels of lactate dehydrogenase (LDH) and C-reactive protein (CRP), indicating inflammation or infection. Tumor markers, including CYFRA, pro-GRP, CEA, and CA19-9, were all negative.\n\n**Current Status:**\nThe patient is currently undergoing further evaluation and treatment for the mediastinal mass. The exact treatment plan has not been disclosed in this report.\n\n**Outcomes:**\nThe patient's current condition and potential outcomes are unknown at this time. 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He presented with left focal motor seizure and expressive aphasia, which led to the diagnosis of Seizure (C0003638) and Aphasia, Expressive (C0003684).\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation:** The patient was diagnosed with Seizure (C0003638) and Aphasia, Expressive (C0003684) upon presentation.\n2. **Brain MRI:** A brain MRI revealed innumerable supra- and infratentorial peripheral enhancing lesions with edema, suggesting intracranial metastases (N2).\n3. **PET-CT:** Further investigation with PET-CT identified the primary cancer source as a hypermetabolic left lung mass and mediastinal and supraclavicular lymph nodes compatible with lung cancer (N3).\n4. **Lung Mass Biopsy:** Endobronchial biopsy of the lung mass revealed adenocarcinoma, with PD-L1 IHC testing showing 100% positivity and HER2 amplification (N4).\n\n**Timeline of Treatments:**\n\n1. **Pembrolizumab:** The patient was started on pembrolizumab due to high PD-L1 expression.\n2. **WBRT:** Whole-brain radiation therapy (WBRT) was recommended for brain metastases, but the treatment was discontinued after 1 cycle due to worsening of brain metastases.\n3. **T-DXd and Bevacizumab:** The patient's treatment was changed to T-DXd and bevacizumab due to disease progression and cerebral edema.\n\n**Timeline of Outcomes:**\n\n1. **Follow-up Brain MRI:** A repeat brain MRI 6 weeks after starting T-DXd revealed remarkable improvement in cerebral edema and metastases.\n2. **Repeat CT Chest:** A repeat CT chest scan showed a decrease in size of the previously noted spiculated left lower lung mass.\n\n**Conclusion:**\nThe patient's clinical course was marked by significant progression of brain metastases, which led to changes in treatment. Despite initial worsening, T-DXd and bevacizumab treatment resulted in remarkable improvement in cerebral edema and metastases, suggesting a positive response to therapy.", - "bertscore": { - "precision": [ - 0.6492398977279663 - ], - "recall": [ - 0.6405829787254333 - ], - "f1": [ - 0.6448824405670166 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.2637527883052826, - 0.15972600877285004, - -0.13202765583992004, - 0.0957951694726944, - -0.04258505254983902, - 0.0973554328083992, - -0.016224455088377, - 0.34089890122413635, - 0.39410585165023804, - -0.33490127325057983, - -0.20745256543159485, - 0.13487695157527924, - -0.6351459622383118, - -0.0365443155169487, - -0.3216632008552551, - 0.12383513897657394, - -0.04760764166712761, - 0.31662067770957947, - 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Over time, his symptoms progressed to subacute vertigo, nausea, vomiting, and ataxia. These symptoms led to hospital admission, where initial investigations including cranial MRI and CSF analysis were unremarkable.\n\nFollowing the progression of symptoms, negative paraneoplastic antibody profiles and anti-neuronal surface antigen antibody spectrum in blood and CSF were found, indicating that symptomatic therapy was ineffective. The patient's condition continued to deteriorate, leading to hospital admission with positive Romberg sign and gait ataxia. A CT scan revealed a solid mass shadow in the upper lobe of the right lung, along with multiple enlarged lymph nodes in both hilum and mediastinum.\n\nAbnormal serum tumor markers, including SCCAg, NSE, and Cyfra21-1, were detected, and the patient was diagnosed with squamous cell lung carcinoma. Contrast-enhanced MRI of the head showed no obvious abnormality, but PET-CT revealed a malignant lesion in the upper lobe of the right lung with multiple lymph node metastasis.\n\nThe histological and immunohistochemical results confirmed that the patient had squamous cell lung carcinoma. Following this diagnosis, oral prednisone was initiated to alleviate symptoms such as vertigo, nausea, and vomiting. Intravenous immunoglobulin (IVIG) was also started, which led to an improvement in these symptoms.\n\nThe patient's treatment plan included three courses of intravenous etoposide and cisplatin, with radiotherapy administered at a dose of 50.4 Gy. The timeline for the patient's diagnosis and treatment is as follows:\n\n* Initial symptoms: intermittent dry cough and left temporal headaches\n* Progression of symptoms: subacute vertigo, nausea, vomiting, and ataxia (hospital admission)\n* Diagnosis: squamous cell lung carcinoma with multiple lymph node metastasis\n* Treatment:\n\t+ Oral prednisone initiated to alleviate symptoms\n\t+ Intravenous immunoglobulin (IVIG) started to alleviate symptoms\n\t+ Three courses of intravenous etoposide and cisplatin\n\t+ Radiotherapy administered at a dose of 50.4 Gy\n\nThe patient's current status is not explicitly stated in the provided data, but it can be inferred that they are receiving ongoing treatment for their squamous cell lung carcinoma. The timeline suggests that the patient has been under treatment for several weeks, with some improvement in symptoms and potentially some progression or stabilization of the disease.\n\nIt is worth noting that the patient's demographics, including age and sex, are not explicitly stated in the provided data. However, based on the information provided, it can be inferred that the patient is a 55-year-old male who has been diagnosed with squamous cell lung carcinoma.", - "bertscore": { - "precision": [ - 0.5163893103599548 - ], - "recall": [ - 0.6056607365608215 - ], - "f1": [ - 0.5574737191200256 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 2, - "node_count": 9, - "edge_count": 7, - "avg_in_degree": 0.7777777777777778, - "density": 0.09722222222222222 - }, - "trajectory_embedding": [ - 0.21283334493637085, - 0.2261987030506134, - -0.18569672107696533, - 0.07250019162893295, - -0.07191392034292221, - 0.026674848049879074, - 0.13202348351478577, - 0.17625777423381805, - 0.3370841145515442, - -0.3352464735507965, - -0.19530074298381805, - 0.2723828852176666, - -0.5447418689727783, - -0.1018790602684021, - -0.38133886456489563, - 0.0197188351303339, - -0.013194016180932522, - 0.2992449104785919, - 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The pulmonary tumor board has recommended this course of action based on imaging findings.\n\nIn summary, the patient was diagnosed with stage IIIC large-cell squamous carcinoma of the left upper lobe in 2023 and underwent treatment with curative intent. Following treatment, there were significant improvements in lung function and tumor regression, but a new lesion suspicious for malignancy was detected in the liver. The patient is now being evaluated for surgical resection of the hepatic metastasis.", - "bertscore": { - "precision": [ - 0.7259575724601746 - ], - "recall": [ - 0.749750554561615 - ], - "f1": [ - 0.7376622557640076 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 8, - "edge_count": 7, - "avg_in_degree": 0.875, - "density": 0.125 - }, - "trajectory_embedding": [ - 0.23916545510292053, - 0.0230923630297184, - -0.08824869245290756, - 0.20278996229171753, - 0.04306795075535774, - 0.1345890760421753, - 0.015297275967895985, - 0.4002745747566223, - 0.5124368071556091, - -0.3175220787525177, - -0.045064736157655716, - -0.16486221551895142, - -0.5308375358581543, - -0.10607318580150604, - -0.2521823048591614, - 0.38863450288772583, - -0.037071093916893005, - 0.2851150929927826, - 0.018904972821474075, - -0.19477026164531708, - -0.47042977809906006, - 0.13593415915966034, - 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She was diagnosed with lung adenocarcinoma, which had metastasized to the brain, mediastinal lymph nodes, and other parts of her body.\n\n**Timeline of Diagnoses:**\n\n1. **May 2024:** The patient presented with cough and headache, leading to a biopsy of the right supraclavicular lymph node (N2). The biopsy confirmed lung adenocarcinoma.\n2. **May 2024:** A diagnosis of advanced lung adenocarcinoma was made, with multiple brain metastases (N3).\n3. **May 2024:** Initial imaging revealed multiple brain metastases, pulmonary lesions, and mediastinal lymphadenopathy.\n\n**Timeline of Treatments:**\n\n1. **May 2024:** The patient underwent whole-brain radiotherapy.\n2. **June 2024:** Next-generation sequencing (NGS) detected a ROS1 fusion and TP53 mutations. The patient started entrectinib therapy.\n3. **July 2024:** The patient experienced significant improvements in headache and insomnia symptoms, indicating a partial response to entrectinib treatment.\n\n**Timeline of Outcomes:**\n\n1. **July 2024:** Imaging showed a reduction in lung nodule size, mediastinal lymph nodes, and intracranial metastatic lesion size, indicating a partial response to entrectinib.\n2. **August 2024:** The patient experienced grade 2 blurred vision and oral mucositis.\n\n**Current Status:**\nThe patient's lung and brain lesions have consistently remained in a state of partial response since starting entrectinib therapy. However, the patient has experienced new symptoms, including blurred vision and oral mucositis, which may indicate a need for further treatment adjustments or additional therapies.\n\nThis clinical case report highlights the importance of personalized medicine approaches, such as targeted therapy with entrectinib, in managing advanced lung cancer with brain metastases.", - "bertscore": { - "precision": [ - 0.6425099968910217 - ], - "recall": [ - 0.6081539392471313 - ], - "f1": [ - 0.6248600482940674 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 8, - "edge_count": 7, - "avg_in_degree": 0.875, - "density": 0.125 - }, - "trajectory_embedding": [ - 0.14966541528701782, - 0.2221803069114685, - -0.19240516424179077, - 0.08077575266361237, - -0.02466701529920101, - 0.20474261045455933, - -0.0013346318155527115, - 0.23096227645874023, - 0.5076491236686707, - -0.410561740398407, - 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He has cerebral infarction and takes 25 mg of clopidogrel.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient's history and routine checkup revealed a 3 cm mass in the left middle lung field during chest radiography.\n2. **Step 2:** Further investigation with CT imaging and blood tests was conducted, which showed a ground-glass nodule with a maximum diameter of 4.6 cm and a solid component measuring 4 cm located in S9/10 of the left lower lobe.\n3. **Step 3:** Pulmonary function tests indicated normal respiratory capacity, but follow-up CT imaging revealed a part-solid nodule measuring 1.6 \u00d7 1.4 cm with a 1.5 cm solid component in the same location.\n4. **Step 4:** PET-CT and MRI of the head were conducted to evaluate the lung nodule and rule out metastasis, showing mild accumulation in the mass with an SUVmax of 2.04.\n5. **Step 5:** Bronchoscopy and biopsy were performed to determine the nature of the lung nodule, leading to a suspected diagnosis of stage IB primary lung cancer.\n\n**Timeline of Treatments:**\n\n1. **Step 6:** Surgical lobectomy was planned following the surgical biopsy.\n\n**Outcomes:**\n\nThe patient underwent bronchoscopy and biopsy, which led to a suspected diagnosis of stage IB primary lung cancer. The patient is scheduled for surgical lobectomy. Further follow-up will be necessary to monitor the patient's condition and assess the effectiveness of treatment.\n\nNote: This narrative is based on the provided data and may not reflect the actual clinical case report or outcomes.", - "bertscore": { - "precision": [ - 0.659263551235199 - ], - "recall": [ - 0.6760050058364868 - ], - "f1": [ - 0.6675293445587158 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.2567644715309143, - 0.054647695273160934, - -0.025133753195405006, - 0.027657220140099525, - 0.0567028634250164, - -0.047446608543395996, - 0.08157778531312943, - 0.12755827605724335, - 0.3595859110355377, - -0.3565047085285187, - -0.2112758755683899, - 0.1016974225640297, - -0.5609835982322693, - -0.06822846084833145, - -0.41357529163360596, - 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He presented to the clinic in February 2022 with chest tightness.\n\n**Initial Diagnosis (Step 1)**\n\nUpon physical examination, left supraclavicular lymphadenopathy was noted, measuring approximately 1 cm in size. Chest CT revealed a 2 cm mass in the posterior basal segment of the left lower lobe, with multiple burrs on the edge and enhancement. Mediastinal lymph nodes were enlarged and fused, surrounding the left main bronchus. Abdominal enhanced CT showed enlargement of the left adrenal gland, considered to be a metastatic lesion.\n\nImaging studies, including whole-body bone imaging and brain-enhanced MRI, did not reveal any obvious abnormalities. Immunohistochemical markers (CK-pan and P40) were positive, suggesting a diagnosis of lung cancer.\n\n**Biopsy and Diagnosis (Step 2)**\n\nOn March 10, 2022, a CT-guided lung puncture biopsy was performed to further characterize the tumor. Pathology suggested poorly differentiated carcinoma. Immunohistochemical markers were CK-pan (+), CK7 (-), TTF-1 (-), P40 (+), BRG-1 (-), and Syn (-). PD-L1 staining revealed a tumor proportion score (TPS) of 8%.\n\n**Diagnosis Confirmation and Treatment (Step 3)**\n\nBased on immunohistochemistry and genetic testing, a diagnosis of SMARCA4-deficient non-small cell lung cancer (SMARCA4-dNSCLC) was made. First-line treatment with tislelizumab combined with fruquintinib was initiated.\n\n**Treatment Outcomes (Step 4)**\n\nFollowing initial treatment, the patient experienced cervical lymph node progression. Subsequent biopsy confirmed the diagnosis, and the patient was treated with local radiotherapy and previous systemic therapy. The patient achieved more than two years of disease control without grade \u22653 adverse events.\n\n**Timeline**\n\n* February 2022: Patient presents to clinic with chest tightness.\n* March 10, 2022: CT-guided lung puncture biopsy is performed.\n* March 2022: Diagnosis of SMARCA4-dNSCLC is confirmed via subsequent biopsy.\n* April 1, 2022: Initial treatment with tislelizumab and fruquintinib begins.\n* April 1, 2022: Patient undergoes local radiotherapy and previous systemic therapy.\n\n**Outcomes**\n\nThe patient achieved more than two years of disease control without grade \u22653 adverse events. The diagnosis of SMARCA4-dNSCLC was confirmed via subsequent biopsy, and the patient responded well to first-line treatment with tislelizumab combined with fruquintinib.", - "bertscore": { - "precision": [ - 0.7477017045021057 - ], - "recall": [ - 0.7287452816963196 - ], - "f1": [ - 0.7381017804145813 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 4, - "edge_count": 3, - "avg_in_degree": 0.75, - "density": 0.25 - }, - "trajectory_embedding": [ - 0.28611698746681213, - 0.13427646458148956, - -0.17884783446788788, - 0.06759999692440033, - -0.12707366049289703, - 0.07035525888204575, - 0.17056792974472046, - -0.0935962051153183, - 0.17258435487747192, - -0.4768597185611725, - -0.167130708694458, - 0.24880175292491913, - -0.5263209342956543, - 0.07364700734615326, - -0.45961248874664307, - 0.04494486376643181, - -0.026198312640190125, - 0.3359876871109009, - 0.012521790340542793, - 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No other significant comorbidities were present at the time of presentation.\n\n**Diagnosis and Timeline:**\n\n1. **Step 1 (N1):**\nThe patient's history of COPD was noted, with a diagnosis code of \"233936005\" for Chronic obstructive lung disease, which is historical in nature.\n2. **Step 2 (N2):**\nTwo months prior to admission, an enhanced CT scan revealed a tumor in the right upper lung.\n3. **Step 3 (N3):**\nBiopsy confirmed that the tumor was squamous cell carcinoma of the lung (SCC), with a TNM stage of T2bNXM1c1.\n4. **Step 4 (N4):**\nThe patient received two cycles of albumin-bound paclitaxel, nedaplatin, and tislelizumab as treatment for SCC.\n\n**Follow-up and Complications:**\n\n5. **Step 5 (N5):**\nA follow-up CT scan showed partial remission of the tumor with cavitation.\n6. **Step 6 (N6):**\nThe patient presented with hemoptysis, which led to further evaluation, including lab tests and imaging.\n7. **Step 7 (N7):**\nEmergency endovascular intervention was performed due to pseudoaneurysm formation in the right upper pulmonary artery located at the SCC cavity wall with an intraluminal hematoma.\n8. **Step 8 (N8):**\nThe patient underwent emergency endovascular intervention, which included embolization using microcoils to occlude the PAP and proximal artery.\n9. **Step 9 (N9):**\nPost-procedure angiography confirmed the disappearance of the pulmonary artery pseudoaneurysm (PAP).\n10. **Step 10 (N10):**\nThe patient experienced no active bleeding postoperatively, and follow-up over 6 months showed no recurrence of hemoptysis.\n11. **Step 11 (N11):**\nA CT scan 3 months post-embolization showed absorption of the tumor cavity with significant tumor reduction.\n\n**Outcomes:**\n\nThe patient's treatment for SCC was successful, with partial remission of the tumor and disappearance of the pulmonary artery pseudoaneurysm. The patient experienced no active bleeding postoperatively and no recurrence of hemoptysis over 6 months. Follow-up imaging showed absorption of the tumor cavity with significant tumor reduction.\n\n**Conclusion:**\nThis case highlights the importance of early diagnosis and treatment for SCC, particularly in patients with a history of COPD. The successful outcome of this patient's treatment underscores the effectiveness of endovascular intervention in managing complications associated with SCC.", - "bertscore": { - "precision": [ - 0.6436575055122375 - ], - "recall": [ - 0.6487551927566528 - ], - "f1": [ - 0.6461962461471558 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 12, - "edge_count": 11, - "avg_in_degree": 0.9166666666666666, - "density": 0.08333333333333333 - }, - "trajectory_embedding": [ - 0.19094891846179962, - 0.14106714725494385, - -0.031158799305558205, - 0.13212095201015472, - -0.034361883997917175, - 0.11214422434568405, - 0.008480226621031761, - 0.27649667859077454, - 0.44355106353759766, - -0.3264440596103668, - -0.24161100387573242, - -0.02264360710978508, - -0.5586544275283813, - -0.07856817543506622, - -0.13135342299938202, - 0.2850583493709564, - -0.02288839966058731, - 0.2912149727344513, - 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He has also experienced pneumonia caused by Legionella pneumophila, hypertension, severe anemia, smoking, and alcohol use.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (N1):**\nThe patient presented with symptoms of a persistent cough, which had worsened over time. His medical history revealed previous episodes of pneumonia, hypertension, anemia, smoking, and alcohol use.\n2. **Step 2 (N2):** One month prior to presentation, the patient developed a Pasteurella pneumotropica infection at an outside facility, as confirmed by bronchoscopy and alveolar lavage fluid mNGS analysis. Despite treatment with anti-infective medications for over two weeks, the patient did not show improvement.\n3. **Step 3 (N3):** The patient presented with a palpable lump on the right thoracic wall, localized pain, and coarse breath sounds in both lungs. Laboratory tests revealed abnormalities in white blood cell count, red blood cell count, hemoglobin, total protein, globulin, albumin, glucose, C-reactive protein, and squamous cell carcinoma antigen.\n4. **Step 4 (N4):** Enhanced CT scans showed a new mass in the left lower lung, multiple enlarged lymph nodes, and bone destruction in the right tenth rib, leading to suspicion of lung cancer with metastasis. Bronchoscopy did not reveal tumor cells.\n\n**Treatments:**\n\n1. **Anti-infective treatment:** The patient received anti-infective medications for over two weeks following the diagnosis of Pasteurella pneumotropica infection.\n2. **Imaging studies:** Enhanced CT scans were performed to evaluate the new mass in the left lower lung and multiple enlarged lymph nodes.\n\n**Outcomes:**\n\n1. **Lung cancer with metastasis:** The patient's symptoms and imaging results suggested a diagnosis of lung cancer with metastasis.\n2. **No tumor cells found on bronchoscopy:** Despite the high suspicion of lung cancer, no tumor cells were found during bronchoscopy.\n3. **Negative antibody tests:** Antibody tests for HIV, HBV, HCV, EBV, and TP were negative, indicating that these infections were not contributing to the patient's condition.\n\n**Conclusion:**\nThe patient presented with a complex clinical picture, including a history of pneumonia, hypertension, anemia, smoking, and alcohol use. The development of Pasteurella pneumotropica infection led to progression in his diagnosis, ultimately resulting in suspicion of lung cancer with metastasis. Despite the high suspicion of lung cancer, no tumor cells were found on bronchoscopy, and antibody tests for common infections were negative. Further evaluation and treatment are necessary to determine the best course of action for this patient.", - "bertscore": { - "precision": [ - 0.5771618485450745 - ], - "recall": [ - 0.6398134231567383 - ], - "f1": [ - 0.606874942779541 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 4, - "edge_count": 3, - "avg_in_degree": 0.75, - "density": 0.25 - }, - "trajectory_embedding": [ - 0.3750039041042328, - -0.018641069531440735, - -0.2502043545246124, - 0.05081702023744583, - -0.05105207860469818, - 0.0839003473520279, - 0.2023211419582367, - 0.19112949073314667, - 0.2581161558628082, - -0.5016443729400635, - -0.10917043685913086, - 0.22764131426811218, - -0.6944714784622192, - -0.16388894617557526, - -0.19019311666488647, - -0.02061181329190731, - 0.21072253584861755, - 0.36244553327560425, - 0.1649523675441742, - -0.19564396142959595, - -0.4511476755142212, - 0.20265279710292816, - 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The diagnosis was made in [year] and marked the beginning of a complex treatment journey.\n\nFollowing the initial diagnosis, the patient transitioned to radiotherapy for the lung and mediastinal lesions (N1 to N2). This marked an important step in the patient's care, as it aimed to alleviate symptoms and slow disease progression. However, this was followed by another significant change when the patient began chemotherapy with albumin-bound paclitaxel and cisplatin, with recombinant human endostatin added in the 4th cycle (N2 to N3). Unfortunately, treatment was not completed due to cardiac reactions, resulting in stable disease.\n\nThe patient's condition continued to evolve as they developed symptoms of chest tightness and shortness of breath. These symptoms persisted despite hospitalization for worsening shortness of breath (N5 to N6), where ECG abnormalities and lab results indicating elevated troponin, BNP, and myoglobin were noted. The initial treatment included a range of medications aimed at managing these complications.\n\nDespite the efforts to manage symptoms, the patient's condition continued to deteriorate. A coronary angiography revealed significant stenosis in the left main trunk (N6 to N7), which further complicated the patient's care. Notably, anticoagulant therapy was not initiated due to concerns about gastrointestinal bleeding secondary to long-term aspirin use.\n\nThroughout this journey, the patient has been managed with a range of treatments, including medications and procedures aimed at addressing complications such as cardiac reactions, chest tightness, and shortness of breath. The timeline of diagnoses and treatments is complex, reflecting the evolving nature of the patient's condition.\n\nThe patient's age and demographic information are not explicitly stated in the provided data, but based on the treatment journey described, it can be inferred that this individual has been living with a serious health condition for several years.", - "bertscore": { - "precision": [ - 0.6489934921264648 - ], - "recall": [ - 0.6017652750015259 - ], - "f1": [ - 0.6244877576828003 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.17100100219249725, - 0.01172204501926899, - -0.21289609372615814, - 0.19774876534938812, - 0.11490162461996078, - 0.15191338956356049, - -0.03697091341018677, - 0.23890110850334167, - 0.5338540077209473, - 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He was admitted to the local hospital with acute abdominal pain, which marked the beginning of his clinical journey.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Initial Presentation:** The patient presented with acute abdominal pain, which led to an enhanced CT scan revealing a 4.0 cm soft tissue mass within the small intestine and mid-lower intestine intussusception (N2).\n2. **Surgical Intervention:** Admitted to the general surgery ward, the patient underwent intussusception surgery on April 8, 2019 (N3). During surgery, an irregular, hard, solid white mass involving the intestine was identified.\n3. **Initial Pathological Diagnosis:** The resected specimen showed a multinodular mass with a tan-white cut surface and firm consistency, thin envelope observed in the periphery of the mass (N4).\n4. **Detailed Pathology and Immunohistochemistry Results:** Histological examination revealed tumor located within the submucosa and lamina propria of the intestinal wall with mucosal erosion, neoplastic cells embedded within the inflammatory background. Immunohistochemistry results confirmed ALK-positive inflammatory myofibroblastic tumor (IMT), highly suspicious for epithelioid inflammatory myofibroblastic sarcoma (EIMS) (N5).\n\n**Diagnosis and Treatment Outcomes:**\n\nThe patient was diagnosed with a suspected case of epithelioid inflammatory myofibroblastic sarcoma (EIMS). Given the ALK-positive status, treatment options were considered. However, no specific treatment details are provided in this data.\n\n**Conclusion:**\nThis clinical case report highlights the importance of a thorough diagnostic workup and the significance of molecular testing in identifying rare and aggressive tumors like EIMS. Further investigation into the patient's treatment plan is necessary to determine the most effective course of action for this unique diagnosis.\n\n**Recommendations:**\n\n1. **Multidisciplinary Team Approach:** Collaboration between surgeons, pathologists, radiologists, and oncologists is crucial for managing complex cases like this.\n2. **Molecular Testing:** Regular molecular testing can help identify potential biomarkers for targeted therapies in EIMS patients.\n3. **Clinical Trials Participation:** Patients with rare tumors like EIMS should be considered for participation in clinical trials to explore new treatment options.\n\n**Future Directions:**\n\n1. **Research on EIMS:** Further studies are needed to understand the biology and behavior of EIMS, as well as to identify potential therapeutic targets.\n2. **Development of New Treatment Strategies:** Researchers should focus on developing novel treatments for EIMS, including targeted therapies and immunotherapies.\n\nBy sharing this clinical case report, we aim to raise awareness about the importance of accurate diagnosis and treatment planning in managing rare and aggressive tumors like EIMS.", - 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0.332520067691803, - -0.08831311017274857 - ] -} \ No newline at end of file diff --git a/src/benchmark/output/results/results_graph_056.json b/src/benchmark/output/results/results_graph_056.json deleted file mode 100644 index a2956f9..0000000 --- a/src/benchmark/output/results/results_graph_056.json +++ /dev/null @@ -1,795 +0,0 @@ -{ - "status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an adult with no publicly available demographic information. However, based on the provided data, it can be inferred that the patient has cancer, as mentioned in Step 1.\n\n**Timeline of Diagnoses and Treatments:**\n\nStep 1:\nThe patient's cancer had no driver gene mutations.\n\nStep 2 (First-line Chemotherapy):\nInitiation of first-line chemotherapy with cisplatin, pemetrexed, and pembrolizumab was administered. This treatment was initiated to target the patient's cancer.\n\nStep 3 (Second-line Chemotherapy):\nProgression to second-line chemotherapy with docetaxel and ramucirumab was administered. This treatment was initiated due to the development of resistance or intolerance to the first-line chemotherapy.\n\nStep 4:\nChemotherapy was delayed for approximately one month due to the development of a perianal abscess, which required surgical intervention under local anesthesia. The patient's cancer treatment was interrupted due to an unexpected complication.\n\nStep 5 (Post-Surgical Complication):\nThe patient developed dyspnea the day following surgery. This symptom suggested that the patient may be experiencing respiratory complications related to the surgery.\n\nStep 6:\nAdmission and Vital Sign Abnormalities:\nFour days after symptom onset, the patient was admitted with vital sign abnormalities, including hypotension, hypoxemia, and tachycardia. These findings indicated that the patient's condition had deteriorated significantly.\n\nStep 7 (Lab Abnormalities):\nElevated D-dimer, C-reactive protein, brain natriuretic peptide, and carcinoembryonic antigen levels were detected in the patient's blood. Additionally, abnormal CBC results and arterial blood gas findings were observed. These lab abnormalities suggested that the patient had developed a systemic inflammatory response syndrome (SIRS) or sepsis.\n\n**Outcomes:**\n\nThe patient's condition continued to deteriorate, with ongoing vital sign abnormalities and lab abnormalities. The exact outcome of this case is not provided in the data, but it can be inferred that the patient required further medical intervention to manage their symptoms and stabilize their condition.\n\nIn conclusion, this clinical case report highlights the complexities of cancer treatment and the potential for unexpected complications. The patient's journey from diagnosis to admission and beyond demonstrates the need for close monitoring and prompt intervention in managing cancer-related symptoms and lab abnormalities.", - "bertscore": { - "precision": [ - 0.6407378911972046 - ], - "recall": [ - 0.6139230132102966 - ], - "f1": [ - 0.6270439624786377 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.22469878196716309, - 0.19692015647888184, - 0.00025188070139847696, - 0.173471599817276, - 0.09548087418079376, - 0.17378945648670197, - -0.016956541687250137, - 0.2958507835865021, - 0.6613865494728088, - -0.4530636966228485, - -0.13141368329524994, - -0.04939684644341469, - -0.6155732274055481, - -0.17467454075813293, - -0.18280437588691711, - 0.12072768062353134, - -0.1693776696920395, - 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This symptomatology was documented as part of her clinical data, including a history of progressive worsening (P3M) and associated symptoms such as involuntary writhing movements.\n\n**Diagnostic Workup:**\nFollowing the patient's presentation, a comprehensive diagnostic workup was conducted, which included imaging studies (Brain MRI and CT), electroencephalogram (EEG), and laboratory tests. The results of these studies were negative for hemorrhage or lesions on the red nucleus or midbrain, seizure activity, and abnormal electrolyte levels.\n\n**Treatment Initiation:**\nDespite the initial negative diagnostic workup, the patient's symptoms worsened, prompting further evaluation and treatment initiation. A ceruloplasmin test was conducted, which revealed a negative result. Subsequent laboratory tests showed positive anti-Hu antibodies at a titer of 1:960, indicating paraneoplastic syndrome.\n\n**Treatment Regimen:**\nThe patient received a treatment regimen consisting of diazepam, primidone, and pramipexole, with the goal of managing her symptoms. However, despite this treatment, the patient's symptoms continued to worsen, leading to hospitalization.\n\n**Intravenous Immunoglobulin (IVIG) Therapy:**\nAs part of her treatment regimen, the patient received IVIG for 4 days. This therapy was aimed at reducing the severity of her paraneoplastic syndrome.\n\n**New Symptoms and Imaging Findings:**\nFollowing the patient's discharge from the hospital, she presented to the emergency department with nausea and vomiting without new abnormal movements or neurologic symptoms. Repeat imaging studies revealed a 3.3 x 2.3 cm mass in the left cerebellar region, involving the left cerebellar peduncle.\n\n**Treatment of New Symptoms:**\nThe patient underwent further evaluation and treatment for her new symptoms. Laboratory tests showed positive anti-Hu antibodies, indicating continued paraneoplastic syndrome.\n\n**Current Status:**\nAt this time, the patient is currently under observation with ongoing management of her paraneoplastic syndrome. The patient's symptoms have improved since the initiation of IVIG therapy, but she continues to experience discomfort and disrupted sleep due to the frequency of her movements.\n\nIn conclusion, this 72-year-old woman with a history of small cell lung cancer presented with progressive involuntary writhing movements in her hands and lower extremities. Despite an initial negative diagnostic workup, further evaluation and treatment initiation revealed paraneoplastic syndrome, which was managed with IVIG therapy. However, new symptoms and imaging findings have necessitated ongoing management and observation.", - "bertscore": { - "precision": [ - 0.5887521505355835 - ], - "recall": [ - 0.5860556364059448 - ], - "f1": [ - 0.5874007940292358 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.10924185812473297, - 0.10171635448932648, - -0.130819171667099, - 0.11970636993646622, - 0.01621156930923462, - -0.025944743305444717, - 0.059883225709199905, - 0.19405730068683624, - 0.5056430101394653, - -0.3832123875617981, - -0.28973308205604553, - 0.21129187941551208, - -0.575080156326294, - -0.07535974681377411, - -0.27020901441574097, - -0.11037592589855194, - 0.01244857907295227, - 0.24032163619995117, - -0.05925019457936287, - -0.07463321834802628, - -0.3116808831691742, - 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He experienced right ocular pain and blurred vision for approximately 1 month prior to presentation.\n\n**Timeline of Diagnoses:**\n\n* **Suspected Uveitis:** The patient was referred to the hospital with suspected uveitis of the right eye, which was diagnosed as a suspected case of uveitis (code C0042095).\n* **Small Cell Lung Cancer (SCLC):** Four months prior to presentation, the patient was diagnosed with SCLC (code C0007106) and had developed right cerebellar metastasis and invasion.\n* **Metastasis:** The patient also had a diagnosis of metastasis (code C0242393), which was active at the time of presentation.\n\n**Timeline of Treatments:**\n\n* **Topical Medications:** Following SCLC diagnosis, the patient started therapy with topical 0.005% latanoprost, 1.0% brinzolamide, and 0.5% timolol maleate.\n* **Oral Acetazolamide:** The patient also took oral acetazolamide at a dose of 500 mg/day.\n* **Intravenous Mannitol:** Due to high IOP and pronounced nausea, the patient required intravenous administration of 200 mL of 20% hypertonic mannitol every 2-3 days for five administrations.\n\n**Timeline of Outcomes:**\n\n* **Iris Metastasis:** Anterior chamber fluid cytology revealed iris metastasis from SCLC, consistent with bronchoalveolar lavage cytology results.\n* **Neovascular Glaucoma:** The patient developed neovascular glaucoma (code C0271198), which was treated with a single intravitreal injection of 2 mg (0.05 mL of 40 mg/mL) aflibercept OD.\n* **Resolution of Symptoms:** Five days post-aflibercept injection, the patient's iris tumor size and iris neovascularization decreased, IOP measured at 18 mm Hg, and symptoms such as ocular pain and nausea were relieved.\n\n**Conclusion:**\nThe patient was diagnosed with suspected uveitis and SCLC, which led to the development of right cerebellar metastasis and invasion. Following diagnosis, the patient received topical medications and oral acetazolamide, as well as intravenous mannitol due to high IOP and nausea. The patient also developed iris metastasis from SCLC, which was treated with an intravitreal injection of aflibercept. Ultimately, the patient's symptoms resolved following treatment, and their IOP returned to normal.", - "bertscore": { - "precision": [ - 0.5613889694213867 - ], - "recall": [ - 0.7224175930023193 - ], - "f1": [ - 0.631804347038269 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.10041718930006027, - 0.16403163969516754, - -0.2795267105102539, - 0.20759916305541992, - 0.1098250150680542, - 0.12031718343496323, - 0.02523813582956791, - 0.28508585691452026, - 0.4031936228275299, - -0.14178399741649628, - -0.1515788584947586, - 0.027539696544408798, - -0.39865249395370483, - -0.16108302772045135, - -0.1848643273115158, - 0.29761239886283875, - -0.348704069852829, - 0.19526958465576172, - -0.07590274512767792, - -0.18397021293640137, - -0.1955096572637558, - 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He has a significant occupational asbestos exposure history while working for a shipbuilding company. The patient denies any history of cigarette smoking or exposure to organic dusts, pet birds, or exotic pets.\n\n**Initial Presentation (Step 1):**\nIn June 2024, the patient presented to the Emergency Department with concerns of weight loss and abdominal distention over the past 4 weeks. He denied any alterations in bowel habits, melena, hematochezia, abdominal pain, nausea, vomiting, dysphagia, or odynophagia.\n\n**Physical Examination and Laboratory Findings (Step 2):**\nAfter initial presentation, the patient underwent multiple abdominal paracenteses, which revealed hazy yellow ascitic fluid with nucleated cells. The cell count was 589 cells/\u03bcL, with lymphocytes 87% and erythrocytes 1461 cells/\u03bcL.\n\n**Imaging Studies (Step 3):**\nA CT scan performed during this time showed massive ascites and a lung nodule.\n\n**Abdominal Paracentesis and Ascitic Fluid Analysis (Steps 4-5):**\nThe patient underwent multiple abdominal paracenteses, which revealed exudative process in the ascitic fluid. The first abdominal paracentesis results showed lactate dehydrogenase 763 IU/L, total protein 4.0 g/dL, albumin 1.7 g/dL, and serum albumin-ascites gradient (SAAG) 0.4 g/dL.\n\n**Repeat Ascitic Fluid Analysis and Abdominal Ultrasonography (Step 6):**\nA repeat ascitic fluid analysis revealed no growth on AFB smear, culture, or fungal culture. An abdominal ultrasonography performed during this time showed normal portal vein size and Doppler indices, with the spleen not enlarged.\n\n**Serum FibroTest-ActiTest (Step 7):**\nThe patient underwent a Serum FibroTest-ActiTest, which suggested no hepatic fibrosis (F0).\n\n**Diagnosis:**\nBased on the results of the various diagnostic tests and imaging studies, the patient was diagnosed with cirrhosis due to chronic liver disease.\n\n**Treatment:**\nNo specific treatment is mentioned in the provided data. However, it can be inferred that the patient may require ongoing management of his ascites and potential complications related to cirrhosis.\n\n**Outcome:**\nThe patient's condition appears to be stable at this point, with no further information provided on any changes or developments since the last update.", - "bertscore": { - "precision": [ - 0.5451638698577881 - ], - "recall": [ - 0.6678067445755005 - ], - "f1": [ - 0.6002851128578186 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 8, - "edge_count": 7, - "avg_in_degree": 0.875, - "density": 0.125 - }, - "trajectory_embedding": [ - 0.3212769627571106, - 0.027124296873807907, - 0.007639573886990547, - 0.1450214982032776, - 0.04273857921361923, - -0.0566130205988884, - 0.15015661716461182, - 0.13063287734985352, - 0.360310435295105, - -0.2895905375480652, - -0.29207170009613037, - 0.0069152191281318665, - -0.5160095691680908, - 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Unfortunately, her demographic information is not explicitly provided in the data, so we will assume that she is an adult female with no other relevant medical history mentioned.\n\n**Initial Presentation (Step 1):**\nThe patient presented to our institution with dyspnea, which was her primary symptom. This presentation led to further investigation and subsequent diagnoses.\n\n**Diagnosis of Adenocarcinoma (Step 2):**\nFollowing a bronchoscopic biopsy of the right upper lobe, the patient was diagnosed with adenocarcinoma. The biopsy results revealed adenocarcinoma, which is a type of non-small cell lung cancer.\n\n**Imaging and Further Diagnosis (Step 3):**\nImaging studies, including bone and brain metastases, were performed to further evaluate the extent of disease. These findings led to a diagnosis of stage IVB lung adenocarcinoma with multiple metastases in the bones and brain.\n\n**Molecular Profiling and Treatment Planning (Step 4):**\nA tumor proportion score was calculated to guide treatment decisions. The results showed that the programmed death-ligand 1 tumor proportion score was 60%. Based on this information, palliative radiation therapy for spinal and brain metastases was initiated, followed by first-line chemotherapy with cisplatin, pemetrexed, and pembrolizumab.\n\n**Progression of Disease (Step 5-6):**\nAfter 13 cycles of chemotherapy, imaging revealed ascites and progressive disease. The patient's condition continued to decline, with worsening ascites and a marked increase in abdominal circumference.\n\n**Second-Line Therapy (Step 7):**\nDue to the progression of disease, second-line therapy was initiated with docetaxel and ramucirumab (DTX+RAM). However, despite this treatment, the patient's condition continued to deteriorate.\n\n**Current Status:**\nThe patient is currently in a poor clinical state, with significant ascites, hypoalbuminemia, and a marked decline in activities of daily living. Her performance status has decreased, and she requires frequent abdominal paracentesis. The patient's abdomen is markedly distended, and her vital signs are concerning.\n\n**Conclusion:**\nThis patient presents with a complex clinical scenario, characterized by rapidly progressive disease despite multiple treatment modalities. 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He denied any fever, sputum or blood production, and chest pain.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (N1):** The patient's chronic recurrent dry cough prompted a chest computed tomography (CT) scan.\n2. **Step 2 (N2):** The CT revealed pulmonary masses at an external hospital, leading to admission to the oncology department for further evaluation and treatment.\n3. **Step 3 (N3):** The patient was admitted to the oncology department for further evaluation and treatment.\n4. **Step 4 (N4):** As part of the evaluation, the patient's medical history was reviewed, revealing no history of hypertension, coronary heart disease, diabetes, cerebral venous thrombosis or hemorrhage, tuberculosis, chronic hepatitis B virus infection and other diseases.\n5. **Step 5 (N5):** Vitals and labs were taken as part of the evaluation, including temperature 37.2\u00b0C, pulse rate 118 bpm, respiratory rate 20 breaths/minute, blood pressure 106/69 mmHg, white blood cells 7.97 \u00d7 109/L, hemoglobin 142 g/L, platelets 287 \u00d7 109/L, and various other lab results.\n6. **Step 6 (N6):** Additional labs were taken as part of the evaluation, including treponema pallidum-specific antibody, hepatitis B surface antigen, and hepatitis C.\n\n**Treatments:**\n\nThe patient underwent a series of evaluations and treatments based on the findings from each step:\n\n* Following the CT scan, the patient was admitted to the oncology department for further evaluation and treatment.\n* As part of the evaluation, the patient's medical history was reviewed, revealing no history of certain diseases.\n* Vitals and labs were taken as part of the evaluation.\n\n**Outcomes:**\n\nThe patient's current status is not explicitly stated in the provided data. However, based on the timeline of diagnoses and treatments, it appears that the patient has undergone a series of evaluations and treatments for pulmonary masses detected by CT scan. The patient's medical history was reviewed, revealing no history of certain diseases, and vitals and labs were taken as part of the evaluation.\n\n**Conclusion:**\n\nThe patient presented with a chronic recurrent dry cough over the course of a month, which prompted a chest CT scan that revealed pulmonary masses. The patient underwent a series of evaluations and treatments based on the findings from each step, including admission to the oncology department for further evaluation and treatment. The patient's medical history was reviewed, revealing no history of certain diseases, and vitals and labs were taken as part of the evaluation.", - "bertscore": { - "precision": [ - 0.47996535897254944 - ], - "recall": [ - 0.5415050387382507 - ], - "f1": [ - 0.5088814496994019 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.29947397112846375, - -0.028808513656258583, - 0.018951475620269775, - 0.24079148471355438, - 0.11866217851638794, - 0.17880016565322876, - 0.11841905117034912, - 0.2565062940120697, - 0.5162163972854614, - -0.40549495816230774, - -0.19314958155155182, - -0.05226249620318413, - -0.6632895469665527, - -0.11044865846633911, - -0.34900379180908203, - 0.20892314612865448, - 0.0023391495924443007, - 0.3613584041595459, - 0.03122534416615963, - 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She presented with a palpable pelvic mass, which was later identified as an anterior wall uterine leiomyoma on gynecological sonography.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1 (N1):**\nThe patient presented with a palpable pelvic mass in January 2010. Physical examination revealed an enlarged uterus, which was mobile, firm in consistency, with no uterine or forniceal tenderness, and mild swelling in the right pubic area.\n\n2. **Step 2 (N2):**\nGynecological sonography on January 30, 2010, identified an anterior wall uterine leiomyoma, measuring 112\u00d794\u00d7108 mm, accompanied by ascites measuring 65\u00d742 mm and a 20\u00d714 mm mass.\n\n3. **Step 3 (N3):**\nLaparotomic myomectomy was performed on February 17, 2020, with incidental discovery of a pelvic tumor. The pelvic tumor described as a cauliflower-like lesion disseminated across the right pelvic wall, cul-de-sac, anterior uterine surface, bladder, and colon.\n\n4. **Step 4 (N4):**\nBiopsy of the sigmoid colon serosa was performed, revealing proliferative mesothelial cells without significant atypia or necrosis. Post-myomectomy CT scan revealed seeding in the lower pelvis, characterized by multiple small, heterogeneous, enhancing nodules on the peritoneum and a prominent soft-tissue mass in the right adnexa.\n\n5. **Step 5 (N5):**\nAnother CT scan performed on February 26th, 2020, revealed moderate ascites and nonspecific peritoneal thickening. Histopathology identified bland mesothelial cells without invasion, and immunohistochemistry showed no significant staining loss. Differential diagnosis included well-differentiated papillary mesothelioma, epithelioid peritoneal mesothelioma, and florid mesothelial hyperplasia; well-differentiated papillary mesothelioma was highly suspected.\n\n**Outcomes:**\n\nThe patient underwent a series of procedures, including laparotomic myomectomy, biopsy, histopathology, and immunohistochemistry. The results of these procedures led to the diagnosis of a pelvic tumor with seeding in the lower pelvis. Despite the presence of seeding, the patient's condition was managed conservatively, with no further surgical interventions reported.\n\n**Conclusion:**\nThis case highlights the complexities of managing a patient with a pelvic mass and subsequent discovery of a pelvic tumor with seeding. The patient's presentation and diagnostic workup led to a series of procedures that ultimately resulted in a diagnosis of a mesothelial tumor. While the patient's condition was managed conservatively, further follow-up is necessary to monitor for any progression or recurrence of the disease.\n\n**Recommendations:**\n\n1. Further imaging studies should be performed to assess the extent of seeding and monitor for any progression or recurrence of the disease.\n2. The patient should be followed up regularly with a multidisciplinary team, including oncologists, radiologists, and pathologists.\n3. Additional diagnostic procedures, such as PET scans or CT scans, may be necessary to further evaluate the patient's condition.\n\n**Limitations:**\n\nThis case report is limited by its retrospective nature and the availability of data. Further research is needed to better understand the management and outcomes of patients with pelvic tumors and seeding.", - "bertscore": { - "precision": [ - 0.514549732208252 - ], - "recall": [ - 0.6133989691734314 - ], - "f1": [ - 0.5596429109573364 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 5, - "edge_count": 4, - "avg_in_degree": 0.8, - "density": 0.2 - }, - "trajectory_embedding": [ - 0.33560317754745483, - -0.032035164535045624, - -0.11456692218780518, - 0.1346358358860016, - 0.020706722512841225, - 0.00046664924593642354, - 0.1556069552898407, - 0.050799597054719925, - 0.29955029487609863, - -0.3043522834777832, - -0.21893103420734406, - 0.13041041791439056, - -0.5819693207740784, - -0.027642954140901566, - -0.3483089804649353, - 0.05678959935903549, - 0.08175595104694366, - 0.18470464646816254, - 0.07032836973667145, - -0.1516115516424179, - -0.3795337677001953, - 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He presented to the emergency room with cough, low back pain, and abdominal pain.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation (October 28, 2023):** The patient was evaluated at the emergency room due to symptoms of cough, low back pain, and abdominal pain. A CT angiogram of the chest was performed, which revealed a large left pleural effusion tracking to the lung apex with near complete opacification of the left lower lobe, a 6-cm left lower lobe mass, and 4-cm left hilar mass with mediastinal adenopathy and pleural nodularity.\n2. **Surgical Intervention (November 9, 2023):** The patient underwent left video-assisted thorascopic surgery with total left lung decortication, removal of fibrin deposits, and placement of a pleural drainage catheter requiring daily drainage.\n3. **Pathology and Imaging Results (November 29, 2023):** Pathology from the left pleural mass revealed malignant epithelial neoplasm with 70% spindle cell and 30% epithelioid cell components consistent with biphasic MPM. PET imaging confirmed advanced disease with extensive left-sided pleural involvement, bilateral mediastinal adenopathy, adrenal, and scattered bone lesions.\n4. **Immune Checkpoint Inhibitor Therapy (December 4, 2023):** The patient began receiving immune checkpoint inhibitor therapy with nivolumab and ipilimumab, which showed initial improvement in pleural drainage output.\n\n**Timeline of Symptoms:**\n\n1. **Initial Presentation:** Cough, low back pain, and abdominal pain.\n2. **Post-Surgical Complication (December 4, 2023):** Lower back pain, lower extremity numbness, and inability to walk after one cycle of therapy.\n\n**Treatment Outcomes:**\nThe patient's treatment with immune checkpoint inhibitors showed initial improvement in pleural drainage output. However, a new symptom of lower back pain, lower extremity numbness, and inability to walk developed after one cycle of therapy, indicating potential side effects or progression of the disease.\n\nThis clinical case report highlights the importance of early diagnosis and treatment of malignant pleural mesothelioma (MPM), as well as the need for careful monitoring of patients receiving immune checkpoint inhibitors.", - "bertscore": { - "precision": [ - 0.7149702310562134 - ], - "recall": [ - 0.7142810821533203 - ], - "f1": [ - 0.7146255373954773 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.1652541607618332, - 0.039438892155885696, - -0.14641372859477997, - 0.18929584324359894, - 0.14937780797481537, - 0.1875849962234497, - -0.10926973819732666, - 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Her demographic information is not explicitly mentioned in the provided data, but based on the age and sex, we can infer that she is an adult female.\n\n**Initial Diagnosis (Step 1):**\nUpon presentation, the patient underwent a lung CT scan, which revealed a space-occupying lesion in the left lower lobe. The lesion was accompanied by peripheral obstructive inflammation, atelectasis, and multiple enlarged lymph nodes in the mediastinum. A biopsy of the lesion was performed, which confirmed the presence of keratinized squamous cell carcinoma. The patient was diagnosed with left lower lobe squamous cell carcinoma (T3N2bM0, Stage IIIB).\n\n**Treatment Initiation (Step 2):**\nThe patient underwent six cycles of albumin-bound paclitaxel (100 mg/m\u00b2 on day 1, day 8, and day 15), cisplatin (75 mg/m\u00b2 on day 1), and carrelizumab (200 mg on day 1). Following this treatment, the left lower lung lesion had significantly reduced in size to approximately 23x25 mm.\n\n**Radiotherapy and Re-emergence of Disease (Step 3):**\nThe patient underwent radiotherapy with a dose of 2 Gy per fraction, administered over a total of 30 fractions. However, after ten fractions, the patient developed dyspnea and fever, with a maximum temperature of 38.5\u00b0C. A lung puncture biopsy was performed, which confirmed the presence of squamous cell carcinoma. The lesion had significantly enlarged to a size of 50 \u00d7 51 mm.\n\n**Outcome:**\nThe patient's condition worsened after radiotherapy, and she developed delayed hypersensitivity pneumonitis (DHP) after 5 months of immunotherapy. Despite this, the patient continued to receive treatment, highlighting the complexities of managing advanced cancer.\n\nIn conclusion, this clinical case report highlights the challenges of treating advanced squamous cell carcinoma in a 59-year-old woman. The patient's initial diagnosis and treatment response were promising, but the disease re-emerged after radiotherapy, leading to worsening symptoms and complications. Further management strategies are needed to improve outcomes for patients with advanced cancer.", - "bertscore": { - "precision": [ - 0.5903757810592651 - ], - "recall": [ - 0.7092682123184204 - ], - "f1": [ - 0.6443838477134705 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 3, - "edge_count": 2, - "avg_in_degree": 0.6666666666666666, - "density": 0.3333333333333333 - }, - "trajectory_embedding": [ - 0.24472539126873016, - 0.05973951891064644, - -0.20621691644191742, - 0.22169888019561768, - -0.08776857703924179, - -0.01297292485833168, - 0.14311833679676056, - 0.19575707614421844, - 0.13809828460216522, - -0.30675601959228516, - -0.19033236801624298, - 0.21958637237548828, - -0.5650694966316223, - -0.03671947494149208, - -0.21233956515789032, - -0.07029158622026443, - 0.05985746905207634, - 0.3540482819080353, - 0.09971606731414795, - -0.21774829924106598, - -0.4880874454975128, - 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Despite this initial treatment, the patient developed metastatic disease in 2022, which led to further evaluation and treatment, including stereotactic radiation therapy for brain metastasis, empirical chemotherapy regimen, histopathological analysis of liver lesions, and treatment with docetaxel. The patient's current status is characterized by ongoing treatment with docetaxel, with modest shrinkage observed in the tumor size.", - "bertscore": { - "precision": [ - 0.707660973072052 - ], - "recall": [ - 0.7203216552734375 - ], - "f1": [ - 0.7139351963996887 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.2563111484050751, - 0.18047350645065308, - -0.12980332970619202, - 0.12957733869552612, - 0.14545029401779175, - 0.19874490797519684, - -0.020612286403775215, - 0.3609883785247803, - 0.5175485610961914, - -0.42774152755737305, - -0.11932812631130219, - -0.07010838389396667, - -0.6297792792320251, - -0.06867539882659912, - -0.2806960642337799, - 0.28194066882133484, - -0.16101223230361938, - 0.2974811792373657, - -0.0320054367184639, - 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However, based on the clinical data, it appears that the patient has a history of lung cancer.\n\n**Timeline of Diagnoses:**\n\n1. **September 2021:** The patient presented to The First Affiliated Hospital of Dalian Medical University with complaints of chest pain and fatigue for half a year. A CT scan revealed partial solid nodules in the posterior segment of the upper lobe of the right lung, which were later diagnosed as malignant neoplasm of bronchus and lung (C34).\n2. **Multiple small lung nodules in both lungs:** Following the initial diagnosis, the patient developed multiple small lung nodules in both lungs, accompanied by abnormal blood test results (lymphocytopenia and neutrophilia). This led to a decision to proceed with surgical resection of lung tissue.\n3. **November 2022:** The patient underwent surgical resection of lung tissue, which revealed invasive adenocarcinoma in the upper lobe of the right lung. The cancer was diagnosed as C2330808 (Adenocarcinoma, Invasive).\n4. **January 2024:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm.\n\n**Timeline of Treatments:**\n\n1. **Surgical resection of lung tissue:** The patient underwent surgical resection of lung tissue in November 2022.\n2. **No second surgical treatment:** The patient refused a second surgical treatment for the recurrence of primary cancer, which presented as ground glass nodules in the left lung.\n\n**Timeline of Outcomes:**\n\n1. **Pathological diagnosis:** The pathological diagnosis of invasive adenocarcinoma was confirmed post-surgery in November 2022.\n2. **Recurrence of primary cancer:** The patient developed recurrence of primary cancer with ground glass nodules in the left lung and new symptoms (fatigue, pale tongue, white fur, and weak pulse) in November 2022.\n3. **Recurrent tumor shrinkage:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm in January 2024.\n\n**Clinical Findings:**\n\nThroughout the patient's treatment, various clinical findings were reported, including:\n\n* Chest pain and fatigue\n* Multiple small lung nodules in both lungs\n* Abnormal blood test results (lymphocytopenia and neutrophilia)\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Laboratory Results:**\n\nThe patient's laboratory results showed:\n\n* Normal blood work (January 2024)\n* Elevated carcinoembryonic antigen level (November 2022)\n\n**Imaging Results:**\n\nThe patient underwent various imaging studies, including CT scans and pathology reports, which revealed:\n\n* Partial solid nodules in the posterior segment of the upper lobe of the right lung (September 2021)\n* Multiple small lung nodules in both lungs\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Prognosis:**\nThe patient's prognosis remains uncertain, as the cancer has recurred and treatment options are limited. Further evaluation and management are necessary to determine the best course of action.\n\n**Conclusion:**\nThis clinical case report highlights the complexities of managing lung cancer, particularly in cases where recurrence occurs. The patient's treatment plan will require careful consideration of various factors, including the patient's overall health, tumor characteristics, and available treatment options.", - "bertscore": { - "precision": [ - 0.6718395352363586 - ], - "recall": [ - 0.6553829908370972 - ], - "f1": [ - 0.66350919008255 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.257910817861557, - 0.11300678551197052, - -0.15380962193012238, - -0.04967570677399635, - -0.14522525668144226, - 0.06221002712845802, - 0.07804203033447266, - 0.17250725626945496, - 0.2976982593536377, - -0.48700565099716187, - -0.2710980474948883, - 0.19328932464122772, - -0.552730143070221, - -0.1464165896177292, - -0.4568333923816681, - 0.13878197968006134, - 0.02563413418829441, - 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He presented to the clinic with a persistent dry cough that had lasted for more than three months.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **July 2019:** The patient was diagnosed with a mass in the central left upper lobe, enlarged bilateral mediastinal lymph nodes, and bilateral pulmonary nodules on contrast-enhanced chest CT (Step 2). Biopsy of the lesion under tracheoscopy confirmed lung adenocarcinoma histologically (Step 3).\n2. **July-September 2019:** The patient underwent whole-body scanning, which revealed macroscopic metastases in the bone. He was clinically classified as stage IVB (T4N0M1c) Non-Small Cell Lung Carcinoma (NSCLC). Zoledronic acid was administered to control bone destruction (Step 4).\n3. **September-October 2019:** The patient underwent tissue biopsy, which detected an acquired T790M mutation in exon 20 (c.2369C>T, frequency as 61.9%) via droplet digital polymerase chain reaction (ddPCR) (Step 7).\n4. **October-November 2019:** Due to the detection of the T790M mutation, the patient was switched to osimertinib 80mg once daily, achieving stable disease with shrinkage of hepatic lesions (Step 8).\n\n**Outcomes:**\n\n1. The patient experienced a rapid clinical benefit lasting 11 months after starting treatment with gefitinib (250 mg once daily) in response to the detection of EGFR exon 19 deletion (Step 6).\n2. After 11 months on gefitinib, tissue biopsy was performed to investigate resistance mechanisms, detecting an acquired T790M mutation in exon 20 (c.2369C>T, frequency as 61.9%) via droplet digital polymerase chain reaction (ddPCR) (Step 7).\n\n**Conclusion:**\nThe patient's clinical course highlights the importance of molecular testing and targeted therapy in the management of NSCLC. The detection of EGFR exon 19 deletion led to treatment with gefitinib, resulting in a rapid clinical benefit. However, the subsequent development of T790M mutation necessitated a switch to osimertinib, achieving stable disease with shrinkage of hepatic lesions.\n\n**Recommendations:**\n\n1. Regular molecular testing for EGFR mutations and T790M status should be performed in patients with NSCLC.\n2. Targeted therapy with gefitinib or osimertinib should be considered based on molecular test results.\n3. Close monitoring of disease progression and response to treatment is essential in managing NSCLC.\n\n**Limitations:**\n\n1. The patient's clinical course was limited by the availability of targeted therapies at the time of diagnosis.\n2. Further research is needed to explore the optimal timing and sequence of molecular testing and targeted therapy in NSCLC.\n\nThis case highlights the importance of personalized medicine in the management of NSCLC, emphasizing the need for regular molecular testing and targeted therapy based on test results.", - "bertscore": { - "precision": [ - 0.7394998073577881 - ], - "recall": [ - 0.7590272426605225 - ], - "f1": [ - 0.7491363286972046 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 8, - "edge_count": 7, - "avg_in_degree": 0.875, - "density": 0.125 - }, - "trajectory_embedding": [ - 0.25666746497154236, - 0.09836211800575256, - -0.10564713180065155, - 0.11217941343784332, - 0.015587031841278076, - 0.07877800613641739, - -0.006527600809931755, - 0.30493852496147156, - 0.5536767244338989, - -0.33620452880859375, - -0.018288739025592804, - -0.09518112242221832, - -0.5867060422897339, - 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Unfortunately, the demographic information provided does not include her name, address, or any other identifying details.\n\n**Timeline of Diagnoses**\n\nThe patient's journey began in [month/year] when she developed memory problems following a COVID-19 infection. Two days later, she underwent lumpectomy due to the worsening symptoms. The pathology report revealed infiltrative breast carcinoma of mixed type (80% non-specific, 20% lobular), histoprognostic grade I (2-2-1), and histological tumor size of 30 mm along the long axis.\n\n**Timeline of Treatments**\n\nFollowing the lumpectomy, the patient was diagnosed with anti-LGI1 limbic encephalitis associated with early-stage breast cancer. MRI, EEG, and positive anti-LGI1 antibodies supported this diagnosis. As a result, she underwent PET scans to further investigate the breast cancer diagnosis.\n\nThe PET scan identified a moderately hypermetabolic lesion in the right breast, leading to resection of the breast tumor with immunohistopathological analysis. The pathological stage was determined as pT2 N0 (sn) G1 R. Following resection, immunosuppressive treatment was started within 24 hours of admission.\n\n**Timeline of Outcomes**\n\nThe patient's condition improved gradually over time. She recovered from the initial symptoms and no longer experienced headaches or focal epileptic seizures since hospitalization. However, partial retrograde and anterograde amnesia persisted during the initial week, followed by a slow and steady improvement.\n\nAfter 12 months of recovery, the patient returned to work with 80% of her previous productivity. Neuropsychological evaluations at baseline showed impairment in verbal episodic memory (Free and Cued Selective Reminding Test) and visual episodic memory (recall of the Rey-Osterrieth complex figure). However, after six months of treatment, objective cognitive improvement was observed.\n\n**Current Status**\n\nThe patient's current status is one of ongoing management and monitoring. She continues to receive immunosuppressive treatment to manage her anti-LGI1 limbic encephalitis. Regular follow-up appointments with her healthcare team are necessary to monitor her condition and adjust treatment as needed.\n\nDespite the challenges she has faced, the patient has demonstrated remarkable resilience and determination in her pursuit of recovery. Her progress is a testament to the importance of comprehensive care and ongoing support for individuals with complex medical conditions.", - "bertscore": { - "precision": [ - 0.5682033896446228 - ], - "recall": [ - 0.5968579053878784 - ], - "f1": [ - 0.5821782946586609 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 12, - "edge_count": 11, - "avg_in_degree": 0.9166666666666666, - "density": 0.08333333333333333 - }, - "trajectory_embedding": [ - 0.13369283080101013, - 0.14433510601520538, - -0.22548367083072662, - 0.060306016355752945, - -0.08639272302389145, - 0.002943794010207057, - 0.23735707998275757, - 0.16482573747634888, - 0.5013976693153381, - -0.3400944769382477, - -0.0792926773428917, - 0.0980411171913147, - -0.5940414071083069, - -0.14733976125717163, - -0.22831867635250092, - 0.1983317881822586, - -0.00968053936958313, - 0.277439147233963, - -0.14450059831142426, - 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Unfortunately, the provided data does not include the patient's demographic information such as age, address, or contact details.\n\nHowever, based on the timeline of diagnoses and treatments provided, we can reconstruct a coherent narrative:\n\nThe patient was first diagnosed with lung cancer, which led to the start of gyroknife radiotherapy for left and right lung malignancies 12 times. This treatment was likely aimed at reducing the size of the tumors in the lungs.\n\nAfter completing this treatment, the patient experienced tumor progression, leading to the start of anlotinib 8mg orally once daily for 14 days every 3 weeks. This medication was intended to slow down the growth of the cancer cells.\n\nHowever, after 14 cycles of anlotinib treatment, the patient presented with hyperglycemia (fasting plasma glucose of 26.1 mmol/L) and urine ketone (+++), leading to a diagnosis of type 1 diabetes. As a result, the patient was discharged with a hypoglycemic regimen of insulin degludec 5 units in the morning and insulin aspartate 4 units three times a day.\n\nOne week after discharge, the patient's blood glucose levels significantly increased after re-starting anlotinib (highest recorded level was 30.1 mmol/L), and the insulin dose was increased. Despite this escalation, the patient continued to experience significant improvements in their laboratory parameters, including GADA, ICA, IAA, Fasting blood glucose, Hemoglobin A1c, Hemoglobin, and Serum albumin.\n\nAfter two cycles of anlotinib treatment, the medication was discontinued due to tumor progression and its significant negative impact on glucose metabolism. However, by the 16th cycle, laboratory parameters showed a marked improvement in these areas.\n\nThe patient's current status is unclear from the provided data, but it appears that they have undergone various treatments for their lung cancer and diabetes. The exact outcome of these treatments is not specified, but the narrative suggests that the patient has experienced significant improvements in their laboratory parameters over time.", - "bertscore": { - "precision": [ - 0.6911485195159912 - ], - "recall": [ - 0.6727587580680847 - ], - "f1": [ - 0.6818296313285828 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 10, - "edge_count": 9, - "avg_in_degree": 0.9, - "density": 0.1 - }, - "trajectory_embedding": [ - 0.1467558592557907, - 0.21578022837638855, - -0.22472743690013885, - 0.1429169625043869, - -0.0391475111246109, - 0.10741577297449112, - 0.24607594311237335, - 0.2464669942855835, - 0.3772128224372864, - -0.3546753525733948, - -0.1136227399110794, - 0.030413171276450157, - -0.4117017686367035, - -0.1751895248889923, - -0.3702186644077301, - 0.24298548698425293, - -0.22810597717761993, - 0.43166160583496094, - -0.07609720528125763, - 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He was admitted to the hospital on day 1 (N1) with symptoms of pneumonia and acute hypoxic respiratory failure requiring intubation. His vital signs were unstable, and he required close monitoring in the intensive care unit.\n\n**Timeline of Diagnoses**\n\n* Day 1 (N1): Admitted with pneumonia and acute hypoxic respiratory failure.\n* Day 14 (N2): Developed septic shock and PICC-line-associated MSSA bacteremia. He was treated with IV cefazolin.\n* Day 28 (N3): Developed SVC syndrome and left upper extremity DVT. He was treated with therapeutic enoxaparin.\n* Day 42 (N4): Recurrent fevers and transfer back to the ICU for septic shock management. Blood cultures grew MSSA, and a transesophageal echocardiogram showed no endocarditis.\n* Day 54 (N5): Repeat blood cultures grew A. fumigatus in addition to MSSA. The infectious disease team recommended continuing IV cefazolin for MSSA bacteremia and adding caspofungin for fungal coverage.\n* Day 56 (N6): Atovaquone continued for pneumocystis jirovecii prophylaxis, and tenofovir discontinued due to concern for contributing to acute kidney injury. The antiretroviral regimen was changed to dolutegravir/rilpivirine plus emtricitabine pending further evaluation of hepatitis B status.\n* Day 62 (N9): Patient died of his illness.\n\n**Timeline of Treatments**\n\n* Day 1-14 (N2): IV cefazolin for MSSA bacteremia\n* Day 28-42 (N3): Therapeutic enoxaparin for SVC syndrome and DVT\n* Day 54 (N5): IV cefazolin continued, caspofungin added for fungal coverage\n* Day 56 (N6): Atovaquone continued, tenofovir discontinued, dolutegravir/rilpivirine plus emtricitabine started\n\n**Outcome**\n\nThe patient's condition worsened over time, and he eventually died on day 62 due to his illness. Despite multiple treatments, including IV cefazolin, therapeutic enoxaparin, and caspofungin, the patient's immune system was unable to overcome the infections.\n\nNote: The narrative is based on the provided data and may not be a comprehensive or entirely accurate representation of the patient's medical history.", - "bertscore": { - "precision": [ - 0.7339485883712769 - ], - "recall": [ - 0.7237894535064697 - ], - "f1": [ - 0.7288336157798767 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 10, - "edge_count": 9, - "avg_in_degree": 0.9, - "density": 0.1 - }, - "trajectory_embedding": [ - 0.18157726526260376, - 0.24173596501350403, - -0.15064290165901184, - 0.07789953052997589, - 0.15454770624637604, - 0.16961298882961273, - -0.11799095571041107, - 0.21222464740276337, - 0.46130186319351196, - -0.346190482378006, - -0.21522000432014465, - 0.06953564286231995, - -0.6833328008651733, - 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However, based on the clinical presentation and imaging findings, it can be inferred that she is likely a young adult.\n\n**Initial Presentation (Step 1):**\nThe patient presented with a fluid collection adjacent to the spleen, which was identified through abdominal ultrasound. The fluid collection had septations, and no malignant cells were found in the aspirated fluid.\n\n**Progression of Disease (Steps 2-5):**\nOver time, the cystic lesion in the left upper quadrant of the abdomen grew in size, with a notable increase from 7.6 x 11.7 cm to 11 x 22 cm. The patient reported feeling pressure and a pulling sensation on the left side of her abdomen, rated as 4/10 for pain. Ultrasound-guided aspiration revealed 33 mL of clear yellow fluid, which was sent to pathology and showed no evidence of malignant cells.\n\n**Imaging Findings:**\nThroughout the course of the disease, various imaging modalities were used, including ultrasound, CT scans, and MRI. These studies consistently demonstrated a large cystic mass extending from the spleen on the left to the left hemipelvis, with enhancing septations.\n\n**Treatment (Step 7):**\nThe patient received doxycycline sclerotherapy over eight months as part of her treatment plan. Post-sclerotherapy ultrasound showed no significant changes in the size or appearance of the cystic mass.\n\n**Outcome:**\nDespite the growth of the cystic lesion, the patient did not experience any symptoms that would suggest malignancy. The sclerotherapy treatment appears to have been effective in stabilizing the lesion, and further imaging studies are scheduled for follow-up.\n\nIn summary, this patient presented with a fluid collection adjacent to the spleen, which progressed over time into a large cystic mass extending from the spleen on the left to the left hemipelvis. The patient received doxycycline sclerotherapy as part of her treatment plan, and post-treatment imaging studies showed no significant changes in the size or appearance of the lesion.", - "bertscore": { - "precision": [ - 0.7009899616241455 - ], - "recall": [ - 0.6653150320053101 - ], - "f1": [ - 0.6826867461204529 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.37995657324790955, - 0.09801924228668213, - 0.029700586572289467, - 0.12594357132911682, - 0.10155230760574341, - 0.09751962870359421, - -0.09553129225969315, - 0.2206941395998001, - 0.4248223304748535, - -0.16399696469306946, - -0.31089702248573303, - -0.05961534380912781, - -0.545925498008728, - 0.12594513595104218, - -0.3283112645149231, - 0.15797248482704163, - -0.0726936012506485, - 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He was admitted for his first cycle of chemotherapy for stage IV small cell lung cancer without cerebral metastases.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Diagnosis:** The patient's diagnosis of stage IV small cell lung cancer was confirmed upon admission.\n2. **Somnolence and Right-Sided Weakness:** 30 minutes after chemotherapy premedication, the patient experienced a sudden change in mental status, progressing to somnolence. Physical examination revealed altered mental status and right-sided weakness (N2).\n3. **Neurological Examination:** The patient's neurological examination showed signs of reduced mobility on the right side, accompanied by right facial paresis (N3).\n4. **Blood Gas Analysis and Brain CT Angiography:** Blood gas analysis showed no respiratory, metabolic, or electrolyte abnormalities, while brain CT angiography did not reveal any vascular lesions or thrombi in major vessels (N4).\n\n**Timeline of Treatments:**\n\n1. **Chemotherapy Premedication:** The patient received 4 mg intravenous ondansetron and 8 mg intravenous dexamethasone as premedication for chemotherapy.\n2. **Aspirin Administration:** Due to the suspicion of a transient ischemic event, a loading dose of 300 mg of aspirin was administered, followed by a daily dose of 100 mg of aspirin (N6).\n\n**Outcome:**\n\nThe patient gradually became more alert approximately one hour after the onset of symptoms and returned to his baseline mental status without any neurological deficits by one hour and thirty minutes after onset. The suspicion of a transient ischemic event as the primary cause of the symptoms was confirmed, and the patient's condition improved with the administration of aspirin.\n\n**Conclusion:**\n\nThis case highlights the importance of prompt recognition and management of acute neurological events in patients undergoing chemotherapy for cancer. Early intervention with aspirin may have contributed to the patient's rapid recovery from a suspected transient ischemic event. Further evaluation and monitoring are necessary to ensure that this patient does not experience any further complications related to his cancer treatment or underlying medical conditions.", - "bertscore": { - "precision": [ - 0.7189599275588989 - ], - "recall": [ - 0.7112793326377869 - ], - "f1": [ - 0.715099036693573 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.045807287096977234, - 0.11770268529653549, - -0.03572636470198631, - 0.021092357113957405, - 0.07645720988512039, - 0.007500001695007086, - 0.008010799996554852, - 0.14289645850658417, - 0.3722045123577118, - -0.33858588337898254, - -0.3850763738155365, - 0.18912379443645477, - -0.6559848189353943, - -0.16191299259662628, - -0.20137447118759155, - 0.0759354755282402, - 0.2702353894710541, - 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She has extensive bone metastases (cT4N3M1c, stage IVB).\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **November 2019:** The patient was diagnosed with left lung adenocarcinoma and had a baseline chest CT scan and head MRI performed.\n2. **December 2019:** Tumor tissue NGS revealed EGFR exon 18 p.G719S mutation and EGFR exon 20 p.S768I mutation, which led to the initiation of first-line afatinib treatment (40 mg daily po).\n3. **January 2020 - October 2020:** The patient experienced therapeutic failure after 10 months of afatinib treatment, as indicated by time to failure.\n4. **October 2020:** The patient developed new brain lesions and had a partial response on afatinib treatment (lung lesion stable disease, head lesions partial response).\n5. **February 2021:** The patient's brain lesions continued to deteriorate, leading to the reversion of third-line afatinib treatment.\n6. **February 2021:** The patient was switched to second-line osimertinib treatment (80 mg daily po).\n\n**Outcomes:**\n\n* Lung lesion stable disease (SD) at October 2020 and February 2021.\n* Head lesions partial response (PR) on afatinib treatment at October 2020 and February 2021.\n* Brain lesions deteriorated over time, with a new onset of symptoms in February 2021.\n\n**Medications:**\n\n* Afatinib (40 mg daily po): initiated in December 2019, experienced therapeutic failure after 10 months, and partially responsive to treatment at October 2020.\n* Osimertinib (80 mg daily po): started in February 2021 as a second-line treatment.\n\n**Imaging:**\n\n* Baseline chest CT scan and head MRI performed in November 2019.\n* Follow-up imaging not specified for each time point, but mentioned to be performed at October 2020 and February 2021.\n\nNote: The patient's timeline is based on the provided data, which may not be comprehensive or up-to-date.", - 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-0.21542488038539886, - 0.10511022061109543, - -0.1617775410413742 - ] -} \ No newline at end of file diff --git a/src/benchmark/output/results/results_graph_077.json b/src/benchmark/output/results/results_graph_077.json deleted file mode 100644 index 6436e0e..0000000 --- a/src/benchmark/output/results/results_graph_077.json +++ /dev/null @@ -1,795 +0,0 @@ -{ - "status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 66-year-old man who presented with persistent respiratory symptoms, including cough, sputum, chest tightness, and pain, for approximately 1 month. He received cefaclor and azithromycin at a local clinic without significant alleviation of his symptoms.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (September 2023):**\nThe patient was initially evaluated in an outpatient setting with persistent respiratory symptoms. A chest X-ray revealed a space-occupying mass in the left lung, prompting hospitalization on September 10, 2023.\n2. **Step 2 (September 10, 2023):**\nUpon admission, laboratory investigations were normal, and CT imaging demonstrated irregularly shaped soft tissue masses in both the upper and lower lobes of the left lung.\n3. **Step 3 (September 11-12, 2023):**\nFurther characterization of the lung mass was performed through additional CT imaging, which showed an oval mass in the lower lobe of the lung measuring approximately 2.3 cm x 1.7 cm with lobulated and spiculated margins.\n4. **Step 4 (September 13-14, 2023):**\nPET-CT imaging revealed high-density lesions in both the upper and lower lobes of the left lung, with increased glucose metabolism. Multiple enlarged lymph nodes were detected in the mediastinum and interlobular spaces.\n\n**Treatments:**\n\n1. **Step 1 (September 2023):**\nThe patient received cefaclor and azithromycin at a local clinic.\n2. **Step 2-4 (September 10-14, 2023):**\nNo specific treatments were mentioned in the provided data.\n\n**Outcomes:**\n\n1. **Imaging:** The initial chest X-ray revealed a space-occupying mass in the left lung, which was later characterized through additional imaging studies.\n2. **Laboratory Investigations:** Normal laboratory results were reported during hospitalization.\n3. **PET-CT Imaging:** High-density lesions with increased glucose metabolism were detected in both the upper and lower lobes of the left lung.\n\n**Conclusion:**\nThe patient's clinical presentation and diagnostic timeline suggest a complex respiratory condition, potentially related to malignancy or other pathologies. Further investigation and characterization are necessary to determine the underlying cause and develop an effective treatment plan.", - "bertscore": { - "precision": [ - 0.5229495763778687 - ], - "recall": [ - 0.6768455505371094 - ], - "f1": [ - 0.5900275707244873 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 4, - "edge_count": 3, - "avg_in_degree": 0.75, - "density": 0.25 - }, - "trajectory_embedding": [ - 0.28606685996055603, - 0.19629862904548645, - -0.1704561412334442, - 0.05046887323260307, - 0.02108978107571602, - -0.05829715356230736, - -0.002245333045721054, - 0.13291165232658386, - 0.2349492609500885, - -0.29417815804481506, - -0.1785058230161667, - 0.17046767473220825, - -0.6892815232276917, - -0.1641303449869156, - -0.12110166251659393, - -0.009564938955008984, - 0.20506024360656738, - 0.19735971093177795, - -0.06371694803237915, - -0.168881356716156, - 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She was diagnosed with stage IVa epidermal growth factor receptor (EGFR)L858R-mutated non-small cell lung cancer (NSCLC).\n\n**Timeline of Diagnoses:**\n\n* September 2019: The patient presented with symptoms of shortness of breath, cough, and hemoptysis, leading to a diagnosis of stage IVa (cT4N2M1a) lung adenocarcinoma in the right upper lobe, with multiple ipsilateral lung metastases, and involvement of the pleura and mediastinal lymph nodes.\n* September 2019: A bronchoscopic lung biopsy revealed the presence of EGFR p.L858R and TP53 p.R248L mutations.\n\n**Timeline of Treatments:**\n\n1. **First-Line Treatment (October 11, 2019 - February 2020)**:\nThe patient received first-line treatment with icotinib (125 mg orally, three times daily) and pemetrexed. After two months, the patient experienced partial response.\n2. **Second-Line Treatment (April 28, 2020 - July 2020)**:\nThe patient commenced second-line treatment with amonertinib (110 mg orally, once daily) in combination with anlotinib (12 mg orally, once daily for 2 weeks, followed by a 1-week drug-free period). The treatment resulted in stable disease initially but progressed after 3 months.\n3. **Third-Line Treatment (August 3, 2020 - November 2020)**:\nThe patient initiated treatment with osimertinib (80 mg orally, once daily) and bevacizumab (350 mg IV, on day 1 of a 21-day cycle). The treatment resulted in partial response after two cycles and significant reduction in tumor lesions after four cycles.\n4. **Fourth-Line Treatment (October 10, 2020 - present)**:\nThe patient received pembrolizumab (200 mg IV on day 1 of every 3 weeks), pemetrexed, and carboplatin. The treatment resulted in partial response after two cycles and significant reduction in tumor lesions after four cycles.\n\n**Outcomes:**\n\n* **Pathological Complete Response (pCR)**:\nThe patient achieved a pathological complete response (pCR) and prolonged survival.\n* **High PD-L1 Expression**:\nTumor microenvironment analysis showed high programmed cell death 1 ligand 1 (PD-L1) expression on tumor cells, indicating potential for immune checkpoint therapy.\n* **Increased Immune Cell Infiltration**:\nThe patient had increased infiltration of immune cells, particularly PD-1+CD8+T cells and PD-L1+macrophages, in the tumor microenvironment.\n\nIn conclusion, this patient's case highlights the importance of personalized medicine approaches in treating advanced NSCLC. The use of targeted therapies, such as EGFR inhibitors and immunotherapies, has led to significant improvements in treatment outcomes and quality of life for patients with this disease.", - "bertscore": { - "precision": [ - 0.5608479976654053 - ], - "recall": [ - 0.6207950711250305 - ], - "f1": [ - 0.5893009901046753 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.28967222571372986, - 0.13287165760993958, - -0.27321428060531616, - 0.1138295978307724, - -0.09009366482496262, - 0.025592172518372536, - 0.09159565716981888, - 0.1864396333694458, - 0.445202499628067, - -0.5484539866447449, - -0.1185631975531578, - 0.20055018365383148, - -0.6732085347175598, - -0.10172402113676071, - -0.23370732367038727, - 0.013881613500416279, - 0.015598686411976814, - 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He presented with a newly diagnosed lung cancer and a progressively increasing lump in the right axilla over 2 months.\n\n**Initial Diagnosis (Step 1):**\nUpon presentation, the patient underwent an ultrasound examination, which revealed a 3.7 cm enlarged lymph node (LN) in the right axilla with effacement and hypervascularity. A biopsy of the LN showed carcinoma with cytokeratin 7 (CK-7) and thyroid transcription factor-1 (TTF-1) positivity, consistent with lung adenocarcinoma, with a possibility of squamous component. Further imaging studies, including a PET scan, revealed multiple F-fluorodeoxyglucose (FDG) avid nodes in the right hilum, thoracic inlet, mediastinum, and right axilla, concerning for metastatic disease.\n\n**Treatment Initiation (Step 2):**\nThe patient was started on single-agent pembrolizumab, a checkpoint inhibitor, with good treatment response. However, after 17 months of treatment, the patient presented to the clinic with worsening shortness of breath (SOB), which he noted a few months ago, was mild in the beginning, and has progressively gotten worse in the last few weeks.\n\n**Progression and Complications (Step 3):**\nA recent PET scan did not show any evidence of disease progression or signs of inflammation in lungs. However, echocardiography revealed severe pulmonary arterial hypertension (PAH), with elevated right ventricular systolic pressure (RVSP) at 86 mm Hg. The patient also had mild regurgitation noted at the pulmonary valve with no structural abnormalities.\n\n**Current Status:**\nThe patient is currently under close observation for worsening symptoms and potential disease progression. Further management strategies, including additional immunotherapies or PAH-specific treatments, are being considered based on ongoing clinical evaluation.\n\n**Timeline of Diagnoses and Treatments:**\n\n* Month 0-2: Patient presents with newly diagnosed lung cancer and progressively increasing lump in the right axilla.\n* Month 2-17: Patient undergoes treatment with pembrolizumab, showing good initial response.\n* Month 17-present: Patient experiences worsening shortness of breath, prompting further evaluation.\n\n**Outcomes:**\n\n* The patient's current disease status is concerning for metastatic lung cancer with PAH.\n* Further management strategies are being considered to address the patient's worsening symptoms and potential disease progression.", - "bertscore": { - "precision": [ - 0.7466033101081848 - ], - "recall": [ - 0.7676594853401184 - ], - "f1": [ - 0.7569850087165833 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - 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"status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 46-year-old woman who was incidentally found to have a pulmonary nodule during a routine health examination. No symptoms were reported, and she had no significant medical history, including no history of tuberculosis or lung infections.\n\n**Initial Diagnosis (Step 1):**\nA chest radiograph revealed a solitary pulmonary nodule in the left lower lung field. The patient was diagnosed with a pulmonary nodule (code: 7225005) and underwent further evaluation.\n\n**Biopsy and Initial Treatment (Steps 2-3):**\nA peripheral pulmonary nodule was identified on a chest CT scan, which led to the performance of an endobronchial ultrasound transbronchial lung biopsy. The procedure was successful, but minor bleeding occurred. Biopsy specimens revealed granulomatous inflammation. Following this, a transbronchial lung cryobiopsy was performed four times through the same guide sheath, also with minor bleeding.\n\n**Post-Biopsy Complications and Treatment Initiation (Step 3):**\nAfter the cryobiopsy, increased density in the lower zone of the left lung was observed on chest radiograph. Tissue sample PCR tests were negative for Mycobacterium tuberculosis and NTM. However, one week post-biopsy, follow-up outpatient chest radiographs revealed an enlarged shadow at the location of the original lesion. The patient reported discharge of a purulent and intermittent blood-tinged sputum, which led to the initiation of antibiotic therapy with moxifloxacin (400 mg daily).\n\n**Response to Antibiotics and Follow-Up (Step 4):**\nTwo weeks after starting antibiotics, chest radiographs indicated a slight increase in the size of the lesion. However, there was an improvement in her symptoms, with no other abnormal findings such as fever. The antibiotic therapy continued with regular outpatient follow-ups.\n\n**Lesion Improvement and Acid-Fast Bacilli Growth (Step 5):**\nThree weeks after tissue biopsy, chest radiographs showed improvement in the lesion size. Notably, growth of acid-fast bacilli was reported in the bronchoalveolar lavage fluid obtained during examination.\n\n**Outcome:**\nThe patient's symptoms improved significantly with antibiotic therapy and follow-up care. The growth of acid-fast bacilli in the bronchoalveolar lavage fluid suggested that the patient had a Mycobacterium tuberculosis infection, which was confirmed by PCR tests. However, due to the presence of granulomatous inflammation in biopsy specimens, it is possible that the patient had an NTM infection as well.\n\n**Conclusion:**\nThe patient's case highlights the importance of prompt evaluation and treatment for pulmonary nodules, particularly those with granulomatous inflammation or acid-fast bacilli growth. Early detection and management can significantly improve outcomes and prevent complications.", - "bertscore": { - "precision": [ - 0.6428266167640686 - ], - "recall": [ - 0.7402181625366211 - ], - "f1": [ - 0.6880933046340942 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 2, - "node_count": 6, - "edge_count": 4, - "avg_in_degree": 0.6666666666666666, - "density": 0.13333333333333333 - }, - "trajectory_embedding": [ - 0.1967584788799286, - 0.11755304038524628, - -0.10197411477565765, - -0.01451544463634491, - -0.10492626577615738, - -0.16041645407676697, - 0.15277233719825745, - 0.07490139454603195, - 0.196526437997818, - -0.2453027218580246, - -0.23723392188549042, - 0.15686118602752686, - -0.45318803191185, - -0.14287793636322021, - -0.1919034719467163, - -0.01922443136572838, - 0.09047435224056244, - 0.2307237833738327, - 0.06612925231456757, - -0.30490654706954956, - -0.5095926523208618, - 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The patient's demographic information is not provided in the data.\n\n**Initial Presentation:**\nThe patient presented with symptoms of intracranial hypertension, including nausea and vomiting (Step 1). This was the initial presentation that led to further investigation.\n\n**Diagnosis:**\nFurther investigation revealed brain MRI suggesting leptomeningeal metastases (Step 2). Lumbar puncture was performed, and cerebrospinal fluid cytology confirmed leptomeningeal metastases (Step 3).\n\n**Treatment:**\nThe patient received treatment for the diagnosed condition. The treatment sequence included initial monotherapy with Olaparib, followed by combination therapy with intrathecal chemotherapy, and eventually a triple combination of Olaparib, Furmonertinib, and intrathecal chemotherapy (Step 5). Intrathecal pemetrexed was administered since October 2021 (Step 8).\n\n**Progression:**\nSymptoms of leptomeningeal metastases worsened dramatically, including lethargy, unresponsiveness, difficulty in eating and swallowing, necessitating intravenous nutritional support. The patient's ECOG performance status declined to 4 (Step 9). This marked a significant progression of the disease.\n\n**Outcome:**\nThe patient experienced a durable response to Olaparib lasting approximately 21 months (Step 6). However, the worsening of leptomeningeal metastases symptoms and decline in functional status necessitated further treatment adjustments.\n\n**Timeline:**\n\n* Step 1: Initial presentation with intracranial hypertension symptoms\n* Step 2: Diagnosis of leptomeningeal metastases confirmed by brain MRI\n* Step 3: Lumbar puncture performed, and cerebrospinal fluid cytology confirmed leptomeningeal metastases\n* Step 4: Placement of Ommaya reservoir for treatment delivery\n* Step 5: Identification of EGFR and BRCA2 mutations\n* Step 6: Initiation of Olaparib therapy with durable response lasting approximately 21 months\n* Step 7: Treatment escalation to combination therapy with intrathecal chemotherapy\n* Step 8: Administration of intrathecal pemetrexed since October 2021\n* Step 9: Worsening of leptomeningeal metastases symptoms and decline in functional status\n\n**Conclusion:**\nThe patient was diagnosed with leptomeningeal metastases and received treatment with Olaparib, Furmonertinib, and intrathecal chemotherapy. The patient experienced a durable response to Olaparib but ultimately required further treatment adjustments due to worsening of symptoms and decline in functional status.", - "bertscore": { - "precision": [ - 0.5512253046035767 - ], - "recall": [ - 0.5020527839660645 - ], - "f1": [ - 0.5254911780357361 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.2321387678384781, - 0.21690434217453003, - -0.13298587501049042, - 0.17195039987564087, - 0.08285973221063614, - 0.15777303278446198, - 0.1095961406826973, - 0.3161073923110962, - 0.6317851543426514, - -0.3226621448993683, - -0.16632980108261108, - -0.09433408826589584, - -0.4814378321170807, - -0.1313047707080841, - -0.1984696239233017, - 0.20387743413448334, - -0.17162606120109558, - 0.3204534351825714, - 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Unfortunately, the patient also had bilateral scattered breast metastases, which made her diagnosis even more complex.\n\nThe patient's journey began when she experienced persistent coughing for one month, which led to a chest CT scan that revealed a 3.1 cm right lower lobe tumor, lymphadenopathy, right pleural effusion, pericardial effusion, and scattered nodules in both breasts. Her CA19-9 level was also elevated at 282 U/mL.\n\nFollowing this initial diagnosis, the patient underwent further testing, including molecular analysis that detected an EML4-ALK fusion gene. This led to a biopsy of her bilateral breast tumors, which revealed adenocarcinoma derived from the lungs or breasts.\n\nThe patient's treatment plan began with oral medication, specifically alectinib (600 mg once daily), which was initiated in response to changes in her lab results and imaging findings. The goal of this treatment was to target the ALK rearrangement present in her cancer cells.\n\nOver time, the patient experienced significant reductions in tumor size, particularly in her breast metastases, which nearly disappeared after a maximum size of 4 mm. Her pleural effusion also resolved, and her CA19-9 level decreased from 282 U/mL to 3.7 U/mL.\n\nSix months after starting treatment with alectinib, the patient underwent another CT scan that showed further tumor shrinkage in her lower right lobe and resolution of her pleural effusion. This marked a significant milestone in her treatment journey, indicating that the medication was effective in controlling her cancer.\n\nThe patient's ongoing treatment with alectinib has been accompanied by regular monitoring of her lab results and imaging findings. Her CA19-9 level remains decreased, and she continues to experience no evidence of recurrence. The resolution of shadows in both breasts on CT scans also suggests that the medication is effective in controlling her breast metastases.\n\nThroughout this journey, the patient's treatment plan has been tailored to address changes in her lab results and imaging findings. Her care team has closely monitored her response to treatment and made adjustments as needed to ensure she receives the most effective therapy possible.\n\nThe patient's story highlights the importance of early detection and targeted therapies in managing complex cancers like pulmonary adenocarcinoma with bilateral breast metastases. With ongoing treatment and close monitoring, this patient is able to manage her disease effectively and maintain a good quality of life.", - "bertscore": { - "precision": [ - 0.6228880882263184 - ], - "recall": [ - 0.5976125597953796 - ], - "f1": [ - 0.6099885702133179 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.2193172574043274, - 0.17341764271259308, - -0.28511232137680054, - 0.06250262260437012, - -0.2072673738002777, - -0.09170977771282196, - 0.21316777169704437, - 0.09700273722410202, - 0.22861331701278687, - -0.39751580357551575, - -0.20688259601593018, - 0.24647818505764008, - -0.7876354455947876, - -0.08496146649122238, - -0.4245613217353821, - 0.042675264179706573, - 0.13037434220314026, - 0.3195406198501587, - 0.007097967900335789, - 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Unfortunately, the demographic information is not provided in the given data.\n\n**Initial Presentation (Step 1):**\nThe patient presented with right locus coeruleus, visceral inversion, sinusitis, and bronchial dilatation. These symptoms led to further cardiac evaluation.\n\n**Diagnostic Journey:**\n\n1. **Electrocardiography (ECG) and Initial Diagnosis (Step 2):**\nAn ECG showed a right-sided heart, prompting further imaging with chest CT and 3D reconstruction of the ribs to evaluate lung and organ positioning.\n\n2. **Chest CT Findings (Step 3):**\nThe chest CT revealed chronic inflammation of both lungs, multiple bronchiectasis in both lungs, nodules in the upper lobe of the right lung, a flaky high-density shadow in the right main bronchus, bilateral pleural thickening, localized calcification of the right pleura, and a right-sided heart with transposition of thoracic and abdominal organs.\n\n3. **Paranasal Sinus CT Findings (Step 4):**\nA paranasal sinus CT showed right maxillary sinusitis, ethmoid sinus, nasal soft tissue shadow, polyps, deviated nasal septum, and bilateral middle and lower turbinate hypertrophy.\n\n4. **Bronchoscopy Evaluation (Steps 5-6):**\nNormal bronchial tubes in the right lung led to further bronchoscopic evaluation of the left lung, where a polypoid neoplasm was found in the opening of the upper lobe of the left lung.\n\n5. **Cancer Diagnosis and Treatment Planning (Step 7):**\nBronchoalveolar lavage fluid cytology showed cancer cells, prompting immunohistochemistry to determine the type of cancer. The diagnosis confirmed small cell lung cancer.\n\n6. **Bone Metastasis Evaluation (Step 8):**\nExtrapulmonary auxiliary examination suggested bone metastasis.\n\n7. **Final Diagnosis and Treatment (Step 10):**\nThe patient was diagnosed with extensive stage small cell lung cancer of the left lung, accompanied by Kartagener Syndrome. The ECOG performance status score was 1.\n\n**Outcomes:**\n\n- The patient has been diagnosed with small cell lung cancer.\n- Bone metastasis is suspected but not confirmed.\n- Treatment plans are pending further evaluation and consultation.\n\nThis clinical case report highlights the importance of a comprehensive diagnostic journey, from initial presentation to final diagnosis. Each step in the diagnostic process builds upon previous findings, ultimately leading to an accurate diagnosis and treatment plan for this patient with small cell lung cancer.", - "bertscore": { - "precision": [ - 0.6484930515289307 - ], - "recall": [ - 0.6397433876991272 - ], - "f1": [ - 0.6440885066986084 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 10, - "edge_count": 9, - "avg_in_degree": 0.9, - "density": 0.1 - }, - "trajectory_embedding": [ - 0.3022826015949249, - -0.0002478778478689492, - 0.07108965516090393, - 0.18501682579517365, - 0.12881651520729065, - 0.13057772815227509, - 0.010211390443146229, - 0.27111274003982544, - 0.48087310791015625, - -0.30358201265335083, - -0.15933957695960999, - -0.05752738192677498, - -0.5778652429580688, - -0.08748479187488556, - -0.32486921548843384, - 0.2844110131263733, - 0.11371511220932007, - 0.32671236991882324, - 0.021662577986717224, - 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She had no history of smoking.\n\n**Timeline of Diagnoses:**\n\n1. **March 2022:** The patient initially presented to the hospital with symptoms of cough and chest pain, which led to a chest computed tomography (CT) scan.\n2. **March 21, 2022:** The CT scan revealed left pleural thickening and pleural effusion, prompting further investigation.\n3. **Thoracoscopic left pleural biopsy** was performed on the same day, followed by plasma DNA analysis via next-generation sequencing (NGS), which identified EGFR exon L858R mutation.\n4. **April 2022:** The diagnosis of stage IV lung adenocarcinoma with EGFR exon L858R mutation was confirmed.\n\n**Timeline of Treatments:**\n\n1. **March 2022:** The patient received osimertinib as the first-line treatment for her lung cancer.\n2. **May 22, 2022:** A follow-up chest CT scan revealed a partial response (PR) to osimertinib treatment.\n3. **April 4, 2024:** Due to progressive disease, the patient's treatment regimen was changed to dabrafenib, trametinib, and aumolertinib concurrently.\n4. **June 3, 2024:** A follow-up chest CT scan revealed a complete response (CR) to the new treatment regimen.\n\n**Timeline of Outcomes:**\n\n1. **May 22, 2022:** The patient experienced a partial response to osimertinib treatment.\n2. **April 4, 2024:** The patient's disease progressed, and she was diagnosed with progressive disease (PD).\n3. **June 3, 2024:** The patient achieved a complete response (CR) to the new treatment regimen.\n\n**Notable Events:**\n\n* During treatment with dabrafenib, trametinib, and aumolertinib, the patient experienced a transient fever.\n* The patient's disease was diagnosed as stage IV lung adenocarcinoma with EGFR exon L858R mutation.\n\n**Conclusion:**\nThe patient's clinical course was marked by an initial presentation of cough and chest pain, followed by a diagnosis of stage IV lung adenocarcinoma with EGFR exon L858R mutation. The patient received osimertinib as the first-line treatment and experienced a partial response. Due to progressive disease, the treatment regimen was changed to dabrafenib, trametinib, and aumolertinib concurrently, resulting in a complete response.", - "bertscore": { - "precision": [ - 0.6942758560180664 - ], - "recall": [ - 0.7067800760269165 - ], - "f1": [ - 0.7004721760749817 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 9, - "edge_count": 8, - "avg_in_degree": 0.8888888888888888, - "density": 0.1111111111111111 - }, - "trajectory_embedding": [ - 0.2675797641277313, - 0.21791553497314453, - -0.22618961334228516, - 0.11571652442216873, - -0.019790956750512123, - 0.05677139014005661, - 0.042519599199295044, - 0.1792418360710144, - 0.5141865611076355, - -0.34321343898773193, - -0.024482721462845802, - 0.13857966661453247, - -0.6468924880027771, - -0.25428396463394165, - -0.1651427149772644, - 0.1542055606842041, - -0.09829944372177124, - 0.31758415699005127, - 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Imaging findings revealed multiple nodular shadows of various sizes within the right cervical region posterior to the sternocleidomastoid muscle and adjacent to the carotid artery sheath, which partially fused.\n\n**Diagnosis (Step 2):**\nCT scans confirmed the presence of a pulmonary malignancy with cervical and mediastinal lymph node metastasis. The largest mass measured approximately 3.8 cm x 2.6 cm with indistinct margins and uneven ring-shaped enhancement.\n\n**Biopsy and Pathological Diagnosis (Step 3):**\nA CT-guided puncture biopsy of the mass in the left inferior lobe of the lung was performed, which led to a pathological diagnosis of lung carcinosarcoma.\n\n**Immunohistochemistry and NGS Testing (Step 4):**\nImmunohistochemistry revealed a Ki-67 index of 80%, while Next-Generation Sequencing (NGS) detected mutations in the TMB gene. These results further supported the presence of pulmonary carcinomas.\n\n**Timeline:**\n\n* January 28, 2023: Patient presents with progressively enlarging neck mass and imaging findings consistent with pulmonary malignancy.\n* January 28, 2023: CT-guided puncture biopsy is performed to confirm diagnosis.\n* (Date not specified): Immunohistochemistry and NGS testing are performed.\n\n**Outcomes:**\nThe patient's condition remains active, with ongoing management of the pulmonary carcinosarcoma. The results of immunohistochemistry and NGS testing have provided valuable information for further treatment planning.\n\nNote: The timeline is incomplete as some dates were not specified in the original data.", - "bertscore": { - "precision": [ - 0.547805905342102 - ], - "recall": [ - 0.6741754412651062 - ], - "f1": [ - 0.6044565439224243 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 4, - "edge_count": 3, - "avg_in_degree": 0.75, - "density": 0.25 - }, - "trajectory_embedding": [ - 0.26591718196868896, - -0.01149221882224083, - -0.05490458011627197, - 0.09002448618412018, - 0.12090761959552765, - -0.02566247433423996, - 0.06007498502731323, - 0.25383898615837097, - 0.2421899437904358, - -0.4905059337615967, - -0.13693289458751678, - 0.12649738788604736, - -0.6974141597747803, - 0.05220205709338188, - -0.4585632383823395, - 0.09128075838088989, - 0.19116288423538208, - 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She was diagnosed with [primary diagnosis] in [month/year].\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1 (N1):** The patient started treatment with osimertinib 160 mg in combination with phenytoin.\n2. **32 months after initiating osimertinib (N2):** A CT scan was performed, showing overall stable visceral and osseous disease. However, the left pleural effusion had completely resolved, while the right pleural effusion remained stable in size.\n3. **Patient developed nail changes with increasing brittleness (grade 1) (N3):** Seizure activity remained well controlled, but persistent dyspnea was noted.\n4. **Echocardiogram, exercise stress testing, cardiopulmonary exercise test, and pulmonary function tests (PFTs) were performed (N4):** These tests showed evidence of chronic obstructive lung disease (COPD) and emphysema.\n5. **Osimertinib dose was reduced to 80 mg daily for one week, then resumed at 160 mg daily due to persistent dyspnea (N5):** Despite the dose reduction, dyspnea did not significantly improve.\n6. **Patient achieved prolonged disease control on osimertinib treatment with continued osimertinib at a dose of 160 mg daily (N6):** Disease progression later stabilized following three cycles of carboplatin/pemetrexed.\n\n**Outcomes:**\n\n* The patient's dyspnea did not significantly improve despite the dose reduction of osimertinib.\n* However, she achieved prolonged disease control on osimertinib treatment with continued osimertinib at a dose of 160 mg daily.\n* The patient's COPD and emphysema were diagnosed and managed effectively.\n\n**Conclusion:**\nThe patient was initially treated with osimertinib 160 mg in combination with phenytoin. After 32 months, a CT scan showed overall stable disease, but persistent dyspnea remained a concern. Despite a dose reduction of osimertinib, the patient's dyspnea did not improve significantly. However, she achieved prolonged disease control on osimertinib treatment with continued dosing at 160 mg daily, and her COPD and emphysema were effectively managed.\n\n**Recommendations:**\n\n* Continue to monitor the patient's dyspnea and adjust the osimertinib dose as needed.\n* Consider adding additional treatments for COPD and emphysema, such as bronchodilators or corticosteroids.\n* Regularly review the patient's disease progression and adjust the treatment plan accordingly.", - "bertscore": { - "precision": [ - 0.5367745161056519 - ], - "recall": [ - 0.6528466939926147 - ], - "f1": [ - 0.5891479849815369 - ] - }, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.0932932123541832, - 0.22252197563648224, - -0.14526592195034027, - 0.15939070284366608, - 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Skipping dependency installation." fi -# echo "Running main..." -# python3 batch_run.py +echo "Running batch run..." +python3 batch_run.py echo "Generating plots..." python3 generate_visuals.py \ No newline at end of file diff --git a/src/graph/__init__.py b/src/graph/__init__.py index 8a3e458..e69de29 100644 --- a/src/graph/__init__.py +++ b/src/graph/__init__.py @@ -1,9 +0,0 @@ -# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) -# -# SPDX-License-Identifier: Apache-2.0 - - -""" - - -""" \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_001.json b/webapp/static/graphs/testset/graph_001.json new file mode 100644 index 0000000..d88caf0 --- /dev/null +++ b/webapp/static/graphs/testset/graph_001.json @@ -0,0 +1,344 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "44-year-old male presented with right-sided chest pain, dry cough, on-off fever, and hematuria for 2 months. Patient has no history of Antitubercular treatment (ATT) intake and was a tobacco chewer for >20 years. Physical examination revealed decreased air entry on the right side of the lung.", + "clinical_data": { + "HPI": [ + { + "summary": "right-sided chest pain, dry cough, on-off fever, and hematuria for 2 months", + "duration": "2 months", + "associated_symptoms": [ + "C0008031", + "C0010200", + "C0015967", + "C0019062" + ] + } + ], + "social_history": [ + { + "category": "tobacco", + "status": "current", + "description": "tobacco chewer for >20 years" + } + ] + } + }, + "custom_id": "graph_001_N0" + }, + { + "id": "N2", + "label": "Step 2", + "customData": { + "node_id": "B", + "node_step_index": 1, + "content": "Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within. Chest imaging showed multiple centrilobular nodules arranged in a linear branching pattern.", + "clinical_data": { + "imaging": [ + { + "type": "Computed tomography", + "body_part": "Thorax", + "modality": "CT", + "finding": "heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within", + "date": null + }, + { + "type": "Chest imaging", + "body_part": "Chest", + "modality": null, + "finding": "multiple centrilobular nodules arranged in a linear branching pattern", + "date": null + } + ] + } + }, + "custom_id": "graph_001_N1" + }, + { + "id": "N3", + "label": "Step 3", + "customData": { + "node_id": "C", + "node_step_index": 3, + "content": "Bronchoscopy with bronchoscopic-guided biopsy and Bronchoalveolar lavage (BAL) was performed. BAL fluid was negative for malignant cells. Biopsy was suggestive of squamous cell carcinoma.", + "clinical_data": { + "procedures": [ + { + "name": "Bronchoscopy", + "approach": "endoscopic", + "location": "lung", + "outcome": "negative for malignant cells" + }, + { + "name": "Biopsy", + "approach": "bronchoscopic-guided", + "location": "lung", + "outcome": "squamous cell carcinoma" + } + ], + "diagnoses": [ + { + "code": "C0007102", + "label": "Squamous Cell Carcinoma", + "status": "suspected" + } + ] + } + }, + "custom_id": "graph_001_N2" + }, + { + "id": "N4", + "label": "Step 4", + "customData": { + "node_id": "D", + "node_step_index": 4, + "content": "Patient reported decreased and blurring of vision. Ophthalmology opinion was within normal limits.", + "clinical_data": { + "HPI": [ + { + "summary": "Patient reported decreased and blurring of vision.", + "associated_symptoms": [ + "Blurring of vision" + ] + } + ] + } + }, + "custom_id": "graph_001_N3" + }, + { + "id": "N5", + "label": "Step 5", + "customData": { + "node_id": "E", + "node_step_index": 5, + "content": "18F-FDG PET/CT scan revealed a FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung. FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits with multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted. Multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary. 18F-FDG-PET/CT showed FDG avid bilateral hypodense renal masses (largest measuring 2.8 cm x 2.6 cm), multiple lytic skeletal lesions with soft tissue component involvement, FDG-avid right-sided lung mass with abdominal lymph node, and FDG-avid soft tissue lesion in the pituitary. Also shows another peripheral enhancing hypodense soft tissue lesion in the left cerebral hemisphere. CT and fused PET/CT axial images showing right parietal-occipital bone lytic lesion with soft tissue component involvement. Metabolically active soft tissue lesions were noted involving bilateral kidneys with extensive metastasis as seen in the FDG PET/CT scan.", + "clinical_data": { + "imaging": [ + { + "type": "Positron emission tomography/computed tomography", + "body_part": "lung", + "modality": "PET", + "finding": "FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography", + "body_part": "mediastinal, abdominopelvic lymph nodes", + "modality": "PET", + "finding": "FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits with multiple sub-centimetric to centimetric-sized bilateral lung nodules", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography", + "body_part": "brain", + "modality": "PET", + "finding": "Multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography", + "body_part": "kidneys", + "modality": "PET", + "finding": "FDG avid bilateral hypodense renal masses (largest measuring 2.8 cm x 2.6 cm)", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography", + "body_part": "skeletal", + "modality": "PET", + "finding": "multiple lytic skeletal lesions with soft tissue component involvement", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography", + "body_part": "pituitary", + "modality": "PET", + "finding": "FDG-avid soft tissue lesion in the pituitary", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography", + "body_part": "left cerebral hemisphere", + "modality": "PET", + "finding": "peripheral enhancing hypodense soft tissue lesion in the left cerebral hemisphere", + "date": null + }, + { + "type": "Computed tomography", + "body_part": "right parietal-occipital bone", + "modality": "CT", + "finding": "right parietal-occipital bone lytic lesion with soft tissue component involvement", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography", + "body_part": "kidneys", + "modality": "PET", + "finding": "Metabolically active soft tissue lesions were noted involving bilateral kidneys with extensive metastasis", + "date": null + } + ] + } + }, + "custom_id": "graph_001_N4" + }, + { + "id": "N6", + "label": "Step 6", + "customData": { + "node_id": "F", + "node_step_index": 7, + "content": "Patient presented with severe headaches and blurring of vision for 15 days.", + "clinical_data": { + "HPI": [ + { + "summary": "Patient presented with severe headaches and blurring of vision for 15 days.", + "duration": "15 days", + "onset": "unknown", + "progression": "unknown", + "associated_symptoms": [ + "C0018681", + "C0234587" + ] + } + ] + } + }, + "custom_id": "graph_001_N5" + }, + { + "id": "N7", + "label": "Step 7", + "customData": { + "node_id": "G", + "node_step_index": 9, + "content": "Biopsy results confirmed metastatic involvement.", + "clinical_data": { + "diagnoses": [ + { + "code": "C0009404", + "label": "Metastasis", + "status": "active" + } + ], + "procedures": [ + { + "name": "Biopsy", + "outcome": "positive for metastatic involvement" + } + ] + } + }, + "custom_id": "graph_001_N6" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Initial presentation and subsequent imaging", + "transition_event": { + "trigger_type": "imaging", + "trigger_entities": [], + "change_type": "addition", + "target_domain": "imaging" + } + }, + "custom_id": "graph_001_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "Bronchoscopy and biopsy performed to investigate the lesion", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "Bronchoscopy", + "Biopsy" + ], + "change_type": "addition", + "target_domain": "procedure" + } + }, + "custom_id": "graph_001_N2_N3" + }, + { + "from": "N3", + "to": "N4", + "data": { + "edge_id": "C_to_D", + "branch_flag": true, + "content": "Patient reported decreased and blurring of vision. Ophthalmology opinion was within normal limits." + }, + "custom_id": "graph_001_N3_N4" + }, + { + "from": "N4", + "to": "N5", + "data": { + "edge_id": "D_to_E", + "branch_flag": true, + "content": "PET/CT scan performed to assess the extent of the disease", + "transition_event": { + "trigger_type": "imaging", + "trigger_entities": [ + "PET/CT" + ], + "change_type": "addition", + "target_domain": "imaging" + } + }, + "custom_id": "graph_001_N4_N5" + }, + { + "from": "N5", + "to": "N6", + "data": { + "edge_id": "E_to_F", + "branch_flag": true, + "content": "Patient presented with severe headaches and blurring of vision.", + "transition_event": { + "trigger_type": "symptom_onset", + "trigger_entities": [ + "C0018681", + "C0234587" + ], + "change_type": "progression", + "target_domain": "symptom" + } + }, + "custom_id": "graph_001_N5_N6" + }, + { + "from": "N6", + "to": "N7", + "data": { + "edge_id": "F_to_G", + "branch_flag": true, + "content": "Biopsy results confirmed metastatic involvement.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "Biopsy" + ], + "change_type": "reinterpretation", + "target_domain": "diagnosis" + } + }, + "custom_id": "graph_001_N6_N7" + } + ] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_012.json b/webapp/static/graphs/testset/graph_012.json new file mode 100644 index 0000000..564a2a2 --- /dev/null +++ b/webapp/static/graphs/testset/graph_012.json @@ -0,0 +1,328 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "79-year-old male, height 174 cm, weight 65 kg, BMI 21.5 kg/m\u00b2, with a smoking history of two packs per day for 55 years (Brinkman Index 1100). History of total thyroidectomy five years prior for papillary thyroid carcinoma (PTC). Comorbidities include chronic obstructive pulmonary disease and hypertension.", + "clinical_data": { + "social_history": [ + { + "category": "smoking", + "status": "past", + "description": "two packs per day for 55 years (Brinkman Index 1100)" + } + ], + "diagnoses": [ + { + "code": "C0009404", + "label": "Chronic Obstructive Airway Disease", + "status": "active" + }, + { + "code": "C0020538", + "label": "Hypertension", + "status": "active" + }, + { + "code": "C0279738", + "label": "Papillary Thyroid Carcinoma", + "status": "historical" + } + ], + "procedures": [ + { + "name": "C0158554", + "date": null, + "location": "Thyroid gland", + "outcome": null + } + ] + } + }, + "custom_id": "graph_012_N0" + }, + { + "id": "N2", + "label": "Step 2", + "customData": { + "node_id": "B", + "node_step_index": 1, + "content": "Six years ago, the patient was found to have left cervical lymphadenopathy of unknown origin, suspected to be cervical lymph node metastasis of papillary thyroid carcinoma (PTC).", + "clinical_data": { + "diagnoses": [ + { + "code": "C0346403", + "label": "Papillary carcinoma of thyroid", + "status": "suspected", + "onset_date": null + } + ], + "imaging": [ + { + "type": "C0024311", + "body_part": "C0007664", + "modality": "other", + "finding": "Left cervical lymphadenopathy of unknown origin", + "impression": "Left cervical lymphadenopathy of unknown origin", + "date": null + } + ] + } + }, + "custom_id": "graph_012_N1" + }, + { + "id": "N3", + "label": "Step 3", + "customData": { + "node_id": "C", + "node_step_index": 2, + "content": "Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathology revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins.", + "clinical_data": { + "procedures": [ + { + "name": "Thyroidectomy, total", + "date": null, + "location": "thyroid gland", + "outcome": null, + "approach": null, + "performed_by": null + }, + { + "name": "Lymph node dissection", + "date": null, + "location": "left cervical lymph node", + "outcome": null, + "approach": null, + "performed_by": null + } + ], + "diagnoses": [ + { + "code": "C73", + "label": "Malignant neoplasm of thyroid gland", + "status": "historical", + "onset_date": null + } + ] + } + }, + "custom_id": "graph_012_N2" + }, + { + "id": "N4", + "label": "Step 4", + "customData": { + "node_id": "D", + "node_step_index": 3, + "content": "Patient was treated with radioiodine therapy (Iodine-131).", + "clinical_data": { + "medications": [ + { + "drug": "C0021843", + "dosage": null, + "frequency": null, + "modality": null, + "start_date": null, + "end_date": null, + "indication": null + } + ] + } + }, + "custom_id": "graph_012_N3" + }, + { + "id": "N5", + "label": "Step 5", + "customData": { + "node_id": "E", + "node_step_index": 4, + "content": "Two years prior to current encounter, a nodule in the right upper lobe of the lung was identified and monitored with chest CT scans. Increase in nodule density observed compared to two years prior, prompting a transbronchial biopsy; however, no definitive diagnosis was made. Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits.", + "clinical_data": { + "imaging": [ + { + "type": "Lung nodule", + "body_part": "Right upper lobe of lung", + "modality": "CT", + "finding": "Increase in nodule density", + "date": null + } + ], + "procedures": [ + { + "name": "Transbronchial biopsy", + "date": null, + "outcome": "No definitive diagnosis" + } + ], + "labs": [ + { + "test": "CYFRA 21-1", + "value": "within normal limits", + "flag": "normal" + }, + { + "test": "Carcinoembryonic antigen", + "value": "within normal limits", + "flag": "normal" + }, + { + "test": "Sialyl Lewis X-i antigen", + "value": "within normal limits", + "flag": "normal" + }, + { + "test": "Pro-gastrin-releasing peptide", + "value": "within normal limits", + "flag": "normal" + }, + { + "test": "Neuron-specific enolase", + "value": "within normal limits", + "flag": "normal" + } + ] + } + }, + "custom_id": "graph_012_N4" + }, + { + "id": "N6", + "label": "Step 6", + "customData": { + "node_id": "F", + "node_step_index": 5, + "content": "Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL. Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15\u00d714 mm in the S1 segment of the right upper lobe. No hilar lymphadenopathy was detected. Pulmonary function and electrocardiogram tests showed no abnormalities.", + "clinical_data": { + "labs": [ + { + "test": "Thyroglobulin Measurement", + "value": "47.7", + "unit": "ng/mL", + "flag": "abnormal" + } + ], + "imaging": [ + { + "type": "Lung X-Ray", + "body_part": "Thorax", + "modality": "X-ray", + "finding": "no abnormalities", + "date": null + }, + { + "type": "CT chest", + "body_part": "Thorax", + "modality": "CT", + "finding": "irregular nodule measuring 15\u00d714 mm in the S1 segment of the right upper lobe", + "impression": "irregular nodule measuring 15\u00d714 mm in the S1 segment of the right upper lobe", + "date": null + } + ] + } + }, + "custom_id": "graph_012_N5" + }, + { + "id": "N7", + "label": "Step 7", + "customData": { + "node_id": "G", + "node_step_index": 6, + "content": "A surgical plan was made to perform intraoperative rapid diagnosis, followed by right upper", + "clinical_data": {} + }, + "custom_id": "graph_012_N6" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Development of left cervical lymphadenopathy of unknown origin, suspected to be cervical lymph node metastasis of papillary thyroid carcinoma (PTC) six years ago." + }, + "custom_id": "graph_012_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "Patient underwent total thyroidectomy and left cervical lymph node dissection five years ago.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C0158554" + ], + "change_type": "addition", + "target_domain": "procedure" + } + }, + "custom_id": "graph_012_N2_N3" + }, + { + "from": "N3", + "to": "N4", + "data": { + "edge_id": "C_to_D", + "branch_flag": true, + "content": "Patient was treated with radioiodine therapy (Iodine-131).", + "transition_event": { + "trigger_type": "medication_change", + "trigger_entities": [ + "C0021843" + ], + "change_type": "addition", + "target_domain": "medication" + } + }, + "custom_id": "graph_012_N3_N4" + }, + { + "from": "N4", + "to": "N5", + "data": { + "edge_id": "D_to_E", + "branch_flag": true, + "content": "Two years prior to current encounter, a nodule in the right upper lobe of the lung was identified and monitored with chest CT scans. Increase in nodule density observed compared to two years prior, prompting a transbronchial biopsy; however, no definitive diagnosis was made. Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits." + }, + "custom_id": "graph_012_N4_N5" + }, + { + "from": "N5", + "to": "N6", + "data": { + "edge_id": "E_to_F", + "branch_flag": true, + "content": "Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL. Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15\u00d714 mm in the S1 segment of the right upper lobe. No hilar lymphadenopathy was detected. Pulmonary function and electrocardiogram tests showed no abnormalities.", + "transition_event": { + "trigger_type": "lab_change", + "trigger_entities": [ + "C0196343" + ], + "change_type": "progression", + "target_domain": "lab" + } + }, + "custom_id": "graph_012_N5_N6" + }, + { + "from": "N6", + "to": "N7", + "data": { + "edge_id": "F_to_G", + "branch_flag": true, + "content": "A surgical plan was made to perform intraoperative rapid diagnosis, followed by right upper" + }, + "custom_id": "graph_012_N6_N7" + } + ] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_013.json b/webapp/static/graphs/testset/graph_013.json new file mode 100644 index 0000000..ce856ea --- /dev/null +++ b/webapp/static/graphs/testset/graph_013.json @@ -0,0 +1,492 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "Patient diagnosed with stage III NSCLC and upper esophageal stricture around the same time.", + "clinical_data": { + "diagnoses": [ + { + "code": "C0678222", + "label": "Non-Small Cell Lung Carcinoma, Stage III", + "status": "active" + }, + { + "code": "C0015008", + "label": "Esophageal Stricture", + "status": "active" + } + ] + } + }, + "custom_id": "graph_013_N0" + }, + { + "id": "N2", + "label": "Step 2", + "customData": { + "node_id": "B", + "node_step_index": 1, + "content": "Initial MRI performed two months after NSCLC diagnosis was unremarkable.", + "clinical_data": { + "imaging": [ + { + "type": "MRI", + "body_part": "unspecified", + "modality": "MRI", + "finding": "unremarkable", + "date": null + } + ], + "diagnoses": [ + { + "code": "SNOMED:254291000", + "label": "Non-small cell lung carcinoma", + "status": "active", + "onset_date": null + } + ] + } + }, + "custom_id": "graph_013_N1" + }, + { + "id": "N3", + "label": "Step 3", + "customData": { + "node_id": "C", + "node_step_index": 2, + "content": "Follow-up CT one year later revealed metastatic spread throughout the brain after presentation to the ED with neurological weakness.", + "clinical_data": { + "imaging": [ + { + "type": "Computed tomography", + "body_part": "Brain", + "modality": "CT", + "finding": "metastatic spread", + "date": null + } + ], + "diagnoses": [ + { + "code": "C0205342", + "label": "Metastasis", + "status": "active", + "onset_date": null + } + ], + "HPI": [ + { + "summary": "neurological weakness", + "onset": null, + "progression": "unknown", + "associated_symptoms": [ + "Neurological deficit" + ], + "alleviating_factors": [], + "exacerbating_factors": [] + } + ] + } + }, + "custom_id": "graph_013_N2" + }, + { + "id": "N4", + "label": "Step 4", + "customData": { + "node_id": "D", + "node_step_index": 3, + "content": "CT head shows multifocal intracranial lesions with vasogenic edema indicative of metastases. Patient admitted to hospital and started on dexamethasone 4 mg twice daily, along with continued treatment for hypokalemia. Patient put on neutropenic precautions with orders to start infectious protocol and broad-spectrum antibiotics if temperature exceeds 100.4\u00b0F. Pantoprazole and enoxaparin sodium initiated for gastrointestinal and deep vein thrombosis prophylaxis.", + "clinical_data": { + "imaging": [ + { + "type": "Lesion (morphologic abnormality) (T019)", + "body_part": "Head (T008)", + "modality": "CT", + "finding": "multifocal intracranial lesions with vasogenic edema indicative of metastases", + "impression": "metastases", + "date": null + } + ], + "medications": [ + { + "drug": "Dexamethasone (C0011575)", + "dosage": "4 mg", + "frequency": "twice daily", + "modality": "oral", + "start_date": null, + "end_date": null, + "indication": "Vasogenic Edema (C0014209)" + }, + { + "drug": "Pantoprazole (C0876366)", + "dosage": null, + "frequency": null, + "modality": null, + "start_date": null, + "end_date": null, + "indication": "Gastrointestinal prophylaxis" + }, + { + "drug": "Enoxaparin sodium (C0701713)", + "dosage": null, + "frequency": null, + "modality": null, + "start_date": null, + "end_date": null, + "indication": "Deep vein thrombosis prophylaxis" + } + ], + "labs": [ + { + "test": "Potassium measurement (C0020144)", + "value": null, + "unit": null, + "flag": "abnormal", + "reference_range": null, + "timestamp": null + } + ], + "procedures": [ + { + "name": "Neutropenic precautions", + "approach": null, + "date": null, + "location": null, + "performed_by": null, + "outcome": null + } + ] + } + }, + "custom_id": "graph_013_N3" + }, + { + "id": "N5", + "label": "Step 5", + "customData": { + "node_id": "E", + "node_step_index": 4, + "content": "MRI confirms multiple new brain metastases with vasogenic edema and possible hemorrhagic components. Oncologist consulted and confirms metastasis to the brain and bone. Dexamethasone increased to 6 mg every eight hours. Enoxaparin sodium discontinued due to possible hemorrhages; mechanical prophylaxis started with thromboembolic deterrent stockings and sequential compression devices. Patient discharged home and began whole brain external radiation therapy dosed at 30 Gy over 10 fractions while holding docetaxel.", + "clinical_data": { + "imaging": [ + { + "type": "Brain MRI", + "body_part": "Brain", + "modality": "MRI", + "finding": "multiple new brain metastases with vasogenic edema and possible hemorrhagic components", + "impression": "multiple new brain metastases with vasogenic edema and possible hemorrhagic components", + "date": null + } + ], + "diagnoses": [ + { + "code": "C0242964", + "label": "Metastasis to the brain", + "status": "active", + "onset_date": null + }, + { + "code": "C0005731", + "label": "bone metastasis", + "status": "active", + "onset_date": null + } + ], + "medications": [ + { + "drug": "C0011872", + "dosage": "6 mg", + "frequency": "every eight hours", + "modality": "oral", + "start_date": null, + "end_date": null, + "indication": "vasogenic edema" + }, + { + "drug": "C0701884", + "dosage": null, + "frequency": null, + "modality": "subcutaneous", + "start_date": null, + "end_date": null, + "indication": "thromboembolic deterrent" + }, + { + "drug": "C0013371", + "dosage": null, + "frequency": null, + "modality": null, + "start_date": null, + "end_date": null, + "indication": "cancer" + } + ], + "procedures": [ + { + "name": "C1523758", + "approach": null, + "date": null, + "location": "brain", + "performed_by": null, + "outcome": null + } + ] + } + }, + "custom_id": "graph_013_N4" + }, + { + "id": "N6", + "label": "Step 6", + "customData": { + "node_id": "F", + "node_step_index": 5, + "content": "Patient tolerated radiation therapy well and docetaxel was re-initiated.", + "clinical_data": { + "procedures": [ + { + "name": "Radiation therapy", + "outcome": "tolerated" + } + ], + "medications": [ + { + "drug": "Docetaxel", + "modality": "IV", + "status": "re-initiated" + } + ] + } + }, + "custom_id": "graph_013_N5" + }, + { + "id": "N7", + "label": "Step 7", + "customData": { + "node_id": "G", + "node_step_index": 6, + "content": "CT scans revealed new developments in the liver and possibly pancreas, indicating refractory disease to second-line docetaxel.", + "clinical_data": { + "imaging": [ + { + "type": "CT scan", + "body_part": "Liver", + "modality": "CT", + "finding": "new developments", + "date": null + }, + { + "type": "CT scan", + "body_part": "Pancreas", + "modality": "CT", + "finding": "possibly new developments", + "date": null + } + ], + "diagnoses": [ + { + "code": null, + "label": "refractory disease to second-line docetaxel", + "status": "active", + "onset_date": null + } + ], + "medications": [ + { + "drug": "Docetaxel", + "dosage": null, + "frequency": null, + "modality": null, + "start_date": null, + "end_date": null, + "indication": null + } + ] + } + }, + "custom_id": "graph_013_N6" + }, + { + "id": "N8", + "label": "Step 8", + "customData": { + "node_id": "H", + "node_step_index": 7, + "content": "Oncologist discussed a third-line option and recommended hospice care.", + "clinical_data": { + "procedures": [ + { + "name": "Hospice care", + "date": null + } + ] + } + }, + "custom_id": "graph_013_N7" + }, + { + "id": "N9", + "label": "Step 9", + "customData": { + "node_id": "I", + "node_step_index": 8, + "content": "Brain MRI displays numerous intracranial lesions involving bilateral cerebral hemispheres, including lesions in the anterior right frontal lobe, left frontoparietal region, and left temporal lobe, with multiple smaller lesions scattered throughout.", + "clinical_data": { + "imaging": [ + { + "type": "Brain MRI", + "body_part": "Brain", + "modality": "MRI", + "finding": "Numerous intracranial lesions involving bilateral cerebral hemispheres, including lesions in the anterior right frontal lobe, left frontoparietal region, and left temporal lobe, with multiple smaller lesions scattered throughout.", + "impression": "Numerous intracranial lesions", + "date": null + } + ] + } + }, + "custom_id": "graph_013_N8" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Two months elapsed between NSCLC diagnosis and initial MRI.", + "transition_event": null + }, + "custom_id": "graph_013_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "One year elapsed between initial MRI and follow-up CT scan. Patient presented to the ED with neurological weakness.", + "transition_event": { + "trigger_type": "symptom_onset", + "trigger_entities": [ + "C0270970" + ], + "change_type": "progression", + "target_domain": "symptom" + } + }, + "custom_id": "graph_013_N2_N3" + }, + { + "from": "N3", + "to": "N4", + "data": { + "edge_id": "C_to_D", + "branch_flag": true, + "content": "Following CT scan, patient was admitted to hospital and started on dexamethasone, continued treatment for hypokalemia, and placed on neutropenic precautions. Pantoprazole and enoxaparin sodium were initiated.", + "transition_event": { + "trigger_type": "interpretation", + "trigger_entities": [ + "C0205342" + ], + "change_type": "progression", + "target_domain": "imaging" + } + }, + "custom_id": "graph_013_N3_N4" + }, + { + "from": "N4", + "to": "N5", + "data": { + "edge_id": "D_to_E", + "branch_flag": true, + "content": "MRI confirms multiple new brain metastases. Dexamethasone increased, enoxaparin sodium discontinued, and mechanical prophylaxis started. Patient discharged home and began whole brain external radiation therapy while holding docetaxel.", + "transition_event": { + "trigger_type": "medication_change", + "trigger_entities": [ + "C0011575", + "C0701713" + ], + "change_type": "escalation", + "target_domain": "medication" + } + }, + "custom_id": "graph_013_N4_N5" + }, + { + "from": "N5", + "to": "N6", + "data": { + "edge_id": "E_to_F", + "branch_flag": true, + "content": "Patient tolerated radiation therapy well.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C1523758" + ], + "change_type": "other", + "target_domain": "procedure" + } + }, + "custom_id": "graph_013_N5_N6" + }, + { + "from": "N6", + "to": "N7", + "data": { + "edge_id": "F_to_G", + "branch_flag": true, + "content": "Docetaxel was re-initiated, but CT scans revealed new developments in the liver and possibly pancreas, indicating refractory disease.", + "transition_event": { + "trigger_type": "medication_change", + "trigger_entities": [ + "C0013371" + ], + "change_type": "addition", + "target_domain": "medication" + } + }, + "custom_id": "graph_013_N6_N7" + }, + { + "from": "N7", + "to": "N8", + "data": { + "edge_id": "G_to_H", + "branch_flag": true, + "content": "Oncologist discussed a third-line option and recommended hospice care.", + "transition_event": { + "trigger_type": "interpretation", + "trigger_entities": [], + "change_type": "other", + "target_domain": "diagnosis" + } + }, + "custom_id": "graph_013_N7_N8" + }, + { + "from": "N8", + "to": "N9", + "data": { + "edge_id": "H_to_I", + "branch_flag": true, + "content": "Brain MRI displays numerous intracranial lesions involving bilateral cerebral hemispheres.", + "transition_event": { + "trigger_type": "imaging", + "trigger_entities": [], + "change_type": "progression", + "target_domain": "imaging" + } + }, + "custom_id": "graph_013_N8_N9" + } + ] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_014.json b/webapp/static/graphs/testset/graph_014.json new file mode 100644 index 0000000..3756dc2 --- /dev/null +++ b/webapp/static/graphs/testset/graph_014.json @@ -0,0 +1,135 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "Vancomycin administered for anti-infection and anti-viral treatment.", + "timestamp": "2023", + "clinical_data": { + "medications": [ + { + "drug": "C0042366", + "dosage": null, + "frequency": null, + "modality": null, + "start_date": null, + "end_date": null, + "indication": "C0003364" + }, + { + "drug": "C0042366", + "dosage": null, + "frequency": null, + "modality": null, + "start_date": null, + "end_date": null, + "indication": "C0043095" + } + ] + } + }, + "custom_id": "graph_014_N0" + }, + { + "id": "N2", + "label": "Step 2", + "customData": { + "node_id": "B", + "node_step_index": 1, + "content": "Repeat enhanced chest CT on May 29, 2023, showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32\u00d725\u00d727 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission.", + "timestamp": "2023-05-29", + "clinical_data": { + "imaging": [ + { + "type": "Cystic lesion", + "body_part": "Right upper lobe", + "modality": "CT", + "finding": "Irregular thin-walled cystic lesion with fine line compartments, measuring approximately 32\u00d725\u00d727 mm", + "date": "2023-05-29" + }, + { + "type": "Lymph node enlargement", + "body_part": "Mediastinum", + "modality": "CT", + "finding": "Enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions", + "date": "2023-05-29" + }, + { + "type": "Mass", + "body_part": "Right upper lobe", + "modality": "CT", + "finding": "Solid component of the right upper lobe mass had essentially disappeared", + "date": "2023-05-29" + } + ] + } + }, + "custom_id": "graph_014_N1" + }, + { + "id": "N3", + "label": "Step 3", + "customData": { + "node_id": "C", + "node_step_index": 2, + "content": "Second cycle of immunotherapy combined with chemotherapy administered.", + "timestamp": "2023-06-27", + "clinical_data": { + "procedures": [ + { + "name": "Immunotherapy", + "date": null + }, + { + "name": "Chemotherapy", + "date": null + } + ] + } + }, + "custom_id": "graph_014_N2" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Patient underwent repeat enhanced chest CT.", + "transition_event": { + "trigger_type": "imaging", + "trigger_entities": [], + "change_type": "other", + "target_domain": "imaging", + "timestamp": "2023-05-29T00:00:00Z" + } + }, + "custom_id": "graph_014_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "Second cycle of immunotherapy combined with chemotherapy administered.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C0019221", + "C0007407" + ], + "change_type": "addition", + "target_domain": "procedure", + "timestamp": "2023-06-27T00:00:00Z" + } + }, + "custom_id": "graph_014_N2_N3" + } + ] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_015.json b/webapp/static/graphs/testset/graph_015.json new file mode 100644 index 0000000..e071d9a --- /dev/null +++ b/webapp/static/graphs/testset/graph_015.json @@ -0,0 +1,45 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "76-year-old male with metastatic non-small cell carcinoma of the lung and history of coronary artery disease status post coronary artery bypass grafting (CABG). Patient presented with intracardiac metastasis and a transient ischemic attack.", + "clinical_data": { + "diagnoses": [ + { + "code": "C34.9", + "label": "Malignant neoplasm of unspecified part of bronchus or lung", + "status": "active" + }, + { + "code": "I25.10", + "label": "Atherosclerotic heart disease of native coronary artery without angina pectoris", + "status": "historical" + }, + { + "code": "I25.82", + "label": "Chronic total occlusion of coronary artery", + "status": "historical" + }, + { + "code": "I63.9", + "label": "Cerebral infarction, unspecified", + "status": "active" + } + ], + "procedures": [ + { + "name": "Coronary Artery Bypass Grafting", + "date": null + } + ] + } + }, + "custom_id": "graph_015_N0" + } + ], + "edges": [] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_016.json b/webapp/static/graphs/testset/graph_016.json new file mode 100644 index 0000000..eff3e6b --- /dev/null +++ b/webapp/static/graphs/testset/graph_016.json @@ -0,0 +1,333 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "51-year-old female patient (born in 1970) presented in April 2013 with a subsolid pulmonary lesion incidentally detected during a routine follow-up for malignant melanoma. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent.", + "timestamp": "2013-04", + "clinical_data": { + "diagnoses": [ + { + "code": "C43", + "label": "Malignant melanoma", + "status": "historical", + "onset_date": null + } + ], + "imaging": [ + { + "type": "Pulmonary lesion", + "body_part": "Lung", + "modality": "CT", + "finding": "subsolid pulmonary lesion", + "impression": "incidental finding", + "date": "2013-04" + } + ], + "procedures": [ + { + "name": "Resection", + "approach": "videothoracoscopic", + "date": null, + "location": "Lung", + "performed_by": null, + "outcome": null + } + ] + } + }, + "custom_id": "graph_016_N0" + }, + { + "id": "N2", + "label": "Step 2", + "customData": { + "node_id": "B", + "node_step_index": 1, + "content": "Patient underwent resection of malignant melanoma. Suspicious lymph node (LU) in the left axilla detected on ultrasound. Biopsy confirmed a metastasis of malignant melanoma in the left axillary lymph node. PET/CT showed a solitary finding in the left axilla.", + "clinical_data": { + "diagnoses": [ + { + "code": "C43", + "label": "Malignant melanoma", + "status": "active" + }, + { + "code": "C77.3", + "label": "Secondary malignant neoplasm of axilla and upper limb", + "status": "active" + } + ], + "imaging": [ + { + "type": "Ultrasound of axilla", + "body_part": "Axilla", + "modality": "Ultrasound", + "finding": "Suspicious lymph node", + "date": null + }, + { + "type": "Positron emission tomography/computed tomography (PET/CT)", + "body_part": "Axilla", + "modality": "PET/CT", + "finding": "Solitary finding in the left axilla", + "date": null + } + ], + "procedures": [ + { + "name": "Resection", + "approach": "open", + "date": null, + "location": "Malignant melanoma", + "performed_by": null, + "outcome": null + }, + { + "name": "Biopsy", + "approach": "percutaneous", + "date": null, + "location": "Left axillary lymph node", + "performed_by": null, + "outcome": "Metastasis of malignant melanoma" + } + ] + } + }, + "custom_id": "graph_016_N1" + }, + { + "id": "N3", + "label": "Step 3", + "customData": { + "node_id": "C", + "node_step_index": 2, + "content": "Left axillary dissection performed in late April 2013, revealing 1 of 19 lymph nodes with metastasis. Molecular genetic testing revealed a BRAF mutation at codon 600. Targeted therapy with BRAF inhibitors initiated. Follow-up at another institution assessed as stable disease.", + "timestamp": "2013-04", + "clinical_data": { + "procedures": [ + { + "name": "Axillary dissection", + "date": "2013-04", + "location": "left axilla", + "outcome": "metastasis in 1 of 19 lymph nodes" + } + ], + "diagnoses": [ + { + "code": "C0497156", + "label": "Metastasis", + "status": "active", + "onset_date": "2013-04" + }, + { + "code": "C0597447", + "label": "BRAF mutation", + "status": "active" + } + ], + "medications": [ + { + "drug": "BRAF inhibitors", + "modality": "oral", + "start_date": "2013-04", + "end_date": null + } + ] + } + }, + "custom_id": "graph_016_N2" + }, + { + "id": "N4", + "label": "Step 4", + "customData": { + "node_id": "D", + "node_step_index": 3, + "content": "November 2017: Routine CT scan of the lungs detected a new asymptomatic 7 mm lesion in segment S10 of the right lower lobe, with a density consistent with a pure ground glass nodule.", + "timestamp": "2017-11", + "clinical_data": { + "imaging": [ + { + "type": "Lung CT", + "body_part": "Lung", + "modality": "CT", + "finding": "7 mm lesion in segment S10 of the right lower lobe, with a density consistent with a pure ground glass nodule", + "impression": "New asymptomatic lesion", + "date": "2017-11" + } + ] + } + }, + "custom_id": "graph_016_N3" + }, + { + "id": "N5", + "label": "Step 5", + "customData": { + "node_id": "E", + "node_step_index": 4, + "content": "June 2020: Follow-up CT scan showed the lesion changed character to a subsolid lesion with the presence of a solid component. July 2020: PET/CT scan confirmed the persistence of the lesion without increased metabolic activity.", + "timestamp": "2020-06", + "clinical_data": { + "imaging": [ + { + "type": "Lesion", + "body_part": "Lung", + "modality": "CT", + "finding": "Subsolid lesion with solid component", + "date": "2020-06" + }, + { + "type": "Lesion", + "body_part": "Lung", + "modality": "PET/CT", + "finding": "Persistence of lesion without increased metabolic activity", + "date": "2020-07" + } + ] + } + }, + "custom_id": "graph_016_N4" + }, + { + "id": "N6", + "label": "Step 6", + "customData": { + "node_id": "F", + "node_step_index": 5, + "content": "April 2021: Follow-up confirmed persistence and slight size progression of the solid component of the lesion. Lesion size 12 mm with a solid component of 7 mm. May 2021: Patient was indicated by the multidisciplinary pulmonary committee for surgical resection.", + "timestamp": "2021-04", + "clinical_data": { + "imaging": [ + { + "type": "Lung lesion", + "body_part": "Lung", + "modality": "CT", + "finding": "Solid component of lesion with slight size progression", + "impression": "Persistence and slight size progression of the solid component of the lesion. Lesion size 12 mm with a solid component of 7 mm.", + "date": "2021-04" + } + ], + "procedures": [ + { + "name": "Surgical resection", + "date": "2021-05", + "indication": "Multidisciplinary pulmonary committee recommendation" + } + ] + } + }, + "custom_id": "graph_016_N5" + }, + { + "id": "N7", + "label": "Step 7", + "customData": { + "node_id": "G", + "clinical_data": {} + }, + "custom_id": "graph_016_N6" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Progression of malignant melanoma and detection of metastasis in the left axillary lymph node." + }, + "custom_id": "graph_016_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "Left axillary dissection and initiation of targeted therapy with BRAF inhibitors following detection of BRAF mutation.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C0004730" + 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"to": "N6", + "data": { + "edge_id": "E_to_F", + "branch_flag": true, + "content": "Persistence and slight size progression of the solid component of the lesion, leading to indication for surgical resection.", + "transition_event": { + "trigger_type": "imaging", + "trigger_entities": [ + "C0023418" + ], + "change_type": "progression", + "target_domain": "imaging", + "timestamp": "2021-04" + } + }, + "custom_id": "graph_016_N5_N6" + }, + { + "from": "N6", + "to": "N7", + "data": { + "edge_id": "F_to_G", + "branch_flag": true, + "content": "Surgical resection of lung lesion." + }, + "custom_id": "graph_016_N6_N7" + } + ] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_018.json b/webapp/static/graphs/testset/graph_018.json new file mode 100644 index 0000000..9e5e84a --- /dev/null +++ b/webapp/static/graphs/testset/graph_018.json @@ -0,0 +1,351 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 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mixed lytic-sclerotic tumor component, with the lytic aspect being more prominent in the anterior portion of the vertebral body.", + "clinical_data": { + "imaging": [ + { + "type": "Computed tomography", + "body_part": "T8 vertebral body", + "modality": "CT", + "finding": "Compression fracture with multiple fracture lines and a mixed lytic-sclerotic tumor component, with the lytic aspect being more prominent in the anterior portion of the vertebral body.", + "impression": "Compression fracture of the T8 vertebral body with mixed lytic-sclerotic tumor component" + } + ] + } + }, + "custom_id": "graph_018_N2" + }, + { + "id": "N4", + "label": "Step 4", + "customData": { + "node_id": "D", + "node_step_index": 3, + "content": "Mild posterior wall prominence without significant stenosis of the vertebral canal.", + "clinical_data": { + "imaging": [ + { + "type": "Posterior wall prominence", + "body_part": "Vertebral canal", + "modality": "X-ray", + "finding": "Mild posterior wall prominence 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"approach": "other", + "location": "spine", + "outcome": "treated" + }, + { + "name": "SpineJack system", + "approach": "other", + "location": "spine", + "outcome": "treated" + } + ], + "diagnoses": [ + { + "code": "compression fracture", + "label": "compression fracture", + "status": "active" + } + ] + } + }, + "custom_id": "graph_018_N5" + }, + { + "id": "N7", + "label": "Step 7", + "customData": { + "node_id": "P", + "node_step_index": 15, + "content": "Initial CT scan to assess the lesion\u2019s size, location, and radiological characteristics.", + "clinical_data": { + "imaging": [ + { + "type": "Computed tomography", + "body_part": "lesion", + "modality": "CT", + "finding": "size, location, and radiological characteristics" + } + ] + } + }, + "custom_id": "graph_018_N6" + }, + { + "id": "N8", + "label": "Step 8", + "customData": { + "node_id": "S", + "node_step_index": 18, + "content": "Patient positioned prone, and conscious sedation is administered using continuous intravenous infusion of fentanyl citrate (0.1 mg/2 mL diluted 1:10 with saline).", + "clinical_data": { + "medications": [ + { + "drug": "C0016007", + "dosage": "0.1 mg", + "modality": "IV", + "indication": "conscious sedation" + } + ], + "procedures": [ + { + "name": "conscious sedation", + "approach": "IV", + "performed_by": "unknown" + } + ] + } + }, + "custom_id": "graph_018_N7" + }, + { + "id": "N9", + "label": "Step 9", + "customData": { + "node_id": "V", + "node_step_index": 21, + "content": "Lidocaine (1\u20132%) is administered subcutaneously at the incision site using a 22-gauge intramuscular needle.", + "clinical_data": { + "medications": [ + { + "drug": "C0023642", + "dosage": "1-2%", + "modality": "subcutaneous" + } + ] + } + }, + "custom_id": "graph_018_N8" + }, + { + "id": "N10", + "label": "Step 10", + "customData": { + "node_id": "W", + "node_step_index": 22, + "content": "Bupivacaine (0.25%\u20130.5%) is infiltrated around the periosteum using an 18-gauge spinal needle (88 mm). Needle placement is verified with fluoroscopic and", + "clinical_data": { + "medications": [ + { + "drug": "C0006401", + "dosage": "0.25%-0.5%", + "modality": "other", + "indication": "C0003123" + } + ], + "procedures": [ + { + "name": "C0016581", + "approach": "percutaneous", + "location": "periosteum" + } + ], + "imaging": [ + { + "modality": "X-ray" + } + ] + } + }, + "custom_id": "graph_018_N9" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Progression from lung adenocarcinoma diagnosis to presentation with severe shoulder pain." + }, + "custom_id": "graph_018_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "Shoulder pain prompts CT scan." + }, + "custom_id": "graph_018_N2_N3" + }, + { + "from": "N3", + "to": "N4", + "data": { + "edge_id": "C_to_D", + "branch_flag": true, + "content": "Further characterization of vertebral canal." + }, + "custom_id": "graph_018_N3_N4" + }, + { + "from": "N4", + "to": "N5", + "data": { + "edge_id": "D_to_T", + "branch_flag": true, + "content": "Diagnosis of pathological fracture due to metastasis." + }, + "custom_id": "graph_018_N4_N5" + }, + { + "from": "N5", + "to": "N6", + "data": { + "edge_id": "T_to_U", + "branch_flag": true, + "content": "Treatment of pathological fracture with microwave ablation and SpineJack system.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "microwave ablation", + "SpineJack system" + ], + "change_type": "addition", + "target_domain": "procedure" + } + }, + "custom_id": "graph_018_N5_N6" + }, + { + "from": "N6", + "to": "N7", + "data": { + "edge_id": "U_to_P", + "branch_flag": true, + "content": "Initial CT scan to assess the lesion\u2019s size, location, and radiological characteristics." + }, + "custom_id": "graph_018_N6_N7" + }, + { + "from": "N7", + "to": "N8", + "data": { + "edge_id": "P_to_S", + "branch_flag": true, + "content": "Patient positioned prone, and conscious sedation is administered using continuous intravenous infusion of fentanyl citrate." + }, + "custom_id": "graph_018_N7_N8" + }, + { + "from": "N8", + "to": "N9", + "data": { + "edge_id": "S_to_V", + "branch_flag": true, + "content": "Lidocaine is administered subcutaneously at the incision site." + }, + "custom_id": "graph_018_N8_N9" + }, + { + "from": "N9", + "to": "N10", + "data": { + "edge_id": "V_to_W", + "branch_flag": true, + "content": "Bupivacaine is infiltrated around the periosteum, verified with fluoroscopic guidance." + }, + "custom_id": "graph_018_N9_N10" + } + ] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_019.json b/webapp/static/graphs/testset/graph_019.json new file mode 100644 index 0000000..16bd66f --- /dev/null +++ b/webapp/static/graphs/testset/graph_019.json @@ -0,0 +1,396 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "July 2023: 54-year-old male presented with facial and dorsal hand edema and was diagnosed with small-cell lung cancer (SCLC) with hilar, mediastinal lymph node, and pleural metastases (cT1N3M1a, extensive stage) and a PS score of 1.", + "clinical_data": { + "diagnoses": [ + { + "code": "C34.9", + "label": "Small cell lung cancer", + "status": "active", + "onset_date": "2023-07" + } + ], + "HPI": [ + { + "summary": "Facial and dorsal hand edema", + "onset": "2023-07" + } + ] + } + }, + "custom_id": "graph_019_N0" + }, + { + "id": "N2", + "label": "Step 2", + "customData": { + "node_id": "B", + "node_step_index": 1, + "content": "Patient started chemotherapy with four cycles of intravenous etoposide 160 mg (days 1\u20133), carboplatin (400 mg) on day 1, and serplulimab 300 mg on day 1 (Q3W). Received serplulimab maintenance therapy (Q3W).", + "clinical_data": { + "medications": [ + { + "drug": "etoposide", + "dosage": "160 mg", + "frequency": "days 1-3", + "modality": "IV", + "start_date": null, + "end_date": null + }, + { + "drug": "carboplatin", + "dosage": "400 mg", + "frequency": "day 1", + "modality": "IV", + "start_date": null, + "end_date": null + }, + { + "drug": "serplulimab", + "dosage": "300 mg", + "frequency": "Q3W", + "modality": "IV", + "start_date": null, + "end_date": null + }, + { + "drug": "serplulimab", + "dosage": "300 mg", + "frequency": "Q3W", + "modality": "IV", + "start_date": null, + "end_date": null + } + ], + "procedures": [ + { + "name": "chemotherapy", + "date": null + } + ] + } + }, + "custom_id": "graph_019_N1" + }, + { + "id": "N3", + "label": "Step 3", + "customData": { + "node_id": "C", + "node_step_index": 2, + "content": "After 18 cycles of chemotherapy and serplulimab maintenance, follow-up evaluations showed partial response (PR).", + "clinical_data": { + "medications": [ + { + "drug": "serplulimab", + "modality": "maintenance", + "indication": "partial response" + } + ], + "procedures": [ + { + "name": "chemotherapy", + "outcome": "partial response" + } + ] + } + }, + "custom_id": "graph_019_N2" + }, + { + "id": "N4", + "label": "Step 4", + "customData": { + "node_id": "D", + "node_step_index": 3, + "content": "After two cycles of serplulimab treatment, the patient intermittently (every 2\u20133 months) experienced hard stools and occasional constipation, relieved with glycerin suppositories.", + "clinical_data": { + "HPI": [ + { + "summary": "Patient experienced hard stools and occasional constipation intermittently (every 2-3 months)", + "duration": "2-3 months", + "alleviating_factors": [ + "glycerin suppositories" + ] + } + ] + } + }, + "custom_id": "graph_019_N3" + }, + { + "id": "N5", + "label": "Step 5", + "customData": { + "node_id": "E", + "node_step_index": 4, + "content": "September 9, 2024: Admitted to gastroenterology department due to 5 days of no bowel movement.", + "clinical_data": { + "HPI": [ + { + "summary": "Admitted to gastroenterology department due to 5 days of no bowel movement.", + "duration": "5 days", + "onset": "5 days prior to admission", + "progression": "unknown", + "associated_symptoms": [], + "alleviating_factors": [], + "exacerbating_factors": [] + } + ], + "diagnoses": [ + { + "code": "53741008", + "label": "Constipation", + "status": "active", + "onset_date": null + } + ] + } + }, + "custom_id": "graph_019_N4" + }, + { + "id": "N6", + "label": "Step 6", + "customData": { + "node_id": "F", + "node_step_index": 5, + "content": "Abdominal CT revealed diffuse dilatation and gas accumulation in the bowel, particularly the colon, suggesting incomplete intestinal obstruction.", + "clinical_data": { + "imaging": [ + { + "type": "Computed tomography of abdomen", + "body_part": "Abdomen", + "modality": "CT", + "finding": "diffuse dilatation and gas accumulation in the bowel, particularly the colon", + "impression": "incomplete intestinal obstruction" + } + ] + } + }, + "custom_id": "graph_019_N5" + }, + { + "id": "N7", + "label": "Step 7", + "customData": { + "node_id": "G", + "node_step_index": 6, + "content": "Gastroscopy showed chronic atrophic gastritis (C2) with bile reflux.", + "clinical_data": { + "diagnoses": [ + { + "code": "C0346239", + "label": "Chronic atrophic gastritis", + "status": "active" + } + ], + "procedures": [ + { + "name": "Gastroscopy", + "date": null + } + ] + } + }, + "custom_id": "graph_019_N6" + }, + { + "id": "N8", + "label": "Step 8", + "customData": { + "node_id": "H", + "node_step_index": 7, + "content": "Colonoscopy revealed a subpedunculated polyp approximately 1.5 cm in size, 20 cm from the anus, with smooth mucosa in the sigmoid colon. Colonoscopy reached the descending colon at 40 cm, where the mucosa and colonic haustra were smooth; however, due to severe pain and copious dry feces, the procedure was terminated.", + "clinical_data": { + "procedures": [ + { + "name": "Colonoscopy", + "date": null, + "location": "sigmoid colon", + "outcome": "terminated due to severe pain and copious dry feces" + } + ], + "imaging": [ + { + "type": "Polyp", + "body_part": "sigmoid colon", + "modality": "Colonoscopy", + "finding": "subpedunculated polyp approximately 1.5 cm in size, 20 cm from the anus, with smooth mucosa", + "date": null + } + ] + } + }, + "custom_id": "graph_019_N7" + }, + { + "id": "N9", + "label": "Step 9", + "customData": { + "node_id": "I", + "node_step_index": 8, + "content": "Patient experienced an inability to defecate and lost 20 kg in weight over 2 months.", + "clinical_data": { + "HPI": [ + { + "summary": "Patient experienced an inability to defecate and lost 20 kg in weight over 2 months.", + "duration": "2 months", + "progression": "gradual", + "associated_symptoms": [ + "C0013067", + "C0043127" + ] + } + ] + } + }, + "custom_id": "graph_019_N8" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Initiation of chemotherapy regimen for small-cell lung cancer." + }, + "custom_id": "graph_019_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "Patient continued chemotherapy and serplulimab maintenance.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C0009331" + ], + "change_type": "other", + "target_domain": "diagnosis" + } + }, + "custom_id": "graph_019_N2_N3" + }, + { + "from": "N3", + "to": "N4", + "data": { + "edge_id": "C_to_D", + "branch_flag": true, + "content": "Patient continued serplulimab treatment.", + "transition_event": { + "trigger_type": "medication_change", + "trigger_entities": [ + "C4721448" + ], + "change_type": "other", + "target_domain": "symptom" + } + }, + "custom_id": "graph_019_N3_N4" + }, + { + "from": "N4", + "to": "N5", + "data": { + "edge_id": "D_to_E", + "branch_flag": true, + "content": "Worsening constipation despite use of glycerin suppositories.", + "transition_event": { + "trigger_type": "symptom_onset", + "trigger_entities": [ + "C0009806" + ], + "change_type": "progression", + "target_domain": "symptom" + } + }, + "custom_id": "graph_019_N4_N5" + }, + { + "from": "N5", + "to": "N6", + "data": { + "edge_id": "E_to_F", + "branch_flag": true, + "content": "Evaluation for constipation.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C0009425" + ], + "change_type": "addition", + "target_domain": "imaging" + } + }, + "custom_id": "graph_019_N5_N6" + }, + { + "from": "N6", + "to": "N7", + "data": { + "edge_id": "F_to_G", + "branch_flag": true, + "content": "Further evaluation for gastrointestinal symptoms.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C0017158" + ], + "change_type": "addition", + "target_domain": "diagnosis" + } + }, + "custom_id": "graph_019_N6_N7" + }, + { + "from": "N7", + "to": "N8", + "data": { + "edge_id": "G_to_H", + "branch_flag": true, + "content": "Further evaluation for gastrointestinal symptoms.", + "transition_event": { + "trigger_type": "procedure", + "trigger_entities": [ + "C0009824" + ], + "change_type": "addition", + "target_domain": "imaging" + } + }, + "custom_id": "graph_019_N7_N8" + }, + { + "from": "N8", + "to": "N9", + "data": { + "edge_id": "H_to_I", + "branch_flag": true, + "content": "Continued gastrointestinal distress.", + "transition_event": { + "trigger_type": "symptom_onset", + "trigger_entities": [ + "C0013067", + "C0043127" + ], + "change_type": "progression", + "target_domain": "symptom" + } + }, + "custom_id": "graph_019_N8_N9" + } + ] +} \ No newline at end of file diff --git a/webapp/static/graphs/testset/graph_020.json b/webapp/static/graphs/testset/graph_020.json new file mode 100644 index 0000000..faa6993 --- /dev/null +++ b/webapp/static/graphs/testset/graph_020.json @@ -0,0 +1,554 @@ +{ + "nodes": [ + { + "id": "N1", + "label": "Step 1", + "customData": { + "node_id": "A", + "node_step_index": 0, + "content": "59-year-old male farmer with a history of hypertension and long-term smoking presented with redness and pain in the second toe of his right foot following a field injury, persisting for two weeks.", + "clinical_data": { + "HPI": [ + { + "summary": "59-year-old male farmer presented with redness and pain in the second toe of his right foot following a field injury, persisting for two weeks.", + "duration": "2 weeks", + "onset": "following a field injury", + "progression": "unknown", + "associated_symptoms": [ + "redness", + "pain" + ] + } + ], + "social_history": [ + { + "category": "smoking", + "status": "current", + "description": "long-term smoking" + } + ], + "diagnoses": [ + { + "code": "http://purl.bioontology.org/ontology/SNOMEDCT/59621000", + "label": "Hypertension", + "status": "historical" + } + ] + } + }, + "custom_id": "graph_020_N0" + }, + { + "id": "N2", + "label": "Step 2", + "customData": { + "node_id": "B", + "node_step_index": 1, + "content": "One week later, the patient developed redness and persistent pain in the left lumbar and groin areas, which was accompanied by coughing, expectoration, and a fever peaking at 38 \u00b0C.", + "clinical_data": { + "HPI": [ + { + "summary": "Patient developed redness and persistent pain in the left lumbar and groin areas one week later.", + "onset": "One week later", + "progression": "sudden", + "associated_symptoms": [ + "Redness", + "Pain" + ] + }, + { + "summary": "Patient experienced coughing, expectoration, and a fever peaking at 38 \u00b0C.", + "associated_symptoms": [ + "Coughing", + "Expectoration", + "Fever" + ] + } + ], + "vitals": [ + { + "type": "Fever", + "value": "38", + "unit": "\u00b0C" + } + ] + } + }, + "custom_id": "graph_020_N1" + }, + { + "id": "N3", + "label": "Step 3", + "customData": { + "node_id": "C", + "node_step_index": 2, + "content": "Admitted to a local hospital. Initial blood tests and a chest CT scan suggested the possibility of a bacterial infection (Table1).", + "clinical_data": { + "labs": [ + { + "test": "Blood test", + "timestamp": null + } + ], + "imaging": [ + { + "type": "CT of chest", + "body_part": "Chest", + "modality": "CT", + "date": null + } + ], + "diagnoses": [ + { + "code": "B0004944", + "label": "Bacterial Infections", + "status": "suspected", + "onset_date": null + } + ] + } + }, + "custom_id": "graph_020_N2" + }, + { + "id": "N4", + "label": "Step 4", + "customData": { + "node_id": "D", + "node_step_index": 3, + "content": "Patient was treated with piperacillin-tazobactam (4.5 g q8 h) for a week with no improvement.", + "clinical_data": { + "medications": [ + { + "drug": "C0724449", + "dosage": "4.5 g", + "frequency": "q8 h", + "modality": "IV", + "start_date": null, + "end_date": null, + "indication": null + } + ] + } + }, + "custom_id": "graph_020_N3" + }, + { + "id": "N5", + "label": "Step 5", + "customData": { + "node_id": "E", + "node_step_index": 4, + "content": "Patient transferred to the hospital with the following vital signs: body temperature 39.1 \u00b0C, heart rate 136 bpm, respiratory rate 36 breaths/minute, blood pressure 140/75 mmHg, and oxygen saturation 85%. Patient was stuporous, responsive to vocal stimuli yet unable to answer questions, with bilateral pupils which were equal, round, and reactive to light.", + "clinical_data": { + "vitals": [ + { + "type": "Body Temperature", + "value": "39.1", + "unit": "\u00b0C" + }, + { + "type": "Heart Rate", + "value": "136", + "unit": "bpm" + }, + { + "type": "Respiratory Rate", + "value": "36", + "unit": "breaths/minute" + }, + { + "type": "Blood Pressure", + "value": "140/75", + "unit": "mmHg" + }, + { + "type": "Oxygen Saturation", + "value": "85", + "unit": "%" + } + ], + "mental_status": [ + { + "domain": "consciousness", + "finding": "stuporous" + }, + { + "domain": "responsiveness", + "finding": "responsive to vocal stimuli" + }, + { + "domain": "speech", + "finding": "unable to answer questions" + }, + { + "domain": "pupils", + "finding": "equal, round, and reactive to light" + } + ] + } + }, + "custom_id": "graph_020_N4" + }, + { + "id": "N6", + "label": "Step 6", + "customData": { + "node_id": "F", + "node_step_index": 5, + "content": "Irregular heartbeat and coarse breath sounds in both lungs (no rales). HIV, AIGA, blood G test, GM test, and blood cultures were negative. Chest/brain CT scans were performed (Table1 and Fig.2(a, d)). Serial sputum cultures were conducted over three consecutive days; the initial specimen was inadequate (WBC < 10/LPF, epithelial cells 201/LPF).", + "clinical_data": { + "vitals": [ + { + "type": "Heart rate (finding)", + "value": "irregular", + "unit": null, + "timestamp": null + } + ], + "diagnoses": [ + { + "code": "B20", + "label": "HIV", + "status": "historical", + "onset_date": null + } + ], + "labs": [ + { + "test": "Blood culture", + "value": "negative", + "unit": null, + "flag": "normal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Sputum culture", + "value": "inadequate", + "unit": null, + "flag": "abnormal", + "reference_range": null, + "timestamp": null + } + ], + "imaging": [ + { + "type": "CT scan", + "body_part": "Chest", + "modality": "CT", + "finding": null, + "impression": null, + "date": null + }, + { + "type": "CT scan", + "body_part": "Brain", + "modality": "CT", + "finding": null, + "impression": null, + "date": null + } + ] + } + }, + "custom_id": "graph_020_N5" + }, + { + "id": "N7", + "label": "Step 7", + "customData": { + "node_id": "G", + "node_step_index": 6, + "content": "Subsequent sputum specimens exhibited cellular profiles consistent with lower respiratory origin (WBC 35\u201350/LPF, epithelial cells 5\u20138/LPF), with persistent isolation of Burkholderia cepacia (2/2 cultures).", + "clinical_data": { + "labs": [ + { + "test": "White blood cell count", + "value": "35-50", + "unit": "/LPF", + "flag": "abnormal" + }, + { + "test": "Epithelial cells", + "value": "5-8", + "unit": "/LPF", + "flag": "abnormal" + }, + { + "test": "Burkholderia cepacia culture", + "value": "positive", + "unit": "2/2 cultures" + } + ] + } + }, + "custom_id": "graph_020_N6" + }, + { + "id": "N8", + "label": "Step 8", + "customData": { + "node_id": "H", + "node_step_index": 7, + "content": "Week 3: Patient experienced cough, expectoration, fever, left lumbar/groin erythema/pain. White blood cell count (\u00d710\u2079/L): 15.41, Neutrophil count (\u00d710\u2079/L): 6.3, Neutrophil percentage: 92.6, Albumin(g/L): 29, C-reactive protein(\u03bcmol/L): 90.8, Procalcitonin(ng/mL): 3.05, N-terminal pro b-type natriuretic peptide(pg/mL): 10675, Alanine aminotransferase(U/L): 11, Aspartate aminotransferase(U/L): 16, Creatinine(\u03bcmol/L): 295.5.", + "clinical_data": { + "HPI": [ + { + "summary": "Patient experienced cough, expectoration, fever, left lumbar/groin erythema/pain.", + "duration": "1 week", + "onset": "3 weeks prior to current encounter", + "progression": "unknown", + "associated_symptoms": [ + "cough", + "expectoration", + "fever", + "erythema", + "pain" + ], + "alleviating_factors": [], + "exacerbating_factors": [] + } + ], + "labs": [ + { + "test": "White blood cell count", + "value": "15.41", + "unit": "\u00d710\u2079/L", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Neutrophil count", + "value": "6.3", + "unit": "\u00d710\u2079/L", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Neutrophil percentage", + "value": "92.6", + "unit": "%", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Albumin", + "value": "29", + "unit": "g/L", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + }, + { + "test": "C-reactive protein", + "value": "90.8", + "unit": "\u03bcmol/L", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Procalcitonin", + "value": "3.05", + "unit": "ng/mL", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + }, + { + "test": "N-terminal pro b-type natriuretic peptide", + "value": "10675", + "unit": "pg/mL", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Alanine aminotransferase", + "value": "11", + "unit": "U/L", + "flag": "normal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Aspartate aminotransferase", + "value": "16", + "unit": "U/L", + "flag": "normal", + "reference_range": null, + "timestamp": null + }, + { + "test": "Creatinine", + "value": "295.5", + "unit": "\u03bcmol/L", + "flag": "abnormal", + "reference_range": null, + "timestamp": null + } + ] + } + }, + "custom_id": "graph_020_N7" + }, + { + "id": "N9", + "label": "Step 9", + "customData": { + "node_id": "I", + "node_step_index": 8, + "content": "Week 4: Patient experienced stupor and hypoxia (SpO\u2082 85%). Cardiac: atrial fibrillation. White blood cell count (\u00d710\u2079/L): 10.01, Neutrophil count (\u00d710\u2079/L): 10.08, Neutrophil percentage: 92.8, Albumin(g/L): 22.8, C-reactive protein(\u03bcmol/L): 176.8, Procalcitonin(ng/mL): 30.58. Electrocardiogram indicated atrial fibrillation. Antimicrobial susceptibility testing indicated sensitivity to meropenem (MIC 4 \u03bcg/mL).", + "clinical_data": { + "vitals": [ + { + "type": "SpO2", + "value": "85", + "unit": "%" + } + ], + "labs": [ + { + "test": "White blood cell count", + "value": "10.01", + "unit": "x10^9/L" + }, + { + "test": "Neutrophil count", + "value": "10.08", + "unit": "x10^9/L" + }, + { + "test": "Neutrophil percentage", + "value": "92.8", + "unit": "%" + }, + { + "test": "Albumin", + "value": "22.8", + "unit": "g/L" + }, + { + "test": "C-reactive protein", + "value": "176.8", + "unit": "\u03bcmol/L" + }, + { + "test": "Procalcitonin", + "value": "30.58", + "unit": "ng/mL" + } + ], + "diagnoses": [ + { + "code": "Atrial fibrillation", + "label": "Atrial fibrillation", + "status": "active" + } + ], + "mental_status": [ + { + "domain": "consciousness", + "finding": "stupor" + } + ], + "medications": [ + { + "drug": "Meropenem", + "indication": "infection", + "sensitivity": "sensitive", + "MIC": "4 \u03bcg/mL" + } + ] + } + }, + "custom_id": "graph_020_N8" + } + ], + "edges": [ + { + "from": "N1", + "to": "N2", + "data": { + "edge_id": "A_to_B", + "branch_flag": true, + "content": "Patient transitioned from toe redness/pain to lumbar/groin redness/pain, coughing, expectoration, and fever." + }, + "custom_id": "graph_020_N1_N2" + }, + { + "from": "N2", + "to": "N3", + "data": { + "edge_id": "B_to_C", + "branch_flag": true, + "content": "Patient was admitted to a local hospital, and initial tests suggested a possible bacterial infection." + }, + "custom_id": "graph_020_N2_N3" + }, + { + "from": "N3", + "to": "N4", + "data": { + "edge_id": "C_to_D", + "branch_flag": true, + "content": "Patient was treated with piperacillin-tazobactam." + }, + "custom_id": "graph_020_N3_N4" + }, + { + "from": "N4", + "to": "N5", + "data": { + "edge_id": "D_to_E", + "branch_flag": true, + "content": "Patient transferred to the hospital with worsening vital signs and altered mental status despite treatment." + }, + "custom_id": "graph_020_N4_N5" + }, + { + "from": "N5", + "to": "N6", + "data": { + "edge_id": "E_to_F", + "branch_flag": true, + "content": "Further testing including cultures and CT scans were performed, with initial negative results for HIV, AIGA, blood G test, GM test, and blood cultures." + }, + "custom_id": "graph_020_N5_N6" + }, + { + "from": "N6", + "to": "N7", + "data": { + "edge_id": "F_to_G", + "branch_flag": true, + "content": "Sputum specimens confirmed Burkholderia cepacia infection." + }, + "custom_id": "graph_020_N6_N7" + }, + { + "from": "N7", + "to": "N8", + "data": { + "edge_id": "G_to_H", + "branch_flag": true, + "content": "Patient experienced persistent symptoms and abnormal lab values." + }, + "custom_id": "graph_020_N7_N8" + }, + { + "from": "N8", + "to": "N9", + "data": { + "edge_id": "H_to_I", + "branch_flag": true, + "content": "Patient developed stupor, hypoxia, and atrial fibrillation, with worsening lab values. Antimicrobial susceptibility testing indicated sensitivity to meropenem." + }, + "custom_id": "graph_020_N8_N9" + } + ] +} \ No newline at end of file From 6aa85eb3e4e02be4976026723ad807b302793de8 Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Sat, 10 May 2025 16:22:05 -0700 Subject: [PATCH 06/11] Add benchmarking results in --- src/benchmark/generate_visuals.py | 2 +- .../output/plots/bertscore_f1_barplot.png | Bin 18136 -> 30152 bytes .../output/plots/metrics_summary.csv | 77 ++ .../output/plots/topology_distributions.png | Bin 31555 -> 45771 bytes .../output/plots/trajectory_tsne.png | Bin 20685 -> 43188 bytes .../output/results/results_graph_001.json | 792 ++++++++++++++++++ .../output/results/results_graph_003.json | 792 ++++++++++++++++++ .../output/results/results_graph_004.json | 792 ++++++++++++++++++ .../output/results/results_graph_005.json | 792 ++++++++++++++++++ .../output/results/results_graph_006.json | 792 ++++++++++++++++++ .../output/results/results_graph_007.json 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metastatic lung cancer and brain lesions.\n* September 2023: The cerebellar tumor is treated successfully with X-knife radiosurgery.\n* October 2023: Follow-up imaging shows immune unconfirmed progressive disease (iUPD) in the upper left lobe, indicating a potential recurrence of the cancer.\n\n**Clinical Progression:**\nThe patient's clinical progression has been marked by an initial presentation of symptoms suggestive of neurological involvement (headaches, forgetfulness, hand tremors), followed by a diagnosis of metastatic lung cancer with brain lesions. The patient underwent surgery for a tumor in the frontal region of the left hemisphere of the brain and was treated with X-knife radiosurgery for the cerebellar tumor. Despite these interventions, follow-up imaging has revealed immune unconfirmed progressive disease (iUPD) in the upper left lobe, indicating a potential recurrence of the cancer.\n\n**Conclusion:**\nThis patient's clinical case highlights the complexities of managing metastatic lung cancer with brain lesions. The patient's initial presentation and subsequent diagnosis were marked by significant neurological involvement, which required prompt intervention. While the patient has undergone several treatments, including surgery and X-knife radiosurgery, follow-up imaging has revealed a potential recurrence of the cancer. 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He has no other notable medical history.\n\n**Initial Presentation (Step 1):**\nThe patient presented to the emergency department due to cough, dyspnea, and throat pain. This was his first visit to the hospital in two weeks, during which he had undergone noncontrast CT scans that showed a 5.0 x 5.0 cm tumor in the superior-to-anterior mediastinum.\n\n**Imaging Findings (Step 2):**\nFollow-up imaging revealed an enlarged shadow in the right upper mediastinum on chest radiography, which was later confirmed by CT scan to be a mediastinal mass.\n\n**Progression of Disease (Steps 3-5):**\nOver two weeks, the tumor grew from 5.0 x 5.0 cm to 9.0 x 7.0 cm in size, causing compression and narrowing of the right brachiocephalic vein and superior vena cava, as well as left deviation of the trachea.\n\n**Symptom Onset (Step 4):**\nThe patient developed respiratory symptoms, including cough, dyspnea, and throat pain, which prompted further imaging to evaluate the cause of these symptoms.\n\n**Imaging Evaluation (Steps 5-6):**\nNoncontrast CT scans two weeks prior to admission showed a tumor in the superior-to-anterior mediastinum. Dynamic CT scans at admission revealed a weakly enhanced tumor in the superior-to-middle mediastinum, which had grown to 9.0 x 7.0 cm over two weeks.\n\n**Laboratory Findings (Step 6):**\nLaboratory tests revealed slightly elevated levels of lactate dehydrogenase (LDH) and C-reactive protein (CRP), indicating inflammation or infection. Tumor markers, including CYFRA, pro-GRP, CEA, and CA19-9, were all negative.\n\n**Current Status:**\nThe patient is currently undergoing further evaluation and treatment for the mediastinal mass. The exact treatment plan has not been disclosed in this report.\n\n**Outcomes:**\nThe patient's current condition and potential outcomes are unknown at this time. Further follow-up will be necessary to determine the effectiveness of any treatments and to monitor for any changes in the patient's condition.", + "bertscore": { + "precision": 0.8157233595848083, + "recall": 0.8282085657119751, + "f1": 0.8219186067581177 + }, + "bleu": 0.08249739602739622, + "rouge1": 0.42085308056872034, + "rougeL": 0.21611374407582937, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.3709355294704437, + 0.02028684876859188, + -0.037475328892469406, + 0.05414177477359772, + 0.11516084522008896, + 0.028672976419329643, + 0.002444108249619603, + 0.26623213291168213, + 0.3955191671848297, + -0.28058165311813354, + -0.18973876535892487, + 0.09418404847383499, + -0.6652488708496094, + -0.08837980031967163, + -0.3189680576324463, + 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significant smoking history (25-pack-year). He presented with left focal motor seizure and expressive aphasia, which led to the diagnosis of Seizure (C0003638) and Aphasia, Expressive (C0003684).\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation:** The patient was diagnosed with Seizure (C0003638) and Aphasia, Expressive (C0003684) upon presentation.\n2. **Brain MRI:** A brain MRI revealed innumerable supra- and infratentorial peripheral enhancing lesions with edema, suggesting intracranial metastases (N2).\n3. **PET-CT:** Further investigation with PET-CT identified the primary cancer source as a hypermetabolic left lung mass and mediastinal and supraclavicular lymph nodes compatible with lung cancer (N3).\n4. **Lung Mass Biopsy:** Endobronchial biopsy of the lung mass revealed adenocarcinoma, with PD-L1 IHC testing showing 100% positivity and HER2 amplification (N4).\n\n**Timeline of Treatments:**\n\n1. **Pembrolizumab:** The patient was started on pembrolizumab due to high PD-L1 expression.\n2. **WBRT:** Whole-brain radiation therapy (WBRT) was recommended for brain metastases, but the treatment was discontinued after 1 cycle due to worsening of brain metastases.\n3. **T-DXd and Bevacizumab:** The patient's treatment was changed to T-DXd and bevacizumab due to disease progression and cerebral edema.\n\n**Timeline of Outcomes:**\n\n1. **Follow-up Brain MRI:** A repeat brain MRI 6 weeks after starting T-DXd revealed remarkable improvement in cerebral edema and metastases.\n2. **Repeat CT Chest:** A repeat CT chest scan showed a decrease in size of the previously noted spiculated left lower lung mass.\n\n**Conclusion:**\nThe patient's clinical course was marked by significant progression of brain metastases, which led to changes in treatment. Despite initial worsening, T-DXd and bevacizumab treatment resulted in remarkable improvement in cerebral edema and metastases, suggesting a positive response to therapy.", + "bertscore": { + "precision": 0.8003971576690674, + "recall": 0.784216046333313, + "f1": 0.7922239899635315 + }, + "bleu": 0.14053318317372476, + "rouge1": 0.4970414201183431, + "rougeL": 0.31952662721893493, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.2637527883052826, + 0.15972600877285004, + -0.13202765583992004, + 0.0957951694726944, + -0.04258505254983902, + 0.0973554328083992, + -0.016224455088377, + 0.34089890122413635, + 0.39410585165023804, + -0.33490127325057983, + -0.20745256543159485, + 0.13487695157527924, + -0.6351459622383118, + -0.0365443155169487, + 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patient in question is a 55-year-old male who was initially diagnosed with intermittent dry cough and left temporal headaches. Over time, his symptoms progressed to subacute vertigo, nausea, vomiting, and ataxia. These symptoms led to hospital admission, where initial investigations including cranial MRI and CSF analysis were unremarkable.\n\nFollowing the progression of symptoms, negative paraneoplastic antibody profiles and anti-neuronal surface antigen antibody spectrum in blood and CSF were found, indicating that symptomatic therapy was ineffective. The patient's condition continued to deteriorate, leading to hospital admission with positive Romberg sign and gait ataxia. A CT scan revealed a solid mass shadow in the upper lobe of the right lung, along with multiple enlarged lymph nodes in both hilum and mediastinum.\n\nAbnormal serum tumor markers, including SCCAg, NSE, and Cyfra21-1, were detected, and the patient was diagnosed with squamous cell lung carcinoma. Contrast-enhanced MRI of the head showed no obvious abnormality, but PET-CT revealed a malignant lesion in the upper lobe of the right lung with multiple lymph node metastasis.\n\nThe histological and immunohistochemical results confirmed that the patient had squamous cell lung carcinoma. Following this diagnosis, oral prednisone was initiated to alleviate symptoms such as vertigo, nausea, and vomiting. Intravenous immunoglobulin (IVIG) was also started, which led to an improvement in these symptoms.\n\nThe patient's treatment plan included three courses of intravenous etoposide and cisplatin, with radiotherapy administered at a dose of 50.4 Gy. The timeline for the patient's diagnosis and treatment is as follows:\n\n* Initial symptoms: intermittent dry cough and left temporal headaches\n* Progression of symptoms: subacute vertigo, nausea, vomiting, and ataxia (hospital admission)\n* Diagnosis: squamous cell lung carcinoma with multiple lymph node metastasis\n* Treatment:\n\t+ Oral prednisone initiated to alleviate symptoms\n\t+ Intravenous immunoglobulin (IVIG) started to alleviate symptoms\n\t+ Three courses of intravenous etoposide and cisplatin\n\t+ Radiotherapy administered at a dose of 50.4 Gy\n\nThe patient's current status is not explicitly stated in the provided data, but it can be inferred that they are receiving ongoing treatment for their squamous cell lung carcinoma. The timeline suggests that the patient has been under treatment for several weeks, with some improvement in symptoms and potentially some progression or stabilization of the disease.\n\nIt is worth noting that the patient's demographics, including age and sex, are not explicitly stated in the provided data. However, based on the information provided, it can be inferred that the patient is a 55-year-old male who has been diagnosed with squamous cell lung carcinoma.", + "bertscore": { + "precision": 0.6984645128250122, + "recall": 0.7505180239677429, + "f1": 0.7235563397407532 + }, + "bleu": 0.0352731369608729, + "rouge1": 0.1935483870967742, + "rougeL": 0.1252371916508539, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 9, + "edge_count": 7, + "avg_in_degree": 0.7777777777777778, + "density": 0.09722222222222222 + }, + "trajectory_embedding": [ + 0.21283334493637085, + 0.2261987030506134, + -0.18569672107696533, + 0.07250019162893295, + -0.07191392034292221, + 0.026674848049879074, + 0.13202348351478577, + 0.17625777423381805, + 0.3370841145515442, + -0.3352464735507965, + -0.19530074298381805, + 0.2723828852176666, + -0.5447418689727783, + -0.1018790602684021, + 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b/src/benchmark/output/results/results_graph_047.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 70-year-old male with a history of asbestos exposure and former smoking (20 pack-years).\n\n**Timeline of Diagnoses:**\n\n1. **2023:** The patient was diagnosed with large-cell squamous carcinoma of the left upper lobe with mediastinal lymph node metastases (cT4 cN3 cM0, stage IIIC).\n2. **2023:** The patient underwent treatment with curative intent, consisting of four cycles of vinorelbine/carboplatin, one cycle of durvalumab, and radiotherapy (total dose: 60 Gy).\n\n**Timeline of Treatments:**\n\n1. **2023:** The patient received four cycles of vinorelbine/carboplatin.\n2. **2023:** The patient received one cycle of durvalumab.\n3. **2023:** The patient underwent radiotherapy.\n\n**Timeline of Outcomes:**\n\n1. **After treatment (2023):** The patient's bilateral radiation pneumonitis progression was monitored.\n2. **After treatment (2023):** A CT scan showed regression of the left central tumor, mediastinal, and right hilar lymph nodes, along with a trend toward resolution of bipulmonary pneumonitis.\n3. **After treatment (2023):** Bronchoscopy revealed marked tumor regression in the left upper lobe, with histology showing bronchial wall reserve cell hyperplasia and mucosal changes, but no recurrence of the previously diagnosed poorly differentiated squamous cell carcinoma or evidence of malignancy.\n4. **After treatment (2023):** A CT scan revealed a new lesion suspicious for malignancy in liver segments V and VI, consistent with metastasis from the known squamous cell carcinoma of the lung.\n\n**Current Status:**\nThe patient is currently undergoing evaluation for surgical resection of solitary centrally located hepatic metastasis. The pulmonary tumor board has recommended this course of action based on imaging findings.\n\nIn summary, the patient was diagnosed with stage IIIC large-cell squamous carcinoma of the left upper lobe in 2023 and underwent treatment with curative intent. Following treatment, there were significant improvements in lung function and tumor regression, but a new lesion suspicious for malignancy was detected in the liver. The patient is now being evaluated for surgical resection of the hepatic metastasis.", + "bertscore": { + "precision": 0.8479164838790894, + "recall": 0.8669500350952148, + "f1": 0.8573276400566101 + }, + "bleu": 0.4280695015351555, + "rouge1": 0.6548148148148148, + "rougeL": 0.5125925925925925, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.23916545510292053, + 0.0230923630297184, + -0.08824869245290756, + 0.20278996229171753, + 0.04306795075535774, + 0.1345890760421753, + 0.015297275967895985, + 0.4002745747566223, + 0.5124368071556091, + -0.3175220787525177, + -0.045064736157655716, + -0.16486221551895142, + -0.5308375358581543, + -0.10607318580150604, + -0.2521823048591614, + 0.38863450288772583, + -0.037071093916893005, + 0.2851150929927826, + 0.018904972821474075, + 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She was diagnosed with lung adenocarcinoma, which had metastasized to the brain, mediastinal lymph nodes, and other parts of her body.\n\n**Timeline of Diagnoses:**\n\n1. **May 2024:** The patient presented with cough and headache, leading to a biopsy of the right supraclavicular lymph node (N2). The biopsy confirmed lung adenocarcinoma.\n2. **May 2024:** A diagnosis of advanced lung adenocarcinoma was made, with multiple brain metastases (N3).\n3. **May 2024:** Initial imaging revealed multiple brain metastases, pulmonary lesions, and mediastinal lymphadenopathy.\n\n**Timeline of Treatments:**\n\n1. **May 2024:** The patient underwent whole-brain radiotherapy.\n2. **June 2024:** Next-generation sequencing (NGS) detected a ROS1 fusion and TP53 mutations. The patient started entrectinib therapy.\n3. **July 2024:** The patient experienced significant improvements in headache and insomnia symptoms, indicating a partial response to entrectinib treatment.\n\n**Timeline of Outcomes:**\n\n1. **July 2024:** Imaging showed a reduction in lung nodule size, mediastinal lymph nodes, and intracranial metastatic lesion size, indicating a partial response to entrectinib.\n2. **August 2024:** The patient experienced grade 2 blurred vision and oral mucositis.\n\n**Current Status:**\nThe patient's lung and brain lesions have consistently remained in a state of partial response since starting entrectinib therapy. However, the patient has experienced new symptoms, including blurred vision and oral mucositis, which may indicate a need for further treatment adjustments or additional therapies.\n\nThis clinical case report highlights the importance of personalized medicine approaches, such as targeted therapy with entrectinib, in managing advanced lung cancer with brain metastases.", + "bertscore": { + "precision": 0.7794458866119385, + "recall": 0.7619431614875793, + "f1": 0.7705951929092407 + }, + "bleu": 0.10900761101947046, + "rouge1": 0.4695201037613489, + "rougeL": 0.2749675745784695, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.14966541528701782, + 0.2221803069114685, + -0.19240516424179077, + 0.08077575266361237, + -0.02466701529920101, + 0.20474261045455933, + 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b/src/benchmark/output/results/results_graph_049.json new file mode 100644 index 0000000..827a933 --- /dev/null +++ b/src/benchmark/output/results/results_graph_049.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 66-year-old man with a history of smoking 20 cigarettes per day until the age of 50, after which he abstained for the past 16 years. He has cerebral infarction and takes 25 mg of clopidogrel.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1:** The patient's history and routine checkup revealed a 3 cm mass in the left middle lung field during chest radiography.\n2. **Step 2:** Further investigation with CT imaging and blood tests was conducted, which showed a ground-glass nodule with a maximum diameter of 4.6 cm and a solid component measuring 4 cm located in S9/10 of the left lower lobe.\n3. **Step 3:** Pulmonary function tests indicated normal respiratory capacity, but follow-up CT imaging revealed a part-solid nodule measuring 1.6 \u00d7 1.4 cm with a 1.5 cm solid component in the same location.\n4. **Step 4:** PET-CT and MRI of the head were conducted to evaluate the lung nodule and rule out metastasis, showing mild accumulation in the mass with an SUVmax of 2.04.\n5. **Step 5:** Bronchoscopy and biopsy were performed to determine the nature of the lung nodule, leading to a suspected diagnosis of stage IB primary lung cancer.\n\n**Timeline of Treatments:**\n\n1. **Step 6:** Surgical lobectomy was planned following the surgical biopsy.\n\n**Outcomes:**\n\nThe patient underwent bronchoscopy and biopsy, which led to a suspected diagnosis of stage IB primary lung cancer. The patient is scheduled for surgical lobectomy. Further follow-up will be necessary to monitor the patient's condition and assess the effectiveness of treatment.\n\nNote: This narrative is based on the provided data and may not reflect the actual clinical case report or outcomes.", + "bertscore": { + "precision": 0.8009686470031738, + "recall": 0.8117077946662903, + "f1": 0.8063024878501892 + }, + "bleu": 0.03576180724801479, + "rouge1": 0.3530326594090203, + "rougeL": 0.2255054432348367, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.2567644715309143, + 0.054647695273160934, + -0.025133753195405006, + 0.027657220140099525, + 0.0567028634250164, + -0.047446608543395996, + 0.08157778531312943, + 0.12755827605724335, + 0.3595859110355377, + -0.3565047085285187, + -0.2112758755683899, + 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"success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics**\n\nThe patient is a 67-year-old man with a history of 40 pack-years of smoking. He presented to the clinic in February 2022 with chest tightness.\n\n**Initial Diagnosis (Step 1)**\n\nUpon physical examination, left supraclavicular lymphadenopathy was noted, measuring approximately 1 cm in size. Chest CT revealed a 2 cm mass in the posterior basal segment of the left lower lobe, with multiple burrs on the edge and enhancement. Mediastinal lymph nodes were enlarged and fused, surrounding the left main bronchus. Abdominal enhanced CT showed enlargement of the left adrenal gland, considered to be a metastatic lesion.\n\nImaging studies, including whole-body bone imaging and brain-enhanced MRI, did not reveal any obvious abnormalities. Immunohistochemical markers (CK-pan and P40) were positive, suggesting a diagnosis of lung cancer.\n\n**Biopsy and Diagnosis (Step 2)**\n\nOn March 10, 2022, a CT-guided lung puncture biopsy was performed to further characterize the tumor. Pathology suggested poorly differentiated carcinoma. Immunohistochemical markers were CK-pan (+), CK7 (-), TTF-1 (-), P40 (+), BRG-1 (-), and Syn (-). PD-L1 staining revealed a tumor proportion score (TPS) of 8%.\n\n**Diagnosis Confirmation and Treatment (Step 3)**\n\nBased on immunohistochemistry and genetic testing, a diagnosis of SMARCA4-deficient non-small cell lung cancer (SMARCA4-dNSCLC) was made. First-line treatment with tislelizumab combined with fruquintinib was initiated.\n\n**Treatment Outcomes (Step 4)**\n\nFollowing initial treatment, the patient experienced cervical lymph node progression. Subsequent biopsy confirmed the diagnosis, and the patient was treated with local radiotherapy and previous systemic therapy. The patient achieved more than two years of disease control without grade \u22653 adverse events.\n\n**Timeline**\n\n* February 2022: Patient presents to clinic with chest tightness.\n* March 10, 2022: CT-guided lung puncture biopsy is performed.\n* March 2022: Diagnosis of SMARCA4-dNSCLC is confirmed via subsequent biopsy.\n* April 1, 2022: Initial treatment with tislelizumab and fruquintinib begins.\n* April 1, 2022: Patient undergoes local radiotherapy and previous systemic therapy.\n\n**Outcomes**\n\nThe patient achieved more than two years of disease control without grade \u22653 adverse events. The diagnosis of SMARCA4-dNSCLC was confirmed via subsequent biopsy, and the patient responded well to first-line treatment with tislelizumab combined with fruquintinib.", + "bertscore": { + "precision": 0.8664990067481995, + "recall": 0.8506335020065308, + "f1": 0.858492910861969 + }, + "bleu": 0.11985709106260009, + "rouge1": 0.4781818181818182, + "rougeL": 0.26363636363636367, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.28611698746681213, + 0.13427646458148956, + -0.17884783446788788, + 0.06759999692440033, + -0.12707366049289703, + 0.07035525888204575, + 0.17056792974472046, + -0.0935962051153183, + 0.17258435487747192, + -0.4768597185611725, + -0.167130708694458, + 0.24880175292491913, + -0.5263209342956543, + 0.07364700734615326, + -0.45961248874664307, + 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history of chronic obstructive pulmonary disease (COPD).\n\n**Initial Presentation:**\nOn [date], the patient was admitted to hospital with sudden massive hemoptysis, which he denied experiencing any chest pain, dyspnea, or fever. No other significant comorbidities were present at the time of presentation.\n\n**Diagnosis and Timeline:**\n\n1. **Step 1 (N1):**\nThe patient's history of COPD was noted, with a diagnosis code of \"233936005\" for Chronic obstructive lung disease, which is historical in nature.\n2. **Step 2 (N2):**\nTwo months prior to admission, an enhanced CT scan revealed a tumor in the right upper lung.\n3. **Step 3 (N3):**\nBiopsy confirmed that the tumor was squamous cell carcinoma of the lung (SCC), with a TNM stage of T2bNXM1c1.\n4. **Step 4 (N4):**\nThe patient received two cycles of albumin-bound paclitaxel, nedaplatin, and tislelizumab as treatment for SCC.\n\n**Follow-up and Complications:**\n\n5. **Step 5 (N5):**\nA follow-up CT scan showed partial remission of the tumor with cavitation.\n6. **Step 6 (N6):**\nThe patient presented with hemoptysis, which led to further evaluation, including lab tests and imaging.\n7. **Step 7 (N7):**\nEmergency endovascular intervention was performed due to pseudoaneurysm formation in the right upper pulmonary artery located at the SCC cavity wall with an intraluminal hematoma.\n8. **Step 8 (N8):**\nThe patient underwent emergency endovascular intervention, which included embolization using microcoils to occlude the PAP and proximal artery.\n9. **Step 9 (N9):**\nPost-procedure angiography confirmed the disappearance of the pulmonary artery pseudoaneurysm (PAP).\n10. **Step 10 (N10):**\nThe patient experienced no active bleeding postoperatively, and follow-up over 6 months showed no recurrence of hemoptysis.\n11. **Step 11 (N11):**\nA CT scan 3 months post-embolization showed absorption of the tumor cavity with significant tumor reduction.\n\n**Outcomes:**\n\nThe patient's treatment for SCC was successful, with partial remission of the tumor and disappearance of the pulmonary artery pseudoaneurysm. The patient experienced no active bleeding postoperatively and no recurrence of hemoptysis over 6 months. Follow-up imaging showed absorption of the tumor cavity with significant tumor reduction.\n\n**Conclusion:**\nThis case highlights the importance of early diagnosis and treatment for SCC, particularly in patients with a history of COPD. The successful outcome of this patient's treatment underscores the effectiveness of endovascular intervention in managing complications associated with SCC.", + "bertscore": { + "precision": 0.7820798754692078, + "recall": 0.7985286116600037, + "f1": 0.7902186512947083 + }, + "bleu": 0.15408828759088924, + "rouge1": 0.4800693240901213, + "rougeL": 0.2998266897746967, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 12, + "edge_count": 11, + "avg_in_degree": 0.9166666666666666, + "density": 0.08333333333333333 + }, + "trajectory_embedding": [ + 0.19094891846179962, + 0.14106714725494385, + -0.031158799305558205, + 0.13212095201015472, + -0.034361883997917175, + 0.11214422434568405, + 0.008480226621031761, + 0.27649667859077454, + 0.44355106353759766, + -0.3264440596103668, + -0.24161100387573242, + -0.02264360710978508, + -0.5586544275283813, + -0.07856817543506622, + 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"reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 61-year-old male with a history of intermittent cough for over two years, worsening in the last month. He has also experienced pneumonia caused by Legionella pneumophila, hypertension, severe anemia, smoking, and alcohol use.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (N1):**\nThe patient presented with symptoms of a persistent cough, which had worsened over time. His medical history revealed previous episodes of pneumonia, hypertension, anemia, smoking, and alcohol use.\n2. **Step 2 (N2):** One month prior to presentation, the patient developed a Pasteurella pneumotropica infection at an outside facility, as confirmed by bronchoscopy and alveolar lavage fluid mNGS analysis. Despite treatment with anti-infective medications for over two weeks, the patient did not show improvement.\n3. **Step 3 (N3):** The patient presented with a palpable lump on the right thoracic wall, localized pain, and coarse breath sounds in both lungs. Laboratory tests revealed abnormalities in white blood cell count, red blood cell count, hemoglobin, total protein, globulin, albumin, glucose, C-reactive protein, and squamous cell carcinoma antigen.\n4. **Step 4 (N4):** Enhanced CT scans showed a new mass in the left lower lung, multiple enlarged lymph nodes, and bone destruction in the right tenth rib, leading to suspicion of lung cancer with metastasis. Bronchoscopy did not reveal tumor cells.\n\n**Treatments:**\n\n1. **Anti-infective treatment:** The patient received anti-infective medications for over two weeks following the diagnosis of Pasteurella pneumotropica infection.\n2. **Imaging studies:** Enhanced CT scans were performed to evaluate the new mass in the left lower lung and multiple enlarged lymph nodes.\n\n**Outcomes:**\n\n1. **Lung cancer with metastasis:** The patient's symptoms and imaging results suggested a diagnosis of lung cancer with metastasis.\n2. **No tumor cells found on bronchoscopy:** Despite the high suspicion of lung cancer, no tumor cells were found during bronchoscopy.\n3. **Negative antibody tests:** Antibody tests for HIV, HBV, HCV, EBV, and TP were negative, indicating that these infections were not contributing to the patient's condition.\n\n**Conclusion:**\nThe patient presented with a complex clinical picture, including a history of pneumonia, hypertension, anemia, smoking, and alcohol use. The development of Pasteurella pneumotropica infection led to progression in his diagnosis, ultimately resulting in suspicion of lung cancer with metastasis. Despite the high suspicion of lung cancer, no tumor cells were found on bronchoscopy, and antibody tests for common infections were negative. Further evaluation and treatment are necessary to determine the best course of action for this patient.", + "bertscore": { + "precision": 0.7502202987670898, + "recall": 0.7783499956130981, + "f1": 0.7640262842178345 + }, + "bleu": 0.024499507708589042, + "rouge1": 0.351493848857645, + "rougeL": 0.1687170474516696, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.3750039041042328, + -0.018641069531440735, + -0.2502043545246124, + 0.05081702023744583, + -0.05105207860469818, + 0.0839003473520279, + 0.2023211419582367, + 0.19112949073314667, + 0.2581161558628082, + -0.5016443729400635, + -0.10917043685913086, + 0.22764131426811218, + -0.6944714784622192, + -0.16388894617557526, + -0.19019311666488647, + -0.02061181329190731, + 0.21072253584861755, + 0.36244553327560425, + 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diagnosed with lung and mediastinal lesions. The diagnosis was made in [year] and marked the beginning of a complex treatment journey.\n\nFollowing the initial diagnosis, the patient transitioned to radiotherapy for the lung and mediastinal lesions (N1 to N2). This marked an important step in the patient's care, as it aimed to alleviate symptoms and slow disease progression. However, this was followed by another significant change when the patient began chemotherapy with albumin-bound paclitaxel and cisplatin, with recombinant human endostatin added in the 4th cycle (N2 to N3). Unfortunately, treatment was not completed due to cardiac reactions, resulting in stable disease.\n\nThe patient's condition continued to evolve as they developed symptoms of chest tightness and shortness of breath. These symptoms persisted despite hospitalization for worsening shortness of breath (N5 to N6), where ECG abnormalities and lab results indicating elevated troponin, BNP, and myoglobin were noted. The initial treatment included a range of medications aimed at managing these complications.\n\nDespite the efforts to manage symptoms, the patient's condition continued to deteriorate. A coronary angiography revealed significant stenosis in the left main trunk (N6 to N7), which further complicated the patient's care. Notably, anticoagulant therapy was not initiated due to concerns about gastrointestinal bleeding secondary to long-term aspirin use.\n\nThroughout this journey, the patient has been managed with a range of treatments, including medications and procedures aimed at addressing complications such as cardiac reactions, chest tightness, and shortness of breath. The timeline of diagnoses and treatments is complex, reflecting the evolving nature of the patient's condition.\n\nThe patient's age and demographic information are not explicitly stated in the provided data, but based on the treatment journey described, it can be inferred that this individual has been living with a serious health condition for several years.", + "bertscore": { + "precision": 0.7764316201210022, + "recall": 0.7502598762512207, + "f1": 0.7631214261054993 + }, + "bleu": 0.010387883712094016, + "rouge1": 0.2814526588845655, + "rougeL": 0.13488975356679636, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.17100100219249725, + 0.01172204501926899, + -0.21289609372615814, + 0.19774876534938812, + 0.11490162461996078, + 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mode 100644 index 0000000..16e9e17 --- /dev/null +++ b/src/benchmark/output/results/results_graph_054.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 49-year-old male with a significant smoking history (37 pack-years). He was admitted to the local hospital with acute abdominal pain, which marked the beginning of his clinical journey.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Initial Presentation:** The patient presented with acute abdominal pain, which led to an enhanced CT scan revealing a 4.0 cm soft tissue mass within the small intestine and mid-lower intestine intussusception (N2).\n2. **Surgical Intervention:** Admitted to the general surgery ward, the patient underwent intussusception surgery on April 8, 2019 (N3). During surgery, an irregular, hard, solid white mass involving the intestine was identified.\n3. **Initial Pathological Diagnosis:** The resected specimen showed a multinodular mass with a tan-white cut surface and firm consistency, thin envelope observed in the periphery of the mass (N4).\n4. **Detailed Pathology and Immunohistochemistry Results:** Histological examination revealed tumor located within the submucosa and lamina propria of the intestinal wall with mucosal erosion, neoplastic cells embedded within the inflammatory background. Immunohistochemistry results confirmed ALK-positive inflammatory myofibroblastic tumor (IMT), highly suspicious for epithelioid inflammatory myofibroblastic sarcoma (EIMS) (N5).\n\n**Diagnosis and Treatment Outcomes:**\n\nThe patient was diagnosed with a suspected case of epithelioid inflammatory myofibroblastic sarcoma (EIMS). Given the ALK-positive status, treatment options were considered. However, no specific treatment details are provided in this data.\n\n**Conclusion:**\nThis clinical case report highlights the importance of a thorough diagnostic workup and the significance of molecular testing in identifying rare and aggressive tumors like EIMS. Further investigation into the patient's treatment plan is necessary to determine the most effective course of action for this unique diagnosis.\n\n**Recommendations:**\n\n1. **Multidisciplinary Team Approach:** Collaboration between surgeons, pathologists, radiologists, and oncologists is crucial for managing complex cases like this.\n2. **Molecular Testing:** Regular molecular testing can help identify potential biomarkers for targeted therapies in EIMS patients.\n3. **Clinical Trials Participation:** Patients with rare tumors like EIMS should be considered for participation in clinical trials to explore new treatment options.\n\n**Future Directions:**\n\n1. **Research on EIMS:** Further studies are needed to understand the biology and behavior of EIMS, as well as to identify potential therapeutic targets.\n2. **Development of New Treatment Strategies:** Researchers should focus on developing novel treatments for EIMS, including targeted therapies and immunotherapies.\n\nBy sharing this clinical case report, we aim to raise awareness about the importance of accurate diagnosis and treatment planning in managing rare and aggressive tumors like EIMS.", + "bertscore": { + "precision": 0.8164544701576233, + "recall": 0.8288332223892212, + "f1": 0.8225972652435303 + }, + "bleu": 0.10046274166922226, + "rouge1": 0.4076539101497504, + "rougeL": 0.25291181364392684, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.2819657325744629, + 0.01156010851264, + -0.19529643654823303, + -0.042242903262376785, + 0.0824071615934372, + -0.062329452484846115, + 0.08502864092588425, + -0.14531011879444122, + 0.2912984788417816, + -0.3691332936286926, + -0.4327576160430908, + 0.2096576988697052, + -0.7493955492973328, + 0.01814318634569645, + -0.5375791788101196, + 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with no publicly available demographic information. However, based on the provided data, it can be inferred that the patient has cancer, as mentioned in Step 1.\n\n**Timeline of Diagnoses and Treatments:**\n\nStep 1:\nThe patient's cancer had no driver gene mutations.\n\nStep 2 (First-line Chemotherapy):\nInitiation of first-line chemotherapy with cisplatin, pemetrexed, and pembrolizumab was administered. This treatment was initiated to target the patient's cancer.\n\nStep 3 (Second-line Chemotherapy):\nProgression to second-line chemotherapy with docetaxel and ramucirumab was administered. This treatment was initiated due to the development of resistance or intolerance to the first-line chemotherapy.\n\nStep 4:\nChemotherapy was delayed for approximately one month due to the development of a perianal abscess, which required surgical intervention under local anesthesia. The patient's cancer treatment was interrupted due to an unexpected complication.\n\nStep 5 (Post-Surgical Complication):\nThe patient developed dyspnea the day following surgery. This symptom suggested that the patient may be experiencing respiratory complications related to the surgery.\n\nStep 6:\nAdmission and Vital Sign Abnormalities:\nFour days after symptom onset, the patient was admitted with vital sign abnormalities, including hypotension, hypoxemia, and tachycardia. These findings indicated that the patient's condition had deteriorated significantly.\n\nStep 7 (Lab Abnormalities):\nElevated D-dimer, C-reactive protein, brain natriuretic peptide, and carcinoembryonic antigen levels were detected in the patient's blood. Additionally, abnormal CBC results and arterial blood gas findings were observed. These lab abnormalities suggested that the patient had developed a systemic inflammatory response syndrome (SIRS) or sepsis.\n\n**Outcomes:**\n\nThe patient's condition continued to deteriorate, with ongoing vital sign abnormalities and lab abnormalities. The exact outcome of this case is not provided in the data, but it can be inferred that the patient required further medical intervention to manage their symptoms and stabilize their condition.\n\nIn conclusion, this clinical case report highlights the complexities of cancer treatment and the potential for unexpected complications. The patient's journey from diagnosis to admission and beyond demonstrates the need for close monitoring and prompt intervention in managing cancer-related symptoms and lab abnormalities.", + "bertscore": { + "precision": 0.7944204211235046, + "recall": 0.7673730254173279, + "f1": 0.7806625366210938 + }, + "bleu": 0.03316548148309143, + "rouge1": 0.2944444444444444, + "rougeL": 0.1625, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.22469878196716309, + 0.19692015647888184, + 0.00025188070139847696, + 0.173471599817276, + 0.09548087418079376, + 0.17378945648670197, + -0.016956541687250137, + 0.2958507835865021, + 0.6613865494728088, + -0.4530636966228485, + -0.13141368329524994, + -0.04939684644341469, + -0.6155732274055481, + -0.17467454075813293, 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Report**\n\n**Patient Demographics:**\nThe patient is a 72-year-old woman with a history of small cell lung cancer (SCLC).\n\n**Initial Presentation:**\nThe patient presented with progressive involuntary writhing movements in her hands and lower extremities over the past 3 months. This symptomatology was documented as part of her clinical data, including a history of progressive worsening (P3M) and associated symptoms such as involuntary writhing movements.\n\n**Diagnostic Workup:**\nFollowing the patient's presentation, a comprehensive diagnostic workup was conducted, which included imaging studies (Brain MRI and CT), electroencephalogram (EEG), and laboratory tests. The results of these studies were negative for hemorrhage or lesions on the red nucleus or midbrain, seizure activity, and abnormal electrolyte levels.\n\n**Treatment Initiation:**\nDespite the initial negative diagnostic workup, the patient's symptoms worsened, prompting further evaluation and treatment initiation. A ceruloplasmin test was conducted, which revealed a negative result. Subsequent laboratory tests showed positive anti-Hu antibodies at a titer of 1:960, indicating paraneoplastic syndrome.\n\n**Treatment Regimen:**\nThe patient received a treatment regimen consisting of diazepam, primidone, and pramipexole, with the goal of managing her symptoms. However, despite this treatment, the patient's symptoms continued to worsen, leading to hospitalization.\n\n**Intravenous Immunoglobulin (IVIG) Therapy:**\nAs part of her treatment regimen, the patient received IVIG for 4 days. This therapy was aimed at reducing the severity of her paraneoplastic syndrome.\n\n**New Symptoms and Imaging Findings:**\nFollowing the patient's discharge from the hospital, she presented to the emergency department with nausea and vomiting without new abnormal movements or neurologic symptoms. Repeat imaging studies revealed a 3.3 x 2.3 cm mass in the left cerebellar region, involving the left cerebellar peduncle.\n\n**Treatment of New Symptoms:**\nThe patient underwent further evaluation and treatment for her new symptoms. Laboratory tests showed positive anti-Hu antibodies, indicating continued paraneoplastic syndrome.\n\n**Current Status:**\nAt this time, the patient is currently under observation with ongoing management of her paraneoplastic syndrome. The patient's symptoms have improved since the initiation of IVIG therapy, but she continues to experience discomfort and disrupted sleep due to the frequency of her movements.\n\nIn conclusion, this 72-year-old woman with a history of small cell lung cancer presented with progressive involuntary writhing movements in her hands and lower extremities. Despite an initial negative diagnostic workup, further evaluation and treatment initiation revealed paraneoplastic syndrome, which was managed with IVIG therapy. However, new symptoms and imaging findings have necessitated ongoing management and observation.", + "bertscore": { + "precision": 0.7369856834411621, + "recall": 0.736884355545044, + "f1": 0.736935019493103 + }, + "bleu": 0.13227885704263823, + "rouge1": 0.4652049571020019, + "rougeL": 0.2421353670162059, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.10924185812473297, + 0.10171635448932648, + -0.130819171667099, + 0.11970636993646622, + 0.01621156930923462, + -0.025944743305444717, + 0.059883225709199905, + 0.19405730068683624, + 0.5056430101394653, + -0.3832123875617981, + -0.28973308205604553, + 0.21129187941551208, + -0.575080156326294, + -0.07535974681377411, + -0.27020901441574097, + -0.11037592589855194, + 0.01244857907295227, + 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Demographics:**\nThe patient is a 65-year-old man who presented to the hospital with suspected uveitis of the right eye. He experienced right ocular pain and blurred vision for approximately 1 month prior to presentation.\n\n**Timeline of Diagnoses:**\n\n* **Suspected Uveitis:** The patient was referred to the hospital with suspected uveitis of the right eye, which was diagnosed as a suspected case of uveitis (code C0042095).\n* **Small Cell Lung Cancer (SCLC):** Four months prior to presentation, the patient was diagnosed with SCLC (code C0007106) and had developed right cerebellar metastasis and invasion.\n* **Metastasis:** The patient also had a diagnosis of metastasis (code C0242393), which was active at the time of presentation.\n\n**Timeline of Treatments:**\n\n* **Topical Medications:** Following SCLC diagnosis, the patient started therapy with topical 0.005% latanoprost, 1.0% brinzolamide, and 0.5% timolol maleate.\n* **Oral Acetazolamide:** The patient also took oral acetazolamide at a dose of 500 mg/day.\n* **Intravenous Mannitol:** Due to high IOP and pronounced nausea, the patient required intravenous administration of 200 mL of 20% hypertonic mannitol every 2-3 days for five administrations.\n\n**Timeline of Outcomes:**\n\n* **Iris Metastasis:** Anterior chamber fluid cytology revealed iris metastasis from SCLC, consistent with bronchoalveolar lavage cytology results.\n* **Neovascular Glaucoma:** The patient developed neovascular glaucoma (code C0271198), which was treated with a single intravitreal injection of 2 mg (0.05 mL of 40 mg/mL) aflibercept OD.\n* **Resolution of Symptoms:** Five days post-aflibercept injection, the patient's iris tumor size and iris neovascularization decreased, IOP measured at 18 mm Hg, and symptoms such as ocular pain and nausea were relieved.\n\n**Conclusion:**\nThe patient was diagnosed with suspected uveitis and SCLC, which led to the development of right cerebellar metastasis and invasion. Following diagnosis, the patient received topical medications and oral acetazolamide, as well as intravenous mannitol due to high IOP and nausea. The patient also developed iris metastasis from SCLC, which was treated with an intravitreal injection of aflibercept. Ultimately, the patient's symptoms resolved following treatment, and their IOP returned to normal.", + "bertscore": { + "precision": 0.7505869269371033, + "recall": 0.845012903213501, + "f1": 0.7950058579444885 + }, + "bleu": 0.06704047393594473, + "rouge1": 0.39263803680981596, + "rougeL": 0.20449897750511245, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.10041718930006027, + 0.16403163969516754, + -0.2795267105102539, + 0.20759916305541992, + 0.1098250150680542, + 0.12031718343496323, + 0.02523813582956791, + 0.28508585691452026, + 0.4031936228275299, + -0.14178399741649628, + -0.1515788584947586, + 0.027539696544408798, + -0.39865249395370483, + -0.16108302772045135, + -0.1848643273115158, + 0.29761239886283875, + -0.348704069852829, + 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67-year-old man born in the United States. He has a significant occupational asbestos exposure history while working for a shipbuilding company. The patient denies any history of cigarette smoking or exposure to organic dusts, pet birds, or exotic pets.\n\n**Initial Presentation (Step 1):**\nIn June 2024, the patient presented to the Emergency Department with concerns of weight loss and abdominal distention over the past 4 weeks. He denied any alterations in bowel habits, melena, hematochezia, abdominal pain, nausea, vomiting, dysphagia, or odynophagia.\n\n**Physical Examination and Laboratory Findings (Step 2):**\nAfter initial presentation, the patient underwent multiple abdominal paracenteses, which revealed hazy yellow ascitic fluid with nucleated cells. The cell count was 589 cells/\u03bcL, with lymphocytes 87% and erythrocytes 1461 cells/\u03bcL.\n\n**Imaging Studies (Step 3):**\nA CT scan performed during this time showed massive ascites and a lung nodule.\n\n**Abdominal Paracentesis and Ascitic Fluid Analysis (Steps 4-5):**\nThe patient underwent multiple abdominal paracenteses, which revealed exudative process in the ascitic fluid. The first abdominal paracentesis results showed lactate dehydrogenase 763 IU/L, total protein 4.0 g/dL, albumin 1.7 g/dL, and serum albumin-ascites gradient (SAAG) 0.4 g/dL.\n\n**Repeat Ascitic Fluid Analysis and Abdominal Ultrasonography (Step 6):**\nA repeat ascitic fluid analysis revealed no growth on AFB smear, culture, or fungal culture. An abdominal ultrasonography performed during this time showed normal portal vein size and Doppler indices, with the spleen not enlarged.\n\n**Serum FibroTest-ActiTest (Step 7):**\nThe patient underwent a Serum FibroTest-ActiTest, which suggested no hepatic fibrosis (F0).\n\n**Diagnosis:**\nBased on the results of the various diagnostic tests and imaging studies, the patient was diagnosed with cirrhosis due to chronic liver disease.\n\n**Treatment:**\nNo specific treatment is mentioned in the provided data. However, it can be inferred that the patient may require ongoing management of his ascites and potential complications related to cirrhosis.\n\n**Outcome:**\nThe patient's condition appears to be stable at this point, with no further information provided on any changes or developments since the last update.", + "bertscore": { + "precision": 0.7324800491333008, + "recall": 0.7999362945556641, + "f1": 0.7647234797477722 + }, + "bleu": 0.03761262491128669, + "rouge1": 0.28633405639913234, + "rougeL": 0.16919739696312364, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.3212769627571106, + 0.027124296873807907, + 0.007639573886990547, + 0.1450214982032776, + 0.04273857921361923, + -0.0566130205988884, + 0.15015661716461182, + 0.13063287734985352, + 0.360310435295105, + 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0000000..9f21883 --- /dev/null +++ b/src/benchmark/output/results/results_graph_061.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 65-year-old woman. Unfortunately, her demographic information is not explicitly provided in the data, so we will assume that she is an adult female with no other relevant medical history mentioned.\n\n**Initial Presentation (Step 1):**\nThe patient presented to our institution with dyspnea, which was her primary symptom. This presentation led to further investigation and subsequent diagnoses.\n\n**Diagnosis of Adenocarcinoma (Step 2):**\nFollowing a bronchoscopic biopsy of the right upper lobe, the patient was diagnosed with adenocarcinoma. The biopsy results revealed adenocarcinoma, which is a type of non-small cell lung cancer.\n\n**Imaging and Further Diagnosis (Step 3):**\nImaging studies, including bone and brain metastases, were performed to further evaluate the extent of disease. These findings led to a diagnosis of stage IVB lung adenocarcinoma with multiple metastases in the bones and brain.\n\n**Molecular Profiling and Treatment Planning (Step 4):**\nA tumor proportion score was calculated to guide treatment decisions. The results showed that the programmed death-ligand 1 tumor proportion score was 60%. Based on this information, palliative radiation therapy for spinal and brain metastases was initiated, followed by first-line chemotherapy with cisplatin, pemetrexed, and pembrolizumab.\n\n**Progression of Disease (Step 5-6):**\nAfter 13 cycles of chemotherapy, imaging revealed ascites and progressive disease. The patient's condition continued to decline, with worsening ascites and a marked increase in abdominal circumference.\n\n**Second-Line Therapy (Step 7):**\nDue to the progression of disease, second-line therapy was initiated with docetaxel and ramucirumab (DTX+RAM). However, despite this treatment, the patient's condition continued to deteriorate.\n\n**Current Status:**\nThe patient is currently in a poor clinical state, with significant ascites, hypoalbuminemia, and a marked decline in activities of daily living. Her performance status has decreased, and she requires frequent abdominal paracentesis. The patient's abdomen is markedly distended, and her vital signs are concerning.\n\n**Conclusion:**\nThis patient presents with a complex clinical scenario, characterized by rapidly progressive disease despite multiple treatment modalities. Further evaluation and management strategies will be necessary to address this challenging case.", + "bertscore": { + "precision": 0.8127667903900146, + "recall": 0.808251142501831, + "f1": 0.8105026483535767 + }, + "bleu": 0.047636868820993244, + "rouge1": 0.37435897435897436, + "rougeL": 0.16923076923076924, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 9, + "edge_count": 7, + "avg_in_degree": 0.7777777777777778, + "density": 0.09722222222222222 + }, + "trajectory_embedding": [ + 0.2474288046360016, + 0.2092151939868927, + -0.12583652138710022, + 0.19021673500537872, + 0.0814264714717865, + 0.177109494805336, + -0.002533096820116043, + 0.3530573844909668, + 0.759898841381073, + -0.3953750431537628, + -0.04731377586722374, + -0.07567942142486572, + -0.6275361180305481, + -0.17365944385528564, + -0.21753628551959991, + 0.26948532462120056, + -0.22064340114593506, + 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with a chronic recurrent dry cough over the course of a month. He denied any fever, sputum or blood production, and chest pain.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (N1):** The patient's chronic recurrent dry cough prompted a chest computed tomography (CT) scan.\n2. **Step 2 (N2):** The CT revealed pulmonary masses at an external hospital, leading to admission to the oncology department for further evaluation and treatment.\n3. **Step 3 (N3):** The patient was admitted to the oncology department for further evaluation and treatment.\n4. **Step 4 (N4):** As part of the evaluation, the patient's medical history was reviewed, revealing no history of hypertension, coronary heart disease, diabetes, cerebral venous thrombosis or hemorrhage, tuberculosis, chronic hepatitis B virus infection and other diseases.\n5. **Step 5 (N5):** Vitals and labs were taken as part of the evaluation, including temperature 37.2\u00b0C, pulse rate 118 bpm, respiratory rate 20 breaths/minute, blood pressure 106/69 mmHg, white blood cells 7.97 \u00d7 109/L, hemoglobin 142 g/L, platelets 287 \u00d7 109/L, and various other lab results.\n6. **Step 6 (N6):** Additional labs were taken as part of the evaluation, including treponema pallidum-specific antibody, hepatitis B surface antigen, and hepatitis C.\n\n**Treatments:**\n\nThe patient underwent a series of evaluations and treatments based on the findings from each step:\n\n* Following the CT scan, the patient was admitted to the oncology department for further evaluation and treatment.\n* As part of the evaluation, the patient's medical history was reviewed, revealing no history of certain diseases.\n* Vitals and labs were taken as part of the evaluation.\n\n**Outcomes:**\n\nThe patient's current status is not explicitly stated in the provided data. However, based on the timeline of diagnoses and treatments, it appears that the patient has undergone a series of evaluations and treatments for pulmonary masses detected by CT scan. The patient's medical history was reviewed, revealing no history of certain diseases, and vitals and labs were taken as part of the evaluation.\n\n**Conclusion:**\n\nThe patient presented with a chronic recurrent dry cough over the course of a month, which prompted a chest CT scan that revealed pulmonary masses. The patient underwent a series of evaluations and treatments based on the findings from each step, including admission to the oncology department for further evaluation and treatment. The patient's medical history was reviewed, revealing no history of certain diseases, and vitals and labs were taken as part of the evaluation.", + "bertscore": { + "precision": 0.6768946051597595, + "recall": 0.7102913856506348, + "f1": 0.6931909322738647 + }, + "bleu": 0.01979863091357997, + "rouge1": 0.20848056537102472, + "rougeL": 0.13780918727915192, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.29947397112846375, + -0.028808513656258583, + 0.018951475620269775, + 0.24079148471355438, + 0.11866217851638794, + 0.17880016565322876, + 0.11841905117034912, + 0.2565062940120697, + 0.5162163972854614, + -0.40549495816230774, + -0.19314958155155182, + -0.05226249620318413, + -0.6632895469665527, + -0.11044865846633911, + -0.34900379180908203, + 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She presented with a palpable pelvic mass, which was later identified as an anterior wall uterine leiomyoma on gynecological sonography.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1 (N1):**\nThe patient presented with a palpable pelvic mass in January 2010. Physical examination revealed an enlarged uterus, which was mobile, firm in consistency, with no uterine or forniceal tenderness, and mild swelling in the right pubic area.\n\n2. **Step 2 (N2):**\nGynecological sonography on January 30, 2010, identified an anterior wall uterine leiomyoma, measuring 112\u00d794\u00d7108 mm, accompanied by ascites measuring 65\u00d742 mm and a 20\u00d714 mm mass.\n\n3. **Step 3 (N3):**\nLaparotomic myomectomy was performed on February 17, 2020, with incidental discovery of a pelvic tumor. The pelvic tumor described as a cauliflower-like lesion disseminated across the right pelvic wall, cul-de-sac, anterior uterine surface, bladder, and colon.\n\n4. **Step 4 (N4):**\nBiopsy of the sigmoid colon serosa was performed, revealing proliferative mesothelial cells without significant atypia or necrosis. Post-myomectomy CT scan revealed seeding in the lower pelvis, characterized by multiple small, heterogeneous, enhancing nodules on the peritoneum and a prominent soft-tissue mass in the right adnexa.\n\n5. **Step 5 (N5):**\nAnother CT scan performed on February 26th, 2020, revealed moderate ascites and nonspecific peritoneal thickening. Histopathology identified bland mesothelial cells without invasion, and immunohistochemistry showed no significant staining loss. Differential diagnosis included well-differentiated papillary mesothelioma, epithelioid peritoneal mesothelioma, and florid mesothelial hyperplasia; well-differentiated papillary mesothelioma was highly suspected.\n\n**Outcomes:**\n\nThe patient underwent a series of procedures, including laparotomic myomectomy, biopsy, histopathology, and immunohistochemistry. The results of these procedures led to the diagnosis of a pelvic tumor with seeding in the lower pelvis. Despite the presence of seeding, the patient's condition was managed conservatively, with no further surgical interventions reported.\n\n**Conclusion:**\nThis case highlights the complexities of managing a patient with a pelvic mass and subsequent discovery of a pelvic tumor with seeding. The patient's presentation and diagnostic workup led to a series of procedures that ultimately resulted in a diagnosis of a mesothelial tumor. While the patient's condition was managed conservatively, further follow-up is necessary to monitor for any progression or recurrence of the disease.\n\n**Recommendations:**\n\n1. Further imaging studies should be performed to assess the extent of seeding and monitor for any progression or recurrence of the disease.\n2. The patient should be followed up regularly with a multidisciplinary team, including oncologists, radiologists, and pathologists.\n3. Additional diagnostic procedures, such as PET scans or CT scans, may be necessary to further evaluate the patient's condition.\n\n**Limitations:**\n\nThis case report is limited by its retrospective nature and the availability of data. Further research is needed to better understand the management and outcomes of patients with pelvic tumors and seeding.", + "bertscore": { + "precision": 0.7205074429512024, + "recall": 0.7689757943153381, + "f1": 0.7439529895782471 + }, + "bleu": 0.020398040132653002, + "rouge1": 0.21212121212121213, + "rougeL": 0.13468013468013468, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.33560317754745483, + -0.032035164535045624, + -0.11456692218780518, + 0.1346358358860016, + 0.020706722512841225, + 0.00046664924593642354, + 0.1556069552898407, + 0.050799597054719925, + 0.29955029487609863, + -0.3043522834777832, + -0.21893103420734406, + 0.13041041791439056, + -0.5819693207740784, + -0.027642954140901566, + -0.3483089804649353, + 0.05678959935903549, + 0.08175595104694366, + 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asbestos as a tunnel inspector. He presented to the emergency room with cough, low back pain, and abdominal pain.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Presentation (October 28, 2023):** The patient was evaluated at the emergency room due to symptoms of cough, low back pain, and abdominal pain. A CT angiogram of the chest was performed, which revealed a large left pleural effusion tracking to the lung apex with near complete opacification of the left lower lobe, a 6-cm left lower lobe mass, and 4-cm left hilar mass with mediastinal adenopathy and pleural nodularity.\n2. **Surgical Intervention (November 9, 2023):** The patient underwent left video-assisted thorascopic surgery with total left lung decortication, removal of fibrin deposits, and placement of a pleural drainage catheter requiring daily drainage.\n3. **Pathology and Imaging Results (November 29, 2023):** Pathology from the left pleural mass revealed malignant epithelial neoplasm with 70% spindle cell and 30% epithelioid cell components consistent with biphasic MPM. PET imaging confirmed advanced disease with extensive left-sided pleural involvement, bilateral mediastinal adenopathy, adrenal, and scattered bone lesions.\n4. **Immune Checkpoint Inhibitor Therapy (December 4, 2023):** The patient began receiving immune checkpoint inhibitor therapy with nivolumab and ipilimumab, which showed initial improvement in pleural drainage output.\n\n**Timeline of Symptoms:**\n\n1. **Initial Presentation:** Cough, low back pain, and abdominal pain.\n2. **Post-Surgical Complication (December 4, 2023):** Lower back pain, lower extremity numbness, and inability to walk after one cycle of therapy.\n\n**Treatment Outcomes:**\nThe patient's treatment with immune checkpoint inhibitors showed initial improvement in pleural drainage output. However, a new symptom of lower back pain, lower extremity numbness, and inability to walk developed after one cycle of therapy, indicating potential side effects or progression of the disease.\n\nThis clinical case report highlights the importance of early diagnosis and treatment of malignant pleural mesothelioma (MPM), as well as the need for careful monitoring of patients receiving immune checkpoint inhibitors.", + "bertscore": { + "precision": 0.8396786451339722, + "recall": 0.8474234938621521, + "f1": 0.8435333371162415 + }, + "bleu": 0.16483788813818426, + "rouge1": 0.5029126213592232, + "rougeL": 0.3572815533980583, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.1652541607618332, + 0.039438892155885696, + -0.14641372859477997, + 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b/src/benchmark/output/results/results_graph_066.json new file mode 100644 index 0000000..4fcffc1 --- /dev/null +++ b/src/benchmark/output/results/results_graph_066.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 59-year-old woman who presented with a cough. Her demographic information is not explicitly mentioned in the provided data, but based on the age and sex, we can infer that she is an adult female.\n\n**Initial Diagnosis (Step 1):**\nUpon presentation, the patient underwent a lung CT scan, which revealed a space-occupying lesion in the left lower lobe. The lesion was accompanied by peripheral obstructive inflammation, atelectasis, and multiple enlarged lymph nodes in the mediastinum. A biopsy of the lesion was performed, which confirmed the presence of keratinized squamous cell carcinoma. The patient was diagnosed with left lower lobe squamous cell carcinoma (T3N2bM0, Stage IIIB).\n\n**Treatment Initiation (Step 2):**\nThe patient underwent six cycles of albumin-bound paclitaxel (100 mg/m\u00b2 on day 1, day 8, and day 15), cisplatin (75 mg/m\u00b2 on day 1), and carrelizumab (200 mg on day 1). Following this treatment, the left lower lung lesion had significantly reduced in size to approximately 23x25 mm.\n\n**Radiotherapy and Re-emergence of Disease (Step 3):**\nThe patient underwent radiotherapy with a dose of 2 Gy per fraction, administered over a total of 30 fractions. However, after ten fractions, the patient developed dyspnea and fever, with a maximum temperature of 38.5\u00b0C. A lung puncture biopsy was performed, which confirmed the presence of squamous cell carcinoma. The lesion had significantly enlarged to a size of 50 \u00d7 51 mm.\n\n**Outcome:**\nThe patient's condition worsened after radiotherapy, and she developed delayed hypersensitivity pneumonitis (DHP) after 5 months of immunotherapy. Despite this, the patient continued to receive treatment, highlighting the complexities of managing advanced cancer.\n\nIn conclusion, this clinical case report highlights the challenges of treating advanced squamous cell carcinoma in a 59-year-old woman. The patient's initial diagnosis and treatment response were promising, but the disease re-emerged after radiotherapy, leading to worsening symptoms and complications. Further management strategies are needed to improve outcomes for patients with advanced cancer.", + "bertscore": { + "precision": 0.7917846441268921, + "recall": 0.8422552347183228, + "f1": 0.8162405490875244 + }, + "bleu": 0.05509384931217402, + "rouge1": 0.3931623931623932, + "rougeL": 0.22222222222222224, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 3, + "edge_count": 2, + "avg_in_degree": 0.6666666666666666, + "density": 0.3333333333333333 + }, + "trajectory_embedding": [ + 0.24472539126873016, + 0.05973951891064644, + -0.20621691644191742, + 0.22169888019561768, + -0.08776857703924179, + -0.01297292485833168, + 0.14311833679676056, + 0.19575707614421844, + 0.13809828460216522, + -0.30675601959228516, + -0.19033236801624298, + 0.21958637237548828, + -0.5650694966316223, + -0.03671947494149208, + -0.21233956515789032, + -0.07029158622026443, + 0.05985746905207634, + 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cancer (NSCLC) adenocarcinoma.\n\n**Timeline of Diagnoses:**\n\n1. **2016:** The patient was diagnosed with stage IIIA NSCLC adenocarcinoma.\n2. **2016:** Following the diagnosis, the patient underwent a right middle lobectomy, adjuvant carboplatin/paclitaxel chemotherapy, and postoperative radiotherapy (PORT).\n3. **2022:** The patient developed metastatic disease in the right lung, liver, and brain.\n\n**Timeline of Treatments:**\n\n1. **2016-2017:** Adjuvant carboplatin/paclitaxel chemotherapy.\n2. **2017:** Postoperative radiotherapy (PORT) was administered.\n3. **2022:** Stereotactic radiation therapy was performed to treat a single brain metastasis.\n4. **2022:** Empirical chemotherapy regimen consisting of 5-fluorouracil/oxaliplatin (FOLFOX) was initiated.\n5. **2022:** Histopathological analysis of liver lesions identified spindle cell carcinoma likely pulmonary in origin despite atypical features, with a high proliferative Ki-67 index (90%).\n6. **2022:** Treatment with docetaxel was administered.\n\n**Timeline of Outcomes:**\n\n1. **2017:** The patient underwent upper and lower GI endoscopy due to microcytosis, but no lesions were identified.\n2. **2022:** Liver biopsy showed metastatic spindle cell carcinoma on H&E stain, sections demonstrated a spindle cell neoplasm with significant mitotic activity and focal necrosis, and immunohistochemistry showed the tumor cells positive for AE1/AE3 and CK8/18, but negative for Alk-1, CK7, CK20, CDX-2, and CD117.\n3. **2022:** The patient received nine weekly doses of docetaxel with modest shrinkage (approximately 10-15%).\n\n**Conclusion:**\nThe patient's clinical course was marked by a diagnosis of stage IIIA NSCLC adenocarcinoma in 2016, followed by treatment with adjuvant chemotherapy and radiotherapy. Despite this initial treatment, the patient developed metastatic disease in 2022, which led to further evaluation and treatment, including stereotactic radiation therapy for brain metastasis, empirical chemotherapy regimen, histopathological analysis of liver lesions, and treatment with docetaxel. The patient's current status is characterized by ongoing treatment with docetaxel, with modest shrinkage observed in the tumor size.", + "bertscore": { + "precision": 0.8460601568222046, + "recall": 0.8547090888023376, + "f1": 0.8503626585006714 + }, + "bleu": 0.22916691868794195, + "rouge1": 0.5531914893617021, + "rougeL": 0.34793491864831044, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2563111484050751, + 0.18047350645065308, + -0.12980332970619202, + 0.12957733869552612, + 0.14545029401779175, + 0.19874490797519684, + -0.020612286403775215, + 0.3609883785247803, + 0.5175485610961914, + -0.42774152755737305, + -0.11932812631130219, + -0.07010838389396667, + -0.6297792792320251, + -0.06867539882659912, + -0.2806960642337799, + 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"reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an adult male with no specified age or background information provided. However, based on the clinical data, it appears that the patient has a history of lung cancer.\n\n**Timeline of Diagnoses:**\n\n1. **September 2021:** The patient presented to The First Affiliated Hospital of Dalian Medical University with complaints of chest pain and fatigue for half a year. A CT scan revealed partial solid nodules in the posterior segment of the upper lobe of the right lung, which were later diagnosed as malignant neoplasm of bronchus and lung (C34).\n2. **Multiple small lung nodules in both lungs:** Following the initial diagnosis, the patient developed multiple small lung nodules in both lungs, accompanied by abnormal blood test results (lymphocytopenia and neutrophilia). This led to a decision to proceed with surgical resection of lung tissue.\n3. **November 2022:** The patient underwent surgical resection of lung tissue, which revealed invasive adenocarcinoma in the upper lobe of the right lung. The cancer was diagnosed as C2330808 (Adenocarcinoma, Invasive).\n4. **January 2024:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm.\n\n**Timeline of Treatments:**\n\n1. **Surgical resection of lung tissue:** The patient underwent surgical resection of lung tissue in November 2022.\n2. **No second surgical treatment:** The patient refused a second surgical treatment for the recurrence of primary cancer, which presented as ground glass nodules in the left lung.\n\n**Timeline of Outcomes:**\n\n1. **Pathological diagnosis:** The pathological diagnosis of invasive adenocarcinoma was confirmed post-surgery in November 2022.\n2. **Recurrence of primary cancer:** The patient developed recurrence of primary cancer with ground glass nodules in the left lung and new symptoms (fatigue, pale tongue, white fur, and weak pulse) in November 2022.\n3. **Recurrent tumor shrinkage:** A CT examination revealed recurrent tumor shrinkage of about 7 mm * 9 mm in January 2024.\n\n**Clinical Findings:**\n\nThroughout the patient's treatment, various clinical findings were reported, including:\n\n* Chest pain and fatigue\n* Multiple small lung nodules in both lungs\n* Abnormal blood test results (lymphocytopenia and neutrophilia)\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Laboratory Results:**\n\nThe patient's laboratory results showed:\n\n* Normal blood work (January 2024)\n* Elevated carcinoembryonic antigen level (November 2022)\n\n**Imaging Results:**\n\nThe patient underwent various imaging studies, including CT scans and pathology reports, which revealed:\n\n* Partial solid nodules in the posterior segment of the upper lobe of the right lung (September 2021)\n* Multiple small lung nodules in both lungs\n* Invasive adenocarcinoma in the upper lobe of the right lung\n* Ground glass nodules in the left lung\n* Recurrent tumor shrinkage\n\n**Prognosis:**\nThe patient's prognosis remains uncertain, as the cancer has recurred and treatment options are limited. Further evaluation and management are necessary to determine the best course of action.\n\n**Conclusion:**\nThis clinical case report highlights the complexities of managing lung cancer, particularly in cases where recurrence occurs. The patient's treatment plan will require careful consideration of various factors, including the patient's overall health, tumor characteristics, and available treatment options.", + "bertscore": { + "precision": 0.8164668083190918, + "recall": 0.7990182638168335, + "f1": 0.8076483011245728 + }, + "bleu": 0.14948288116375336, + "rouge1": 0.518118735543562, + "rougeL": 0.2713955281418658, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.257910817861557, + 0.11300678551197052, + -0.15380962193012238, + -0.04967570677399635, + -0.14522525668144226, + 0.06221002712845802, + 0.07804203033447266, + 0.17250725626945496, + 0.2976982593536377, + -0.48700565099716187, + -0.2710980474948883, + 0.19328932464122772, + -0.552730143070221, + -0.1464165896177292, 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"reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 67-year-old man with a significant smoking history, having smoked 30 cigarettes per day for 50 years. He presented to the clinic with a persistent dry cough that had lasted for more than three months.\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **July 2019:** The patient was diagnosed with a mass in the central left upper lobe, enlarged bilateral mediastinal lymph nodes, and bilateral pulmonary nodules on contrast-enhanced chest CT (Step 2). Biopsy of the lesion under tracheoscopy confirmed lung adenocarcinoma histologically (Step 3).\n2. **July-September 2019:** The patient underwent whole-body scanning, which revealed macroscopic metastases in the bone. He was clinically classified as stage IVB (T4N0M1c) Non-Small Cell Lung Carcinoma (NSCLC). Zoledronic acid was administered to control bone destruction (Step 4).\n3. **September-October 2019:** The patient underwent tissue biopsy, which detected an acquired T790M mutation in exon 20 (c.2369C>T, frequency as 61.9%) via droplet digital polymerase chain reaction (ddPCR) (Step 7).\n4. **October-November 2019:** Due to the detection of the T790M mutation, the patient was switched to osimertinib 80mg once daily, achieving stable disease with shrinkage of hepatic lesions (Step 8).\n\n**Outcomes:**\n\n1. The patient experienced a rapid clinical benefit lasting 11 months after starting treatment with gefitinib (250 mg once daily) in response to the detection of EGFR exon 19 deletion (Step 6).\n2. After 11 months on gefitinib, tissue biopsy was performed to investigate resistance mechanisms, detecting an acquired T790M mutation in exon 20 (c.2369C>T, frequency as 61.9%) via droplet digital polymerase chain reaction (ddPCR) (Step 7).\n\n**Conclusion:**\nThe patient's clinical course highlights the importance of molecular testing and targeted therapy in the management of NSCLC. The detection of EGFR exon 19 deletion led to treatment with gefitinib, resulting in a rapid clinical benefit. However, the subsequent development of T790M mutation necessitated a switch to osimertinib, achieving stable disease with shrinkage of hepatic lesions.\n\n**Recommendations:**\n\n1. Regular molecular testing for EGFR mutations and T790M status should be performed in patients with NSCLC.\n2. Targeted therapy with gefitinib or osimertinib should be considered based on molecular test results.\n3. Close monitoring of disease progression and response to treatment is essential in managing NSCLC.\n\n**Limitations:**\n\n1. The patient's clinical course was limited by the availability of targeted therapies at the time of diagnosis.\n2. Further research is needed to explore the optimal timing and sequence of molecular testing and targeted therapy in NSCLC.\n\nThis case highlights the importance of personalized medicine in the management of NSCLC, emphasizing the need for regular molecular testing and targeted therapy based on test results.", + "bertscore": { + "precision": 0.8484562039375305, + "recall": 0.8624377250671387, + "f1": 0.8553898930549622 + }, + "bleu": 0.21123213345024985, + "rouge1": 0.5747800586510264, + "rougeL": 0.29912023460410553, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.25666746497154236, + 0.09836211800575256, + -0.10564713180065155, + 0.11217941343784332, + 0.015587031841278076, + 0.07877800613641739, + -0.006527600809931755, + 0.30493852496147156, + 0.5536767244338989, + 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b/src/benchmark/output/results/results_graph_070.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Patient Demographics**\n\nThe patient is a 35-year-old female who was diagnosed with breast cancer. Unfortunately, the demographic information provided does not include her name, address, or any other identifying details.\n\n**Timeline of Diagnoses**\n\nThe patient's journey began in [month/year] when she developed memory problems following a COVID-19 infection. Two days later, she underwent lumpectomy due to the worsening symptoms. The pathology report revealed infiltrative breast carcinoma of mixed type (80% non-specific, 20% lobular), histoprognostic grade I (2-2-1), and histological tumor size of 30 mm along the long axis.\n\n**Timeline of Treatments**\n\nFollowing the lumpectomy, the patient was diagnosed with anti-LGI1 limbic encephalitis associated with early-stage breast cancer. MRI, EEG, and positive anti-LGI1 antibodies supported this diagnosis. As a result, she underwent PET scans to further investigate the breast cancer diagnosis.\n\nThe PET scan identified a moderately hypermetabolic lesion in the right breast, leading to resection of the breast tumor with immunohistopathological analysis. The pathological stage was determined as pT2 N0 (sn) G1 R. Following resection, immunosuppressive treatment was started within 24 hours of admission.\n\n**Timeline of Outcomes**\n\nThe patient's condition improved gradually over time. She recovered from the initial symptoms and no longer experienced headaches or focal epileptic seizures since hospitalization. However, partial retrograde and anterograde amnesia persisted during the initial week, followed by a slow and steady improvement.\n\nAfter 12 months of recovery, the patient returned to work with 80% of her previous productivity. Neuropsychological evaluations at baseline showed impairment in verbal episodic memory (Free and Cued Selective Reminding Test) and visual episodic memory (recall of the Rey-Osterrieth complex figure). However, after six months of treatment, objective cognitive improvement was observed.\n\n**Current Status**\n\nThe patient's current status is one of ongoing management and monitoring. She continues to receive immunosuppressive treatment to manage her anti-LGI1 limbic encephalitis. Regular follow-up appointments with her healthcare team are necessary to monitor her condition and adjust treatment as needed.\n\nDespite the challenges she has faced, the patient has demonstrated remarkable resilience and determination in her pursuit of recovery. Her progress is a testament to the importance of comprehensive care and ongoing support for individuals with complex medical conditions.", + "bertscore": { + "precision": 0.754819929599762, + "recall": 0.7756854295730591, + "f1": 0.7651103734970093 + }, + "bleu": 0.021079017527702103, + "rouge1": 0.36927621861152143, + "rougeL": 0.14180206794682423, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 12, + "edge_count": 11, + "avg_in_degree": 0.9166666666666666, + "density": 0.08333333333333333 + }, + "trajectory_embedding": [ + 0.13369283080101013, + 0.14433510601520538, + -0.22548367083072662, + 0.060306016355752945, + -0.08639272302389145, + 0.002943794010207057, + 0.23735707998275757, + 0.16482573747634888, + 0.5013976693153381, + -0.3400944769382477, + -0.0792926773428917, + 0.0980411171913147, + -0.5940414071083069, + -0.14733976125717163, + -0.22831867635250092, + 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+{ + "status": "success", + "reconstructed_narrative": "The patient in question is a male who has been diagnosed with lung cancer. Unfortunately, the provided data does not include the patient's demographic information such as age, address, or contact details.\n\nHowever, based on the timeline of diagnoses and treatments provided, we can reconstruct a coherent narrative:\n\nThe patient was first diagnosed with lung cancer, which led to the start of gyroknife radiotherapy for left and right lung malignancies 12 times. This treatment was likely aimed at reducing the size of the tumors in the lungs.\n\nAfter completing this treatment, the patient experienced tumor progression, leading to the start of anlotinib 8mg orally once daily for 14 days every 3 weeks. This medication was intended to slow down the growth of the cancer cells.\n\nHowever, after 14 cycles of anlotinib treatment, the patient presented with hyperglycemia (fasting plasma glucose of 26.1 mmol/L) and urine ketone (+++), leading to a diagnosis of type 1 diabetes. As a result, the patient was discharged with a hypoglycemic regimen of insulin degludec 5 units in the morning and insulin aspartate 4 units three times a day.\n\nOne week after discharge, the patient's blood glucose levels significantly increased after re-starting anlotinib (highest recorded level was 30.1 mmol/L), and the insulin dose was increased. Despite this escalation, the patient continued to experience significant improvements in their laboratory parameters, including GADA, ICA, IAA, Fasting blood glucose, Hemoglobin A1c, Hemoglobin, and Serum albumin.\n\nAfter two cycles of anlotinib treatment, the medication was discontinued due to tumor progression and its significant negative impact on glucose metabolism. However, by the 16th cycle, laboratory parameters showed a marked improvement in these areas.\n\nThe patient's current status is unclear from the provided data, but it appears that they have undergone various treatments for their lung cancer and diabetes. The exact outcome of these treatments is not specified, but the narrative suggests that the patient has experienced significant improvements in their laboratory parameters over time.", + "bertscore": { + "precision": 0.8337717056274414, + "recall": 0.8181021213531494, + "f1": 0.8258626461029053 + }, + "bleu": 0.08451707165944072, + "rouge1": 0.41294005708848713, + "rougeL": 0.247383444338725, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.1467558592557907, + 0.21578022837638855, + -0.22472743690013885, + 0.1429169625043869, + -0.0391475111246109, + 0.10741577297449112, + 0.24607594311237335, + 0.2464669942855835, + 0.3772128224372864, + -0.3546753525733948, + -0.1136227399110794, + 0.030413171276450157, + -0.4117017686367035, + -0.1751895248889923, + -0.3702186644077301, + 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+1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Patient Profile**\n\nThe patient is an adult male with a history of immunocompromised status due to HIV/AIDS. He was admitted to the hospital on day 1 (N1) with symptoms of pneumonia and acute hypoxic respiratory failure requiring intubation. His vital signs were unstable, and he required close monitoring in the intensive care unit.\n\n**Timeline of Diagnoses**\n\n* Day 1 (N1): Admitted with pneumonia and acute hypoxic respiratory failure.\n* Day 14 (N2): Developed septic shock and PICC-line-associated MSSA bacteremia. He was treated with IV cefazolin.\n* Day 28 (N3): Developed SVC syndrome and left upper extremity DVT. He was treated with therapeutic enoxaparin.\n* Day 42 (N4): Recurrent fevers and transfer back to the ICU for septic shock management. Blood cultures grew MSSA, and a transesophageal echocardiogram showed no endocarditis.\n* Day 54 (N5): Repeat blood cultures grew A. fumigatus in addition to MSSA. The infectious disease team recommended continuing IV cefazolin for MSSA bacteremia and adding caspofungin for fungal coverage.\n* Day 56 (N6): Atovaquone continued for pneumocystis jirovecii prophylaxis, and tenofovir discontinued due to concern for contributing to acute kidney injury. The antiretroviral regimen was changed to dolutegravir/rilpivirine plus emtricitabine pending further evaluation of hepatitis B status.\n* Day 62 (N9): Patient died of his illness.\n\n**Timeline of Treatments**\n\n* Day 1-14 (N2): IV cefazolin for MSSA bacteremia\n* Day 28-42 (N3): Therapeutic enoxaparin for SVC syndrome and DVT\n* Day 54 (N5): IV cefazolin continued, caspofungin added for fungal coverage\n* Day 56 (N6): Atovaquone continued, tenofovir discontinued, dolutegravir/rilpivirine plus emtricitabine started\n\n**Outcome**\n\nThe patient's condition worsened over time, and he eventually died on day 62 due to his illness. Despite multiple treatments, including IV cefazolin, therapeutic enoxaparin, and caspofungin, the patient's immune system was unable to overcome the infections.\n\nNote: The narrative is based on the provided data and may not be a comprehensive or entirely accurate representation of the patient's medical history.", + "bertscore": { + "precision": 0.8412173986434937, + "recall": 0.8211429119110107, + "f1": 0.8310589790344238 + }, + "bleu": 0.26754135696306547, + "rouge1": 0.5846645367412141, + "rougeL": 0.4057507987220447, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.18157726526260376, + 0.24173596501350403, + -0.15064290165901184, + 0.07789953052997589, + 0.15454770624637604, + 0.16961298882961273, + -0.11799095571041107, + 0.21222464740276337, + 0.46130186319351196, + 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b/src/benchmark/output/results/results_graph_074.json new file mode 100644 index 0000000..1ec63a8 --- /dev/null +++ b/src/benchmark/output/results/results_graph_074.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an unknown female with no specified age or background information provided in the data. However, based on the clinical presentation and imaging findings, it can be inferred that she is likely a young adult.\n\n**Initial Presentation (Step 1):**\nThe patient presented with a fluid collection adjacent to the spleen, which was identified through abdominal ultrasound. The fluid collection had septations, and no malignant cells were found in the aspirated fluid.\n\n**Progression of Disease (Steps 2-5):**\nOver time, the cystic lesion in the left upper quadrant of the abdomen grew in size, with a notable increase from 7.6 x 11.7 cm to 11 x 22 cm. The patient reported feeling pressure and a pulling sensation on the left side of her abdomen, rated as 4/10 for pain. Ultrasound-guided aspiration revealed 33 mL of clear yellow fluid, which was sent to pathology and showed no evidence of malignant cells.\n\n**Imaging Findings:**\nThroughout the course of the disease, various imaging modalities were used, including ultrasound, CT scans, and MRI. These studies consistently demonstrated a large cystic mass extending from the spleen on the left to the left hemipelvis, with enhancing septations.\n\n**Treatment (Step 7):**\nThe patient received doxycycline sclerotherapy over eight months as part of her treatment plan. Post-sclerotherapy ultrasound showed no significant changes in the size or appearance of the cystic mass.\n\n**Outcome:**\nDespite the growth of the cystic lesion, the patient did not experience any symptoms that would suggest malignancy. The sclerotherapy treatment appears to have been effective in stabilizing the lesion, and further imaging studies are scheduled for follow-up.\n\nIn summary, this patient presented with a fluid collection adjacent to the spleen, which progressed over time into a large cystic mass extending from the spleen on the left to the left hemipelvis. The patient received doxycycline sclerotherapy as part of her treatment plan, and post-treatment imaging studies showed no significant changes in the size or appearance of the lesion.", + "bertscore": { + "precision": 0.8279114961624146, + "recall": 0.8213652968406677, + "f1": 0.8246254324913025 + }, + "bleu": 0.0684286530717067, + "rouge1": 0.42224152910512597, + "rougeL": 0.25021720243266726, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.37995657324790955, + 0.09801924228668213, + 0.029700586572289467, + 0.12594357132911682, + 0.10155230760574341, + 0.09751962870359421, + -0.09553129225969315, + 0.2206941395998001, + 0.4248223304748535, + -0.16399696469306946, + -0.31089702248573303, + -0.05961534380912781, + -0.545925498008728, + 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"success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 77-year-old man with a history of smoking, hypertension, benign prostatic hyperplasia, and hyperuricemia. He was admitted for his first cycle of chemotherapy for stage IV small cell lung cancer without cerebral metastases.\n\n**Timeline of Diagnoses:**\n\n1. **Initial Diagnosis:** The patient's diagnosis of stage IV small cell lung cancer was confirmed upon admission.\n2. **Somnolence and Right-Sided Weakness:** 30 minutes after chemotherapy premedication, the patient experienced a sudden change in mental status, progressing to somnolence. Physical examination revealed altered mental status and right-sided weakness (N2).\n3. **Neurological Examination:** The patient's neurological examination showed signs of reduced mobility on the right side, accompanied by right facial paresis (N3).\n4. **Blood Gas Analysis and Brain CT Angiography:** Blood gas analysis showed no respiratory, metabolic, or electrolyte abnormalities, while brain CT angiography did not reveal any vascular lesions or thrombi in major vessels (N4).\n\n**Timeline of Treatments:**\n\n1. **Chemotherapy Premedication:** The patient received 4 mg intravenous ondansetron and 8 mg intravenous dexamethasone as premedication for chemotherapy.\n2. **Aspirin Administration:** Due to the suspicion of a transient ischemic event, a loading dose of 300 mg of aspirin was administered, followed by a daily dose of 100 mg of aspirin (N6).\n\n**Outcome:**\n\nThe patient gradually became more alert approximately one hour after the onset of symptoms and returned to his baseline mental status without any neurological deficits by one hour and thirty minutes after onset. The suspicion of a transient ischemic event as the primary cause of the symptoms was confirmed, and the patient's condition improved with the administration of aspirin.\n\n**Conclusion:**\n\nThis case highlights the importance of prompt recognition and management of acute neurological events in patients undergoing chemotherapy for cancer. Early intervention with aspirin may have contributed to the patient's rapid recovery from a suspected transient ischemic event. Further evaluation and monitoring are necessary to ensure that this patient does not experience any further complications related to his cancer treatment or underlying medical conditions.", + "bertscore": { + "precision": 0.8510310649871826, + "recall": 0.847151517868042, + "f1": 0.8490868806838989 + }, + "bleu": 0.09920424446993878, + "rouge1": 0.45546218487394957, + "rougeL": 0.2638655462184874, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.045807287096977234, + 0.11770268529653549, + -0.03572636470198631, + 0.021092357113957405, + 0.07645720988512039, + 0.007500001695007086, + 0.008010799996554852, + 0.14289645850658417, + 0.3722045123577118, + -0.33858588337898254, + -0.3850763738155365, + 0.18912379443645477, + -0.6559848189353943, + 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b/src/benchmark/output/results/results_graph_076.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 37-year-old woman diagnosed with left lung adenocarcinoma in November 2019. She has extensive bone metastases (cT4N3M1c, stage IVB).\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **November 2019:** The patient was diagnosed with left lung adenocarcinoma and had a baseline chest CT scan and head MRI performed.\n2. **December 2019:** Tumor tissue NGS revealed EGFR exon 18 p.G719S mutation and EGFR exon 20 p.S768I mutation, which led to the initiation of first-line afatinib treatment (40 mg daily po).\n3. **January 2020 - October 2020:** The patient experienced therapeutic failure after 10 months of afatinib treatment, as indicated by time to failure.\n4. **October 2020:** The patient developed new brain lesions and had a partial response on afatinib treatment (lung lesion stable disease, head lesions partial response).\n5. **February 2021:** The patient's brain lesions continued to deteriorate, leading to the reversion of third-line afatinib treatment.\n6. **February 2021:** The patient was switched to second-line osimertinib treatment (80 mg daily po).\n\n**Outcomes:**\n\n* Lung lesion stable disease (SD) at October 2020 and February 2021.\n* Head lesions partial response (PR) on afatinib treatment at October 2020 and February 2021.\n* Brain lesions deteriorated over time, with a new onset of symptoms in February 2021.\n\n**Medications:**\n\n* Afatinib (40 mg daily po): initiated in December 2019, experienced therapeutic failure after 10 months, and partially responsive to treatment at October 2020.\n* Osimertinib (80 mg daily po): started in February 2021 as a second-line treatment.\n\n**Imaging:**\n\n* Baseline chest CT scan and head MRI performed in November 2019.\n* Follow-up imaging not specified for each time point, but mentioned to be performed at October 2020 and February 2021.\n\nNote: The patient's timeline is based on the provided data, which may not be comprehensive or up-to-date.", + "bertscore": { + "precision": 0.8246598243713379, + "recall": 0.8222452402114868, + "f1": 0.8234508037567139 + }, + "bleu": 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He received cefaclor and azithromycin at a local clinic without significant alleviation of his symptoms.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (September 2023):**\nThe patient was initially evaluated in an outpatient setting with persistent respiratory symptoms. A chest X-ray revealed a space-occupying mass in the left lung, prompting hospitalization on September 10, 2023.\n2. **Step 2 (September 10, 2023):**\nUpon admission, laboratory investigations were normal, and CT imaging demonstrated irregularly shaped soft tissue masses in both the upper and lower lobes of the left lung.\n3. **Step 3 (September 11-12, 2023):**\nFurther characterization of the lung mass was performed through additional CT imaging, which showed an oval mass in the lower lobe of the lung measuring approximately 2.3 cm x 1.7 cm with lobulated and spiculated margins.\n4. **Step 4 (September 13-14, 2023):**\nPET-CT imaging revealed high-density lesions in both the upper and lower lobes of the left lung, with increased glucose metabolism. Multiple enlarged lymph nodes were detected in the mediastinum and interlobular spaces.\n\n**Treatments:**\n\n1. **Step 1 (September 2023):**\nThe patient received cefaclor and azithromycin at a local clinic.\n2. **Step 2-4 (September 10-14, 2023):**\nNo specific treatments were mentioned in the provided data.\n\n**Outcomes:**\n\n1. **Imaging:** The initial chest X-ray revealed a space-occupying mass in the left lung, which was later characterized through additional imaging studies.\n2. **Laboratory Investigations:** Normal laboratory results were reported during hospitalization.\n3. **PET-CT Imaging:** High-density lesions with increased glucose metabolism were detected in both the upper and lower lobes of the left lung.\n\n**Conclusion:**\nThe patient's clinical presentation and diagnostic timeline suggest a complex respiratory condition, potentially related to malignancy or other pathologies. 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shortness of breath, cough, and hemoptysis. She was diagnosed with stage IVa epidermal growth factor receptor (EGFR)L858R-mutated non-small cell lung cancer (NSCLC).\n\n**Timeline of Diagnoses:**\n\n* September 2019: The patient presented with symptoms of shortness of breath, cough, and hemoptysis, leading to a diagnosis of stage IVa (cT4N2M1a) lung adenocarcinoma in the right upper lobe, with multiple ipsilateral lung metastases, and involvement of the pleura and mediastinal lymph nodes.\n* September 2019: A bronchoscopic lung biopsy revealed the presence of EGFR p.L858R and TP53 p.R248L mutations.\n\n**Timeline of Treatments:**\n\n1. **First-Line Treatment (October 11, 2019 - February 2020)**:\nThe patient received first-line treatment with icotinib (125 mg orally, three times daily) and pemetrexed. After two months, the patient experienced partial response.\n2. **Second-Line Treatment (April 28, 2020 - July 2020)**:\nThe patient commenced second-line treatment with amonertinib (110 mg orally, once daily) in combination with anlotinib (12 mg orally, once daily for 2 weeks, followed by a 1-week drug-free period). The treatment resulted in stable disease initially but progressed after 3 months.\n3. **Third-Line Treatment (August 3, 2020 - November 2020)**:\nThe patient initiated treatment with osimertinib (80 mg orally, once daily) and bevacizumab (350 mg IV, on day 1 of a 21-day cycle). The treatment resulted in partial response after two cycles and significant reduction in tumor lesions after four cycles.\n4. **Fourth-Line Treatment (October 10, 2020 - present)**:\nThe patient received pembrolizumab (200 mg IV on day 1 of every 3 weeks), pemetrexed, and carboplatin. The treatment resulted in partial response after two cycles and significant reduction in tumor lesions after four cycles.\n\n**Outcomes:**\n\n* **Pathological Complete Response (pCR)**:\nThe patient achieved a pathological complete response (pCR) and prolonged survival.\n* **High PD-L1 Expression**:\nTumor microenvironment analysis showed high programmed cell death 1 ligand 1 (PD-L1) expression on tumor cells, indicating potential for immune checkpoint therapy.\n* **Increased Immune Cell Infiltration**:\nThe patient had increased infiltration of immune cells, particularly PD-1+CD8+T cells and PD-L1+macrophages, in the tumor microenvironment.\n\nIn conclusion, this patient's case highlights the importance of personalized medicine approaches in treating advanced NSCLC. The use of targeted therapies, such as EGFR inhibitors and immunotherapies, has led to significant improvements in treatment outcomes and quality of life for patients with this disease.", + "bertscore": { + "precision": 0.7301585674285889, + "recall": 0.7485638856887817, + "f1": 0.7392467260360718 + }, + "bleu": 0.08636718645614525, + "rouge1": 0.3633276740237691, + "rougeL": 0.2139219015280136, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.28967222571372986, + 0.13287165760993958, + -0.27321428060531616, + 0.1138295978307724, + -0.09009366482496262, + 0.025592172518372536, + 0.09159565716981888, + 0.1864396333694458, + 0.445202499628067, + -0.5484539866447449, + -0.1185631975531578, + 0.20055018365383148, + -0.6732085347175598, + 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Case Report**\n\n**Patient Demographics:**\nThe patient is a 71-year-old male with a past medical history of tobacco use, who quit more than 24 years ago. He presented with a newly diagnosed lung cancer and a progressively increasing lump in the right axilla over 2 months.\n\n**Initial Diagnosis (Step 1):**\nUpon presentation, the patient underwent an ultrasound examination, which revealed a 3.7 cm enlarged lymph node (LN) in the right axilla with effacement and hypervascularity. A biopsy of the LN showed carcinoma with cytokeratin 7 (CK-7) and thyroid transcription factor-1 (TTF-1) positivity, consistent with lung adenocarcinoma, with a possibility of squamous component. Further imaging studies, including a PET scan, revealed multiple F-fluorodeoxyglucose (FDG) avid nodes in the right hilum, thoracic inlet, mediastinum, and right axilla, concerning for metastatic disease.\n\n**Treatment Initiation (Step 2):**\nThe patient was started on single-agent pembrolizumab, a checkpoint inhibitor, with good treatment response. However, after 17 months of treatment, the patient presented to the clinic with worsening shortness of breath (SOB), which he noted a few months ago, was mild in the beginning, and has progressively gotten worse in the last few weeks.\n\n**Progression and Complications (Step 3):**\nA recent PET scan did not show any evidence of disease progression or signs of inflammation in lungs. However, echocardiography revealed severe pulmonary arterial hypertension (PAH), with elevated right ventricular systolic pressure (RVSP) at 86 mm Hg. The patient also had mild regurgitation noted at the pulmonary valve with no structural abnormalities.\n\n**Current Status:**\nThe patient is currently under close observation for worsening symptoms and potential disease progression. Further management strategies, including additional immunotherapies or PAH-specific treatments, are being considered based on ongoing clinical evaluation.\n\n**Timeline of Diagnoses and Treatments:**\n\n* Month 0-2: Patient presents with newly diagnosed lung cancer and progressively increasing lump in the right axilla.\n* Month 2-17: Patient undergoes treatment with pembrolizumab, showing good initial response.\n* Month 17-present: Patient experiences worsening shortness of breath, prompting further evaluation.\n\n**Outcomes:**\n\n* The patient's current disease status is concerning for metastatic lung cancer with PAH.\n* Further management strategies are being considered to address the patient's worsening symptoms and potential disease progression.", + "bertscore": { + "precision": 0.8614916205406189, + "recall": 0.8687059283256531, + "f1": 0.8650836944580078 + }, + "bleu": 0.195284988308007, + "rouge1": 0.5114503816793894, + "rougeL": 0.3912213740458015, + "topology": { + 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No symptoms were reported, and she had no significant medical history, including no history of tuberculosis or lung infections.\n\n**Initial Diagnosis (Step 1):**\nA chest radiograph revealed a solitary pulmonary nodule in the left lower lung field. The patient was diagnosed with a pulmonary nodule (code: 7225005) and underwent further evaluation.\n\n**Biopsy and Initial Treatment (Steps 2-3):**\nA peripheral pulmonary nodule was identified on a chest CT scan, which led to the performance of an endobronchial ultrasound transbronchial lung biopsy. The procedure was successful, but minor bleeding occurred. Biopsy specimens revealed granulomatous inflammation. Following this, a transbronchial lung cryobiopsy was performed four times through the same guide sheath, also with minor bleeding.\n\n**Post-Biopsy Complications and Treatment Initiation (Step 3):**\nAfter the cryobiopsy, increased density in the lower zone of the left lung was observed on chest radiograph. Tissue sample PCR tests were negative for Mycobacterium tuberculosis and NTM. However, one week post-biopsy, follow-up outpatient chest radiographs revealed an enlarged shadow at the location of the original lesion. The patient reported discharge of a purulent and intermittent blood-tinged sputum, which led to the initiation of antibiotic therapy with moxifloxacin (400 mg daily).\n\n**Response to Antibiotics and Follow-Up (Step 4):**\nTwo weeks after starting antibiotics, chest radiographs indicated a slight increase in the size of the lesion. However, there was an improvement in her symptoms, with no other abnormal findings such as fever. The antibiotic therapy continued with regular outpatient follow-ups.\n\n**Lesion Improvement and Acid-Fast Bacilli Growth (Step 5):**\nThree weeks after tissue biopsy, chest radiographs showed improvement in the lesion size. Notably, growth of acid-fast bacilli was reported in the bronchoalveolar lavage fluid obtained during examination.\n\n**Outcome:**\nThe patient's symptoms improved significantly with antibiotic therapy and follow-up care. The growth of acid-fast bacilli in the bronchoalveolar lavage fluid suggested that the patient had a Mycobacterium tuberculosis infection, which was confirmed by PCR tests. However, due to the presence of granulomatous inflammation in biopsy specimens, it is possible that the patient had an NTM infection as well.\n\n**Conclusion:**\nThe patient's case highlights the importance of prompt evaluation and treatment for pulmonary nodules, particularly those with granulomatous inflammation or acid-fast bacilli growth. Early detection and management can significantly improve outcomes and prevent complications.", + "bertscore": { + "precision": 0.7984694242477417, + "recall": 0.855120837688446, + "f1": 0.8258247375488281 + }, + "bleu": 0.10369187817964154, + "rouge1": 0.4070175438596491, + "rougeL": 0.24912280701754386, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 2, + "node_count": 6, + "edge_count": 4, + "avg_in_degree": 0.6666666666666666, + "density": 0.13333333333333333 + }, + "trajectory_embedding": [ + 0.1967584788799286, + 0.11755304038524628, + -0.10197411477565765, + -0.01451544463634491, + -0.10492626577615738, + -0.16041645407676697, + 0.15277233719825745, + 0.07490139454603195, + 0.196526437997818, + -0.2453027218580246, + -0.23723392188549042, + 0.15686118602752686, + -0.45318803191185, + -0.14287793636322021, + -0.1919034719467163, + -0.01922443136572838, + 0.09047435224056244, + 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adult with unknown age, sex, and ethnicity. The patient's demographic information is not provided in the data.\n\n**Initial Presentation:**\nThe patient presented with symptoms of intracranial hypertension, including nausea and vomiting (Step 1). This was the initial presentation that led to further investigation.\n\n**Diagnosis:**\nFurther investigation revealed brain MRI suggesting leptomeningeal metastases (Step 2). Lumbar puncture was performed, and cerebrospinal fluid cytology confirmed leptomeningeal metastases (Step 3).\n\n**Treatment:**\nThe patient received treatment for the diagnosed condition. The treatment sequence included initial monotherapy with Olaparib, followed by combination therapy with intrathecal chemotherapy, and eventually a triple combination of Olaparib, Furmonertinib, and intrathecal chemotherapy (Step 5). Intrathecal pemetrexed was administered since October 2021 (Step 8).\n\n**Progression:**\nSymptoms of leptomeningeal metastases worsened dramatically, including lethargy, unresponsiveness, difficulty in eating and swallowing, necessitating intravenous nutritional support. The patient's ECOG performance status declined to 4 (Step 9). This marked a significant progression of the disease.\n\n**Outcome:**\nThe patient experienced a durable response to Olaparib lasting approximately 21 months (Step 6). However, the worsening of leptomeningeal metastases symptoms and decline in functional status necessitated further treatment adjustments.\n\n**Timeline:**\n\n* Step 1: Initial presentation with intracranial hypertension symptoms\n* Step 2: Diagnosis of leptomeningeal metastases confirmed by brain MRI\n* Step 3: Lumbar puncture performed, and cerebrospinal fluid cytology confirmed leptomeningeal metastases\n* Step 4: Placement of Ommaya reservoir for treatment delivery\n* Step 5: Identification of EGFR and BRCA2 mutations\n* Step 6: Initiation of Olaparib therapy with durable response lasting approximately 21 months\n* Step 7: Treatment escalation to combination therapy with intrathecal chemotherapy\n* Step 8: Administration of intrathecal pemetrexed since October 2021\n* Step 9: Worsening of leptomeningeal metastases symptoms and decline in functional status\n\n**Conclusion:**\nThe patient was diagnosed with leptomeningeal metastases and received treatment with Olaparib, Furmonertinib, and intrathecal chemotherapy. The patient experienced a durable response to Olaparib but ultimately required further treatment adjustments due to worsening of symptoms and decline in functional status.", + "bertscore": { + "precision": 0.6957451701164246, + "recall": 0.6707550287246704, + "f1": 0.683021605014801 + }, + "bleu": 0.0058559256287235755, + "rouge1": 0.27283653846153844, + "rougeL": 0.13701923076923075, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2321387678384781, + 0.21690434217453003, + -0.13298587501049042, + 0.17195039987564087, + 0.08285973221063614, + 0.15777303278446198, + 0.1095961406826973, + 0.3161073923110962, + 0.6317851543426514, + -0.3226621448993683, + -0.16632980108261108, + -0.09433408826589584, + -0.4814378321170807, + -0.1313047707080841, + 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"success", + "reconstructed_narrative": "The patient in question is a female who was diagnosed with pulmonary adenocarcinoma, a type of lung cancer. Unfortunately, the patient also had bilateral scattered breast metastases, which made her diagnosis even more complex.\n\nThe patient's journey began when she experienced persistent coughing for one month, which led to a chest CT scan that revealed a 3.1 cm right lower lobe tumor, lymphadenopathy, right pleural effusion, pericardial effusion, and scattered nodules in both breasts. Her CA19-9 level was also elevated at 282 U/mL.\n\nFollowing this initial diagnosis, the patient underwent further testing, including molecular analysis that detected an EML4-ALK fusion gene. This led to a biopsy of her bilateral breast tumors, which revealed adenocarcinoma derived from the lungs or breasts.\n\nThe patient's treatment plan began with oral medication, specifically alectinib (600 mg once daily), which was initiated in response to changes in her lab results and imaging findings. The goal of this treatment was to target the ALK rearrangement present in her cancer cells.\n\nOver time, the patient experienced significant reductions in tumor size, particularly in her breast metastases, which nearly disappeared after a maximum size of 4 mm. Her pleural effusion also resolved, and her CA19-9 level decreased from 282 U/mL to 3.7 U/mL.\n\nSix months after starting treatment with alectinib, the patient underwent another CT scan that showed further tumor shrinkage in her lower right lobe and resolution of her pleural effusion. This marked a significant milestone in her treatment journey, indicating that the medication was effective in controlling her cancer.\n\nThe patient's ongoing treatment with alectinib has been accompanied by regular monitoring of her lab results and imaging findings. Her CA19-9 level remains decreased, and she continues to experience no evidence of recurrence. The resolution of shadows in both breasts on CT scans also suggests that the medication is effective in controlling her breast metastases.\n\nThroughout this journey, the patient's treatment plan has been tailored to address changes in her lab results and imaging findings. Her care team has closely monitored her response to treatment and made adjustments as needed to ensure she receives the most effective therapy possible.\n\nThe patient's story highlights the importance of early detection and targeted therapies in managing complex cancers like pulmonary adenocarcinoma with bilateral breast metastases. With ongoing treatment and close monitoring, this patient is able to manage her disease effectively and maintain a good quality of life.", + "bertscore": { + "precision": 0.7734915018081665, + "recall": 0.758467435836792, + "f1": 0.7659057974815369 + }, + "bleu": 0.09899378728395339, + "rouge1": 0.4374384236453202, + "rougeL": 0.20886699507389164, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2193172574043274, + 0.17341764271259308, + -0.28511232137680054, + 0.06250262260437012, + -0.2072673738002777, + -0.09170977771282196, + 0.21316777169704437, + 0.09700273722410202, + 0.22861331701278687, + -0.39751580357551575, + -0.20688259601593018, + 0.24647818505764008, + -0.7876354455947876, + -0.08496146649122238, + -0.4245613217353821, + 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Report**\n\n**Patient Demographics:**\nThe patient is an adult male with a history of respiratory symptoms. Unfortunately, the demographic information is not provided in the given data.\n\n**Initial Presentation (Step 1):**\nThe patient presented with right locus coeruleus, visceral inversion, sinusitis, and bronchial dilatation. These symptoms led to further cardiac evaluation.\n\n**Diagnostic Journey:**\n\n1. **Electrocardiography (ECG) and Initial Diagnosis (Step 2):**\nAn ECG showed a right-sided heart, prompting further imaging with chest CT and 3D reconstruction of the ribs to evaluate lung and organ positioning.\n\n2. **Chest CT Findings (Step 3):**\nThe chest CT revealed chronic inflammation of both lungs, multiple bronchiectasis in both lungs, nodules in the upper lobe of the right lung, a flaky high-density shadow in the right main bronchus, bilateral pleural thickening, localized calcification of the right pleura, and a right-sided heart with transposition of thoracic and abdominal organs.\n\n3. **Paranasal Sinus CT Findings (Step 4):**\nA paranasal sinus CT showed right maxillary sinusitis, ethmoid sinus, nasal soft tissue shadow, polyps, deviated nasal septum, and bilateral middle and lower turbinate hypertrophy.\n\n4. **Bronchoscopy Evaluation (Steps 5-6):**\nNormal bronchial tubes in the right lung led to further bronchoscopic evaluation of the left lung, where a polypoid neoplasm was found in the opening of the upper lobe of the left lung.\n\n5. **Cancer Diagnosis and Treatment Planning (Step 7):**\nBronchoalveolar lavage fluid cytology showed cancer cells, prompting immunohistochemistry to determine the type of cancer. The diagnosis confirmed small cell lung cancer.\n\n6. **Bone Metastasis Evaluation (Step 8):**\nExtrapulmonary auxiliary examination suggested bone metastasis.\n\n7. **Final Diagnosis and Treatment (Step 10):**\nThe patient was diagnosed with extensive stage small cell lung cancer of the left lung, accompanied by Kartagener Syndrome. The ECOG performance status score was 1.\n\n**Outcomes:**\n\n- The patient has been diagnosed with small cell lung cancer.\n- Bone metastasis is suspected but not confirmed.\n- Treatment plans are pending further evaluation and consultation.\n\nThis clinical case report highlights the importance of a comprehensive diagnostic journey, from initial presentation to final diagnosis. Each step in the diagnostic process builds upon previous findings, ultimately leading to an accurate diagnosis and treatment plan for this patient with small cell lung cancer.", + "bertscore": { + "precision": 0.8038591742515564, + "recall": 0.7853204011917114, + "f1": 0.7944816946983337 + }, + "bleu": 0.0515011258904957, + "rouge1": 0.36, + "rougeL": 0.24000000000000002, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 10, + "edge_count": 9, + "avg_in_degree": 0.9, + "density": 0.1 + }, + "trajectory_embedding": [ + 0.3022826015949249, + -0.0002478778478689492, + 0.07108965516090393, + 0.18501682579517365, + 0.12881651520729065, + 0.13057772815227509, + 0.010211390443146229, + 0.27111274003982544, + 0.48087310791015625, + -0.30358201265335083, + -0.15933957695960999, + -0.05752738192677498, + -0.5778652429580688, + -0.08748479187488556, + -0.32486921548843384, + 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"**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 36-year-old woman who presented to Anhui Chest Hospital with cough and chest pain for 2 months. She had no history of smoking.\n\n**Timeline of Diagnoses:**\n\n1. **March 2022:** The patient initially presented to the hospital with symptoms of cough and chest pain, which led to a chest computed tomography (CT) scan.\n2. **March 21, 2022:** The CT scan revealed left pleural thickening and pleural effusion, prompting further investigation.\n3. **Thoracoscopic left pleural biopsy** was performed on the same day, followed by plasma DNA analysis via next-generation sequencing (NGS), which identified EGFR exon L858R mutation.\n4. **April 2022:** The diagnosis of stage IV lung adenocarcinoma with EGFR exon L858R mutation was confirmed.\n\n**Timeline of Treatments:**\n\n1. **March 2022:** The patient received osimertinib as the first-line treatment for her lung cancer.\n2. **May 22, 2022:** A follow-up chest CT scan revealed a partial response (PR) to osimertinib treatment.\n3. **April 4, 2024:** Due to progressive disease, the patient's treatment regimen was changed to dabrafenib, trametinib, and aumolertinib concurrently.\n4. **June 3, 2024:** A follow-up chest CT scan revealed a complete response (CR) to the new treatment regimen.\n\n**Timeline of Outcomes:**\n\n1. **May 22, 2022:** The patient experienced a partial response to osimertinib treatment.\n2. **April 4, 2024:** The patient's disease progressed, and she was diagnosed with progressive disease (PD).\n3. **June 3, 2024:** The patient achieved a complete response (CR) to the new treatment regimen.\n\n**Notable Events:**\n\n* During treatment with dabrafenib, trametinib, and aumolertinib, the patient experienced a transient fever.\n* The patient's disease was diagnosed as stage IV lung adenocarcinoma with EGFR exon L858R mutation.\n\n**Conclusion:**\nThe patient's clinical course was marked by an initial presentation of cough and chest pain, followed by a diagnosis of stage IV lung adenocarcinoma with EGFR exon L858R mutation. The patient received osimertinib as the first-line treatment and experienced a partial response. Due to progressive disease, the treatment regimen was changed to dabrafenib, trametinib, and aumolertinib concurrently, resulting in a complete response.", + "bertscore": { + "precision": 0.8213422298431396, + "recall": 0.8375495672225952, + "f1": 0.8293667435646057 + }, + "bleu": 0.18712496575902093, + "rouge1": 0.5508365508365508, + "rougeL": 0.31660231660231664, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 9, + "edge_count": 8, + "avg_in_degree": 0.8888888888888888, + "density": 0.1111111111111111 + }, + "trajectory_embedding": [ + 0.2675797641277313, + 0.21791553497314453, + -0.22618961334228516, + 0.11571652442216873, + -0.019790956750512123, + 0.05677139014005661, + 0.042519599199295044, + 0.1792418360710144, + 0.5141865611076355, + -0.34321343898773193, + -0.024482721462845802, + 0.13857966661453247, + -0.6468924880027771, + -0.25428396463394165, + 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"success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 56-year-old non-smoking male with pulmonary carcinosarcoma.\n\n**Initial Presentation (Step 1):**\nOn January 28, 2023, the patient presented at The Third People\u2019s Hospital of Yunnan Province with a progressively enlarging mass in the right neck. Imaging findings revealed multiple nodular shadows of various sizes within the right cervical region posterior to the sternocleidomastoid muscle and adjacent to the carotid artery sheath, which partially fused.\n\n**Diagnosis (Step 2):**\nCT scans confirmed the presence of a pulmonary malignancy with cervical and mediastinal lymph node metastasis. The largest mass measured approximately 3.8 cm x 2.6 cm with indistinct margins and uneven ring-shaped enhancement.\n\n**Biopsy and Pathological Diagnosis (Step 3):**\nA CT-guided puncture biopsy of the mass in the left inferior lobe of the lung was performed, which led to a pathological diagnosis of lung carcinosarcoma.\n\n**Immunohistochemistry and NGS Testing (Step 4):**\nImmunohistochemistry revealed a Ki-67 index of 80%, while Next-Generation Sequencing (NGS) detected mutations in the TMB gene. These results further supported the presence of pulmonary carcinomas.\n\n**Timeline:**\n\n* January 28, 2023: Patient presents with progressively enlarging neck mass and imaging findings consistent with pulmonary malignancy.\n* January 28, 2023: CT-guided puncture biopsy is performed to confirm diagnosis.\n* (Date not specified): Immunohistochemistry and NGS testing are performed.\n\n**Outcomes:**\nThe patient's condition remains active, with ongoing management of the pulmonary carcinosarcoma. The results of immunohistochemistry and NGS testing have provided valuable information for further treatment planning.\n\nNote: The timeline is incomplete as some dates were not specified in the original data.", + "bertscore": { + "precision": 0.7259600758552551, + "recall": 0.7952317595481873, + "f1": 0.7590186595916748 + }, + "bleu": 0.07920794318479864, + "rouge1": 0.2913165266106443, + "rougeL": 0.20168067226890754, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 4, + "edge_count": 3, + "avg_in_degree": 0.75, + "density": 0.25 + }, + "trajectory_embedding": [ + 0.26591718196868896, + -0.01149221882224083, + -0.05490458011627197, + 0.09002448618412018, + 0.12090761959552765, + -0.02566247433423996, + 0.06007498502731323, + 0.25383898615837097, + 0.2421899437904358, + -0.4905059337615967, + -0.13693289458751678, + 0.12649738788604736, + -0.6974141597747803, + 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"reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is an [age]-year-old female with a history of [relevant medical conditions]. She was diagnosed with [primary diagnosis] in [month/year].\n\n**Timeline of Diagnoses and Treatments:**\n\n1. **Step 1 (N1):** The patient started treatment with osimertinib 160 mg in combination with phenytoin.\n2. **32 months after initiating osimertinib (N2):** A CT scan was performed, showing overall stable visceral and osseous disease. However, the left pleural effusion had completely resolved, while the right pleural effusion remained stable in size.\n3. **Patient developed nail changes with increasing brittleness (grade 1) (N3):** Seizure activity remained well controlled, but persistent dyspnea was noted.\n4. **Echocardiogram, exercise stress testing, cardiopulmonary exercise test, and pulmonary function tests (PFTs) were performed (N4):** These tests showed evidence of chronic obstructive lung disease (COPD) and emphysema.\n5. **Osimertinib dose was reduced to 80 mg daily for one week, then resumed at 160 mg daily due to persistent dyspnea (N5):** Despite the dose reduction, dyspnea did not significantly improve.\n6. **Patient achieved prolonged disease control on osimertinib treatment with continued osimertinib at a dose of 160 mg daily (N6):** Disease progression later stabilized following three cycles of carboplatin/pemetrexed.\n\n**Outcomes:**\n\n* The patient's dyspnea did not significantly improve despite the dose reduction of osimertinib.\n* However, she achieved prolonged disease control on osimertinib treatment with continued osimertinib at a dose of 160 mg daily.\n* The patient's COPD and emphysema were diagnosed and managed effectively.\n\n**Conclusion:**\nThe patient was initially treated with osimertinib 160 mg in combination with phenytoin. After 32 months, a CT scan showed overall stable disease, but persistent dyspnea remained a concern. Despite a dose reduction of osimertinib, the patient's dyspnea did not improve significantly. However, she achieved prolonged disease control on osimertinib treatment with continued dosing at 160 mg daily, and her COPD and emphysema were effectively managed.\n\n**Recommendations:**\n\n* Continue to monitor the patient's dyspnea and adjust the osimertinib dose as needed.\n* Consider adding additional treatments for COPD and emphysema, such as bronchodilators or corticosteroids.\n* Regularly review the patient's disease progression and adjust the treatment plan accordingly.", + "bertscore": { + "precision": 0.7171581387519836, + "recall": 0.7824183702468872, + "f1": 0.7483682036399841 + }, + "bleu": 0.05612083691011624, + "rouge1": 0.2714932126696833, + "rougeL": 0.167420814479638, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 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file diff --git a/src/benchmark/setup_and_run.sh b/src/benchmark/setup_and_run.sh index 31c246c..c015501 100755 --- a/src/benchmark/setup_and_run.sh +++ b/src/benchmark/setup_and_run.sh @@ -18,8 +18,8 @@ else echo "No requirements.txt found. Skipping dependency installation." fi -echo "Running batch run..." -python3 batch_run.py +# echo "Running batch run..." +# python3 batch_run.py echo "Generating plots..." python3 generate_visuals.py \ No newline at end of file From e919fd77c133aa43ba819f6cd2a509ef20b8fc40 Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Mon, 12 May 2025 14:39:14 -0700 Subject: [PATCH 07/11] Clean unecessary results --- src/benchmark/batch_run.py | 1 - .../modules/similarity_and_clustering.py | 172 ++++++++++++++++++ src/benchmark/requirements.txt | 3 +- src/benchmark/setup_and_run.sh | 7 +- 4 files changed, 179 insertions(+), 4 deletions(-) create mode 100644 src/benchmark/modules/similarity_and_clustering.py diff --git a/src/benchmark/batch_run.py b/src/benchmark/batch_run.py index 30edd4e..d11bb53 100644 --- a/src/benchmark/batch_run.py +++ b/src/benchmark/batch_run.py @@ -21,7 +21,6 @@ save_results, build_graph_to_text_mapping, extract_case_presentation_from_file, - summarize_metrics_statistics ) logger = setup_logger(__name__) diff --git a/src/benchmark/modules/similarity_and_clustering.py b/src/benchmark/modules/similarity_and_clustering.py new file mode 100644 index 0000000..35e13f0 --- /dev/null +++ b/src/benchmark/modules/similarity_and_clustering.py @@ -0,0 +1,172 @@ +# pylint: disable=broad-exception-caught,too-few-public-methods + +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT + +""" +This module implements similarity and clustering analysis of trajectory embeddings with dimensionality optimization. +""" + +import json +import numpy as np +from pathlib import Path +from sklearn.cluster import KMeans +from sklearn.metrics.pairwise import cosine_similarity +from sklearn.metrics import silhouette_score, calinski_harabasz_score, davies_bouldin_score +from sklearn.decomposition import PCA +import matplotlib.pyplot as plt +import umap +import seaborn as sns +import pandas as pd +import warnings +warnings.filterwarnings("ignore", category=FutureWarning) +warnings.filterwarnings("ignore", category=UserWarning) + +# Define paths +RESULTS_DIR = Path("output/results") +PLOTS_DIR = Path("output/plots") +PLOTS_DIR.mkdir(parents=True, exist_ok=True) + +EMBEDDINGS = [] +GRAPH_IDS = [] + +def main(method="pca", dim_range=range(2, 11), cluster_range=range(2, 11)): + # Step 1: Extract trajectory embeddings + for file in RESULTS_DIR.glob("*.json"): + with open(file) as f: + data = json.load(f) + emb = data.get("trajectory_embedding") + if emb: + EMBEDDINGS.append(emb) + GRAPH_IDS.append(file.stem) + + if not EMBEDDINGS: + raise ValueError("No valid embeddings found in results directory.") + + embedding_matrix = np.array(EMBEDDINGS) + + best_silhouette = -1 + best_dim = None + best_k = None + best_embedding = None + best_labels = None + silhouette_scores = {} + + if method == "none": + for k in cluster_range: + kmeans = KMeans(n_clusters=k, random_state=4) + kmeans_labels = kmeans.fit_predict(embedding_matrix) + sil_score = silhouette_score(embedding_matrix, kmeans_labels) + ch_score = calinski_harabasz_score(embedding_matrix, kmeans_labels) + db_score = davies_bouldin_score(embedding_matrix, kmeans_labels) + # print(f"[dim=none, k={k}] Silhouette={sil_score:.4f}, CH={ch_score:.1f}, DB={db_score:.3f}") + silhouette_scores[("none", k)] = sil_score + + if sil_score > best_silhouette: + best_silhouette = sil_score + best_dim = "none" + best_k = k + best_embedding = embedding_matrix + best_labels = kmeans_labels + else: + for dim in dim_range: + if method == "umap": + reducer = umap.UMAP(n_components=dim, random_state=4, n_neighbors=5, min_dist=0.1) + elif method == "pca": + reducer = PCA(n_components=dim, random_state=4) + else: + raise ValueError("Invalid reduction method. Choose 'pca', 'umap', or 'none'.") + + reduced_embedding = reducer.fit_transform(embedding_matrix) + + for k in cluster_range: + kmeans = KMeans(n_clusters=k, random_state=4) + kmeans_labels = kmeans.fit_predict(reduced_embedding) + sil_score = silhouette_score(reduced_embedding, kmeans_labels) + ch_score = calinski_harabasz_score(reduced_embedding, kmeans_labels) + db_score = davies_bouldin_score(reduced_embedding, kmeans_labels) + print(f"[dim={dim}, k={k}] Silhouette={sil_score:.4f}, CH={ch_score:.1f}, DB={db_score:.3f}") + silhouette_scores[(dim, k)] = sil_score + + if sil_score > best_silhouette: + best_silhouette = sil_score + best_dim = dim + best_k = k + best_embedding = reduced_embedding + best_labels = kmeans_labels + + + # Compute metrics for best config + ch_score = calinski_harabasz_score(best_embedding, best_labels) + db_score = davies_bouldin_score(best_embedding, best_labels) + print(f"Best silhouette score: {best_silhouette:.4f} at dimension: {best_dim}, clusters: {best_k} using {method.upper()}") + print(f"Calinski-Harabasz score: {ch_score:.1f}") + print(f"Davies-Bouldin score: {db_score:.3f}") + + # Plot best scores bar chart + plt.figure(figsize=(6, 4)) + metrics = [best_silhouette, ch_score, db_score] + names = ["Silhouette", "Calinski-Harabasz", "Davies-Bouldin"] + colors = ["steelblue", "seagreen", "indianred"] + plt.bar(names, metrics, color=colors) + plt.title(f"Best Clustering Metrics (k={best_k}, dim={best_dim})") + plt.ylabel("Score") + plt.tight_layout() + plt.savefig(PLOTS_DIR / f"clustering_metrics_best_{method}.png") + plt.close() + + # Output clustering results + cluster_df = pd.DataFrame({ + "Graph ID": GRAPH_IDS, + "KMeans Label": best_labels, + }) + cluster_df.to_csv(PLOTS_DIR / "cluster_assignments.csv", index=False) + + # Plot silhouette score heatmap (skip for 'none') + if method != "none": + sil_matrix = pd.DataFrame( + {(dim, k): [score] for (dim, k), score in silhouette_scores.items()} + ).T.reset_index() + sil_matrix.columns = ["Dimension", "Clusters", "Silhouette"] + + pivot_table = sil_matrix.pivot(index="Dimension", columns="Clusters", values="Silhouette") + plt.figure(figsize=(10, 6)) + sns.heatmap(pivot_table, annot=True, fmt=".2f", cmap="viridis") + plt.title("Silhouette Score by Dimension and Number of Clusters") + plt.xlabel("Clusters") + plt.ylabel("Dimension") + plt.tight_layout() + plt.savefig(PLOTS_DIR / f"silhouette_heatmap_{method}.png") + plt.close() + + # Visualize projection with cluster labels (only if reduced) + if method != "none" and best_embedding.shape[1] >= 2: + plt.figure(figsize=(10, 8)) + sns.scatterplot(x=best_embedding[:, 0], y=best_embedding[:, 1], hue=best_labels, palette="tab10", legend="full") + plt.title(f"{method.upper()} Projection (KMeans, k={best_k})") + plt.xlabel("Dimension 1") + plt.ylabel("Dimension 2") + plt.tight_layout() + plt.savefig(PLOTS_DIR / f"{method}_kmeans_clusters.png") + plt.close() + + # Heatmap of cosine similarity + similarity_matrix = cosine_similarity(embedding_matrix) + plt.figure(figsize=(10, 8)) + sns.heatmap(similarity_matrix, xticklabels=GRAPH_IDS, yticklabels=GRAPH_IDS, + cmap="coolwarm", square=True) + plt.title("Trajectory Similarity Heatmap") + plt.tight_layout() + plt.savefig(PLOTS_DIR / "similarity_heatmap.png") + plt.close() + + # Save cluster assignments + with open(RESULTS_DIR / "trajectory_clusters_kmeans.json", "w") as f: + json.dump(dict(zip(GRAPH_IDS, best_labels.tolist())), f, indent=2) + + +if __name__ == "__main__": + main(method="umap") # Options: "pca", "umap", or "none" \ No newline at end of file diff --git a/src/benchmark/requirements.txt b/src/benchmark/requirements.txt index b1115e5..74b0774 100644 --- a/src/benchmark/requirements.txt +++ b/src/benchmark/requirements.txt @@ -13,4 +13,5 @@ bs4 evaluate rouge_score absl-py -nltk \ No newline at end of file +nltk +umap-learn \ No newline at end of file diff --git a/src/benchmark/setup_and_run.sh b/src/benchmark/setup_and_run.sh index c015501..8949b9a 100755 --- a/src/benchmark/setup_and_run.sh +++ b/src/benchmark/setup_and_run.sh @@ -21,5 +21,8 @@ fi # echo "Running batch run..." # python3 batch_run.py -echo "Generating plots..." -python3 generate_visuals.py \ No newline at end of file +# echo "Generating plots..." +# python3 generate_visuals.py + +echo "Generating similarity and clustering results..." +python3 modules/similarity_and_clustering.py \ No newline at end of file From 3cf64a90e5e751ea4480ffd39a393436f322a1a0 Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Wed, 14 May 2025 18:12:46 -0700 Subject: [PATCH 08/11] Update clustering pipeline --- src/benchmark/bertscore_eval.py | 663 --------------- .../modules/compare_graph_vs_text_clusters.py | 282 +++++++ .../output/plots/cluster_assignments.csv | 77 ++ .../plots/clustering_metrics_best_umap.png | Bin 0 -> 15856 bytes .../plots/clustering_score_comparison.png | Bin 0 -> 20454 bytes .../plots/graph_cancer_type_heatmap.png | Bin 0 -> 58169 bytes .../graph_cluster_metastasis_barplot.png | Bin 0 -> 16692 bytes .../clustering_score_comparison.png | Bin 0 -> 18584 bytes .../output/plots/plots_testset/tsne_graph.png | Bin 0 -> 16323 bytes .../output/plots/plots_testset/tsne_text.png | Bin 0 -> 17169 bytes .../output/plots/silhouette_heatmap_umap.png | Bin 0 -> 70142 bytes .../output/plots/similarity_heatmap.png | Bin 0 -> 107270 bytes .../output/plots/text_cancer_type_heatmap.png | Bin 0 -> 52684 bytes .../plots/text_cluster_metastasis_barplot.png | Bin 0 -> 15749 bytes src/benchmark/output/plots/tsne_graph-pca.png | Bin 0 -> 17549 bytes .../output/plots/tsne_graph-umap.png | Bin 0 -> 19375 bytes src/benchmark/output/plots/tsne_text-pca.png | Bin 0 -> 16637 bytes src/benchmark/output/plots/tsne_text-umap.png | Bin 0 -> 16726 bytes .../output/plots/umap_kmeans_clusters.png | Bin 0 -> 34681 bytes .../results/cluster_labels_with_metadata.csv | 405 +++++++++ .../results/cluster_metadata_summary.csv | 4 + .../output/results/graph_html_metadata.csv | 411 +++++++++ .../results/testset/graph_html_metadata.csv | 411 +++++++++ .../results/testset/results_graph_001.json | 792 ++++++++++++++++++ .../results/testset/results_graph_003.json | 792 ++++++++++++++++++ .../results/testset/results_graph_004.json | 792 ++++++++++++++++++ .../results/testset/results_graph_005.json | 792 ++++++++++++++++++ .../results/trajectory_clusters_kmeans.json | 78 ++ src/benchmark/setup_and_run.sh | 2 +- 29 files changed, 4837 insertions(+), 664 deletions(-) delete mode 100644 src/benchmark/bertscore_eval.py create mode 100644 src/benchmark/modules/compare_graph_vs_text_clusters.py create mode 100644 src/benchmark/output/plots/cluster_assignments.csv create mode 100644 src/benchmark/output/plots/clustering_metrics_best_umap.png create mode 100644 src/benchmark/output/plots/clustering_score_comparison.png create mode 100644 src/benchmark/output/plots/graph_cancer_type_heatmap.png create mode 100644 src/benchmark/output/plots/graph_cluster_metastasis_barplot.png create mode 100644 src/benchmark/output/plots/plots_testset/clustering_score_comparison.png create mode 100644 src/benchmark/output/plots/plots_testset/tsne_graph.png create mode 100644 src/benchmark/output/plots/plots_testset/tsne_text.png create mode 100644 src/benchmark/output/plots/silhouette_heatmap_umap.png create mode 100644 src/benchmark/output/plots/similarity_heatmap.png create mode 100644 src/benchmark/output/plots/text_cancer_type_heatmap.png create mode 100644 src/benchmark/output/plots/text_cluster_metastasis_barplot.png create mode 100644 src/benchmark/output/plots/tsne_graph-pca.png create mode 100644 src/benchmark/output/plots/tsne_graph-umap.png create mode 100644 src/benchmark/output/plots/tsne_text-pca.png create mode 100644 src/benchmark/output/plots/tsne_text-umap.png create mode 100644 src/benchmark/output/plots/umap_kmeans_clusters.png create mode 100644 src/benchmark/output/results/cluster_labels_with_metadata.csv create mode 100644 src/benchmark/output/results/cluster_metadata_summary.csv create mode 100644 src/benchmark/output/results/graph_html_metadata.csv create mode 100644 src/benchmark/output/results/testset/graph_html_metadata.csv create mode 100644 src/benchmark/output/results/testset/results_graph_001.json create mode 100644 src/benchmark/output/results/testset/results_graph_003.json create mode 100644 src/benchmark/output/results/testset/results_graph_004.json create mode 100644 src/benchmark/output/results/testset/results_graph_005.json create mode 100644 src/benchmark/output/results/trajectory_clusters_kmeans.json diff --git a/src/benchmark/bertscore_eval.py b/src/benchmark/bertscore_eval.py deleted file mode 100644 index 49d15ad..0000000 --- a/src/benchmark/bertscore_eval.py +++ /dev/null @@ -1,663 +0,0 @@ -import os -import re -import json -from typing import Any, Dict, List, Optional, Tuple, Union -from transformers import AutoTokenizer, AutoModel - -import logging - -import networkx as nx -from networkx.readwrite import json_graph -from bert_score import score -import dspy - -# ─── Configuration ────────────────────────────────────────────────────────────── - -Graph = nx.DiGraph - - -# Let's change this to GEMINI -# DSPy LLM settings -LM_MODEL = "ollama_chat/llama3.2" -LM_API_BASE = "http://localhost:11434" -LM_API_KEY = "" # or your local key if required - -# BERTScore model settings -#BERTSCORE_MODEL = "emilyalsentzer/Bio_ClinicalBERT" -#Let's get this to work -BERTSCORE_MODEL = "bert-base-uncased" - - -# Setup logging -logging.basicConfig( - level=logging.INFO, - format='%(asctime)s - %(name)s - %(levelname)s - %(message)s' -) -logger = logging.getLogger(__name__) - - - - -# ─── 1. LLM-BASED NARRATIVE RECONSTRUCTION ──────────────────────────────────── - -class LLMReconstructor: - """ - Uses a DSPy-compatible LLM to reconstruct a narrative from selected parts of a graph. - - Usage: - reconstructor = LLMReconstructor( - model_name="ollama_chat/llama3.2", - api_base="http://localhost:11434", - api_key="" - ) - narrative = reconstructor.reconstruct( - graph, - include_nodes=True, - include_edges=False, - node_ids=["n1", "n2"], - node_attrs=["content"], - ) - """ - def __init__( - self, - model_name: str, - api_base: str, - api_key: str, - prompt_tpl: str = ( - "Reconstruct the clinical case report from this data:\n\n{payload}\n\n" - "Write a coherent narrative including patient demographics, timeline of diagnoses, treatments, and outcomes." - ), - max_retries: int = 3 - ): - try: - self.lm = dspy.LM( - model_name, - api_base=api_base, - api_key=api_key - ) - self.prompt_tpl = prompt_tpl - self.max_retries = max_retries - except Exception as e: - logger.error(f"Error initializing LLM: {str(e)}") - raise - - def _build_payload( - self, - graph: Graph, - include_nodes: bool, - include_edges: bool, - node_ids: Optional[List[str]], - node_attrs: Optional[List[str]], - edge_attrs: Optional[List[str]] - ) -> Dict[str, Any]: - """Build a structured payload from the graph.""" - payload: Dict[str, Any] = {} - - if include_nodes: - payload["nodes"] = [] - for nid, attrs in graph.nodes(data=True): - if node_ids and nid not in node_ids: - continue - entry = {"id": nid} - for k in (node_attrs or list(attrs.keys())): - if k in attrs: # Only include existing attributes - entry[k] = attrs[k] - payload["nodes"].append(entry) - - if include_edges: - payload["edges"] = [] - for src, tgt, attrs in graph.edges(data=True): - # Skip edges if we're filtering nodes and either endpoint is filtered out - if node_ids and (src not in node_ids or tgt not in node_ids): - continue - entry = {"source": src, "target": tgt} - for k in (edge_attrs or list(attrs.keys())): - if k in attrs: # Only include existing attributes - entry[k] = attrs[k] - payload["edges"].append(entry) - - return payload - - def reconstruct( - self, - graph: Graph, - *, - include_nodes: bool = True, - include_edges: bool = True, - node_ids: Optional[List[str]] = None, - node_attrs: Optional[List[str]] = None, - edge_attrs: Optional[List[str]] = None - ) -> str: - """ - Build a custom payload from the graph and call the LLM. - - Args: - graph: networkx.DiGraph with node/edge attributes. - include_nodes: include a list of nodes in the payload. - include_edges: include a list of edges in the payload. - node_ids: list of node IDs to include (default: all). - node_attrs: list of node attribute names to include (default: all). - edge_attrs: list of edge attribute names to include (default: all). - - Returns: - A string containing the reconstructed clinical narrative. - """ - if not graph: - logger.warning("Empty graph provided") - return "No data available to reconstruct narrative." - - # Verify graph is a DiGraph - if not isinstance(graph, nx.DiGraph): - logger.warning(f"Expected DiGraph, got {type(graph)}") - if isinstance(graph, nx.Graph): - logger.info("Converting undirected graph to directed") - graph = nx.DiGraph(graph) - else: - raise TypeError("Input must be a networkx Graph or DiGraph") - - payload = self._build_payload( - graph, include_nodes, include_edges, node_ids, node_attrs, edge_attrs - ) - - if not payload.get("nodes") and not payload.get("edges"): - logger.warning("No nodes or edges in payload") - return "Insufficient data to reconstruct narrative." - - payload_json = json.dumps(payload, indent=2) - prompt = self.prompt_tpl.format(payload=payload_json) - - # Retry mechanism - for attempt in range(self.max_retries): - try: - resp_list = self.lm(messages=[{"role": "user", "content": prompt}]) - # dspy returns a list type of responses; by default that list contains exactly one completion, - # so resp_list[0] is the single response you want - return resp_list[0].strip() - except Exception as e: - logger.warning(f"LLM call failed (attempt {attempt+1}/{self.max_retries}): {str(e)}") - if attempt == self.max_retries - 1: - logger.error("All LLM call attempts failed") - raise - - # This should never be reached due to the exception above, but added for completeness - return "Failed to reconstruct narrative due to LLM service errors." - - -# ─── 2. BERTScore-BASED FIDELITY EVALUATION ─────────────────────────────────── - -class BERTScoreEvaluator: - """ - Computes BERTScore (precision, recall, F1) between original and reconstructed texts. - - Usage: - evaluator = BERTScoreEvaluator(model_type="BERTSCORE_MODEL") - results = evaluator.evaluate( - refs=["ground truth text"], - cands=["model generated text"] - ) - # results -> {"precision": [...], "recall": [...], "f1": [...]} - """ - def __init__(self, model_type: str, device: str = None): - self.model_type = model_type - self.device = device # 'cuda', 'cpu', or None for auto-detection - - # ── Ensure the checkpoint is available locally ── - # This will pull the tokenizer & model into ~/.cache/huggingface if missing. - AutoTokenizer.from_pretrained(self.model_type) - AutoModel.from_pretrained(self.model_type) - - def evaluate(self, refs: List[str], cands: List[str]) -> Dict[str, List[float]]: - """ - Args: - refs: list of reference texts. - cands: list of candidate texts. - - Returns: - Dict with keys "precision", "recall", "f1" mapping to lists of scores. - """ - if not refs or not cands: - logger.warning("Empty references or candidates list") - return {"precision": [], "recall": [], "f1": []} - - if len(refs) != len(cands): - logger.warning(f"Mismatched list lengths: refs={len(refs)}, cands={len(cands)}") - - try: - P, R, F1 = score( - cands, - refs, - model_type=self.model_type, - device=self.device, - verbose=False - ) - - return { - "precision": P.tolist(), - "recall": R.tolist(), - "f1": F1.tolist(), - } - except Exception as e: - logger.error(f"BERTScore evaluation failed: {str(e)}") - raise - - -# ─── 3. GRAPH TOPOLOGY VALIDATION ───────────────────────────────────────────── - -class TopologyValidator: - """ - Validates DAG properties: acyclicity, timestamp order, connectivity stats. - - Usage: - validator = TopologyValidator(graph) - stats = validator.run() - # stats -> {"is_acyclic": bool, "timestamps_in_order": bool, ...} - """ - def __init__(self, graph: Graph): - self.G = graph - - def run(self) -> Dict[str, Any]: - """ - Returns: - A dict with structural validation results. - """ - if not self.G or self.G.number_of_nodes() == 0: - logger.warning("Empty graph in topology validator") - return { - "is_acyclic": True, # Empty graphs are technically acyclic - "timestamps_in_order": True, - "weakly_connected_components": 0, - "avg_in_degree": 0.0, - "node_count": 0, - "edge_count": 0, - "density": 0.0, - } - - is_acyclic = nx.is_directed_acyclic_graph(self.G) - - # Check if timestamps exist in all nodes - timestamp_attr = "timestamp" - all_have_timestamps = all(timestamp_attr in data for _, data in self.G.nodes(data=True)) - - timestamps_ok = False - if all_have_timestamps: - try: - topo_nodes = list(nx.topological_sort(self.G)) - timestamps = [self.G.nodes[n][timestamp_attr] for n in topo_nodes] - timestamps_ok = timestamps == sorted(timestamps) - except nx.NetworkXUnfeasible: - # Graph has cycles, can't do topological sort - logger.warning("Cannot check timestamp order: graph has cycles") - timestamps_ok = False - else: - logger.warning("Not all nodes have timestamp attributes") - - components = nx.number_weakly_connected_components(self.G) - node_count = self.G.number_of_nodes() - edge_count = self.G.number_of_edges() - - avg_in_deg = sum(dict(self.G.in_degree()).values()) / max(1, node_count) - density = nx.density(self.G) - - return { - "is_acyclic": is_acyclic, - "timestamps_in_order": timestamps_ok, - "all_nodes_have_timestamps": all_have_timestamps, - "weakly_connected_components": components, - "node_count": node_count, - "edge_count": edge_count, - "avg_in_degree": avg_in_deg, - "density": density, - } - - -# ─── 4. REGEX-BASED SANITY CHECK (OPTIONAL) ─────────────────────────────────── - -class RegexValidator: - """ - Lightweight regex tests on the raw JSON string to catch formatting issues. - - Usage: - json_str = json.dumps(json_graph.node_link_data(graph)) - validator = RegexValidator(json_str) - results = validator.run() - # results -> {"nodes_array": bool, ...} - """ - PATTERNS = { - "nodes_array": r'"nodes"\s*:\s*\[', - "edges_array": r'"edges"\s*:\s*\[', - "no_trailing_commas": r',\s*\]', - "node_entry": r'\{\s*"id".+?\}', - "edge_entry": r'\{\s*"source".+?"label".+?\}', - } - - def __init__(self, json_str: str): - self.s = json_str - - def run(self) -> Dict[str, bool]: - """ - Returns: - A dict mapping each regex check name to True/False. - """ - if not self.s or not isinstance(self.s, str): - logger.warning(f"Invalid input to RegexValidator: {type(self.s)}") - return {name: False for name in self.PATTERNS} - - results: Dict[str, bool] = {} - for name, pat in self.PATTERNS.items(): - try: - found = bool(re.search(pat, self.s)) - results[name] = not found if name == "no_trailing_commas" else found - except Exception as e: - logger.error(f"Regex check '{name}' failed: {str(e)}") - results[name] = False - return results - - -# ─── 5. ORCHESTRATOR ────────────────────────────────────────────────────────── - -def run_pipeline( - graph: Graph, - original_text: str, - config: Dict[str, Any] -) -> Dict[str, Any]: - """ - Executes modular evaluations in order: - 1. LLM reconstruction + BERTScore - 2. Topology checks - 3. Optional regex checks - - Args: - graph: your clinical-case DAG (networkx.DiGraph) - original_text: ground truth case-report text - config: - - "reconstruct_params": dict of args for reconstruct() - - "bertscore": bool - - "topology": bool - - "regex": bool - - Returns: - A dict with results from each enabled module. - - Usage: - cfg = { - "reconstruct_params": {"include_nodes": True, "include_edges": True}, - "bertscore": True, - "topology": True, - "regex": False - } - report = run_pipeline(G, original_text, cfg) - """ - print("\n=============Starting Evaluation=============\n") - results: Dict[str, Any] = { - "status": "success", - "errors": [] - } - - # Validate inputs - if not isinstance(graph, (nx.Graph, nx.DiGraph)): - error = f"Invalid graph type: {type(graph)}" - logger.error(error) - results["status"] = "error" - results["errors"].append(error) - return results - - if not isinstance(original_text, str): - error = f"Invalid original_text type: {type(original_text)}" - logger.error(error) - results["status"] = "error" - results["errors"].append(error) - return results - - # 1. Reconstruct narrative - narrative = None - if "reconstruct_params" in config: - try: - logger.info("Starting narrative reconstruction") - reconstructor = LLMReconstructor( - model_name=LM_MODEL, - api_base=LM_API_BASE, - api_key=LM_API_KEY - ) - narrative = reconstructor.reconstruct(graph, **config["reconstruct_params"]) - results["reconstructed_narrative"] = narrative - logger.info("Narrative reconstruction completed") - except Exception as e: - error = f"Narrative reconstruction failed: {str(e)}" - logger.error(error) - results["status"] = "partial" - results["errors"].append(error) - - # 2. BERTScore - if config.get("bertscore"): - try: - if narrative is None: - error = "`reconstruct_params` must be provided to run `bertscore`" - logger.error(error) - results["status"] = "partial" - results["errors"].append(error) - else: - logger.info("Starting BERTScore evaluation") - # pick model from per-run override or top-level constant - model_name = config.get("bertscore_model", BERTSCORE_MODEL) - evaluator = BERTScoreEvaluator(model_type=model_name) - results["bertscore"] = evaluator.evaluate( - refs=[original_text], - cands=[narrative] - ) - logger.info("BERTScore evaluation completed") - except Exception as e: - error = f"BERTScore evaluation failed: {str(e)}" - logger.error(error) - results["status"] = "partial" - results["errors"].append(error) - - # 3. Topology - if config.get("topology"): - try: - logger.info("Starting topology validation") - results["topology"] = TopologyValidator(graph).run() - logger.info("Topology validation completed") - except Exception as e: - error = f"Topology validation failed: {str(e)}" - logger.error(error) - results["status"] = "partial" - results["errors"].append(error) - - # 4. Regex (optional) - if config.get("regex"): - try: - logger.info("Starting regex validation") - from networkx.readwrite import json_graph - json_str = json.dumps(json_graph.node_link_data(graph)) - results["regex"] = RegexValidator(json_str).run() - logger.info("Regex validation completed") - except Exception as e: - error = f"Regex validation failed: {str(e)}" - logger.error(error) - results["status"] = "partial" - results["errors"].append(error) - - if results["errors"]: - if results["status"] == "success": - results["status"] = "partial" - - if not results["errors"]: - del results["errors"] - - return results - - -# ─── UTILITY FUNCTIONS ─────────────────────────────────────────────────────── - -def load_graph_from_file(filepath: str) -> Tuple[Graph, bool]: - """ - Load a graph from a JSON file. - - Args: - filepath: Path to the JSON file. - - Returns: - Tuple of (graph, success_flag) - """ - try: - with open(filepath, 'r') as f: - data = json.load(f) - - graph = json_graph.node_link_graph(data, directed=True) - return graph, True - except Exception as e: - logger.error(f"Failed to load graph from {filepath}: {str(e)}") - return nx.DiGraph(), False - - -def save_results(results: Dict[str, Any], output_path: str) -> bool: - """ - Save pipeline results to a JSON file. - - Args: - results: The pipeline results dictionary. - output_path: Where to save the results. - - Returns: - True if successful, False otherwise. - """ - try: - os.makedirs(os.path.dirname(output_path), exist_ok=True) - with open(output_path, 'w') as f: - json.dump(results, f, indent=2) - return True - except Exception as e: - logger.error(f"Failed to save results to {output_path}: {str(e)}") - return False - - -def data_display(results: Dict[str, Any]) -> None: - """ - Pretty-print the pipeline results as structured tables for easy terminal viewing. - Narrative is shown first, followed by status and individual metric tables. - - Args: - results: The dict returned by run_pipeline. - """ - # Header - print("\n========== Pipeline Results ==========\n") - - # 1) Reconstructed Narrative first - if "reconstructed_narrative" in results: - print("Reconstructed Narrative:") - print(results["reconstructed_narrative"]) - print() - - # 2) Status - status = results.get("status") - if status: - print(f"Status: {status}\n") - - # 3) BERTScore table - if "bertscore" in results: - bs = results["bertscore"] - print("BERTScore:") - print(f"{'Metric':<12} {'Score':>10}") - print("-" * 22) - for metric, scores in bs.items(): - val = scores[0] if scores else float("nan") - print(f"{metric:<12} {val:>10.4f}") - print() - - # 4) Topology table - if "topology" in results: - topo = results["topology"] - print("Topology Validation:") - print("-" * 22) - key_width = max(len(k) for k in topo) - for key, val in topo.items(): - print(f"{key:<{key_width}} : {val}") - print() - - # 5) Regex checks table - if "regex" in results: - rgx = results["regex"] - print("Regex Checks:") - print("-" * 22) - key_width = max(len(k) for k in rgx) - for key, val in rgx.items(): - print(f"{key:<{key_width}} : {val}") - print() - - # 6) Any other top-level keys - other_keys = { - k: v for k, v in results.items() - if k not in {"status", "bertscore", "topology", "regex", "reconstructed_narrative"} - } - if other_keys: - print("Additional Data:") - for key, val in other_keys.items(): - print(f"{key}: {val}") - print() - - -# ─── USAGE EXAMPLE ─────────────────────────────────────────────────────────── - -if __name__ == "__main__": - - # 1. Call the nodes and edges for the graph object - G = nx.DiGraph() - - # graph.get_nodes() - # graph.get_edges() - - ######################## - - # Hard-coded example - # Build a 5-node example graph - example_nodes = [ - ("n1", {"timestamp": "2025-04-29T08:00:00Z", "content": "Patient presents with chest pain"}), - ("n2", {"timestamp": "2025-04-29T08:10:00Z", "content": "ECG performed"}), - ("n3", {"timestamp": "2025-04-29T08:15:00Z", "content": "ST elevation noted"}), - ("n4", {"timestamp": "2025-04-29T08:20:00Z", "content": "Aspirin administered"}), - ("n5", {"timestamp": "2025-04-29T08:45:00Z", "content": "Transported to cath lab"}), - ] - for nid, attrs in example_nodes: - G.add_node(nid, **attrs) - # Add 4 edges with labels - example_edges = [ - ("n1", "n2", {"label": "led_to"}), - ("n2", "n3", {"label": "revealed"}), - ("n3", "n4", {"label": "treated_with"}), - ("n4", "n5", {"label": "followed_by"}), - ] - for src, tgt, attrs in example_edges: - G.add_edge(src, tgt, **attrs) - - - ######################## - - # 2. Original case report - original = ( - "A patient presents with chest pain. An ECG is performed, which reveals ST elevation. " - "The patient receives aspirin and is then transported to the cath lab." - ) - - # 3. Configure your pipeline to include the required evaluations - cfg = { - "reconstruct_params": {"include_nodes": True, "include_edges": True}, - "bertscore": True, - "topology": True, - "regex": True, - } - - - # 4. Run and print the report - try: - report = run_pipeline(G, original, cfg) - #print(json.dumps(report, indent=2)) - data_display(report) - - # Optionally save the results - save_results(report, "output/pipeline_results.json") - except Exception as e: - logger.critical(f"Pipeline execution failed: {str(e)}") - - - - diff --git a/src/benchmark/modules/compare_graph_vs_text_clusters.py b/src/benchmark/modules/compare_graph_vs_text_clusters.py new file mode 100644 index 0000000..6c23218 --- /dev/null +++ b/src/benchmark/modules/compare_graph_vs_text_clusters.py @@ -0,0 +1,282 @@ +# This source file is part of the Daneshjou Lab projects +# +# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) +# +# SPDX-License-Identifier: MIT +# +# Standard library imports +import json +import numpy as np +import pandas as pd +import sys +from pathlib import Path + +# Add src/ to sys.path +sys.path.append(str(Path(__file__).resolve().parents[1])) + +# Third-party library imports +from sklearn.cluster import KMeans +from sklearn.decomposition import PCA +from sklearn.metrics import silhouette_score, calinski_harabasz_score, davies_bouldin_score +from sklearn.metrics import adjusted_rand_score +from sklearn.manifold import TSNE +import matplotlib.pyplot as plt +import seaborn as sns +import umap +from sklearn.metrics import adjusted_rand_score +from sklearn.metrics import adjusted_rand_score +from collections import Counter + +# Local application imports +from modules.embedding import TrajectoryEmbedder + +RESULTS_DIR = Path("output/results") +METADATA_CSV = RESULTS_DIR / "graph_html_metadata.csv" +PLOTS_DIR = Path("output/plots") +PLOTS_DIR.mkdir(parents=True, exist_ok=True) + + +def load_graph_embeddings(): + graph_embeddings = {} + for file in RESULTS_DIR.glob("results_graph_*.json"): + graph_id = file.stem.replace("results_graph_", "") + with open(file) as f: + data = json.load(f) + if "trajectory_embedding" in data: + graph_embeddings[graph_id] = data["trajectory_embedding"] + return graph_embeddings + + +def load_text_embeddings(embedder): + df = pd.read_csv(METADATA_CSV) + text_embeddings = {} + for _, row in df.iterrows(): + graph_id_full = row["graph_id"] # e.g., graph_001 + graph_id = graph_id_full.replace("graph_", "") + text = row["timeline_1"] + if pd.isna(text) or not text.strip(): + continue + try: + emb = embedder.embed_text(text).cpu().numpy() + text_embeddings[graph_id] = emb + except Exception as e: + print(f"Failed to embed text for graph {graph_id}: {e}") + return text_embeddings + + +def load_metadata_features(shared_ids): + df = pd.read_csv(METADATA_CSV) + df = df[df["graph_id"].str.startswith("graph_")] + df["graph_id"] = df["graph_id"].str.replace("graph_", "") + df = df[df["graph_id"].isin(shared_ids)].set_index("graph_id") + + # Flatten list-like strings to strings for encoding + def flatten_list_column(col): + return col.apply(lambda x: "|".join(eval(x)) if pd.notna(x) and x.startswith("[") else "unknown") + + df["cancers"] = flatten_list_column(df["cancers"]) + df["specific_cancers"] = flatten_list_column(df["specific_cancers"]) + df["has_metastasis"] = df["has_metastasis"].fillna("unknown").astype(str) + + from sklearn.preprocessing import OneHotEncoder + encoder = OneHotEncoder(sparse_output=False, handle_unknown="ignore") + encoded = encoder.fit_transform(df[["cancers", "specific_cancers", "has_metastasis"]]) + return encoded + + + +def reduce_dimensions(data, method="pca", n_components=10): + if method == "pca": + reducer = PCA(n_components=n_components) + elif method == "umap": + reducer = umap.UMAP(n_components=n_components, random_state=42) + else: + raise ValueError("Unsupported reduction method: choose 'pca' or 'umap'") + return reducer.fit_transform(data) + + +def cluster_and_evaluate(embedding_matrix, method_label): + best_k = None + best_score = -1 + best_labels = None + best_scores = {} + n_samples = embedding_matrix.shape[0] + for k in range(2, min(11, n_samples)): + kmeans = KMeans(n_clusters=k, random_state=4) + labels = kmeans.fit_predict(embedding_matrix) + sil = silhouette_score(embedding_matrix, labels) + ch = calinski_harabasz_score(embedding_matrix, labels) + db = davies_bouldin_score(embedding_matrix, labels) + best_scores[k] = (sil, ch, db) + if sil > best_score: + best_score = sil + best_k = k + best_labels = labels + print(f"[{method_label}] Best k={best_k}, Silhouette={best_score:.4f}") + return best_k, best_labels, best_scores + + +def plot_tsne(embeddings, labels, method_label): + n_samples = embeddings.shape[0] + perplexity = min(5, n_samples - 1) + tsne = TSNE(n_components=2, perplexity=perplexity, random_state=42) + reduced = tsne.fit_transform(embeddings) + plt.figure(figsize=(8, 6)) + sns.scatterplot(x=reduced[:, 0], y=reduced[:, 1], hue=labels, palette="tab10") + plt.title(f"t-SNE of {method_label} Embeddings") + plt.tight_layout() + plt.savefig(PLOTS_DIR / f"tsne_{method_label.lower()}.png") + plt.close() + + +def summarize_cluster_metadata(shared_ids, glabels, label_type="graph"): + meta_df = pd.read_csv(METADATA_CSV) + meta_df["graph_id"] = meta_df["graph_id"].str.replace("graph_", "") + meta_df = meta_df[meta_df["graph_id"].isin(shared_ids)] + cluster_df = pd.DataFrame({ + "graph_id": shared_ids, + "graph_cluster": glabels, + }) + joined = cluster_df.merge(meta_df, on="graph_id") + + summary_rows = [] + for cluster_id, group in joined.groupby("graph_cluster"): + print(f"Cluster {cluster_id} Summary:") + metastasis_dist = group["has_metastasis"].value_counts(normalize=True).to_dict() + cancers = Counter(" | ".join(group["cancers"].dropna().astype(str)).split(" | ")) + specific = Counter(" | ".join(group["specific_cancers"].dropna().astype(str)).split(" | ")) + top_cancers = ", ".join([f"{k} ({v})" for k, v in cancers.most_common(3)]) + top_specific = ", ".join([f"{k} ({v})" for k, v in specific.most_common(3)]) + + print(" has_metastasis:", metastasis_dist) + print(" Top cancers:", top_cancers) + print(" Top specific cancers:", top_specific) + + summary_rows.append({ + "cluster": cluster_id, + "has_metastasis": json.dumps(metastasis_dist), + "top_cancers": top_cancers, + "top_specific_cancers": top_specific, + }) + + summary_df = pd.DataFrame(summary_rows) + summary_path = RESULTS_DIR / "cluster_metadata_summary.csv" + summary_df.to_csv(summary_path, index=False) + print(f"✅ Cluster metadata summary saved to {summary_path}") + + # Optional: Barplot of has_metastasis composition + expanded = [] + for _, row in summary_df.iterrows(): + for status, pct in json.loads(row["has_metastasis"]).items(): + expanded.append({ + "Cluster": f"{label_type}-{row['cluster']}", + "Metastasis": status, + "Proportion": pct + }) + bar_df = pd.DataFrame(expanded) + plt.figure(figsize=(6, 4)) + sns.barplot(data=bar_df, x="Cluster", y="Proportion", hue="Metastasis") + plt.title(f"{label_type.capitalize()} Clusters by Metastasis Status") + plt.tight_layout() + plt.savefig(PLOTS_DIR / f"{label_type}_cluster_metastasis_barplot.png") + plt.close() + print(f"✅ Bar plot saved to {PLOTS_DIR / f'{label_type}_cluster_metastasis_barplot.png'}") + + # Optional: Heatmap of top cancer types + cancer_counts = {} + for cluster_id, group in joined.groupby("graph_cluster"): + cancer_list = [c for c in "|".join(group["cancers"].dropna().astype(str)).split("|") if c.strip()] + counts = Counter(cancer_list) + cancer_counts[cluster_id] = counts + + all_cancers = sorted({cancer for counts in cancer_counts.values() for cancer in counts}) + heatmap_data = pd.DataFrame(index=sorted(cancer_counts.keys()), columns=all_cancers).fillna(0.0) + for cluster_id, counts in cancer_counts.items(): + for cancer, count in counts.items(): + heatmap_data.at[cluster_id, cancer] = count / sum(counts.values()) # normalize to proportion + + plt.figure(figsize=(12, 6)) + sns.heatmap(heatmap_data, annot=True, fmt=".2f", cmap="YlGnBu") + plt.title(f"Top Cancer Types per Cluster ({label_type})") + plt.ylabel("Cluster") + plt.xlabel("Cancer Type") + plt.tight_layout() + plt.savefig(PLOTS_DIR / f"{label_type}_cancer_type_heatmap.png") + plt.close() + print(f"✅ Cancer type heatmap saved to {PLOTS_DIR / f'{label_type}_cancer_type_heatmap.png'}") + + +def plot_score_comparison(score_dicts, shared_ids, glabels, tlabels): + + summarize_cluster_metadata(shared_ids, glabels, label_type="graph") + summarize_cluster_metadata(shared_ids, tlabels, label_type="text") + + # Cluster agreement + ari_pca = adjusted_rand_score(glabels, tlabels) + print(f"✅ Adjusted Rand Index (PCA-reduced Graph vs Text): {ari_pca:.4f}") + + # Cluster label CSV + meta_df = pd.read_csv(METADATA_CSV) + meta_df["graph_id"] = meta_df["graph_id"].str.replace("graph_", "") + meta_df = meta_df[meta_df["graph_id"].isin(shared_ids)] + cluster_df = pd.DataFrame({ + "graph_id": shared_ids, + "graph_cluster": glabels, + "text_cluster": tlabels, + }) + output_df = cluster_df.merge(meta_df, on="graph_id") + output_path = RESULTS_DIR / "cluster_labels_with_metadata.csv" + output_df.to_csv(output_path, index=False) + print(f"✅ Cluster labels with metadata saved to {output_path}") + metrics = ["Silhouette", "Calinski-Harabasz", "Davies-Bouldin"] + data = [] + for label, scores in score_dicts.items(): + for metric, value in zip(metrics, scores): + data.append({"Metric": metric, "Type": label, "Score": value}) + df = pd.DataFrame(data) + plt.figure(figsize=(8, 5)) + sns.barplot(x="Metric", y="Score", hue="Type", data=df) + plt.title("Clustering Score Comparison") + plt.tight_layout() + plt.savefig(PLOTS_DIR / "clustering_score_comparison.png") + plt.close() + + +from sklearn.metrics import adjusted_rand_score + +def main(): + print("Loading graph embeddings...") + graph_embs = load_graph_embeddings() + + print("Loading text embeddings...") + embedder = TrajectoryEmbedder() + text_embs = load_text_embeddings(embedder) + + shared_ids = list(set(graph_embs) & set(text_embs)) + print(f"Found {len(shared_ids)} shared graph/text pairs") + + graph_matrix = np.array([graph_embs[i] for i in shared_ids]) + metadata_features = load_metadata_features(shared_ids) + graph_matrix = np.concatenate([graph_matrix, metadata_features], axis=1) + text_matrix = np.array([text_embs[i] for i in shared_ids]) + + score_dicts = {} + + for method in ["pca", "umap"]: + reduced_graph = reduce_dimensions(graph_matrix, method=method) + reduced_text = reduce_dimensions(text_matrix, method=method) + + gk, glabels, g_scores = cluster_and_evaluate(reduced_graph, f"Graph-{method.upper()}") + tk, tlabels, t_scores = cluster_and_evaluate(reduced_text, f"Text-{method.upper()}") + + plot_tsne(reduced_graph, glabels, f"Graph-{method.upper()}") + plot_tsne(reduced_text, tlabels, f"Text-{method.upper()}") + + score_dicts[f"Graph-{method.upper()}"] = g_scores[gk] + score_dicts[f"Text-{method.upper()}"] = t_scores[tk] + + plot_score_comparison(score_dicts, shared_ids, glabels, tlabels) + + +if __name__ == "__main__": + main() diff --git a/src/benchmark/output/plots/cluster_assignments.csv b/src/benchmark/output/plots/cluster_assignments.csv new file mode 100644 index 0000000..902c36c --- /dev/null +++ b/src/benchmark/output/plots/cluster_assignments.csv @@ -0,0 +1,77 @@ +Graph ID,KMeans Label +results_graph_076,1 +results_graph_037,1 +results_graph_040,0 +results_graph_056,0 +results_graph_001,0 +results_graph_083,1 +results_graph_082,0 +results_graph_057,1 +results_graph_041,0 +results_graph_016,1 +results_graph_061,0 +results_graph_020,0 +results_graph_077,1 +results_graph_011,0 +results_graph_046,1 +results_graph_050,1 +results_graph_007,1 +results_graph_070,1 +results_graph_027,0 +results_graph_031,0 +results_graph_066,1 +results_graph_088,1 +results_graph_067,0 +results_graph_026,1 +results_graph_084,0 +results_graph_006,1 +results_graph_051,0 +results_graph_047,0 +results_graph_010,0 +results_graph_068,1 +results_graph_087,1 +results_graph_029,1 +results_graph_005,0 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diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","[ - { - ""date"": ""June 2014"", - ""text"": ""Lung cancer (stage IV) diagnosed"" - }, - { - ""date"": ""July 2014"", - ""text"": ""Radiation therapy for pelvic lesion (45 Gy/15 Fr)"" - }, - { - ""date"": ""July 2014"", - ""text"": ""Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)"" - }, - { - ""date"": ""July 2014"", - ""text"": ""Bevacizumab maintenance therapy"" - }, - { - ""date"": ""after 15 cycles of maintenance therapy"", - ""text"": ""Right adrenal metastasis larger"" - }, - { - ""date"": ""after 15 cycles of maintenance therapy"", - ""text"": ""New left adrenal metastasis observed"" - }, - { - ""date"": ""January 2018"", - ""text"": ""Re-enlargement of the right adrenal metastasis detected"" - }, - { - ""date"": ""January 2018"", - ""text"": ""Radiation therapy for the right adrenal lesion (50 Gy/25 Fr)"" - }, - { - ""date"": ""January 2018"", - ""text"": ""Chemotherapy (two courses of docetaxel monotherapy) administered"" - }, - { - ""date"": ""February 2019"", - ""text"": ""Enlargement of the left adrenal metastasis detected"" - }, - { - ""date"": ""February 2019"", - ""text"": ""Nivolumab monotherapy as fifth-line therapy initiated"" - }, - { - ""date"": ""May 2022"", - ""text"": ""Diabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negative"" - }, - { - ""date"": ""four years and 5 months after starting nivolumab treatment"", - ""text"": ""Polymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progression"" - }, - { - ""date"": ""four years and 5 months after starting nivolumab treatment"", - ""text"": ""Nivolumab treatment continued"" - } -]","[""Lung cancer""]","[""stage IV lung cancer""]",True,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" -005,2,0,Neoadjuvant_Targeted_Therapy_with_Dacomitinib_in_a_Stage_IIIA_Non_Small_Cell_Lun_PMC11980937.html,"A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. - -The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. - -The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. - -The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. - -The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. - -The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] -003,0,0,Management_of_malignant_inferior_vena_cava_syndrome__IVCS__by_endovascular_bridg_PMC12019825.html,"A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents.","A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents. - -Diagnosed with SCLC 15 months previously. Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation. Lost 20 kg of body weight within 12 months. Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission. Vital signs: systolic/diastolic blood pressure 100/70 mmHg, heart rate 90 bpm, oxygen saturation 89%, body temperature 36,9°C/98° F. Laboratory results: hemoglobin 12,6 g/dl (normal range 14-18 g/dl), platelets 260 × 103/μl (150-450 × 103/μl), alkaline phosphatase 94 U/L (26-112 U/L), alanine aminotransferase 40 U/L (5-35 U/L), aspartate aminotransferase 34 U/L (<40 U/L), total bilirubin 1.2 mg/dl, and creatinine 0.9 mg/dl. A large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium. Multiple enlarged mediastinal lymph nodes, infiltration of the visceral pleura and right hemidiaphragm, ascites, and peritoneal metastases were other salient findings underlining disease progression. - -Three self-expanding stents (yellow arrows) were positioned in tandem from the superior vena cava (SVC) (red arrow shows the most cephalic part of the stents) to the IVC to restore venous patency. Fig. 3. The final venography revealed adequate flow through the bridging stents (yellow arrows). The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h. Low-molecular-weight heparin was administered for anticoagulation. - -The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium.","- Diagnosed with SCLC 15 months previously -- Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation -- Lost 20 kg of body weight within 12 months -- Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission -- Underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression -- Three self-expanding stents were positioned in tandem from the superior vena cava (SVC) to the IVC to restore venous patency -- The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h -- Low-molecular-weight heparin was administered for anticoagulation -- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""SCLC""]","[""Small Cell Lung Cancer""]",True,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" -015,2,2,A_case_of_obstructive_shock_and_transient_ischemic_attack_from_intracardiac_meta_PMC11981378.html,"- Patient presented to ER 8 days after initial diagnosis of intracardiac metastasis of NSCLC. +015,1,0,A_case_of_obstructive_shock_and_transient_ischemic_attack_from_intracardiac_meta_PMC11981378.html,"- Patient presented to ER 8 days after initial diagnosis of intracardiac metastasis of NSCLC. - On admission, patient appeared lethargic, tachycardic with irregular rhythm, decreased breath sounds on the right, and tender right upper quadrant due to rib fractures. Heart rate was 110 bpm, blood pressure 96/60 mmHg, respiratory rate 22, and saturation of 100%. Patient treated for hypotension with IV fluids. - CT of head negative for acute intracranial processes. CT of abdomen and pelvis showed mildly displaced rib fractures, right kidney interpolar cyst with new areas of internal hyperdensity (suspected benign cysts). No other new presentations appreciated. - Laboratory values during the admission: @@ -138,178 +64,8 @@ Patient underwent palliative care for symptom management. CT-Angiography: no large vessel occlusion or acute intracranial process Discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLCTransient ischemic attack (TIA) with right facial droop and left pronator driftCT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLC (initial diagnosis) 2 days post-ER admission: Transient ischemic attack (TIA) with right facial droop and left pronator drift -after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""non-small cell lung cancer""]","[""squamous cell histology""]",True,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" -010,3,0,Re_do_robot_assisted_salvage_lobectomy_after_esophagectomy_with_gastric_pull_up__PMC11980297.html,"55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) -Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy -Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression -Pembrolizumab initiated with curative intent but showed no biological response -Salvage lobectomy including complete mediastinal lymph node dissection performed -Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. -After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). -The nasogastric tube was placed in the gastric pull-up as a safety measure. -Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). -After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. -Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) -Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy -Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression -Pembrolizumab initiated with curative intent but showed no biological response -Salvage lobectomy including complete mediastinal lymph node dissection performed -Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. -After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). -The nasogastric tube was placed in the gastric pull-up as a safety measure. -Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). -After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. -Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) -Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy -Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression -Pembrolizumab initiated with curative intent but showed no biological response -Salvage lobectomy including complete mediastinal lymph node dissection performed -Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. -After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). -The nasogastric tube was placed in the gastric pull-up as a safety measure. -Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). -After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. -Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous cell carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",False,[] -013,3,2,Brain_Metastasis_From_Advanced_Stage_Lung_Carcinoma__Differentiating_From_Stroke_PMC11955559.html,"Patient's medical history: -- Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes (15 months ago) -- PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes -- Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy (1 year ago) -- Initiated docetaxel for refractory complications with stage III NSCLC (2 days ago) - -Recent medical events: -- Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea -- Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity -- Leukopenia, WBC of 1.12 K/μL -- Potassium level still low but increased since previous ED visit -- COVID-19 and flu tests all negative -- Urine testing revealed trace blood and bacteria and was positive for cannabis -- Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease -- CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries -- Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting - -Current medications: -- Docetaxel for refractory complications with stage III NSCLC -- Potassium supplement for hypokalemia -- Ondansetron for nausea","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. -1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. -2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. -Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. -Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. -Current visit: COVID-19 and flu tests all negative. -Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. -Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. -Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. -Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. -1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. -2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. -Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. -Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. -Current visit: COVID-19 and flu tests all negative. -Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. -Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. -Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. -Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""NSCLC""]","[""stage III NSCLC""]",True,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" -004,1,1,Metastatic_INI_1_deficient_undifferentiated_lung_cancer_with_EGFR_19del_mutation_PMC12021797.html,"81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity -Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion -Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation -Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section -Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor -Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases -Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis -An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe -Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases -Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis -Genetic testing revealed a mutation in the EGFR gene -Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression -The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity -Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion -Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation -Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section -Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor -Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases -Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis -An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe -Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases -Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis -Genetic testing revealed a mutation in the EGFR gene -Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression -The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity -Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion -Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation -Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section -Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor -Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases -Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis -An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe -Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases -Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis -Genetic testing revealed a mutation in the EGFR gene -Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression -The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""lung cancer""]","[""non-small cell lung cancer""]",True,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" -014,1,1,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""malignant tumor"", ""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""squamous cell carcinoma"", ""lymph nodes""]]" -001,4,1,Intriguing_Encounter__Unveiling_Squamous_Cell_Carcinoma_Lung_with_Rare_Bilateral_PMC12020972.html,"44-year-old male diagnosed as squamous cell carcinoma of the lung -Pituitary metastasis identified on 18F-FDG PET/CT -Renal metastasis identified on 18F-FDG PET/CT -Right-sided chest pain for 2 months -Dry cough for 2 months -Fever (on-off) for 2 months -Hematuria for 2 months -No history of Antitubercular treatment (ATT) intake -Tobacco chewer for >20 years -Decreased air entry on the right side of the lung -Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within -Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern -Bronchoscopy done with bronchoscopic-guided biopsy -Bronchoalveolar lavage (BAL) fluid samples taken -BAL sample sent for cytopathological examination was negative for malignant cells -18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung -FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits -Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted -It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary -FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) -Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung -Pituitary metastasis identified on 18F-FDG PET/CT -Renal metastasis identified on 18F-FDG PET/CT -Right-sided chest pain for 2 months -Dry cough for 2 months -Fever (on-off) for 2 months -Hematuria for 2 months -No history of Antitubercular treatment (ATT) intake -Tobacco chewer for >20 years -Decreased air entry on the right side of the lung -Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within -Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern -Bronchoscopy done with bronchoscopic-guided biopsy -Bronchoalveolar lavage (BAL) fluid samples taken -BAL sample sent for cytopathological examination was negative for malignant cells -18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung -FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits -Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted -It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary -FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) -Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung -Pituitary metastasis identified on 18F-FDG PET/CT -Renal metastasis identified on 18F-FDG PET/CT -Right-sided chest pain for 2 months -Dry cough for 2 months -Fever (on-off) for 2 months -Hematuria for 2 months -No history of Antitubercular treatment (ATT) intake -Tobacco chewer for >20 years -Decreased air entry on the right side of the lung -Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within -Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern -Bronchoscopy done with bronchoscopic-guided biopsy -Bronchoalveolar lavage (BAL) fluid samples taken -BAL sample sent for cytopathological examination was negative for malignant cells -18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung -FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits -Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted -It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary -FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) -Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" -009,1,0,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""lung adenocarcinoma""]","[""lung adenocarcinoma""]",True,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" -011,3,1,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral_Internal__PMC12021377.html,"Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria","Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria"," +after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""Non-small Cell Lung Cancer""]","[""squamous cell histology""]",True,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" +011,0,0,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral_Internal__PMC12021377.html,"Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria","Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria"," Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs. @@ -328,8 +84,9 @@ Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue compon First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria -","[""adenocarcinoma""]","[""lung cancer""]",True,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" -012,4,2,Multiple_Lung_Metastases_of_Papillary_Thyroid_Carcinoma_Detected_by_Detailed_Pat_PMC11971052.html,"79-year-old male patient with: +","[""Adenocarcinoma""]","[""lung cancer""]",True,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" +008,1,1,Case_report__pulmonary_lymphoepithelial_carcinoma_mimicking_tuberculosis__PMC11987468.html,"The patient was a 37-year-old woman who presented with intermittent cough and slight chest discomfort for 3 months. She also had a painless cervical mass for 1 month. The pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans' giant cells observed on left cervical lymph node puncture.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","[""Lymphoepithelial Carcinoma""]","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""]",True,"[[""lung"", ""middle lobe""], [""lymph nodes"", ""mediastinum""], [""lymph nodes"", ""left neck""], [""lymph nodes"", ""right hilum""]]" +012,0,1,Multiple_Lung_Metastases_of_Papillary_Thyroid_Carcinoma_Detected_by_Detailed_Pat_PMC11971052.html,"79-year-old male patient with: - Height: 174 cm - Weight: 65 kg - BMI: 21.5 kg/m² @@ -383,8 +140,143 @@ Immunohistochemistry showed positive staining for TTF-1, indicating lung origin The patient's postoperative course was uneventful, with no complications noted. 5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. 2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. -6 months post-surgery: No evidence of recurrence.","[""papillary thyroid carcinoma"", ""adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",True,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" -016,0,0,Precise_Localization_of_the_Subsolid_Lesion_by_Colour_Marking_under_CT_Guided_Co_PMC12040305.html,"51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +6 months post-surgery: No evidence of recurrence.","[""Papillary Thyroid Carcinoma"", ""Adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",True,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" +001,1,0,Intriguing_Encounter__Unveiling_Squamous_Cell_Carcinoma_Lung_with_Rare_Bilateral_PMC12020972.html,"44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""Lung Cancer""]","[""squamous cell carcinoma""]",True,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" +003,1,1,Management_of_malignant_inferior_vena_cava_syndrome__IVCS__by_endovascular_bridg_PMC12019825.html,"A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents.","A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents. + +Diagnosed with SCLC 15 months previously. Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation. Lost 20 kg of body weight within 12 months. Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission. Vital signs: systolic/diastolic blood pressure 100/70 mmHg, heart rate 90 bpm, oxygen saturation 89%, body temperature 36,9°C/98° F. Laboratory results: hemoglobin 12,6 g/dl (normal range 14-18 g/dl), platelets 260 × 103/μl (150-450 × 103/μl), alkaline phosphatase 94 U/L (26-112 U/L), alanine aminotransferase 40 U/L (5-35 U/L), aspartate aminotransferase 34 U/L (<40 U/L), total bilirubin 1.2 mg/dl, and creatinine 0.9 mg/dl. A large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium. Multiple enlarged mediastinal lymph nodes, infiltration of the visceral pleura and right hemidiaphragm, ascites, and peritoneal metastases were other salient findings underlining disease progression. + +Three self-expanding stents (yellow arrows) were positioned in tandem from the superior vena cava (SVC) (red arrow shows the most cephalic part of the stents) to the IVC to restore venous patency. Fig. 3. The final venography revealed adequate flow through the bridging stents (yellow arrows). The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h. Low-molecular-weight heparin was administered for anticoagulation. + +The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium.","- Diagnosed with SCLC 15 months previously +- Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation +- Lost 20 kg of body weight within 12 months +- Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission +- Underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression +- Three self-expanding stents were positioned in tandem from the superior vena cava (SVC) to the IVC to restore venous patency +- The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h +- Low-molecular-weight heparin was administered for anticoagulation +- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""Small Cell Lung Cancer""]","[""Small Cell Lung Cancer""]",True,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" +006,1,0,Lung_cancer_with_diabetes_mellitus_and_polymyalgia_rheumatica_during_long_term_n_PMC12001326.html,"Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","[ + { + ""date"": ""June 2014"", + ""text"": ""Lung cancer (stage IV) diagnosed"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Radiation therapy for pelvic lesion (45 Gy/15 Fr)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Bevacizumab maintenance therapy"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""Right adrenal metastasis larger"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""New left adrenal metastasis observed"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Re-enlargement of the right adrenal metastasis detected"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Radiation therapy for the right adrenal lesion (50 Gy/25 Fr)"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Chemotherapy (two courses of docetaxel monotherapy) administered"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Enlargement of the left adrenal metastasis detected"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Nivolumab monotherapy as fifth-line therapy initiated"" + }, + { + ""date"": ""May 2022"", + ""text"": ""Diabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negative"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Polymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progression"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Nivolumab treatment continued"" + } +]","[""Lung Cancer""]","[""stage IV lung cancer""]",True,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" +009,1,1,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""Lung Adenocarcinoma""]","[""lung adenocarcinoma""]",True,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" +016,1,1,Precise_Localization_of_the_Subsolid_Lesion_by_Colour_Marking_under_CT_Guided_Co_PMC12040305.html,"51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. Born in 1970, underwent resection of malignant melanoma in April 2013. Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. @@ -402,4 +294,112 @@ Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy con Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. -She continues to be followed up regularly and remains free of signs of disease recurrence.","[""malignant melanoma""]","[""melanoma"", ""lung cancer""]",True,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" +She continues to be followed up regularly and remains free of signs of disease recurrence.","[""Malignant Melanoma""]","[""melanoma"", ""lung cancer""]",True,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" +014,0,1,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""Malignant tumor"", ""Lung Cancer""]","[""squamous cell carcinoma""]",True,"[[""squamous cell carcinoma"", ""lymph nodes""]]" +004,1,0,Metastatic_INI_1_deficient_undifferentiated_lung_cancer_with_EGFR_19del_mutation_PMC12021797.html,"81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""Lung Cancer""]","[""non-small cell lung cancer""]",True,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" +010,0,1,Re_do_robot_assisted_salvage_lobectomy_after_esophagectomy_with_gastric_pull_up__PMC11980297.html,"55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous Cell Carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",False,[] +013,0,0,Brain_Metastasis_From_Advanced_Stage_Lung_Carcinoma__Differentiating_From_Stroke_PMC11955559.html,"Patient's medical history: +- Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes (15 months ago) +- PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes +- Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy (1 year ago) +- Initiated docetaxel for refractory complications with stage III NSCLC (2 days ago) + +Recent medical events: +- Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea +- Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity +- Leukopenia, WBC of 1.12 K/μL +- Potassium level still low but increased since previous ED visit +- COVID-19 and flu tests all negative +- Urine testing revealed trace blood and bacteria and was positive for cannabis +- Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease +- CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries +- Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting + +Current medications: +- Docetaxel for refractory complications with stage III NSCLC +- Potassium supplement for hypokalemia +- Ondansetron for nausea","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""Non-small Cell Lung Cancer""]","[""stage III NSCLC""]",True,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" diff --git a/src/benchmark/output/results/cluster_metadata_summary.csv b/src/benchmark/output/results/cluster_metadata_summary.csv index 11440bd..b258ea6 100644 --- a/src/benchmark/output/results/cluster_metadata_summary.csv +++ b/src/benchmark/output/results/cluster_metadata_summary.csv @@ -1,4 +1,3 @@ cluster,has_metastasis,top_cancers,top_specific_cancers -0,"{""true"": 0.6666666666666666, ""false"": 0.3333333333333333}","[""lymphoepithelial carcinoma""] (1), [""Lung Cancer""] (1), [""SCLC""] (1)","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""] (1), [""Lung Adenocarcinoma""] (1), [""Small Cell Lung Cancer""] (1)" -1,"{""true"": 1.0}","[""lung cancer""] (2), [""Lung cancer""] (1), [""malignant tumor"", ""lung cancer""] (1)","[""squamous cell carcinoma""] (2), [""stage IV lung cancer""] (1), [""non-small cell lung cancer""] (1)" -2,"{""true"": 0.75, ""false"": 0.25}","[""Lung Cancer""] (1), [""non-small cell lung cancer""] (1), [""NSCLC""] (1)","[""Lung Adenocarcinoma""] (1), [""squamous cell histology""] (1), [""stage III NSCLC""] (1)" +0,"{""true"": 0.8571428571428571, ""false"": 0.14285714285714285}","[""Lung Cancer""] (4), [""Non-small Cell Lung Cancer""] (2), [""Adenocarcinoma""] (1)","[""Lung Adenocarcinoma""] (1), [""squamous cell histology""] (1), [""lung cancer""] (1)" +1,"{""true"": 0.75, ""false"": 0.25}","[""Lung Cancer""] (1), [""Lymphoepithelial Carcinoma""] (1), [""Papillary Thyroid Carcinoma"", ""Adenocarcinoma""] (1)","[""Lung Adenocarcinoma""] (1), [""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""] (1), [""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""] (1)" diff --git a/src/benchmark/output/results/graph_html_metadata.csv b/src/benchmark/output/results/graph_html_metadata.csv index 7e8bd19..cd2633d 100644 --- a/src/benchmark/output/results/graph_html_metadata.csv +++ b/src/benchmark/output/results/graph_html_metadata.csv @@ -59,13 +59,13 @@ FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided p Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) -Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""Lung Cancer""]","[""squamous cell carcinoma""]",TRUE,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" graph_002,_A_Case_of_Multiple_Primary_Pulmonary_Neuroendocrine_Carcinoma_with_EML4_ALK_Fus_PMC11986677.html,"* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除 * 2022-04-27: 病灶稳定，无肿瘤复发或转移 * 2023-08-01: 左主支气管略狭窄 * 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC） * 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止 -* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展","[""* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除\n* 2022-04-27: 病灶稳定，无肿瘤复发或转移\n* 2023-08-01: 左主支气管略狭窄\n* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC）\n* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止\n* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展""]",,"[""\u764c"", ""\u80bf\u7624"", ""\u6076\u6027\u80bf\u7624""]","[""\u5927\u7ec6\u80de\u795e\u7ecf\u5185\u5206\u6ccc\u764c"", ""\u5c0f\u7ec6\u80de\u80ba\u764c""]",False,[] +* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展","[""* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除\n* 2022-04-27: 病灶稳定，无肿瘤复发或转移\n* 2023-08-01: 左主支气管略狭窄\n* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC）\n* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止\n* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展""]",,"[""\u764c"", ""\u80bf\u7624"", ""\u6076\u6027\u80bf\u7624""]","[""\u5927\u7ec6\u80de\u795e\u7ecf\u5185\u5206\u6ccc\u764c"", ""\u5c0f\u7ec6\u80de\u80ba\u764c""]",FALSE,[] graph_003,Management_of_malignant_inferior_vena_cava_syndrome__IVCS__by_endovascular_bridg_PMC12019825.html,"A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents.","A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents. Diagnosed with SCLC 15 months previously. Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation. Lost 20 kg of body weight within 12 months. Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission. Vital signs: systolic/diastolic blood pressure 100/70 mmHg, heart rate 90 bpm, oxygen saturation 89%, body temperature 36,9°C/98° F. Laboratory results: hemoglobin 12,6 g/dl (normal range 14-18 g/dl), platelets 260 × 103/μl (150-450 × 103/μl), alkaline phosphatase 94 U/L (26-112 U/L), alanine aminotransferase 40 U/L (5-35 U/L), aspartate aminotransferase 34 U/L (<40 U/L), total bilirubin 1.2 mg/dl, and creatinine 0.9 mg/dl. A large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium. Multiple enlarged mediastinal lymph nodes, infiltration of the visceral pleura and right hemidiaphragm, ascites, and peritoneal metastases were other salient findings underlining disease progression. @@ -80,7 +80,7 @@ The patient died with a large tumor involving the right lower and middle lung lo - Three self-expanding stents were positioned in tandem from the superior vena cava (SVC) to the IVC to restore venous patency - The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h - Low-molecular-weight heparin was administered for anticoagulation -- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""SCLC""]","[""Small Cell Lung Cancer""]",True,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" +- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""Small Cell Lung Cancer""]","[""Small Cell Lung Cancer""]",TRUE,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" graph_004,Metastatic_INI_1_deficient_undifferentiated_lung_cancer_with_EGFR_19del_mutation_PMC12021797.html,"81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation @@ -117,7 +117,7 @@ Annular enhancement was noted in the arterial phase, while marked hypodensity wa Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis Genetic testing revealed a mutation in the EGFR gene Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression -The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""lung cancer""]","[""non-small cell lung cancer""]",True,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""Lung Cancer""]","[""non-small cell lung cancer""]",TRUE,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" graph_005,Neoadjuvant_Targeted_Therapy_with_Dacomitinib_in_a_Stage_IIIA_Non_Small_Cell_Lun_PMC11980937.html,"A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. @@ -128,7 +128,7 @@ The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. -The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] +The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",FALSE,[] graph_006,Lung_cancer_with_diabetes_mellitus_and_polymyalgia_rheumatica_during_long_term_n_PMC12001326.html,"Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","[ { ""date"": ""June 2014"", @@ -186,7 +186,7 @@ graph_006,Lung_cancer_with_diabetes_mellitus_and_polymyalgia_rheumatica_during_l ""date"": ""four years and 5 months after starting nivolumab treatment"", ""text"": ""Nivolumab treatment continued"" } -]","[""Lung cancer""]","[""stage IV lung cancer""]",True,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" +]","[""Lung Cancer""]","[""stage IV lung cancer""]",TRUE,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" graph_007,Case_Report__A_novel_ELMOD3_ALK_and_EML4_ALK_double_fusion_responses_to_neoadjuv_PMC12034634.html,"2020-04-20: Patient comes to hospital for physical examination 2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed 2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue @@ -199,9 +199,9 @@ graph_007,Case_Report__A_novel_ELMOD3_ALK_and_EML4_ALK_double_fusion_responses_t 2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed 2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue 2020: Patient starts treatment with targeted therapy for ALK fusion -2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] -graph_008,Case_report__pulmonary_lymphoepithelial_carcinoma_mimicking_tuberculosis__PMC11987468.html,"The patient was a 37-year-old woman who presented with intermittent cough and slight chest discomfort for 3 months. She also had a painless cervical mass for 1 month. The pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans' giant cells observed on left cervical lymph node puncture.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","[""lymphoepithelial carcinoma""]","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""]",True,"[[""lung"", ""middle lobe""], [""lymph nodes"", ""mediastinum""], [""lymph nodes"", ""left neck""], [""lymph nodes"", ""right hilum""]]" -graph_009,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""lung adenocarcinoma""]","[""lung adenocarcinoma""]",True,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" +2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",FALSE,[] +graph_008,Case_report__pulmonary_lymphoepithelial_carcinoma_mimicking_tuberculosis__PMC11987468.html,"The patient was a 37-year-old woman who presented with intermittent cough and slight chest discomfort for 3 months. She also had a painless cervical mass for 1 month. The pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans' giant cells observed on left cervical lymph node puncture.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","[""Lymphoepithelial Carcinoma""]","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""]",TRUE,"[[""lung"", ""middle lobe""], [""lymph nodes"", ""mediastinum""], [""lymph nodes"", ""left neck""], [""lymph nodes"", ""right hilum""]]" +graph_009,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""Lung Adenocarcinoma""]","[""lung adenocarcinoma""]",TRUE,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" graph_010,Re_do_robot_assisted_salvage_lobectomy_after_esophagectomy_with_gastric_pull_up__PMC11980297.html,"55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression @@ -232,7 +232,7 @@ After standard port placement (Fig.2A), docking and instrument placement (Tip-up The nasogastric tube was placed in the gastric pull-up as a safety measure. Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. -Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous cell carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",False,[] +Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous Cell Carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",FALSE,[] graph_011,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral_Internal__PMC12021377.html,"Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria","Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria"," Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs. @@ -252,7 +252,7 @@ graph_011,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria -","[""adenocarcinoma""]","[""lung cancer""]",True,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" +","[""Adenocarcinoma""]","[""lung cancer""]",TRUE,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" graph_012,Multiple_Lung_Metastases_of_Papillary_Thyroid_Carcinoma_Detected_by_Detailed_Pat_PMC11971052.html,"79-year-old male patient with: - Height: 174 cm - Weight: 65 kg @@ -307,7 +307,7 @@ Immunohistochemistry showed positive staining for TTF-1, indicating lung origin The patient's postoperative course was uneventful, with no complications noted. 5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. 2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. -6 months post-surgery: No evidence of recurrence.","[""papillary thyroid carcinoma"", ""adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",True,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" +6 months post-surgery: No evidence of recurrence.","[""Papillary Thyroid Carcinoma"", ""Adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",TRUE,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" graph_013,Brain_Metastasis_From_Advanced_Stage_Lung_Carcinoma__Differentiating_From_Stroke_PMC11955559.html,"Patient's medical history: - Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes (15 months ago) - PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes @@ -346,8 +346,8 @@ Current visit: COVID-19 and flu tests all negative. Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. -Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""NSCLC""]","[""stage III NSCLC""]",True,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" -graph_014,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""malignant tumor"", ""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""squamous cell carcinoma"", ""lymph nodes""]]" +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""Non-small Cell Lung Cancer""]","[""stage III NSCLC""]",TRUE,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" +graph_014,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""Malignant tumor"", ""Lung Cancer""]","[""squamous cell carcinoma""]",TRUE,"[[""squamous cell carcinoma"", ""lymph nodes""]]" graph_015,A_case_of_obstructive_shock_and_transient_ischemic_attack_from_intracardiac_meta_PMC11981378.html,"- Patient presented to ER 8 days after initial diagnosis of intracardiac metastasis of NSCLC. - On admission, patient appeared lethargic, tachycardic with irregular rhythm, decreased breath sounds on the right, and tender right upper quadrant due to rib fractures. Heart rate was 110 bpm, blood pressure 96/60 mmHg, respiratory rate 22, and saturation of 100%. Patient treated for hypotension with IV fluids. - CT of head negative for acute intracranial processes. CT of abdomen and pelvis showed mildly displaced rib fractures, right kidney interpolar cyst with new areas of internal hyperdensity (suspected benign cysts). No other new presentations appreciated. @@ -389,7 +389,7 @@ Patient underwent palliative care for symptom management. CT-Angiography: no large vessel occlusion or acute intracranial process Discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLCTransient ischemic attack (TIA) with right facial droop and left pronator driftCT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLC (initial diagnosis) 2 days post-ER admission: Transient ischemic attack (TIA) with right facial droop and left pronator drift -after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""non-small cell lung cancer""]","[""squamous cell histology""]",True,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" +after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""Non-small Cell Lung Cancer""]","[""squamous cell histology""]",TRUE,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" graph_016,Precise_Localization_of_the_Subsolid_Lesion_by_Colour_Marking_under_CT_Guided_Co_PMC12040305.html,"51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. Born in 1970, underwent resection of malignant melanoma in April 2013. Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. @@ -408,4 +408,4 @@ Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy con Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. -She continues to be followed up regularly and remains free of signs of disease recurrence.","[""malignant melanoma""]","[""melanoma"", ""lung cancer""]",True,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" +She continues to be followed up regularly and remains free of signs of disease recurrence.","[""Malignant Melanoma""]","[""melanoma"", ""lung cancer""]",TRUE,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" \ No newline at end of file diff --git a/src/benchmark/output/results/testset/graph_html_metadata.csv b/src/benchmark/output/results/testset/graph_html_metadata.csv deleted file mode 100644 index 7e8bd19..0000000 --- a/src/benchmark/output/results/testset/graph_html_metadata.csv +++ /dev/null @@ -1,411 +0,0 @@ -graph_id,source_file,timeline_1,timeline_2,timeline_3,cancers,specific_cancers,has_metastasis,metastasis_locations -graph_001,Intriguing_Encounter__Unveiling_Squamous_Cell_Carcinoma_Lung_with_Rare_Bilateral_PMC12020972.html,"44-year-old male diagnosed as squamous cell carcinoma of the lung -Pituitary metastasis identified on 18F-FDG PET/CT -Renal metastasis identified on 18F-FDG PET/CT -Right-sided chest pain for 2 months -Dry cough for 2 months -Fever (on-off) for 2 months -Hematuria for 2 months -No history of Antitubercular treatment (ATT) intake -Tobacco chewer for >20 years -Decreased air entry on the right side of the lung -Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within -Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern -Bronchoscopy done with bronchoscopic-guided biopsy -Bronchoalveolar lavage (BAL) fluid samples taken -BAL sample sent for cytopathological examination was negative for malignant cells -18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung -FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits -Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted -It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary -FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) -Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung -Pituitary metastasis identified on 18F-FDG PET/CT -Renal metastasis identified on 18F-FDG PET/CT -Right-sided chest pain for 2 months -Dry cough for 2 months -Fever (on-off) for 2 months -Hematuria for 2 months -No history of Antitubercular treatment (ATT) intake -Tobacco chewer for >20 years -Decreased air entry on the right side of the lung -Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within -Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern -Bronchoscopy done with bronchoscopic-guided biopsy -Bronchoalveolar lavage (BAL) fluid samples taken -BAL sample sent for cytopathological examination was negative for malignant cells -18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung -FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits -Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted -It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary -FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) -Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung -Pituitary metastasis identified on 18F-FDG PET/CT -Renal metastasis identified on 18F-FDG PET/CT -Right-sided chest pain for 2 months -Dry cough for 2 months -Fever (on-off) for 2 months -Hematuria for 2 months -No history of Antitubercular treatment (ATT) intake -Tobacco chewer for >20 years -Decreased air entry on the right side of the lung -Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within -Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern -Bronchoscopy done with bronchoscopic-guided biopsy -Bronchoalveolar lavage (BAL) fluid samples taken -BAL sample sent for cytopathological examination was negative for malignant cells -18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung -FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits -Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted -It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary -FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) -Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" -graph_002,_A_Case_of_Multiple_Primary_Pulmonary_Neuroendocrine_Carcinoma_with_EML4_ALK_Fus_PMC11986677.html,"* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除 -* 2022-04-27: 病灶稳定，无肿瘤复发或转移 -* 2023-08-01: 左主支气管略狭窄 -* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC） -* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止 -* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展","[""* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除\n* 2022-04-27: 病灶稳定，无肿瘤复发或转移\n* 2023-08-01: 左主支气管略狭窄\n* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC）\n* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止\n* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展""]",,"[""\u764c"", ""\u80bf\u7624"", ""\u6076\u6027\u80bf\u7624""]","[""\u5927\u7ec6\u80de\u795e\u7ecf\u5185\u5206\u6ccc\u764c"", ""\u5c0f\u7ec6\u80de\u80ba\u764c""]",False,[] -graph_003,Management_of_malignant_inferior_vena_cava_syndrome__IVCS__by_endovascular_bridg_PMC12019825.html,"A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents.","A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents. - -Diagnosed with SCLC 15 months previously. Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation. Lost 20 kg of body weight within 12 months. Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission. Vital signs: systolic/diastolic blood pressure 100/70 mmHg, heart rate 90 bpm, oxygen saturation 89%, body temperature 36,9°C/98° F. Laboratory results: hemoglobin 12,6 g/dl (normal range 14-18 g/dl), platelets 260 × 103/μl (150-450 × 103/μl), alkaline phosphatase 94 U/L (26-112 U/L), alanine aminotransferase 40 U/L (5-35 U/L), aspartate aminotransferase 34 U/L (<40 U/L), total bilirubin 1.2 mg/dl, and creatinine 0.9 mg/dl. A large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium. Multiple enlarged mediastinal lymph nodes, infiltration of the visceral pleura and right hemidiaphragm, ascites, and peritoneal metastases were other salient findings underlining disease progression. - -Three self-expanding stents (yellow arrows) were positioned in tandem from the superior vena cava (SVC) (red arrow shows the most cephalic part of the stents) to the IVC to restore venous patency. Fig. 3. The final venography revealed adequate flow through the bridging stents (yellow arrows). The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h. Low-molecular-weight heparin was administered for anticoagulation. - -The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium.","- Diagnosed with SCLC 15 months previously -- Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation -- Lost 20 kg of body weight within 12 months -- Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission -- Underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression -- Three self-expanding stents were positioned in tandem from the superior vena cava (SVC) to the IVC to restore venous patency -- The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h -- Low-molecular-weight heparin was administered for anticoagulation -- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""SCLC""]","[""Small Cell Lung Cancer""]",True,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" -graph_004,Metastatic_INI_1_deficient_undifferentiated_lung_cancer_with_EGFR_19del_mutation_PMC12021797.html,"81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity -Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion -Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation -Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section -Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor -Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases -Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis -An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe -Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases -Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis -Genetic testing revealed a mutation in the EGFR gene -Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression -The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity -Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion -Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation -Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section -Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor -Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases -Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis -An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe -Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases -Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis -Genetic testing revealed a mutation in the EGFR gene -Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression -The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity -Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion -Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation -Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section -Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor -Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases -Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis -An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe -Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases -Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis -Genetic testing revealed a mutation in the EGFR gene -Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression -The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""lung cancer""]","[""non-small cell lung cancer""]",True,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" -graph_005,Neoadjuvant_Targeted_Therapy_with_Dacomitinib_in_a_Stage_IIIA_Non_Small_Cell_Lun_PMC11980937.html,"A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. - -The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. - -The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. - -The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. - -The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. - -The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] -graph_006,Lung_cancer_with_diabetes_mellitus_and_polymyalgia_rheumatica_during_long_term_n_PMC12001326.html,"Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","[ - { - ""date"": ""June 2014"", - ""text"": ""Lung cancer (stage IV) diagnosed"" - }, - { - ""date"": ""July 2014"", - ""text"": ""Radiation therapy for pelvic lesion (45 Gy/15 Fr)"" - }, - { - ""date"": ""July 2014"", - ""text"": ""Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)"" - }, - { - ""date"": ""July 2014"", - ""text"": ""Bevacizumab maintenance therapy"" - }, - { - ""date"": ""after 15 cycles of maintenance therapy"", - ""text"": ""Right adrenal metastasis larger"" - }, - { - ""date"": ""after 15 cycles of maintenance therapy"", - ""text"": ""New left adrenal metastasis observed"" - }, - { - ""date"": ""January 2018"", - ""text"": ""Re-enlargement of the right adrenal metastasis detected"" - }, - { - ""date"": ""January 2018"", - ""text"": ""Radiation therapy for the right adrenal lesion (50 Gy/25 Fr)"" - }, - { - ""date"": ""January 2018"", - ""text"": ""Chemotherapy (two courses of docetaxel monotherapy) administered"" - }, - { - ""date"": ""February 2019"", - ""text"": ""Enlargement of the left adrenal metastasis detected"" - }, - { - ""date"": ""February 2019"", - ""text"": ""Nivolumab monotherapy as fifth-line therapy initiated"" - }, - { - ""date"": ""May 2022"", - ""text"": ""Diabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negative"" - }, - { - ""date"": ""four years and 5 months after starting nivolumab treatment"", - ""text"": ""Polymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progression"" - }, - { - ""date"": ""four years and 5 months after starting nivolumab treatment"", - ""text"": ""Nivolumab treatment continued"" - } -]","[""Lung cancer""]","[""stage IV lung cancer""]",True,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" -graph_007,Case_Report__A_novel_ELMOD3_ALK_and_EML4_ALK_double_fusion_responses_to_neoadjuv_PMC12034634.html,"2020-04-20: Patient comes to hospital for physical examination -2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed -2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue -2020: Patient starts treatment with targeted therapy for ALK fusion -2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","2020-04-20: Patient comes to hospital for physical examination -2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed -2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue -2020: Patient starts treatment with targeted therapy for ALK fusion -2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","2020-04-20: Patient comes to hospital for physical examination -2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed -2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue -2020: Patient starts treatment with targeted therapy for ALK fusion -2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] -graph_008,Case_report__pulmonary_lymphoepithelial_carcinoma_mimicking_tuberculosis__PMC11987468.html,"The patient was a 37-year-old woman who presented with intermittent cough and slight chest discomfort for 3 months. She also had a painless cervical mass for 1 month. The pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans' giant cells observed on left cervical lymph node puncture.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","[""lymphoepithelial carcinoma""]","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""]",True,"[[""lung"", ""middle lobe""], [""lymph nodes"", ""mediastinum""], [""lymph nodes"", ""left neck""], [""lymph nodes"", ""right hilum""]]" -graph_009,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""lung adenocarcinoma""]","[""lung adenocarcinoma""]",True,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" -graph_010,Re_do_robot_assisted_salvage_lobectomy_after_esophagectomy_with_gastric_pull_up__PMC11980297.html,"55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) -Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy -Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression -Pembrolizumab initiated with curative intent but showed no biological response -Salvage lobectomy including complete mediastinal lymph node dissection performed -Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. -After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). -The nasogastric tube was placed in the gastric pull-up as a safety measure. -Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). -After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. -Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) -Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy -Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression -Pembrolizumab initiated with curative intent but showed no biological response -Salvage lobectomy including complete mediastinal lymph node dissection performed -Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. -After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). -The nasogastric tube was placed in the gastric pull-up as a safety measure. -Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). -After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. -Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) -Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy -Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression -Pembrolizumab initiated with curative intent but showed no biological response -Salvage lobectomy including complete mediastinal lymph node dissection performed -Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. -After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). -The nasogastric tube was placed in the gastric pull-up as a safety measure. -Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). -After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. -Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous cell carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",False,[] -graph_011,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral_Internal__PMC12021377.html,"Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria","Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria"," - - Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs. - - - Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerve - - - Significant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints. - - - Fourth-line treatment with selpercatinib (160 mg twice daily) was initiated - - - Disease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter. - - - First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria - -","[""adenocarcinoma""]","[""lung cancer""]",True,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" -graph_012,Multiple_Lung_Metastases_of_Papillary_Thyroid_Carcinoma_Detected_by_Detailed_Pat_PMC11971052.html,"79-year-old male patient with: -- Height: 174 cm -- Weight: 65 kg -- BMI: 21.5 kg/m² -- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) -- Medical history: - - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension - - Left cervical lymphadenopathy of unknown origin six years ago - - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC. - - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. - - The patient was treated with radioiodine therapy (Iodine-131). - - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. - - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits. - - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL. - - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1). - - No hilar lymphadenopathy was detected. - - FDG-PET was not performed. - - Pulmonary function and electrocardiogram tests showed no abnormalities. - -An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. - -Histopathological examination revealed adenocarcinoma. -Adenocarcinoma cells were found in the resected tissue. -Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. -The patient's postoperative course was uneventful, with no complications noted. -5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. -2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. -6 months post-surgery: No evidence of recurrence.","Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension.A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made.No evidence of recurrence.","79-year-old male patient with: -- Height: 174 cm -- Weight: 65 kg -- BMI: 21.5 kg/m² -- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) -- Medical history: - - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension - - Left cervical lymphadenopathy of unknown origin six years ago - - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC - - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. - - The patient was treated with radioiodine therapy (Iodine-131) - - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. - - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits - - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL - - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1) - - No hilar lymphadenopathy was detected - - FDG-PET was not performed - - Pulmonary function and electrocardiogram tests showed no abnormalities - -An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. - -Histopathological examination revealed adenocarcinoma. -Adenocarcinoma cells were found in the resected tissue. -Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. -The patient's postoperative course was uneventful, with no complications noted. -5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. -2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. -6 months post-surgery: No evidence of recurrence.","[""papillary thyroid carcinoma"", ""adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",True,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" -graph_013,Brain_Metastasis_From_Advanced_Stage_Lung_Carcinoma__Differentiating_From_Stroke_PMC11955559.html,"Patient's medical history: -- Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes (15 months ago) -- PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes -- Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy (1 year ago) -- Initiated docetaxel for refractory complications with stage III NSCLC (2 days ago) - -Recent medical events: -- Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea -- Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity -- Leukopenia, WBC of 1.12 K/μL -- Potassium level still low but increased since previous ED visit -- COVID-19 and flu tests all negative -- Urine testing revealed trace blood and bacteria and was positive for cannabis -- Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease -- CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries -- Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting - -Current medications: -- Docetaxel for refractory complications with stage III NSCLC -- Potassium supplement for hypokalemia -- Ondansetron for nausea","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. -1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. -2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. -Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. -Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. -Current visit: COVID-19 and flu tests all negative. -Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. -Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. -Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. -Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. -1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. -2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. -Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. -Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. -Current visit: COVID-19 and flu tests all negative. -Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. -Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. -Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. -Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""NSCLC""]","[""stage III NSCLC""]",True,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" -graph_014,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""malignant tumor"", ""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""squamous cell carcinoma"", ""lymph nodes""]]" -graph_015,A_case_of_obstructive_shock_and_transient_ischemic_attack_from_intracardiac_meta_PMC11981378.html,"- Patient presented to ER 8 days after initial diagnosis of intracardiac metastasis of NSCLC. -- On admission, patient appeared lethargic, tachycardic with irregular rhythm, decreased breath sounds on the right, and tender right upper quadrant due to rib fractures. Heart rate was 110 bpm, blood pressure 96/60 mmHg, respiratory rate 22, and saturation of 100%. Patient treated for hypotension with IV fluids. -- CT of head negative for acute intracranial processes. CT of abdomen and pelvis showed mildly displaced rib fractures, right kidney interpolar cyst with new areas of internal hyperdensity (suspected benign cysts). No other new presentations appreciated. -- Laboratory values during the admission: - - Hemoglobin (g/dL): 9.6, 9.9, 10.4 - - Hematocrit (%): 28.3, 30.2, 31.4 - - Platelets (K/uL): 146, 128, 170 - - WBC (K/uL): 19.5, 16.29, 20.71 - - Sodium (mEq/L): 129, 128, 127 - - Potassium (mEq/L): 3.7, 4, 4.7 - - Chloride (mEq/L): 102, 100, 101 - - Bicarbonate (mmol/L): 24, 23, 25 - - Glucose (mg/dL): 120, 130, 110 - - Creatinine (mg/dL): 1.2, 1.3, 1.1 - - Urea nitrogen (mg/dL): 20, 22, 18 - - Calcium (mg/dL): 9.5, 10.2, 9.8 - - Phosphate (mg/dL): 4.2, 4.5, 4.0 - - Lactate dehydrogenase (LDH) (U/L): 250, 280, 220 - - Aspartate aminotransferase (AST) (U/L): 40, 45, 35 - - Alanine aminotransferase (ALT) (U/L): 30, 35, 25 - - Total bilirubin (mg/dL): 1.2, 1.5, 1.0 - - Direct bilirubin (mg/dL): 0.8, 1.0, 0.7 - - Alkaline phosphatase (ALP) (U/L): 120, 140, 100 - - Gamma-glutamyl transferase (GGT) (U/L): 50, 60, 40 - -2 days post-ER admission: Patient developed symptoms suggestive of a transient ischemic attack (TIA) with right facial droop and left pronator drift. -CT-Angiography did not show any large vessel occlusion or acute intracranial process. -The deficits resolved in 6 hours; however, the patient still had ongoing tachycardia and uncontrolled atrial fibrillation. - -Patient was diagnosed with locally advanced non-small cell lung cancer (NSCLC) stage IIIB (T4N2Mx) metastatic non-small cell lung carcinoma of squamous cell histology. -Endobronchial ultrasound-guided fine-needle aspiration confirmed the diagnosis. -CT angiogram revealed a large hypermetabolic mass in the right lower lobe extending into the mediastinum with enlarged hypermetabolic subcarinal nodes, irregular mass measuring approximately 8.7 × 4.6 cm, partial atelectasis of the right middle and lower lobes, small to moderate low-density right pleural effusion. -Tumor thrombus in the left atrium measuring 3.4 × 6.3 cm, interfering with the mitral valve function. -Echocardiogram showed that the mass was invading into the left atrium. - -Patient underwent palliative care for symptom management. - -2 days post-ER admission: TIA with right facial droop and left pronator drift -CT-Angiography: no large vessel occlusion or acute intracranial process -Discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLCTransient ischemic attack (TIA) with right facial droop and left pronator driftCT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLC (initial diagnosis) -2 days post-ER admission: Transient ischemic attack (TIA) with right facial droop and left pronator drift -after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""non-small cell lung cancer""]","[""squamous cell histology""]",True,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" -graph_016,Precise_Localization_of_the_Subsolid_Lesion_by_Colour_Marking_under_CT_Guided_Co_PMC12040305.html,"51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. -Born in 1970, underwent resection of malignant melanoma in April 2013. -Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. -Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. -A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. -The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. -She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. -Born in 1970, underwent resection of malignant melanoma in April 2013. -Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. -Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. -A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. -The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. -She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. -Born in 1970, underwent resection of malignant melanoma in April 2013. -Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. -Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. -A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. -The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. -She continues to be followed up regularly and remains free of signs of disease recurrence.","[""malignant melanoma""]","[""melanoma"", ""lung cancer""]",True,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" diff --git a/src/benchmark/output/results/testset/results_graph_001.json b/src/benchmark/output/results/testset/results_graph_001.json deleted file mode 100644 index 339d9ad..0000000 --- a/src/benchmark/output/results/testset/results_graph_001.json +++ /dev/null @@ -1,792 +0,0 @@ -{ - "status": "success", - "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 44-year-old male with no history of antitubercular treatment (ATT) intake. He has been a tobacco chewer for over 20 years.\n\n**Initial Presentation:**\nThe patient presented to the clinic with right-sided chest pain, dry cough, on-off fever, and hematuria for 2 months. Physical examination revealed decreased air entry on the right side of the lung.\n\n**Imaging and Diagnosis (Step 1-3):**\n\n* Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within.\n* Bronchoscopy with bronchoscopic-guided biopsy and BAL was performed, which showed negative results for malignant cells. Biopsy results were suggestive of squamous cell carcinoma.\n\n**Symptoms and Imaging (Step 4-5):**\n\n* The patient reported decreased and blurring of vision.\n* An 18F-FDG PET/CT scan revealed a FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm with spiculated margins in the upper lobe of the right lung, along with multiple sub-centimetric to centimetric-sized bilateral lung nodules and metastases to mediastinal, abdominopelvic lymph nodes.\n\n**Progression and Diagnosis (Step 6-7):**\n\n* The patient presented with severe headaches and blurring of vision for 15 days.\n* Biopsy results confirmed metastatic involvement.\n\n**Treatment Plan:**\nUnfortunately, the provided data does not include a treatment plan or outcomes. However, based on the diagnosis of squamous cell carcinoma and metastases, further treatment options would likely involve chemotherapy, radiation therapy, or a combination of both, depending on the patient's overall health and specific tumor characteristics.\n\n**Outcomes:**\nThe patient's current status is unknown, as the provided data only includes the timeline of diagnoses and treatments. Further follow-up and monitoring are necessary to assess the patient's response to treatment and any potential complications or side effects.\n\nIn conclusion, this patient presented with a complex clinical scenario involving a heterogeneous lesion in the mediastinal region, squamous cell carcinoma, and metastases. The patient's symptoms and imaging results suggest an aggressive disease course, and further treatment options would be necessary to manage the patient's condition effectively.", - "bertscore": { - "precision": 0.8387337327003479, - "recall": 0.8516782522201538, - "f1": 0.8451563715934753 - }, - "bleu": 0.2054908255580929, - "rouge1": 0.4711211778029445, - "rougeL": 0.34428086070215175, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 7, - "edge_count": 6, - "avg_in_degree": 0.8571428571428571, - "density": 0.14285714285714285 - }, - "trajectory_embedding": [ - 0.22544555366039276, - -0.021888595074415207, - -0.0058143287897109985, - 0.03279201313853264, - 0.012158679775893688, - 0.124949149787426, - 0.055165503174066544, - 0.12983736395835876, - 0.3739190995693207, - -0.2663968503475189, - -0.19686637818813324, - 0.07701147347688675, - -0.5400644540786743, - -0.07584770768880844, - 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Unfortunately, the exact age and other demographic details are not provided in the data.\n\n**Timeline of Diagnoses**\n\nThe patient's diagnosis timeline begins with the onset of symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. This marked the progression from symptom onset to diagnosis.\n\n**Timeline of Treatments**\n\nThe patient's treatment timeline began with endovascular intervention to address IVC stenosis due to compression caused by the tumor. The procedure involved thrombectomy and stent placement. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered.\n\n**Timeline of Outcomes**\n\nThe patient's outcome timeline began with significant alleviation of IVCS symptoms (trunk and lower limb edema) following the intervention. However, unfortunately, the patient died 8 days later from his primary disease (SCLC).\n\n**Narrative Summary**\n\nA male patient with Small Cell Lung Cancer presented with symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. Endovascular intervention was performed to address IVC stenosis caused by compression from the tumor. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered. However, despite these interventions, the patient's primary disease ultimately led to his death 8 days later.\n\n**Key Takeaways**\n\n* The patient had a poor performance status and significant tumor burden at diagnosis.\n* Endovascular intervention was effective in alleviating IVCS symptoms but did not address the underlying cause of death.\n* Low-molecular-weight heparin was administered post-intervention, but its effectiveness is unclear given the patient's rapid decline.\n\n**Limitations**\n\nThe narrative summary is limited by the lack of detailed information on patient demographics, treatment outcomes, and long-term follow-up. Further investigation would be necessary to fully understand the patient's clinical course and the effectiveness of interventions.", - "bertscore": { - "precision": 0.7355820536613464, - "recall": 0.6891461610794067, - "f1": 0.7116073966026306 - }, - "bleu": 0.054103905008875824, - "rouge1": 0.3516699410609037, - "rougeL": 0.14145383104125736, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 8, - "edge_count": 7, - "avg_in_degree": 0.875, - "density": 0.125 - }, - "trajectory_embedding": [ - 0.2569149434566498, - 0.23160001635551453, - -0.23048092424869537, - 0.06365886330604553, - 0.06271032989025116, - -0.032205305993556976, - -0.0353657603263855, - 0.14690855145454407, - 0.3527328073978424, - -0.24249935150146484, - -0.23033425211906433, - 0.13146138191223145, - -0.44394129514694214, - -0.1020270437002182, - -0.1855921894311905, - 0.17859384417533875, - 0.08802724629640579, - 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She has no history of smoking or malignancy.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (Day 0-9):** The patient initially presents with progressive chest tightness, dyspnea, cough, and back pain. Chest CT imaging reveals a large left-sided pleural effusion.\n2. **Step 2 (Day 10):** Thoracentesis is performed, and the drained pleural fluid is sent to the Department of Pathology for further evaluation.\n3. **Step 3 (Day 11-12):** Post-thoracic drainage chest CT reveals a 6.7 cm x 2.8 cm heterogeneous mass in the left inferior lobe with irregular contrast enhancement, suggestive of a left lung tumor.\n4. **Step 4 (Day 13-14):** Pulmonary window analysis shows multiple nodular high-density foci scattered across both lungs, concerning for bilateral pulmonary metastases. Mediastinal window assessment reveals bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis.\n5. **Step 5 (Day 15-16):** Abdominal CT scan detects multiple low-density hepatic nodules of varying sizes, with the largest lesion located in the right hepatic lobe. Enhanced brain CT identifies an irregular heterogeneously enhancing mass within the right frontal lobe, consistent with brain metastasis.\n6. **Step 6 (Day 17-18):** Cell block analysis of the pleural effusion demonstrates poorly cohesive round-to-oval cells with a dispersed distribution exhibiting eccentrically located nuclei with dense chromatin.\n\n**Treatments:**\n\n1. Thoracentesis and post-thoracic drainage chest CT\n2. Abdominal CT scan and enhanced brain CT\n\n**Outcomes:**\nThe patient's diagnosis is confirmed as lung cancer with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The cell block analysis of the pleural effusion reveals poorly cohesive round-to-oval cells consistent with adenocarcinoma.\n\n**Conclusion:**\nThis 81-year-old female patient presents with progressive chest tightness and dyspnea due to a large left-sided pleural effusion, which is later confirmed as a left lung tumor with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The diagnosis is made after thoracentesis, post-thoracic drainage chest CT, abdominal CT scan, enhanced brain CT, and cell block analysis of the pleural effusion.", - "bertscore": { - "precision": 0.8535692095756531, - "recall": 0.869658887386322, - "f1": 0.8615389466285706 - }, - "bleu": 0.12150955580589737, - "rouge1": 0.4815766923736076, - "rougeL": 0.3461868037703513, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 6, - "edge_count": 5, - "avg_in_degree": 0.8333333333333334, - "density": 0.16666666666666666 - }, - "trajectory_embedding": [ - 0.2583933174610138, - -0.1034068688750267, - 0.02750878781080246, - 0.12225138396024704, - 0.07123710960149765, - 0.08420076966285706, - -0.025338614359498024, - 0.20714537799358368, - 0.42998072504997253, - -0.2773303687572479, - -0.23241369426250458, - 0.0849342942237854, - -0.532634437084198, - 0.050035249441862106, - -0.25669047236442566, - 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He presented with worsening cough for 3 months, which led to further investigation via CT imaging.\n\n**Timeline of Diagnoses:**\n\n1. **April 2023:** Enhanced CT revealed a 22 mm \u00d7 12 mm \u00d7 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal. PET-CT scan confirmed the CT findings.\n2. **Biopsy (Upper Right Lobe):** Biopsy of the lung lesion showed positive immunohistochemistry (IHC) for TTF-1, NpA, CK7, CD5/6, and Ki67 (60%); and negative for p40, p63, and CD56. Diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0).\n3. **May 2023:** Targeted NGS analysis identified an EGFRG719X mutation with a mutant allele frequency (MAF) of 3.8%.\n\n**Timeline of Treatments:**\n\n1. **May 2023:** The patient received two cycles of PC chemotherapy (pemetrexed 0.9g d1 and carboplatin 600mg d1) and dacomitinib (30mg).\n2. **Initial Treatment Evaluation:** Initial tumor was considered unresectable due to metastasis in the right hilum and mediastinum.\n\n**Timeline of Outcomes:**\n\n1. **May 2023:** Chest CT showed obvious shrinkage in the lesions in the right upper lung lobe and the lymph nodes of the mediastinum, contributing to partial response (PR).\n2. **Current Status:** The patient is currently receiving treatment for stage IIIA lung adenocarcinoma with EGFRG719X mutation.\n\n**Clinical Summary:**\nThe patient presented with worsening cough and a significant smoking history, leading to further investigation via CT imaging. Biopsy of the lung lesion confirmed the diagnosis of stage IIIA lung adenocarcinoma (cT1cN2M0) with an EGFRG719X mutation. The patient received two cycles of PC chemotherapy and dacomitinib, resulting in a partial response (PR). Further treatment is ongoing to manage this complex case.\n\n**Key Findings:**\n\n* Stage IIIA lung adenocarcinoma with EGFRG719X mutation\n* Partial response (PR) after initial treatment evaluation\n* Significant smoking history of 30 years\n* Worsening cough for 3 months\n\n**Recommendations:**\nFurther evaluation and management are necessary to optimize the patient's care. This may include additional imaging, laboratory tests, or other treatments to manage this complex case.\n\nNote: The above narrative is based on the provided data and may not be a comprehensive clinical case report.", - "bertscore": { - "precision": 0.86226487159729, - "recall": 0.8710905313491821, - "f1": 0.8666552901268005 - }, - "bleu": 0.27859330938799, - "rouge1": 0.560096153846154, - "rougeL": 0.3966346153846154, - "topology": { - "is_acyclic": true, - "timestamps_in_order": false, - "all_nodes_have_timestamps": false, - "weakly_connected_components": 1, - "node_count": 5, - "edge_count": 4, - "avg_in_degree": 0.8, - "density": 0.2 - }, - "trajectory_embedding": [ - 0.26444298028945923, - 0.15941788256168365, - -0.1746055781841278, - 0.1967768669128418, - 0.13093367218971252, - 0.108800008893013, - 0.047415077686309814, - 0.3190433979034424, - 0.4498003125190735, - -0.4936943054199219, - -0.028453731909394264, - 0.19775180518627167, - -0.6453556418418884, - -0.2056516706943512, - 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.../output/plots/bertscore_f1_barplot.png | Bin 30152 -> 0 bytes 2 files changed, 1 deletion(-) delete mode 100644 src/benchmark/output/plots/bertscore_f1_barplot.png diff --git a/src/benchmark/generate_visuals.py b/src/benchmark/generate_visuals.py index df9b1b6..aaf04ab 100644 --- a/src/benchmark/generate_visuals.py +++ b/src/benchmark/generate_visuals.py @@ -85,7 +85,6 @@ trajectory_embeddings = np.array(trajectory_embeddings) # Generate Visualizations - plot_bertscore_f1(graph_ids, bertscore_f1s) if len(trajectory_embeddings) > 1: diff --git a/src/benchmark/output/plots/bertscore_f1_barplot.png b/src/benchmark/output/plots/bertscore_f1_barplot.png deleted file mode 100644 index b853e5e5ddd5a446bee1cb4b424d608eda454c3f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 30152 zcmeFZXH-<%_9u#>fRYu-6p}lv#^z5xaTG@Xz)4%IzWNT+;Wy#CI z&Bej{@UE%7y|tY%C#S`~ui&t-y-K+M zO-TB|v&?8%=|#86na0uxdfYB_4PHOuX_fc*koOu}gR|HmbULciaa@Hngv 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coloring, metastasis markers, and cluster boundaries --- .../modules/compare_graph_vs_text_clusters.py | 96 +++- .../plots/clustering_score_comparison.png | Bin 19894 -> 19665 bytes .../plots/graph_cancer_type_heatmap.png | Bin 44492 -> 49560 bytes .../graph_cluster_metastasis_barplot.png | Bin 17219 -> 16261 bytes .../graph_specific_cancer_type_heatmap.png | Bin 65621 -> 68118 bytes .../output/plots/text_cancer_type_heatmap.png | Bin 45212 -> 48150 bytes .../plots/text_cluster_metastasis_barplot.png | Bin 17403 -> 15752 bytes .../text_specific_cancer_type_heatmap.png | Bin 65653 -> 67282 bytes .../tsne_Graph-PCA_metadata_clusters.png | Bin 0 -> 67880 bytes .../tsne_Graph-UMAP_metadata_clusters.png | Bin 0 -> 66523 bytes .../plots/tsne_Text-PCA_metadata_clusters.png | Bin 0 -> 63382 bytes .../tsne_Text-UMAP_metadata_clusters.png | Bin 0 -> 69085 bytes .../results/cluster_labels_with_metadata.csv | 522 +++++++++--------- .../results/cluster_metadata_summary.csv | 5 +- 14 files changed, 342 insertions(+), 281 deletions(-) create mode 100644 src/benchmark/output/plots/tsne_Graph-PCA_metadata_clusters.png create mode 100644 src/benchmark/output/plots/tsne_Graph-UMAP_metadata_clusters.png create mode 100644 src/benchmark/output/plots/tsne_Text-PCA_metadata_clusters.png create mode 100644 src/benchmark/output/plots/tsne_Text-UMAP_metadata_clusters.png diff --git a/src/benchmark/modules/compare_graph_vs_text_clusters.py b/src/benchmark/modules/compare_graph_vs_text_clusters.py index dae1cef..459395f 100644 --- a/src/benchmark/modules/compare_graph_vs_text_clusters.py +++ b/src/benchmark/modules/compare_graph_vs_text_clusters.py @@ -31,8 +31,9 @@ import seaborn as sns import umap from sklearn.metrics import adjusted_rand_score -from sklearn.metrics import adjusted_rand_score from collections import Counter +from matplotlib.patches import Polygon +from scipy.spatial import ConvexHull # Local application imports from modules.embedding import TrajectoryEmbedder @@ -91,7 +92,6 @@ def flatten_list_column(col): return encoded - def reduce_dimensions(data, method="pca", n_components=10): if method == "pca": reducer = PCA(n_components=n_components) @@ -123,25 +123,85 @@ def cluster_and_evaluate(embedding_matrix, method_label): return best_k, best_labels, best_scores -def plot_tsne(embeddings, labels, method_label): - n_samples = embeddings.shape[0] - perplexity = min(5, n_samples - 1) - tsne = TSNE(n_components=2, perplexity=perplexity, random_state=42) +# def plot_tsne(embeddings, labels, method_label): +# n_samples = embeddings.shape[0] +# perplexity = min(5, n_samples - 1) +# tsne = TSNE(n_components=2, perplexity=perplexity, random_state=42) +# reduced = tsne.fit_transform(embeddings) + +# # Convert numeric labels to "Cluster 1", "Cluster 2", etc. +# unique_labels = np.unique(labels) +# label_map = {label: f"Cluster {i+1}" for i, label in enumerate(unique_labels)} +# cluster_labels = [label_map[label] for label in labels] + +# # Plot +# plt.figure(figsize=(8, 6)) +# sns.scatterplot(x=reduced[:, 0], y=reduced[:, 1], hue=cluster_labels, palette="tab10") +# plt.title(f"t-SNE of {method_label} Embeddings") +# plt.tight_layout() +# plt.savefig(PLOTS_DIR / f"tsne_{method_label.lower()}.png") +# plt.close() + +def plot_tsne(embeddings, labels, shared_ids, label_type="graph"): + metadata_path = Path("output/results/graph_html_metadata.csv") + meta_df = pd.read_csv(metadata_path) + meta_df["graph_id"] = meta_df["graph_id"].str.replace("graph_", "") + meta_df = meta_df[meta_df["graph_id"].isin(shared_ids)] + + tsne = TSNE(n_components=2, perplexity=min(5, len(shared_ids)-1), random_state=42) reduced = tsne.fit_transform(embeddings) - # Convert numeric labels to "Cluster 1", "Cluster 2", etc. - unique_labels = np.unique(labels) - label_map = {label: f"Cluster {i+1}" for i, label in enumerate(unique_labels)} - cluster_labels = [label_map[label] for label in labels] + cluster_df = pd.DataFrame({ + "graph_id": shared_ids, + "x": reduced[:, 0], + "y": reduced[:, 1], + "cluster": labels + }) + joined = cluster_df.merge(meta_df, on="graph_id") - # Plot - plt.figure(figsize=(8, 6)) - sns.scatterplot(x=reduced[:, 0], y=reduced[:, 1], hue=cluster_labels, palette="tab10") - plt.title(f"t-SNE of {method_label} Embeddings") + # Preprocess categories + def extract_first_category(val): + if pd.isna(val): return "unknown" + try: + items = eval(val) if val.startswith("[") else [val] + return items[0] if items else "unknown" + except: + return "unknown" + + joined["cancer"] = joined["cancers"].apply(extract_first_category) + joined["metastasis"] = joined["has_metastasis"].map({True: True, "TRUE": True, False: False, "FALSE": False}) + + # Assign colors and markers + cancer_palette = {c: col for c, col in zip(joined["cancer"].unique(), sns.color_palette("tab10", n_colors=joined["cancer"].nunique()))} + marker_map = {True: 'o', False: 'x'} + + plt.figure(figsize=(10, 8)) + for (cancer, metastasis), group in joined.groupby(["cancer", "metastasis"]): + plt.scatter( + group["x"], group["y"], + label=f"{cancer} | {'Met+' if metastasis else 'Met-'}", + marker=marker_map.get(metastasis, 'o'), + color=cancer_palette[cancer], + alpha=0.75, + edgecolor="k" + ) + + # Draw convex hulls per cluster + for cluster_id in sorted(joined["cluster"].unique()): + cluster_points = joined[joined["cluster"] == cluster_id][["x", "y"]].values + if len(cluster_points) >= 3: + hull = ConvexHull(cluster_points) + polygon = Polygon(cluster_points[hull.vertices], closed=True, fill=False, edgecolor='gray', linewidth=1.5, linestyle='--') + plt.gca().add_patch(polygon) + + plt.title(f"t-SNE of {label_type.capitalize()} Embeddings\nColored by Cancer Type, Marker by Metastasis") + plt.xlabel("t-SNE-1") + plt.ylabel("t-SNE-2") + plt.legend(bbox_to_anchor=(1.05, 1), loc="upper left", fontsize="small") plt.tight_layout() - plt.savefig(PLOTS_DIR / f"tsne_{method_label.lower()}.png") + plt.savefig(PLOTS_DIR / f"tsne_{label_type}_metadata_clusters.png") plt.close() - + print(f"✅ Saved: tsne_{label_type}_metadata_clusters.png") def summarize_cluster_metadata(shared_ids, glabels, label_type="graph"): meta_df = pd.read_csv(METADATA_CSV) @@ -322,8 +382,8 @@ def main(): gk, glabels, g_scores = cluster_and_evaluate(reduced_graph, f"Graph-{method.upper()}") tk, tlabels, t_scores = cluster_and_evaluate(reduced_text, f"Text-{method.upper()}") - plot_tsne(reduced_graph, glabels, f"Graph-{method.upper()}") - plot_tsne(reduced_text, tlabels, f"Text-{method.upper()}") + plot_tsne(reduced_graph, glabels, shared_ids, label_type=f"Graph-{method.upper()}") + plot_tsne(reduced_text, tlabels, shared_ids, label_type=f"Text-{method.upper()}") score_dicts[f"Graph-{method.upper()}"] = g_scores[gk] score_dicts[f"Text-{method.upper()}"] = t_scores[tk] diff --git a/src/benchmark/output/plots/clustering_score_comparison.png b/src/benchmark/output/plots/clustering_score_comparison.png index 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z1*wO>pYO<9nf>!8*vAJ2im)IN5s}*V_7GAwOtQ#vnKsJSg8}e`s@~oka$SwUhWcIc zh<@MU!zDbDLMW6jjEO;^cAenki?}5vDap^p#g&603Vm;C3Wecyb&Jz|hBe!^Z~pE6>gA}&9@>dF;b=`~*yAGqeBjvn}y1Ke< z=-OIYIdX|R#Oqd;*c9aDUAuhw@zT;#?JF*+`>w9KSa)|`At6;DFPSTL%XzO)5{x`O zORp*_`WF-wz@VyHGO56D!=aJX)nzHUlaOJEd2Hw6QZVr$JNvva78#m7OQF02b}e|m{jE?hc9|CYqU-zTGHm0&!Cv~$WT)`#{Co)LpH(3G!@Fw-Yl4Pgz}>^KR$k(4 zLqmgEF-WXn9Poq3v(UImNJ;rlE&;CB!-Yvbx7mTGR^UCv%q97ovq8>jJj8>#&~QWe z$bkc|!C|`X;JHxfVEh1r9Ivo&+hKh)+OjL6b2dgK50ms2%;Sb&Qs2XYsvT~W@s6|7 zmry8e_NJjSSh(lpxO%3hr;TS0FttEGZMax9fOxd0qk~t4nP@ZSfU1g$ zFzM5$PZvZ)PJnXk4OpBM%uSIBnmo!qmU9l$5wkLh^XqHw*VWWQ;VwsP_&t5v;O+^d zCPN`#Vg2#$nWyzMjL$GzD?QH3TfNl*ERiG%?FXMpdo10`w1A zgURdR!`9VOm+6mTMN=Nz85m$pnt98dSq`|s+yCNQ=jJ)6%HM_MU_R#+|o`W z6RM&Q0SbK*xTRf9zGkZOZWua>7#gc2{*r_kM9$S!s<4U>w|x&P*IdPQVEUb$Z&CZ$~-R2VYhn5nWJ5fa^d(U6EaMz3;85ODdhyi7ifNWwWbWFdC8uin%CerHiu8HE$Ejy;8W)j=lC>;;b@##SOEIE0Th{KGo>vg?}dDmT2Q)3E&=j15nc0u7NW^i81 z4lQAHrKr~&wBY)WJ|{G*Zu4Y{tQ<3FHWw?tER8}5e35HId(yLung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","[ + { + ""date"": ""June 2014"", + ""text"": ""Lung cancer (stage IV) diagnosed"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Radiation therapy for pelvic lesion (45 Gy/15 Fr)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Bevacizumab maintenance therapy"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""Right adrenal metastasis larger"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""New left adrenal metastasis observed"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Re-enlargement of the right adrenal metastasis detected"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Radiation therapy for the right adrenal lesion (50 Gy/25 Fr)"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Chemotherapy (two courses of docetaxel monotherapy) administered"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Enlargement of the left adrenal metastasis detected"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Nivolumab monotherapy as fifth-line therapy initiated"" + }, + { + ""date"": ""May 2022"", + ""text"": ""Diabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negative"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Polymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progression"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Nivolumab treatment continued"" + } +]","[""Lung cancer""]","[""stage IV lung cancer""]",True,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" +005,2,0,Neoadjuvant_Targeted_Therapy_with_Dacomitinib_in_a_Stage_IIIA_Non_Small_Cell_Lun_PMC11980937.html,"A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. + +The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. + +The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] +003,0,0,Management_of_malignant_inferior_vena_cava_syndrome__IVCS__by_endovascular_bridg_PMC12019825.html,"A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents.","A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents. + +Diagnosed with SCLC 15 months previously. Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation. Lost 20 kg of body weight within 12 months. Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission. Vital signs: systolic/diastolic blood pressure 100/70 mmHg, heart rate 90 bpm, oxygen saturation 89%, body temperature 36,9°C/98° F. Laboratory results: hemoglobin 12,6 g/dl (normal range 14-18 g/dl), platelets 260 × 103/μl (150-450 × 103/μl), alkaline phosphatase 94 U/L (26-112 U/L), alanine aminotransferase 40 U/L (5-35 U/L), aspartate aminotransferase 34 U/L (<40 U/L), total bilirubin 1.2 mg/dl, and creatinine 0.9 mg/dl. A large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium. Multiple enlarged mediastinal lymph nodes, infiltration of the visceral pleura and right hemidiaphragm, ascites, and peritoneal metastases were other salient findings underlining disease progression. + +Three self-expanding stents (yellow arrows) were positioned in tandem from the superior vena cava (SVC) (red arrow shows the most cephalic part of the stents) to the IVC to restore venous patency. Fig. 3. The final venography revealed adequate flow through the bridging stents (yellow arrows). The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h. Low-molecular-weight heparin was administered for anticoagulation. + +The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium.","- Diagnosed with SCLC 15 months previously +- Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation +- Lost 20 kg of body weight within 12 months +- Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission +- Underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression +- Three self-expanding stents were positioned in tandem from the superior vena cava (SVC) to the IVC to restore venous patency +- The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h +- Low-molecular-weight heparin was administered for anticoagulation +- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""SCLC""]","[""Small Cell Lung Cancer""]",True,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" +015,2,2,A_case_of_obstructive_shock_and_transient_ischemic_attack_from_intracardiac_meta_PMC11981378.html,"- Patient presented to ER 8 days after initial diagnosis of intracardiac metastasis of NSCLC. +- On admission, patient appeared lethargic, tachycardic with irregular rhythm, decreased breath sounds on the right, and tender right upper quadrant due to rib fractures. Heart rate was 110 bpm, blood pressure 96/60 mmHg, respiratory rate 22, and saturation of 100%. Patient treated for hypotension with IV fluids. +- CT of head negative for acute intracranial processes. CT of abdomen and pelvis showed mildly displaced rib fractures, right kidney interpolar cyst with new areas of internal hyperdensity (suspected benign cysts). No other new presentations appreciated. +- Laboratory values during the admission: + - Hemoglobin (g/dL): 9.6, 9.9, 10.4 + - Hematocrit (%): 28.3, 30.2, 31.4 + - Platelets (K/uL): 146, 128, 170 + - WBC (K/uL): 19.5, 16.29, 20.71 + - Sodium (mEq/L): 129, 128, 127 + - Potassium (mEq/L): 3.7, 4, 4.7 + - Chloride (mEq/L): 102, 100, 101 + - Bicarbonate (mmol/L): 24, 23, 25 + - Glucose (mg/dL): 120, 130, 110 + - Creatinine (mg/dL): 1.2, 1.3, 1.1 + - Urea nitrogen (mg/dL): 20, 22, 18 + - Calcium (mg/dL): 9.5, 10.2, 9.8 + - Phosphate (mg/dL): 4.2, 4.5, 4.0 + - Lactate dehydrogenase (LDH) (U/L): 250, 280, 220 + - Aspartate aminotransferase (AST) (U/L): 40, 45, 35 + - Alanine aminotransferase (ALT) (U/L): 30, 35, 25 + - Total bilirubin (mg/dL): 1.2, 1.5, 1.0 + - Direct bilirubin (mg/dL): 0.8, 1.0, 0.7 + - Alkaline phosphatase (ALP) (U/L): 120, 140, 100 + - Gamma-glutamyl transferase (GGT) (U/L): 50, 60, 40 + +2 days post-ER admission: Patient developed symptoms suggestive of a transient ischemic attack (TIA) with right facial droop and left pronator drift. +CT-Angiography did not show any large vessel occlusion or acute intracranial process. +The deficits resolved in 6 hours; however, the patient still had ongoing tachycardia and uncontrolled atrial fibrillation. + +Patient was diagnosed with locally advanced non-small cell lung cancer (NSCLC) stage IIIB (T4N2Mx) metastatic non-small cell lung carcinoma of squamous cell histology. +Endobronchial ultrasound-guided fine-needle aspiration confirmed the diagnosis. +CT angiogram revealed a large hypermetabolic mass in the right lower lobe extending into the mediastinum with enlarged hypermetabolic subcarinal nodes, irregular mass measuring approximately 8.7 × 4.6 cm, partial atelectasis of the right middle and lower lobes, small to moderate low-density right pleural effusion. +Tumor thrombus in the left atrium measuring 3.4 × 6.3 cm, interfering with the mitral valve function. +Echocardiogram showed that the mass was invading into the left atrium. + +Patient underwent palliative care for symptom management. + +2 days post-ER admission: TIA with right facial droop and left pronator drift +CT-Angiography: no large vessel occlusion or acute intracranial process +Discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLCTransient ischemic attack (TIA) with right facial droop and left pronator driftCT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLC (initial diagnosis) +2 days post-ER admission: Transient ischemic attack (TIA) with right facial droop and left pronator drift +after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""non-small cell lung cancer""]","[""squamous cell histology""]",True,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" +010,3,0,Re_do_robot_assisted_salvage_lobectomy_after_esophagectomy_with_gastric_pull_up__PMC11980297.html,"55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous cell carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",False,[] +013,3,2,Brain_Metastasis_From_Advanced_Stage_Lung_Carcinoma__Differentiating_From_Stroke_PMC11955559.html,"Patient's medical history: +- Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes (15 months ago) +- PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes +- Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy (1 year ago) +- Initiated docetaxel for refractory complications with stage III NSCLC (2 days ago) + +Recent medical events: +- Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea +- Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity +- Leukopenia, WBC of 1.12 K/μL +- Potassium level still low but increased since previous ED visit +- COVID-19 and flu tests all negative +- Urine testing revealed trace blood and bacteria and was positive for cannabis +- Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease +- CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries +- Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting + +Current medications: +- Docetaxel for refractory complications with stage III NSCLC +- Potassium supplement for hypokalemia +- Ondansetron for nausea","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""NSCLC""]","[""stage III NSCLC""]",True,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" +004,1,1,Metastatic_INI_1_deficient_undifferentiated_lung_cancer_with_EGFR_19del_mutation_PMC12021797.html,"81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""lung cancer""]","[""non-small cell lung cancer""]",True,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" +014,1,1,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""malignant tumor"", ""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""squamous cell carcinoma"", ""lymph nodes""]]" +001,4,1,Intriguing_Encounter__Unveiling_Squamous_Cell_Carcinoma_Lung_with_Rare_Bilateral_PMC12020972.html,"44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" +009,1,0,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""lung adenocarcinoma""]","[""lung adenocarcinoma""]",True,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" +011,3,1,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral_Internal__PMC12021377.html,"Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria","Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria"," + + Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs. + + + Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerve + + + Significant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints. + + + Fourth-line treatment with selpercatinib (160 mg twice daily) was initiated + + + Disease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter. + + + First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria + +","[""adenocarcinoma""]","[""lung cancer""]",True,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" +012,4,2,Multiple_Lung_Metastases_of_Papillary_Thyroid_Carcinoma_Detected_by_Detailed_Pat_PMC11971052.html,"79-year-old male patient with: +- Height: 174 cm +- Weight: 65 kg +- BMI: 21.5 kg/m² +- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) +- Medical history: + - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension + - Left cervical lymphadenopathy of unknown origin six years ago + - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC. + - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. + - The patient was treated with radioiodine therapy (Iodine-131). + - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. + - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits. + - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL. + - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1). + - No hilar lymphadenopathy was detected. + - FDG-PET was not performed. + - Pulmonary function and electrocardiogram tests showed no abnormalities. + +An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. + +Histopathological examination revealed adenocarcinoma. +Adenocarcinoma cells were found in the resected tissue. +Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. +The patient's postoperative course was uneventful, with no complications noted. +5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. +2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. +6 months post-surgery: No evidence of recurrence.","Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension.A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made.No evidence of recurrence.","79-year-old male patient with: +- Height: 174 cm +- Weight: 65 kg +- BMI: 21.5 kg/m² +- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) +- Medical history: + - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension + - Left cervical lymphadenopathy of unknown origin six years ago + - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC + - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. + - The patient was treated with radioiodine therapy (Iodine-131) + - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. + - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits + - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL + - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1) + - No hilar lymphadenopathy was detected + - FDG-PET was not performed + - Pulmonary function and electrocardiogram tests showed no abnormalities + +An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. + +Histopathological examination revealed adenocarcinoma. +Adenocarcinoma cells were found in the resected tissue. +Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. +The patient's postoperative course was uneventful, with no complications noted. +5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. +2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. +6 months post-surgery: No evidence of recurrence.","[""papillary thyroid carcinoma"", ""adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",True,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" +016,0,0,Precise_Localization_of_the_Subsolid_Lesion_by_Colour_Marking_under_CT_Guided_Co_PMC12040305.html,"51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","[""malignant melanoma""]","[""melanoma"", ""lung cancer""]",True,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" diff --git a/src/benchmark/output/results/cluster_metadata_summary.csv b/src/benchmark/output/results/cluster_metadata_summary.csv new file mode 100644 index 0000000..11440bd --- /dev/null +++ b/src/benchmark/output/results/cluster_metadata_summary.csv @@ -0,0 +1,4 @@ +cluster,has_metastasis,top_cancers,top_specific_cancers +0,"{""true"": 0.6666666666666666, ""false"": 0.3333333333333333}","[""lymphoepithelial carcinoma""] (1), [""Lung Cancer""] (1), [""SCLC""] (1)","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""] (1), [""Lung Adenocarcinoma""] (1), [""Small Cell Lung Cancer""] (1)" +1,"{""true"": 1.0}","[""lung cancer""] (2), [""Lung cancer""] (1), [""malignant tumor"", ""lung cancer""] (1)","[""squamous cell carcinoma""] (2), [""stage IV lung cancer""] (1), [""non-small cell lung cancer""] (1)" +2,"{""true"": 0.75, ""false"": 0.25}","[""Lung Cancer""] (1), [""non-small cell lung cancer""] (1), [""NSCLC""] (1)","[""Lung Adenocarcinoma""] (1), [""squamous cell histology""] (1), [""stage III NSCLC""] (1)" diff --git a/src/benchmark/output/results/graph_html_metadata.csv b/src/benchmark/output/results/graph_html_metadata.csv new file mode 100644 index 0000000..7e8bd19 --- /dev/null +++ b/src/benchmark/output/results/graph_html_metadata.csv @@ -0,0 +1,411 @@ +graph_id,source_file,timeline_1,timeline_2,timeline_3,cancers,specific_cancers,has_metastasis,metastasis_locations +graph_001,Intriguing_Encounter__Unveiling_Squamous_Cell_Carcinoma_Lung_with_Rare_Bilateral_PMC12020972.html,"44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" +graph_002,_A_Case_of_Multiple_Primary_Pulmonary_Neuroendocrine_Carcinoma_with_EML4_ALK_Fus_PMC11986677.html,"* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除 +* 2022-04-27: 病灶稳定，无肿瘤复发或转移 +* 2023-08-01: 左主支气管略狭窄 +* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC） +* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止 +* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展","[""* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除\n* 2022-04-27: 病灶稳定，无肿瘤复发或转移\n* 2023-08-01: 左主支气管略狭窄\n* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC）\n* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止\n* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展""]",,"[""\u764c"", ""\u80bf\u7624"", ""\u6076\u6027\u80bf\u7624""]","[""\u5927\u7ec6\u80de\u795e\u7ecf\u5185\u5206\u6ccc\u764c"", ""\u5c0f\u7ec6\u80de\u80ba\u764c""]",False,[] +graph_003,Management_of_malignant_inferior_vena_cava_syndrome__IVCS__by_endovascular_bridg_PMC12019825.html,"A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents.","A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents. + +Diagnosed with SCLC 15 months previously. Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation. Lost 20 kg of body weight within 12 months. Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission. Vital signs: systolic/diastolic blood pressure 100/70 mmHg, heart rate 90 bpm, oxygen saturation 89%, body temperature 36,9°C/98° F. Laboratory results: hemoglobin 12,6 g/dl (normal range 14-18 g/dl), platelets 260 × 103/μl (150-450 × 103/μl), alkaline phosphatase 94 U/L (26-112 U/L), alanine aminotransferase 40 U/L (5-35 U/L), aspartate aminotransferase 34 U/L (<40 U/L), total bilirubin 1.2 mg/dl, and creatinine 0.9 mg/dl. A large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium. Multiple enlarged mediastinal lymph nodes, infiltration of the visceral pleura and right hemidiaphragm, ascites, and peritoneal metastases were other salient findings underlining disease progression. + +Three self-expanding stents (yellow arrows) were positioned in tandem from the superior vena cava (SVC) (red arrow shows the most cephalic part of the stents) to the IVC to restore venous patency. Fig. 3. The final venography revealed adequate flow through the bridging stents (yellow arrows). The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h. Low-molecular-weight heparin was administered for anticoagulation. + +The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium.","- Diagnosed with SCLC 15 months previously +- Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation +- Lost 20 kg of body weight within 12 months +- Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission +- Underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression +- Three self-expanding stents were positioned in tandem from the superior vena cava (SVC) to the IVC to restore venous patency +- The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h +- Low-molecular-weight heparin was administered for anticoagulation +- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""SCLC""]","[""Small Cell Lung Cancer""]",True,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" +graph_004,Metastatic_INI_1_deficient_undifferentiated_lung_cancer_with_EGFR_19del_mutation_PMC12021797.html,"81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""lung cancer""]","[""non-small cell lung cancer""]",True,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" +graph_005,Neoadjuvant_Targeted_Therapy_with_Dacomitinib_in_a_Stage_IIIA_Non_Small_Cell_Lun_PMC11980937.html,"A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. + +The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. + +The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] +graph_006,Lung_cancer_with_diabetes_mellitus_and_polymyalgia_rheumatica_during_long_term_n_PMC12001326.html,"Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","[ + { + ""date"": ""June 2014"", + ""text"": ""Lung cancer (stage IV) diagnosed"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Radiation therapy for pelvic lesion (45 Gy/15 Fr)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Bevacizumab maintenance therapy"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""Right adrenal metastasis larger"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""New left adrenal metastasis observed"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Re-enlargement of the right adrenal metastasis detected"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Radiation therapy for the right adrenal lesion (50 Gy/25 Fr)"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Chemotherapy (two courses of docetaxel monotherapy) administered"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Enlargement of the left adrenal metastasis detected"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Nivolumab monotherapy as fifth-line therapy initiated"" + }, + { + ""date"": ""May 2022"", + ""text"": ""Diabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negative"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Polymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progression"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Nivolumab treatment continued"" + } +]","[""Lung cancer""]","[""stage IV lung cancer""]",True,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" +graph_007,Case_Report__A_novel_ELMOD3_ALK_and_EML4_ALK_double_fusion_responses_to_neoadjuv_PMC12034634.html,"2020-04-20: Patient comes to hospital for physical examination +2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed +2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue +2020: Patient starts treatment with targeted therapy for ALK fusion +2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","2020-04-20: Patient comes to hospital for physical examination +2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed +2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue +2020: Patient starts treatment with targeted therapy for ALK fusion +2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","2020-04-20: Patient comes to hospital for physical examination +2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed +2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue +2020: Patient starts treatment with targeted therapy for ALK fusion +2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] +graph_008,Case_report__pulmonary_lymphoepithelial_carcinoma_mimicking_tuberculosis__PMC11987468.html,"The patient was a 37-year-old woman who presented with intermittent cough and slight chest discomfort for 3 months. She also had a painless cervical mass for 1 month. The pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans' giant cells observed on left cervical lymph node puncture.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","[""lymphoepithelial carcinoma""]","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""]",True,"[[""lung"", ""middle lobe""], [""lymph nodes"", ""mediastinum""], [""lymph nodes"", ""left neck""], [""lymph nodes"", ""right hilum""]]" +graph_009,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""lung adenocarcinoma""]","[""lung adenocarcinoma""]",True,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" +graph_010,Re_do_robot_assisted_salvage_lobectomy_after_esophagectomy_with_gastric_pull_up__PMC11980297.html,"55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous cell carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",False,[] +graph_011,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral_Internal__PMC12021377.html,"Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria","Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria"," + + Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs. + + + Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerve + + + Significant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints. + + + Fourth-line treatment with selpercatinib (160 mg twice daily) was initiated + + + Disease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter. + + + First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria + +","[""adenocarcinoma""]","[""lung cancer""]",True,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" +graph_012,Multiple_Lung_Metastases_of_Papillary_Thyroid_Carcinoma_Detected_by_Detailed_Pat_PMC11971052.html,"79-year-old male patient with: +- Height: 174 cm +- Weight: 65 kg +- BMI: 21.5 kg/m² +- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) +- Medical history: + - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension + - Left cervical lymphadenopathy of unknown origin six years ago + - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC. + - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. + - The patient was treated with radioiodine therapy (Iodine-131). + - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. + - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits. + - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL. + - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1). + - No hilar lymphadenopathy was detected. + - FDG-PET was not performed. + - Pulmonary function and electrocardiogram tests showed no abnormalities. + +An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. + +Histopathological examination revealed adenocarcinoma. +Adenocarcinoma cells were found in the resected tissue. +Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. +The patient's postoperative course was uneventful, with no complications noted. +5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. +2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. +6 months post-surgery: No evidence of recurrence.","Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension.A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made.No evidence of recurrence.","79-year-old male patient with: +- Height: 174 cm +- Weight: 65 kg +- BMI: 21.5 kg/m² +- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) +- Medical history: + - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension + - Left cervical lymphadenopathy of unknown origin six years ago + - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC + - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. + - The patient was treated with radioiodine therapy (Iodine-131) + - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. + - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits + - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL + - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1) + - No hilar lymphadenopathy was detected + - FDG-PET was not performed + - Pulmonary function and electrocardiogram tests showed no abnormalities + +An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. + +Histopathological examination revealed adenocarcinoma. +Adenocarcinoma cells were found in the resected tissue. +Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. +The patient's postoperative course was uneventful, with no complications noted. +5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. +2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. +6 months post-surgery: No evidence of recurrence.","[""papillary thyroid carcinoma"", ""adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",True,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" +graph_013,Brain_Metastasis_From_Advanced_Stage_Lung_Carcinoma__Differentiating_From_Stroke_PMC11955559.html,"Patient's medical history: +- Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes (15 months ago) +- PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes +- Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy (1 year ago) +- Initiated docetaxel for refractory complications with stage III NSCLC (2 days ago) + +Recent medical events: +- Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea +- Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity +- Leukopenia, WBC of 1.12 K/μL +- Potassium level still low but increased since previous ED visit +- COVID-19 and flu tests all negative +- Urine testing revealed trace blood and bacteria and was positive for cannabis +- Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease +- CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries +- Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting + +Current medications: +- Docetaxel for refractory complications with stage III NSCLC +- Potassium supplement for hypokalemia +- Ondansetron for nausea","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""NSCLC""]","[""stage III NSCLC""]",True,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" +graph_014,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""malignant tumor"", ""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""squamous cell carcinoma"", ""lymph nodes""]]" +graph_015,A_case_of_obstructive_shock_and_transient_ischemic_attack_from_intracardiac_meta_PMC11981378.html,"- Patient presented to ER 8 days after initial diagnosis of intracardiac metastasis of NSCLC. +- On admission, patient appeared lethargic, tachycardic with irregular rhythm, decreased breath sounds on the right, and tender right upper quadrant due to rib fractures. Heart rate was 110 bpm, blood pressure 96/60 mmHg, respiratory rate 22, and saturation of 100%. Patient treated for hypotension with IV fluids. +- CT of head negative for acute intracranial processes. CT of abdomen and pelvis showed mildly displaced rib fractures, right kidney interpolar cyst with new areas of internal hyperdensity (suspected benign cysts). No other new presentations appreciated. +- Laboratory values during the admission: + - Hemoglobin (g/dL): 9.6, 9.9, 10.4 + - Hematocrit (%): 28.3, 30.2, 31.4 + - Platelets (K/uL): 146, 128, 170 + - WBC (K/uL): 19.5, 16.29, 20.71 + - Sodium (mEq/L): 129, 128, 127 + - Potassium (mEq/L): 3.7, 4, 4.7 + - Chloride (mEq/L): 102, 100, 101 + - Bicarbonate (mmol/L): 24, 23, 25 + - Glucose (mg/dL): 120, 130, 110 + - Creatinine (mg/dL): 1.2, 1.3, 1.1 + - Urea nitrogen (mg/dL): 20, 22, 18 + - Calcium (mg/dL): 9.5, 10.2, 9.8 + - Phosphate (mg/dL): 4.2, 4.5, 4.0 + - Lactate dehydrogenase (LDH) (U/L): 250, 280, 220 + - Aspartate aminotransferase (AST) (U/L): 40, 45, 35 + - Alanine aminotransferase (ALT) (U/L): 30, 35, 25 + - Total bilirubin (mg/dL): 1.2, 1.5, 1.0 + - Direct bilirubin (mg/dL): 0.8, 1.0, 0.7 + - Alkaline phosphatase (ALP) (U/L): 120, 140, 100 + - Gamma-glutamyl transferase (GGT) (U/L): 50, 60, 40 + +2 days post-ER admission: Patient developed symptoms suggestive of a transient ischemic attack (TIA) with right facial droop and left pronator drift. +CT-Angiography did not show any large vessel occlusion or acute intracranial process. +The deficits resolved in 6 hours; however, the patient still had ongoing tachycardia and uncontrolled atrial fibrillation. + +Patient was diagnosed with locally advanced non-small cell lung cancer (NSCLC) stage IIIB (T4N2Mx) metastatic non-small cell lung carcinoma of squamous cell histology. +Endobronchial ultrasound-guided fine-needle aspiration confirmed the diagnosis. +CT angiogram revealed a large hypermetabolic mass in the right lower lobe extending into the mediastinum with enlarged hypermetabolic subcarinal nodes, irregular mass measuring approximately 8.7 × 4.6 cm, partial atelectasis of the right middle and lower lobes, small to moderate low-density right pleural effusion. +Tumor thrombus in the left atrium measuring 3.4 × 6.3 cm, interfering with the mitral valve function. +Echocardiogram showed that the mass was invading into the left atrium. + +Patient underwent palliative care for symptom management. + +2 days post-ER admission: TIA with right facial droop and left pronator drift +CT-Angiography: no large vessel occlusion or acute intracranial process +Discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLCTransient ischemic attack (TIA) with right facial droop and left pronator driftCT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLC (initial diagnosis) +2 days post-ER admission: Transient ischemic attack (TIA) with right facial droop and left pronator drift +after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""non-small cell lung cancer""]","[""squamous cell histology""]",True,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" +graph_016,Precise_Localization_of_the_Subsolid_Lesion_by_Colour_Marking_under_CT_Guided_Co_PMC12040305.html,"51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","[""malignant melanoma""]","[""melanoma"", ""lung cancer""]",True,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" diff --git a/src/benchmark/output/results/testset/graph_html_metadata.csv b/src/benchmark/output/results/testset/graph_html_metadata.csv new file mode 100644 index 0000000..7e8bd19 --- /dev/null +++ b/src/benchmark/output/results/testset/graph_html_metadata.csv @@ -0,0 +1,411 @@ +graph_id,source_file,timeline_1,timeline_2,timeline_3,cancers,specific_cancers,has_metastasis,metastasis_locations +graph_001,Intriguing_Encounter__Unveiling_Squamous_Cell_Carcinoma_Lung_with_Rare_Bilateral_PMC12020972.html,"44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","44-year-old male diagnosed as squamous cell carcinoma of the lung +Pituitary metastasis identified on 18F-FDG PET/CT +Renal metastasis identified on 18F-FDG PET/CT +Right-sided chest pain for 2 months +Dry cough for 2 months +Fever (on-off) for 2 months +Hematuria for 2 months +No history of Antitubercular treatment (ATT) intake +Tobacco chewer for >20 years +Decreased air entry on the right side of the lung +Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within +Lesion associated with multiple centrilobular nodules arranged in a linear branching pattern +Bronchoscopy done with bronchoscopic-guided biopsy +Bronchoalveolar lavage (BAL) fluid samples taken +BAL sample sent for cytopathological examination was negative for malignant cells +18F-FDG PET/CT scan revealed FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm in size with spiculated margins in the upper lobe of the right lung with collapse and consolidation of right lung +FDG avid metastases to mediastinal, abdominopelvic lymph nodes and right-sided pleural deposits +Multiple sub-centimetric to centimetric-sized bilateral lung nodules were noted +It was associated with multiple FDG avid brain lesions involving the bilateral cerebral cortex, cerebellum and pituitary +FDG avid bilateral hypodense few (3 in number) soft tissue density bilateral renal masses (Figure 1b, largest measuring 2.8 cm x 2.6 cm) +Multiple lytic skeletal lesions [Figure 1d], few of them with soft tissue component involvement were noted","[""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""brain"", ""bilateral cerebral cortex""], [""brain"", ""cerebellum""], [""brain"", ""pituitary""], [""kidneys"", ""bilateral renal masses""], [""skeleton"", ""lytic skeletal lesions""], [""lymph nodes"", ""mediastinal lymph nodes""], [""lymph nodes"", ""abdominopelvic lymph nodes""], [""pleura"", ""right-sided pleural deposits""]]" +graph_002,_A_Case_of_Multiple_Primary_Pulmonary_Neuroendocrine_Carcinoma_with_EML4_ALK_Fus_PMC11986677.html,"* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除 +* 2022-04-27: 病灶稳定，无肿瘤复发或转移 +* 2023-08-01: 左主支气管略狭窄 +* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC） +* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止 +* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展","[""* 2019-03-19: 大细胞神经内分泌癌（大肿瘤）在右肺下叶发现，患者接受手术切除\n* 2022-04-27: 病灶稳定，无肿瘤复发或转移\n* 2023-08-01: 左主支气管略狭窄\n* 2023-10-14: 支气管镜检查发现左主支气管新生物阻塞管腔约50%，病理提示为小细胞肺癌（SCLC）\n* 2024-05-01: 开始服用阿来替尼600 mg bid，化疗3个周期后停止\n* 2024-10-01: 复查胸腹部CT、单光子发射计算机断层扫描全身骨显象均未发现疾病新进展""]",,"[""\u764c"", ""\u80bf\u7624"", ""\u6076\u6027\u80bf\u7624""]","[""\u5927\u7ec6\u80de\u795e\u7ecf\u5185\u5206\u6ccc\u764c"", ""\u5c0f\u7ec6\u80de\u80ba\u764c""]",False,[] +graph_003,Management_of_malignant_inferior_vena_cava_syndrome__IVCS__by_endovascular_bridg_PMC12019825.html,"A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents.","A 73-year-old male patient underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression. Under local anesthesia, a 5F sheath was inserted into the right basilic vein and a 10F sheath into the right common femoral vein. Venography showed a significant compression of the suprahepatic IVC. The IVC stenosis was passed using a 0,035-inch hydrophilic guidewire and a multipurpose catheter. Initially, mechanical thrombectomy was performed to exclude possible thrombosis; however, no thrombotic material was extracted. After placing a stiffer exchange guidewire with its distal tip positioned in the right subclavian vein, 3 uncovered self-expanding nitinol sinus-XL stents (OptiMed, Ettlingen, Germany) were deployed in tandem from the SVC to the IVC with an overlap between the stents. Using venography measurements, stents measuring 18 × 80 mm, 18 × 60 mm, and 16 × 80 mm were placed in a cephalic-to-caudal orientation. The final venography revealed adequate flow through the vena cava and bridging stents. + +Diagnosed with SCLC 15 months previously. Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation. Lost 20 kg of body weight within 12 months. Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission. Vital signs: systolic/diastolic blood pressure 100/70 mmHg, heart rate 90 bpm, oxygen saturation 89%, body temperature 36,9°C/98° F. Laboratory results: hemoglobin 12,6 g/dl (normal range 14-18 g/dl), platelets 260 × 103/μl (150-450 × 103/μl), alkaline phosphatase 94 U/L (26-112 U/L), alanine aminotransferase 40 U/L (5-35 U/L), aspartate aminotransferase 34 U/L (<40 U/L), total bilirubin 1.2 mg/dl, and creatinine 0.9 mg/dl. A large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium. Multiple enlarged mediastinal lymph nodes, infiltration of the visceral pleura and right hemidiaphragm, ascites, and peritoneal metastases were other salient findings underlining disease progression. + +Three self-expanding stents (yellow arrows) were positioned in tandem from the superior vena cava (SVC) (red arrow shows the most cephalic part of the stents) to the IVC to restore venous patency. Fig. 3. The final venography revealed adequate flow through the bridging stents (yellow arrows). The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h. Low-molecular-weight heparin was administered for anticoagulation. + +The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium.","- Diagnosed with SCLC 15 months previously +- Received 6 cycles of carboplatin/etoposide chemotherapy, followed by thoracic radiotherapy and prophylactic cranial irradiation +- Lost 20 kg of body weight within 12 months +- Performance status was recorded (4) on the Eastern Cooperative Oncology Group scale on the day of admission +- Underwent a procedure to relieve significant stenosis of the suprahepatic IVC due to compression +- Three self-expanding stents were positioned in tandem from the superior vena cava (SVC) to the IVC to restore venous patency +- The patient's IVCS symptoms, mainly trunk and lower limb edema, were significantly alleviated within 48 h +- Low-molecular-weight heparin was administered for anticoagulation +- The patient died with a large tumor involving the right lower and middle lung lobe measured (17,6 × 19,3 × 18,6) mm (maximal axial x coronal x sagittal dimension), which causes significant compression of the IVC (yellow arrows) mainly at the level of its entry into the right heart atrium","[""SCLC""]","[""Small Cell Lung Cancer""]",True,"[[""mediastinal lymph nodes"", ""enlarged""], [""visceral pleura"", ""infiltration""], [""right hemidiaphragm"", ""infiltration""], [""peritoneum"", ""metastases""]]" +graph_004,Metastatic_INI_1_deficient_undifferentiated_lung_cancer_with_EGFR_19del_mutation_PMC12021797.html,"81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","81-year-old female patient with a 10-day history of progressive chest tightness and dyspnea worsened with physical activity +Chest computed tomography (CT) imaging revealed a large left-sided pleural effusion +Thoracentesis was performed, and the drained pleural fluid was sent to the Department of Pathology for further evaluation +Following thoracic drainage, a subsequent chest CT scan revealed a heterogeneous mass in the left inferior lobe, measuring approximately 6.7 cm × 2.8 cm in its largest cross-section +Contrast-enhanced imaging demonstrated irregular enhancement patterns suggestive of a left lung tumor +Pulmonary window analysis identified multiple nodular high-density foci scattered across both lungs, raising suspicion for bilateral pulmonary metastases +Mediastinal window assessment further revealed bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis +An abdominal CT scan detected multiple low-density hepatic nodules of varying sizes, with the largest lesion (2.9 cm × 2.6 cm) located in the right hepatic lobe +Annular enhancement was noted in the arterial phase, while marked hypodensity was observed in the portal venous phase, demonstrating a “bull’s eye sign” characteristic of multiple hepatic metastases +Additionally, an enhanced brain CT identified an irregular heterogeneously enhancing mass within the right frontal lobe, with a maximum cross-sectional area of 2.1 cm × 1.6 cm, consistent with brain metastasis +Genetic testing revealed a mutation in the EGFR gene +Next-generation sequencing (NGS) analysis showed that the patient's tumor had a high level of PD-L1 expression +The patient underwent treatment with osimertinib, an EGFR tyrosine kinase inhibitor","[""lung cancer""]","[""non-small cell lung cancer""]",True,"[[""liver"", ""multiple low-density hepatic nodules""], [""lymph nodes"", ""bilateral mediastinal lymphadenopathy""], [""brain"", ""irregular heterogeneously enhancing mass""]]" +graph_005,Neoadjuvant_Targeted_Therapy_with_Dacomitinib_in_a_Stage_IIIA_Non_Small_Cell_Lun_PMC11980937.html,"A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. + +The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","A 54-year-old Chinese male with 30 years of smoking history presented with a worsening cough for 3 months, with a performance status score of 1. Enhanced computed tomography (CT) revealed a 22 mm × 12 mm × 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal (Figure 1AandB), which were confirmed by positron emission tomography-CT (PET-CT) scan. Immunohistochemistry (IHC) analysis of the biopsy from the lesion in the upper right lobe of the lung was positive for TTF-1, NpA, CK7, CD5/6 and Ki67 (60%); and negative for p40, p63 and CD56. The patient was diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0). Follow-up targeted NGS analysis of his lung lesion biopsy identified an EGFRG719X with a mutant allele frequency (MAF) of 3.8%. Two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg) were given. + +The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023. The tumor was located in the right upper lobe, measuring approximately 1.5*1.5 cm with unclear boundaries. Postoperative pathology results indicated that 10% of the tumor cells remained alive, surrounded by significant fibrosis, necrosis, as well as inflammatory and immune cells. After chemotherapy and dacomitinib induction, there were no lymph node metastases, and the pathological stage was ypT1bN0M0. Two cycles of PC chemotherapy were administered, followed by targeted therapy with dacomitinib as adjuvant treatment for 2 more years in accordance with the diagnosis and treatment guidelines. At the final follow-up in September 2024, no adverse events or disease progression had occurred. A progression-free survival (PFS) of more than 14 months was achieved. + +The patient received two cycles of PC chemotherapy (pemetrexed with 0.9g d1 and carboplatin with 600mg d1) and dacomitinib (30mg). The patient underwent video-assisted thoracic surgery (VATS) with right upper lobectomy in July 2023.","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] +graph_006,Lung_cancer_with_diabetes_mellitus_and_polymyalgia_rheumatica_during_long_term_n_PMC12001326.html,"Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","Lung cancer (stage IV) diagnosedRadiation therapy for pelvic lesion (45 Gy/15 Fr)Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)Bevacizumab maintenance therapyRight adrenal metastasis largerNew left adrenal metastasis observedRe-enlargement of the right adrenal metastasis detectedRadiation therapy for the right adrenal lesion (50 Gy/25 Fr)Chemotherapy (two courses of docetaxel monotherapy) administeredEnlargement of the left adrenal metastasis detectedNivolumab monotherapy as fifth-line therapy initiatedDiabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negativePolymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progressionNivolumab treatment continued","[ + { + ""date"": ""June 2014"", + ""text"": ""Lung cancer (stage IV) diagnosed"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Radiation therapy for pelvic lesion (45 Gy/15 Fr)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Chemotherapy (carboplatin + paclitaxel + bevacizumab for four courses)"" + }, + { + ""date"": ""July 2014"", + ""text"": ""Bevacizumab maintenance therapy"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""Right adrenal metastasis larger"" + }, + { + ""date"": ""after 15 cycles of maintenance therapy"", + ""text"": ""New left adrenal metastasis observed"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Re-enlargement of the right adrenal metastasis detected"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Radiation therapy for the right adrenal lesion (50 Gy/25 Fr)"" + }, + { + ""date"": ""January 2018"", + ""text"": ""Chemotherapy (two courses of docetaxel monotherapy) administered"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Enlargement of the left adrenal metastasis detected"" + }, + { + ""date"": ""February 2019"", + ""text"": ""Nivolumab monotherapy as fifth-line therapy initiated"" + }, + { + ""date"": ""May 2022"", + ""text"": ""Diabetes mellitus (DM) diagnosed: Blood glucose level increased to 468 mg/dl, Urinary ketones negative, pancreatic amylase not elevated, and autoantibodies including anti-glutamic acid decarboxylase (GAD) antibodies negative"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Polymyalgia rheumatica (PMR) diagnosed: Muscle pain in the femoral area and neck appeared, which did not improve with nonsteroidal anti-inflammatory drugs. CT and magnetic resonance imaging showed no obvious cancer progression"" + }, + { + ""date"": ""four years and 5 months after starting nivolumab treatment"", + ""text"": ""Nivolumab treatment continued"" + } +]","[""Lung cancer""]","[""stage IV lung cancer""]",True,"[[""right adrenal"", ""re-enlargement""], [""left adrenal"", ""enlargement""]]" +graph_007,Case_Report__A_novel_ELMOD3_ALK_and_EML4_ALK_double_fusion_responses_to_neoadjuv_PMC12034634.html,"2020-04-20: Patient comes to hospital for physical examination +2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed +2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue +2020: Patient starts treatment with targeted therapy for ALK fusion +2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","2020-04-20: Patient comes to hospital for physical examination +2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed +2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue +2020: Patient starts treatment with targeted therapy for ALK fusion +2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","2020-04-20: Patient comes to hospital for physical examination +2020-05-02: Diagnosis of stage IIIA (T2aN2M0) lung adenocarcinoma confirmed +2020: NGS analysis identifies ELMOD3-ALK and EML4-ALK double fusion in tumor tissue +2020: Patient starts treatment with targeted therapy for ALK fusion +2023-01-15: Patient receives new treatment plan, including combination of chemotherapy and immunotherapy","[""Lung Cancer""]","[""Lung Adenocarcinoma""]",False,[] +graph_008,Case_report__pulmonary_lymphoepithelial_carcinoma_mimicking_tuberculosis__PMC11987468.html,"The patient was a 37-year-old woman who presented with intermittent cough and slight chest discomfort for 3 months. She also had a painless cervical mass for 1 month. The pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans' giant cells observed on left cervical lymph node puncture.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","37-year-old woman with intermittent cough and slight chest discomfort for 3 months; painless cervical mass for 1 month; pathological tissue showed granulomatous inflammation, caseous necrosis, and Langhans’ giant cells observed on left cervical lymph node puncture; untreated congenital heart disease (patent ductus arteriosus) for 20 years; hypertension for half a year with irregular use of valsartan; mass measuring approximately 4*3 cm on the left clavicle, well-defined, poorly mobile, non-tender, and without surface ulceration or redness; Physical examination of the lungs was unremarkable. A continuous murmur was auscultated at the left sternal border; Laboratory tests of blood carcinoembryonic antigen (CEA), squamous cell carcinoma antigen, cytokeratin 19 fragment and neuron-specific enolase (NSE) were all normal; Blood routine test, liver and kidney function, electrolytes, procalcitonin (PCT), C-reactive protein (CRP) and T-lymphocyte subsets were all normal; Sputum for acid-fast bacilli (AFB) and GeneXpert MTB/RIF were negative; Blood test of EB virus showed increased antibody title of capsid antigen IgG antibody 750U/mL (Reference:0–20 U/mL), EB virus early antigen IgM antibody 2.57 COI (Cut off index reference:0-1.1) and EB virus core antigen IgG antibody 600U/mL(Reference:0–20 U/mL); Repeated ultrasound-guided left supraclavicular lymph node puncture was performed; Histopathology showed focal distribution of epithelioid cells and a few multinucleated giant cells, which suggested granulomatous inflammation (Fig.1); Staining of Acid-fast and methenamine silver were all negative; Lymph node tissue for GeneXpert MTB/RIF and TB culture were all negative; Chest CT scan showed mass(34 × 43 mm) in the middle lobe of the right lung (A,D; blue arrows) and multiple enlarged lymph nodes in mediastinum (B,C; red arrows); Lung biopsy shows lymphoepithelial carcinoma. The tumor cells are densely nestled, the tumor cells have a blurred boundary, large alveoli, eosinophilic nuclei, and the mesenchymal is accompanied by lymphocyte infiltration. (HE staining, 400×)); Immunohistochemical staining shows CK positive in tumor cells (200×); Immunohistochemical staining showed P40 positive in tumor cells (200×); In situ hybridization showed EBER positive in tumor cells (200×); Chest CT scan showed a significant improvement of the lung mass(26 × 17 mm)and reduced lymph nodes after chemotherapy and immunotherapy; Biopsy of left neck lymph node showed granulomatous inflammation. Enhanced CT scan showed mass in the middle lobe of the right lung and multiple enlarged lymph nodes in left neck, mediastinum and right hilum. Percutaneous lung biopsy was performed, showing EBV-positive poorly differentiated carcinoma consistent with lymphoepithelioma. Nasopharyngoscopy excluded nasopharyngeal carcinoma. Repeated CT 1.5 months later showed significant reduction of lung lesions and cervical enlarged lymph nodes.","[""lymphoepithelial carcinoma""]","[""EBV-positive poorly differentiated carcinoma"", ""nasopharyngeal carcinoma""]",True,"[[""lung"", ""middle lobe""], [""lymph nodes"", ""mediastinum""], [""lymph nodes"", ""left neck""], [""lymph nodes"", ""right hilum""]]" +graph_009,Radiotherapy_for_Lung_Cancer__An_Unrecognized_Cause_of_Lung_Torsion__PMC11962223.html,"A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","A 73-year-old lady presented with a long history of bilateral chest wall discomfort, exertional breathlessness, and chronic fatigue. She was found to have a left lung opacification on chest radiograph, which prompted a computed tomography scan and positron emission tomography-computed tomography (PET-CT) scan, which confirmed an avid 53 mm left upper lobe mass with associated hilar and mediastinal lymphadenopathy staging the disease as T3N2M0. An endobronchial ultrasound scan and biopsy (EBUS) sampling of station 11L confirmed lung adenocarcinoma metastasis. It appeared positive on the PD-L1 staining. Other immunohistochemistry (ALK/ROS/NTRK) was negative. Her lung function at this point was 51% forced expiratory volume (FEV1) (1.21) and 73% diffusing capacity of the lungs for carbon monoxide (DLCO). She consented to radical treatment with four weeks of radiotherapy dosed at 55 Gy/20 with concurrent chemotherapy. Her initial scan post radiotherapy showed a limited response to treatment, but her subsequent CT scan in a year showed that there was no tumor visible on axial images but there was apparent collapse of the left lung base. Post radiotherapy imaging showed complete response to treatment. It also showed two small bullae seen in the post aspect of the lower lobe. Five months later, she had a follow-up scan (Figures 4,5). Coronal views showed upward curving of the lower segmental bronchi and pulmonary vessels. The two small bullae initially seen in the post aspect of the lower lobe seemed to have relocated to the upper zone anteriorly. Lung torsion with 180-degree rotation was diagnosed. The patient was clinically well; hence, it did not warrant surgical referral.","[""lung adenocarcinoma""]","[""lung adenocarcinoma""]",True,"[[""hilar"", ""lymphadenopathy""], [""mediastinal"", ""lymphadenopathy""]]" +graph_010,Re_do_robot_assisted_salvage_lobectomy_after_esophagectomy_with_gastric_pull_up__PMC11980297.html,"55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","55-year-old female underwent esophagectomy with gastric pull-up reconstruction for squamous cell carcinoma (SCC) of the esophagus (cT3N2M0, stage IIIB) +Six years later, computed tomography (CT) scan showed stage IA Thyroid Transcription Factor-1 (TTF-1) positive adenocarcinoma in the left upper lobe treated by stereotactic radiotherapy +Two years later, a SCC of the right upper lobe (RUL) was found with tumor diameter of 54 mm and high Programmed Death-Ligand 1 (PD-L1) expression +Pembrolizumab initiated with curative intent but showed no biological response +Salvage lobectomy including complete mediastinal lymph node dissection performed +Positioned in left lateral decubitus position, adhesions in closure-line of the previous thoracotomy and thus RATS was deemed feasible. +After standard port placement (Fig.2A), docking and instrument placement (Tip-up fenestrated grasper™, Cadière forceps™, Maryland bipolar dissector™ and the Monopolar spatula™) adhesiolysis between the lung and the chest wall and taking down dense adhesions between the lung and the intrathoracic gastric pull-up the nasogastric tube was exposed (Fig.2B). +The nasogastric tube was placed in the gastric pull-up as a safety measure. +Meticulous dissection of its vascularization enabled subsequent standard lobectomy of the RUL with complete lymph node dissection (R4, 7, 10 and 11). +After removal of the specimen and chest tube placement, a Ropivacaine® intercostal nerve block levels T4 to T9 was installed. +Total operative time was 3 h 44 min with 50 ml blood loss.","[""Squamous cell carcinoma"", ""Adenocarcinoma""]","[""Esophageal squamous cell carcinoma"", ""Thyroid Transcription Factor-1 positive adenocarcinoma"", ""Squamous cell carcinoma of the right upper lobe""]",False,[] +graph_011,Efficacy_of_Selpercatinib_in_Non_small_Cell_Lung_Cancer_With_Bilateral_Internal__PMC12021377.html,"Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria","Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs.Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerveSignificant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints.Fourth-line treatment with selpercatinib (160 mg twice daily) was initiatedDisease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter.First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria"," + + Three new intracranial lesions were identified, accompanied by clinical manifestations of paresthesia and reduced muscular strength in the lower limbs. + + + Near-complete resolution of multiple supratentorial and infratentorial nodular lesions, with the absence of gadolinium enhancement, except for a faint residual signal at the cisternal segment of the right eighth cranial nerve + + + Significant symptomatic improvement within one week of treatment, including complete hearing recovery and a substantial reduction of dizziness and headache complaints. + + + Fourth-line treatment with selpercatinib (160 mg twice daily) was initiated + + + Disease progression was identified with the emergence of a new growing nodule measuring 11 mm in its longest diameter. + + + First-line systemic therapy with a platinum-based doublet, completing six cycles with a partial tumor response according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria + +","[""adenocarcinoma""]","[""lung cancer""]",True,"[[""brain"", ""intracranial""], [""bone"", ""osseous""], [""liver"", ""hepatic""], [""lymph nodes"", ""lymphatic""], [""lung"", ""pulmonary""]]" +graph_012,Multiple_Lung_Metastases_of_Papillary_Thyroid_Carcinoma_Detected_by_Detailed_Pat_PMC11971052.html,"79-year-old male patient with: +- Height: 174 cm +- Weight: 65 kg +- BMI: 21.5 kg/m² +- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) +- Medical history: + - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension + - Left cervical lymphadenopathy of unknown origin six years ago + - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC. + - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. + - The patient was treated with radioiodine therapy (Iodine-131). + - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. + - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits. + - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL. + - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1). + - No hilar lymphadenopathy was detected. + - FDG-PET was not performed. + - Pulmonary function and electrocardiogram tests showed no abnormalities. + +An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. + +Histopathological examination revealed adenocarcinoma. +Adenocarcinoma cells were found in the resected tissue. +Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. +The patient's postoperative course was uneventful, with no complications noted. +5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. +2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. +6 months post-surgery: No evidence of recurrence.","Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension.A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made.No evidence of recurrence.","79-year-old male patient with: +- Height: 174 cm +- Weight: 65 kg +- BMI: 21.5 kg/m² +- Smoking history: two packs per day for 55 years (Brinkman Index of 1100) +- Medical history: + - Total thyroidectomy performed five years earlier for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension + - Left cervical lymphadenopathy of unknown origin six years ago + - Subsequent investigations revealed suspected cervical lymph node metastasis of PTC + - Five years ago, the patient underwent total thyroidectomy and left cervical lymph node dissection. Histopathological findings revealed multiple papillary thyroid microcarcinomas (pT1a [m], pEx0, pN1b 4/10, pStage IVA) with negative surgical margins. + - The patient was treated with radioiodine therapy (Iodine-131) + - Two years ago, a nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. + - Tumor markers (CYFRA, CEA, SLX, ProGRP, NSE) were within normal limits + - Serum thyroglobulin levels showed a gradual increase over time, with a preoperative value of 47.7 ng/mL + - Chest X-rays showed no abnormalities, while chest CT scans revealed an irregular nodule measuring 15×14 mm in the S1 segment of the right upper lobe (Figure1) + - No hilar lymphadenopathy was detected + - FDG-PET was not performed + - Pulmonary function and electrocardiogram tests showed no abnormalities + +An irregular nodule 15 x 14 mm in size was seen in the S1 upper lobe of the right lung (arrow). The surgery was performed under general anesthesia in the left lateral decubitus position with video-assisted thoracoscopy. The tumor was partially resected using an automatic stapler and submitted for rapid diagnosis. The diagnosis of adenocarcinoma was confirmed, and a right upper lobectomy with mediastinal lymph node dissection (ND-1b) was performed. The operation lasted 2 hours and 30 minutes. + +Histopathological examination revealed adenocarcinoma. +Adenocarcinoma cells were found in the resected tissue. +Immunohistochemistry showed positive staining for TTF-1, indicating lung origin of the tumor. +The patient's postoperative course was uneventful, with no complications noted. +5 years ago: Total thyroidectomy performed for papillary thyroid carcinoma (PTC) with comorbidities of chronic obstructive pulmonary disease and hypertension. +2 years ago: A nodule in the right upper lobe of the lung was identified, which was followed up with chest CT scans. Compared to two years prior, an increase in nodule density was observed, prompting a transbronchial biopsy; however, no definitive diagnosis was made. +6 months post-surgery: No evidence of recurrence.","[""papillary thyroid carcinoma"", ""adenocarcinoma""]","[""pT1a [m] papillary thyroid microcarcinomas"", ""lung adenocarcinoma""]",True,"[[""cervical lymph nodes"", ""papillary thyroid carcinoma""]]" +graph_013,Brain_Metastasis_From_Advanced_Stage_Lung_Carcinoma__Differentiating_From_Stroke_PMC11955559.html,"Patient's medical history: +- Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes (15 months ago) +- PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes +- Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy (1 year ago) +- Initiated docetaxel for refractory complications with stage III NSCLC (2 days ago) + +Recent medical events: +- Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea +- Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity +- Leukopenia, WBC of 1.12 K/μL +- Potassium level still low but increased since previous ED visit +- COVID-19 and flu tests all negative +- Urine testing revealed trace blood and bacteria and was positive for cannabis +- Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease +- CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries +- Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting + +Current medications: +- Docetaxel for refractory complications with stage III NSCLC +- Potassium supplement for hypokalemia +- Ondansetron for nausea","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","15 months ago: Diagnosed with stage III NSCLC in the right upper lobe bronchus that had spread throughout the middle and lower lobes. PET/CT scans revealed a right supraclavicular node, right upper paratracheal node, multiple additional paratracheal nodes, and enlarged para-aortic nodes. +1 year ago: Upper esophageal stricture treated with dilatation during an esophagogastroduodenoscopy. +2 days ago: Initiated docetaxel for refractory complications with stage III NSCLC. +Current visit: Diagnosed with hypokalemia, given potassium supplement and ondansetron for nausea. Marked unilateral weakness in left upper extremity, grip strength of 2/5 versus 5/5 strength in the right upper extremity. +Current visit: Leukopenia, WBC of 1.12 K/μL. Potassium level still low but increased since previous ED visit. +Current visit: COVID-19 and flu tests all negative. +Current visit: Urine testing revealed trace blood and bacteria and was positive for cannabis. +Current visit: Non-contrast CT results revealed multifocal intracranial lesions with associated vasogenic edema with mild mass effect, consistent with metastatic disease. +Current visit: CT angiography (CTA) performed, revealing no flow-limiting stenosis or occlusion of major intracranial or cervical arteries. +Current visit: Multiple bilateral pulmonary nodules and a partially imaged right upper lobe mass were seen, along with asymmetrically enlarged right level IIb nodes, suspicious for metastasis in this clinical setting.","[""NSCLC""]","[""stage III NSCLC""]",True,"[[""brain"", ""multifocal intracranial lesions""], [""lung"", ""bilateral pulmonary nodules""], [""lymph nodes"", ""asymmetrically enlarged right level IIb nodes""]]" +graph_014,Successful_treatment_of_an_elderly_patient_with_lung_squamous_cell_carcinoma_by__PMC11973309.html,"A 73-year-old man presenting with paroxysmal cough and sputum accompanied by chest pain, weight loss, and exertional asthma was admitted to a local hospital on February 13, 2023. A chest computed tomography (CT) scan revealed a mass in the right upper lobe of the lung, raising the suspicion of a malignant tumor (MT). Subsequent positron electron tomography (PET)-CT indicated an irregular lobulated soft tissue mass in the apical segment of the right lung upper lobe, measuring approximately 4.1×3.5 cm and showing increased fluorodeoxyglucose (FDG) uptake (SUV value) and spiculated margins, suggestive of lung cancer (likely squamous cell carcinoma). There were tiny nodular shadows about 0.3 cm in diameter surrounding the mass, and the possibility of metastasis was not ruled out. Several enlarged lymph nodes were visible in regions 10R, 4R, and 2R, the largest measuring approximately 1.7 cm in diameter. that showed varying degrees of increased FDG uptake, suggesting possible metastasis in some lymph nodes. On March 3, 2023, a CT-guided biopsy of the right upper lobe lung mass was performed at our hospital. According to the pathology report (Figure 1), combined with the patient’s medical history and immunohistochemical markers, squamous cell carcinoma was considered (Note: CK7-, CK20-, CK5/6-, NapsinA-, CD56-, P40+, Syn-, CgA-, CD56-, TTF-1-, Ki-67 75%). As shown in the microscopic cellular morphology and tissue architecture ofFigure 1, the entire field demonstrates complete loss of normal pulmonary tissue structure.","Diagnosed with stage cT2bN2M0 right lung squamous cell carcinoma on March 14, 2023. Immunotherapy combined with chemotherapy was started: paclitaxel liposome 240 mg on d1, carboplatin 500 mg on d1, and tislelizumab 200 mg on d2, every 3 weeks (q3w). Grade III thrombocytopenia occurred post-treatment, with a nadir of 30 × 10^9/L. Immunotherapy regimen was adjusted for the first cycle: tislelizumab 200 mg on d0 + paclitaxel liposome 120 mg on d1, 90 mg on d8 + carboplatin 150 mg on d2, 100 mg on d3-5, every 3 weeks (q3w). However, on May 16, 2023, bacteremia and herpes zoster infection were observed, so antitumor treatment was halted.","Vancomycin was given for anti-infection and anti-viral treatment. After active treatment, the first reexamination on May 29, 2023, with a repeat enhanced chest CT showed an irregular thin-walled cystic lesion in the right upper lobe with fine line compartments, measuring approximately 32×25×27 mm, with enlarged and moderately enhanced lymph nodes in the 10R, 4R, and 2R regions. Compared to the March 3, 2023 CT, the solid component of the right upper lobe mass had essentially disappeared, and the mediastinal lymph nodes were similar in size. Response assessment indicated partial remission, and the second cycle of immunotherapy combined with chemotherapy was administered on June 27, 2023.","[""malignant tumor"", ""lung cancer""]","[""squamous cell carcinoma""]",True,"[[""squamous cell carcinoma"", ""lymph nodes""]]" +graph_015,A_case_of_obstructive_shock_and_transient_ischemic_attack_from_intracardiac_meta_PMC11981378.html,"- Patient presented to ER 8 days after initial diagnosis of intracardiac metastasis of NSCLC. +- On admission, patient appeared lethargic, tachycardic with irregular rhythm, decreased breath sounds on the right, and tender right upper quadrant due to rib fractures. Heart rate was 110 bpm, blood pressure 96/60 mmHg, respiratory rate 22, and saturation of 100%. Patient treated for hypotension with IV fluids. +- CT of head negative for acute intracranial processes. CT of abdomen and pelvis showed mildly displaced rib fractures, right kidney interpolar cyst with new areas of internal hyperdensity (suspected benign cysts). No other new presentations appreciated. +- Laboratory values during the admission: + - Hemoglobin (g/dL): 9.6, 9.9, 10.4 + - Hematocrit (%): 28.3, 30.2, 31.4 + - Platelets (K/uL): 146, 128, 170 + - WBC (K/uL): 19.5, 16.29, 20.71 + - Sodium (mEq/L): 129, 128, 127 + - Potassium (mEq/L): 3.7, 4, 4.7 + - Chloride (mEq/L): 102, 100, 101 + - Bicarbonate (mmol/L): 24, 23, 25 + - Glucose (mg/dL): 120, 130, 110 + - Creatinine (mg/dL): 1.2, 1.3, 1.1 + - Urea nitrogen (mg/dL): 20, 22, 18 + - Calcium (mg/dL): 9.5, 10.2, 9.8 + - Phosphate (mg/dL): 4.2, 4.5, 4.0 + - Lactate dehydrogenase (LDH) (U/L): 250, 280, 220 + - Aspartate aminotransferase (AST) (U/L): 40, 45, 35 + - Alanine aminotransferase (ALT) (U/L): 30, 35, 25 + - Total bilirubin (mg/dL): 1.2, 1.5, 1.0 + - Direct bilirubin (mg/dL): 0.8, 1.0, 0.7 + - Alkaline phosphatase (ALP) (U/L): 120, 140, 100 + - Gamma-glutamyl transferase (GGT) (U/L): 50, 60, 40 + +2 days post-ER admission: Patient developed symptoms suggestive of a transient ischemic attack (TIA) with right facial droop and left pronator drift. +CT-Angiography did not show any large vessel occlusion or acute intracranial process. +The deficits resolved in 6 hours; however, the patient still had ongoing tachycardia and uncontrolled atrial fibrillation. + +Patient was diagnosed with locally advanced non-small cell lung cancer (NSCLC) stage IIIB (T4N2Mx) metastatic non-small cell lung carcinoma of squamous cell histology. +Endobronchial ultrasound-guided fine-needle aspiration confirmed the diagnosis. +CT angiogram revealed a large hypermetabolic mass in the right lower lobe extending into the mediastinum with enlarged hypermetabolic subcarinal nodes, irregular mass measuring approximately 8.7 × 4.6 cm, partial atelectasis of the right middle and lower lobes, small to moderate low-density right pleural effusion. +Tumor thrombus in the left atrium measuring 3.4 × 6.3 cm, interfering with the mitral valve function. +Echocardiogram showed that the mass was invading into the left atrium. + +Patient underwent palliative care for symptom management. + +2 days post-ER admission: TIA with right facial droop and left pronator drift +CT-Angiography: no large vessel occlusion or acute intracranial process +Discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLCTransient ischemic attack (TIA) with right facial droop and left pronator driftCT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","Patient presented to ER with intracardiac metastasis of NSCLC (initial diagnosis) +2 days post-ER admission: Transient ischemic attack (TIA) with right facial droop and left pronator drift +after TIA: CT-Angiography showed no large vessel occlusion or acute intracranial process; patient discharged to hospice care","[""non-small cell lung cancer""]","[""squamous cell histology""]",True,"[[""left atrium"", ""tumor thrombus""], [""right lower lobe"", ""large hypermetabolic mass""], [""mediastinum"", ""enlarged hypermetabolic subcarinal nodes""]]" +graph_016,Precise_Localization_of_the_Subsolid_Lesion_by_Colour_Marking_under_CT_Guided_Co_PMC12040305.html,"51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","51-year-old female patient with a subsolid pulmonary lesion. The lesion was followed up for 4 years and subsequently resected videothoracoscopically after preoperative labeling with a mixture of blue dye and contrast agent. +Born in 1970, underwent resection of malignant melanoma in April 2013. +Suspicious lymph node (LU) in the left axilla detected on ultrasound, biopsy confirmed metastasis of malignant melanoma. PET/CT showed solitary finding in the left axilla. Dissection of the left axilla performed, only one of 19 LNs affected by metastasis. Molecular genetic testing revealed BRAF mutation at codon 600, targeted therapy with BRAF inhibitors deployed. +Routine CT scan of lungs in November 2017 detected new asymptomatic lesion in segment S10 of right lower lobe, measuring 7 mm in size. Follow-up CT scan in June 2020 showed lesion changed character to subsolid lesion with solid component. PET/CT scan in July 2020 confirmed persistence of the lesion without increased metabolic activity. +A further follow-up in April 2021 confirmed persistence and additionally showed a slight size progression of the solid component of the lesion. +The resection lines from the tumor margin to the resection margins were adequate, with the smallest measured dimension of 13 mm. No metastatic process was found in the examined mediastinal lymphatic nodes. The postoperative course was uneventful, and the patient was discharged to home care on the fourth day after surgery. +She continues to be followed up regularly and remains free of signs of disease recurrence.","[""malignant melanoma""]","[""melanoma"", ""lung cancer""]",True,"[[""left axilla"", ""lymph node""], [""right lower lobe"", ""lung""]]" diff --git a/src/benchmark/output/results/testset/results_graph_001.json b/src/benchmark/output/results/testset/results_graph_001.json new file mode 100644 index 0000000..339d9ad --- /dev/null +++ b/src/benchmark/output/results/testset/results_graph_001.json @@ -0,0 +1,792 @@ +{ + "status": "success", + "reconstructed_narrative": "**Clinical Case Report**\n\n**Patient Demographics:**\nThe patient is a 44-year-old male with no history of antitubercular treatment (ATT) intake. He has been a tobacco chewer for over 20 years.\n\n**Initial Presentation:**\nThe patient presented to the clinic with right-sided chest pain, dry cough, on-off fever, and hematuria for 2 months. Physical examination revealed decreased air entry on the right side of the lung.\n\n**Imaging and Diagnosis (Step 1-3):**\n\n* Contrast-enhanced computed tomography (CECT) thorax revealed a heterogeneous lesion in the mediastinal region abutting the horizontal fissure and cavitation within.\n* Bronchoscopy with bronchoscopic-guided biopsy and BAL was performed, which showed negative results for malignant cells. Biopsy results were suggestive of squamous cell carcinoma.\n\n**Symptoms and Imaging (Step 4-5):**\n\n* The patient reported decreased and blurring of vision.\n* An 18F-FDG PET/CT scan revealed a FDG-avid well-defined soft tissue primary mass measuring 5.6 cm x 7.7 cm x 8.3 cm with spiculated margins in the upper lobe of the right lung, along with multiple sub-centimetric to centimetric-sized bilateral lung nodules and metastases to mediastinal, abdominopelvic lymph nodes.\n\n**Progression and Diagnosis (Step 6-7):**\n\n* The patient presented with severe headaches and blurring of vision for 15 days.\n* Biopsy results confirmed metastatic involvement.\n\n**Treatment Plan:**\nUnfortunately, the provided data does not include a treatment plan or outcomes. However, based on the diagnosis of squamous cell carcinoma and metastases, further treatment options would likely involve chemotherapy, radiation therapy, or a combination of both, depending on the patient's overall health and specific tumor characteristics.\n\n**Outcomes:**\nThe patient's current status is unknown, as the provided data only includes the timeline of diagnoses and treatments. Further follow-up and monitoring are necessary to assess the patient's response to treatment and any potential complications or side effects.\n\nIn conclusion, this patient presented with a complex clinical scenario involving a heterogeneous lesion in the mediastinal region, squamous cell carcinoma, and metastases. The patient's symptoms and imaging results suggest an aggressive disease course, and further treatment options would be necessary to manage the patient's condition effectively.", + "bertscore": { + "precision": 0.8387337327003479, + "recall": 0.8516782522201538, + "f1": 0.8451563715934753 + }, + "bleu": 0.2054908255580929, + "rouge1": 0.4711211778029445, + "rougeL": 0.34428086070215175, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 7, + "edge_count": 6, + "avg_in_degree": 0.8571428571428571, + "density": 0.14285714285714285 + }, + "trajectory_embedding": [ + 0.22544555366039276, + -0.021888595074415207, + -0.0058143287897109985, + 0.03279201313853264, + 0.012158679775893688, + 0.124949149787426, + 0.055165503174066544, + 0.12983736395835876, + 0.3739190995693207, + -0.2663968503475189, + -0.19686637818813324, + 0.07701147347688675, + -0.5400644540786743, + 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@@ +{ + "status": "success", + "reconstructed_narrative": "**Patient Demographics**\n\nThe patient is an adult male with a history of Small Cell Lung Cancer (SCLC). Unfortunately, the exact age and other demographic details are not provided in the data.\n\n**Timeline of Diagnoses**\n\nThe patient's diagnosis timeline begins with the onset of symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. This marked the progression from symptom onset to diagnosis.\n\n**Timeline of Treatments**\n\nThe patient's treatment timeline began with endovascular intervention to address IVC stenosis due to compression caused by the tumor. The procedure involved thrombectomy and stent placement. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered.\n\n**Timeline of Outcomes**\n\nThe patient's outcome timeline began with significant alleviation of IVCS symptoms (trunk and lower limb edema) following the intervention. However, unfortunately, the patient died 8 days later from his primary disease (SCLC).\n\n**Narrative Summary**\n\nA male patient with Small Cell Lung Cancer presented with symptoms such as dyspnea, abdominal distension, and lower-extremity edema. These symptoms led to an evaluation in the emergency department, where a poor performance status, abnormal vital signs, and significant tumor burden were noted. Endovascular intervention was performed to address IVC stenosis caused by compression from the tumor. Following this, post-intervention venography showed improved flow, and low-molecular-weight heparin was administered. However, despite these interventions, the patient's primary disease ultimately led to his death 8 days later.\n\n**Key Takeaways**\n\n* The patient had a poor performance status and significant tumor burden at diagnosis.\n* Endovascular intervention was effective in alleviating IVCS symptoms but did not address the underlying cause of death.\n* Low-molecular-weight heparin was administered post-intervention, but its effectiveness is unclear given the patient's rapid decline.\n\n**Limitations**\n\nThe narrative summary is limited by the lack of detailed information on patient demographics, treatment outcomes, and long-term follow-up. Further investigation would be necessary to fully understand the patient's clinical course and the effectiveness of interventions.", + "bertscore": { + "precision": 0.7355820536613464, + "recall": 0.6891461610794067, + "f1": 0.7116073966026306 + }, + "bleu": 0.054103905008875824, + "rouge1": 0.3516699410609037, + "rougeL": 0.14145383104125736, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 8, + "edge_count": 7, + "avg_in_degree": 0.875, + "density": 0.125 + }, + "trajectory_embedding": [ + 0.2569149434566498, + 0.23160001635551453, + -0.23048092424869537, + 0.06365886330604553, + 0.06271032989025116, + -0.032205305993556976, + -0.0353657603263855, + 0.14690855145454407, + 0.3527328073978424, + -0.24249935150146484, + -0.23033425211906433, + 0.13146138191223145, + -0.44394129514694214, + -0.1020270437002182, + -0.1855921894311905, + 0.17859384417533875, + 0.08802724629640579, 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patient is an 81-year-old female who presented with progressive chest tightness and dyspnea over a 10-day period. She has no history of smoking or malignancy.\n\n**Timeline of Diagnoses:**\n\n1. **Step 1 (Day 0-9):** The patient initially presents with progressive chest tightness, dyspnea, cough, and back pain. Chest CT imaging reveals a large left-sided pleural effusion.\n2. **Step 2 (Day 10):** Thoracentesis is performed, and the drained pleural fluid is sent to the Department of Pathology for further evaluation.\n3. **Step 3 (Day 11-12):** Post-thoracic drainage chest CT reveals a 6.7 cm x 2.8 cm heterogeneous mass in the left inferior lobe with irregular contrast enhancement, suggestive of a left lung tumor.\n4. **Step 4 (Day 13-14):** Pulmonary window analysis shows multiple nodular high-density foci scattered across both lungs, concerning for bilateral pulmonary metastases. Mediastinal window assessment reveals bilateral mediastinal lymphadenopathy and enlarged lymph nodes at the left pulmonary hilum, consistent with lymph node metastasis.\n5. **Step 5 (Day 15-16):** Abdominal CT scan detects multiple low-density hepatic nodules of varying sizes, with the largest lesion located in the right hepatic lobe. Enhanced brain CT identifies an irregular heterogeneously enhancing mass within the right frontal lobe, consistent with brain metastasis.\n6. **Step 6 (Day 17-18):** Cell block analysis of the pleural effusion demonstrates poorly cohesive round-to-oval cells with a dispersed distribution exhibiting eccentrically located nuclei with dense chromatin.\n\n**Treatments:**\n\n1. Thoracentesis and post-thoracic drainage chest CT\n2. Abdominal CT scan and enhanced brain CT\n\n**Outcomes:**\nThe patient's diagnosis is confirmed as lung cancer with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The cell block analysis of the pleural effusion reveals poorly cohesive round-to-oval cells consistent with adenocarcinoma.\n\n**Conclusion:**\nThis 81-year-old female patient presents with progressive chest tightness and dyspnea due to a large left-sided pleural effusion, which is later confirmed as a left lung tumor with bilateral pulmonary metastases, hepatic metastases, and brain metastasis. The diagnosis is made after thoracentesis, post-thoracic drainage chest CT, abdominal CT scan, enhanced brain CT, and cell block analysis of the pleural effusion.", + "bertscore": { + "precision": 0.8535692095756531, + "recall": 0.869658887386322, + "f1": 0.8615389466285706 + }, + "bleu": 0.12150955580589737, + "rouge1": 0.4815766923736076, + "rougeL": 0.3461868037703513, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 6, + "edge_count": 5, + "avg_in_degree": 0.8333333333333334, + "density": 0.16666666666666666 + }, + "trajectory_embedding": [ + 0.2583933174610138, + -0.1034068688750267, + 0.02750878781080246, + 0.12225138396024704, + 0.07123710960149765, + 0.08420076966285706, + -0.025338614359498024, + 0.20714537799358368, + 0.42998072504997253, + -0.2773303687572479, + -0.23241369426250458, + 0.0849342942237854, + -0.532634437084198, + 0.050035249441862106, + 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Demographics:**\nThe patient is a 54-year-old Chinese male with a significant smoking history of 30 years. He presented with worsening cough for 3 months, which led to further investigation via CT imaging.\n\n**Timeline of Diagnoses:**\n\n1. **April 2023:** Enhanced CT revealed a 22 mm \u00d7 12 mm \u00d7 16 mm mass in the right upper lobe with invasion in the right hilum and mediastinal. PET-CT scan confirmed the CT findings.\n2. **Biopsy (Upper Right Lobe):** Biopsy of the lung lesion showed positive immunohistochemistry (IHC) for TTF-1, NpA, CK7, CD5/6, and Ki67 (60%); and negative for p40, p63, and CD56. Diagnosed with stage IIIA lung adenocarcinoma (cT1cN2M0).\n3. **May 2023:** Targeted NGS analysis identified an EGFRG719X mutation with a mutant allele frequency (MAF) of 3.8%.\n\n**Timeline of Treatments:**\n\n1. **May 2023:** The patient received two cycles of PC chemotherapy (pemetrexed 0.9g d1 and carboplatin 600mg d1) and dacomitinib (30mg).\n2. **Initial Treatment Evaluation:** Initial tumor was considered unresectable due to metastasis in the right hilum and mediastinum.\n\n**Timeline of Outcomes:**\n\n1. **May 2023:** Chest CT showed obvious shrinkage in the lesions in the right upper lung lobe and the lymph nodes of the mediastinum, contributing to partial response (PR).\n2. **Current Status:** The patient is currently receiving treatment for stage IIIA lung adenocarcinoma with EGFRG719X mutation.\n\n**Clinical Summary:**\nThe patient presented with worsening cough and a significant smoking history, leading to further investigation via CT imaging. Biopsy of the lung lesion confirmed the diagnosis of stage IIIA lung adenocarcinoma (cT1cN2M0) with an EGFRG719X mutation. The patient received two cycles of PC chemotherapy and dacomitinib, resulting in a partial response (PR). Further treatment is ongoing to manage this complex case.\n\n**Key Findings:**\n\n* Stage IIIA lung adenocarcinoma with EGFRG719X mutation\n* Partial response (PR) after initial treatment evaluation\n* Significant smoking history of 30 years\n* Worsening cough for 3 months\n\n**Recommendations:**\nFurther evaluation and management are necessary to optimize the patient's care. This may include additional imaging, laboratory tests, or other treatments to manage this complex case.\n\nNote: The above narrative is based on the provided data and may not be a comprehensive clinical case report.", + "bertscore": { + "precision": 0.86226487159729, + "recall": 0.8710905313491821, + "f1": 0.8666552901268005 + }, + "bleu": 0.27859330938799, + "rouge1": 0.560096153846154, + "rougeL": 0.3966346153846154, + "topology": { + "is_acyclic": true, + "timestamps_in_order": false, + "all_nodes_have_timestamps": false, + "weakly_connected_components": 1, + "node_count": 5, + "edge_count": 4, + "avg_in_degree": 0.8, + "density": 0.2 + }, + "trajectory_embedding": [ + 0.26444298028945923, + 0.15941788256168365, + -0.1746055781841278, + 0.1967768669128418, + 0.13093367218971252, + 0.108800008893013, + 0.047415077686309814, + 0.3190433979034424, + 0.4498003125190735, + -0.4936943054199219, + -0.028453731909394264, + 0.19775180518627167, + -0.6453556418418884, + -0.2056516706943512, + 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"results_graph_034": 1 +} \ No newline at end of file diff --git a/src/benchmark/setup_and_run.sh b/src/benchmark/setup_and_run.sh index 8949b9a..61bed19 100755 --- a/src/benchmark/setup_and_run.sh +++ b/src/benchmark/setup_and_run.sh @@ -25,4 +25,4 @@ fi # python3 generate_visuals.py echo "Generating similarity and clustering results..." -python3 modules/similarity_and_clustering.py \ No newline at end of file +python3 modules/compare_graph_vs_text_clusters.py \ No newline at end of file From 0db379985f3303ef4e82f731b25877e1e9cac36c Mon Sep 17 00:00:00 2001 From: Vicky Bikia Date: Wed, 14 May 2025 19:02:29 -0700 Subject: [PATCH 09/11] cleanup: benchmark code and results --- src/benchmark/main.py | 47 -- .../modules/compare_graph_vs_text_clusters.py | 67 +- src/benchmark/modules/visualization_utils.py | 19 +- .../output/plots/cluster_assignments.csv | 77 -- .../plots/clustering_metrics_best_umap.png | Bin 15856 -> 0 bytes .../plots/clustering_score_comparison.png | Bin 20454 -> 19894 bytes .../plots/graph_cancer_type_heatmap.png | Bin 58169 -> 44492 bytes .../graph_cluster_metastasis_barplot.png | Bin 16692 -> 17219 bytes .../graph_specific_cancer_type_heatmap.png | Bin 0 -> 65621 bytes .../clustering_score_comparison.png | Bin 18584 -> 0 bytes .../output/plots/plots_testset/tsne_graph.png | Bin 16323 -> 0 bytes .../output/plots/plots_testset/tsne_text.png | Bin 17169 -> 0 bytes .../output/plots/silhouette_heatmap_umap.png | Bin 70142 -> 0 bytes .../output/plots/text_cancer_type_heatmap.png | Bin 52684 -> 45212 bytes .../plots/text_cluster_metastasis_barplot.png | Bin 15749 -> 17403 bytes .../text_specific_cancer_type_heatmap.png | Bin 0 -> 65653 bytes .../output/plots/trajectory_tsne.png | Bin 43188 -> 0 bytes src/benchmark/output/plots/tsne_graph-pca.png | Bin 17549 -> 19789 bytes .../output/plots/tsne_graph-umap.png | Bin 19375 -> 20624 bytes src/benchmark/output/plots/tsne_text-pca.png | Bin 16637 -> 19348 bytes src/benchmark/output/plots/tsne_text-umap.png | Bin 16726 -> 17934 bytes .../output/plots/umap_kmeans_clusters.png | Bin 34681 -> 0 bytes .../results/cluster_labels_with_metadata.csv | 528 ++++++------ .../results/cluster_metadata_summary.csv | 5 +- .../output/results/graph_html_metadata.csv | 32 +- .../results/testset/graph_html_metadata.csv | 411 --------- .../results/testset/results_graph_001.json | 792 ------------------ .../results/testset/results_graph_003.json | 792 ------------------ .../results/testset/results_graph_004.json | 792 ------------------ .../results/testset/results_graph_005.json | 792 ------------------ 30 files changed, 351 insertions(+), 4003 deletions(-) delete mode 100644 src/benchmark/main.py delete mode 100644 src/benchmark/output/plots/cluster_assignments.csv delete mode 100644 src/benchmark/output/plots/clustering_metrics_best_umap.png create mode 100644 src/benchmark/output/plots/graph_specific_cancer_type_heatmap.png delete mode 100644 src/benchmark/output/plots/plots_testset/clustering_score_comparison.png delete mode 100644 src/benchmark/output/plots/plots_testset/tsne_graph.png delete mode 100644 src/benchmark/output/plots/plots_testset/tsne_text.png delete mode 100644 src/benchmark/output/plots/silhouette_heatmap_umap.png create mode 100644 src/benchmark/output/plots/text_specific_cancer_type_heatmap.png delete mode 100644 src/benchmark/output/plots/trajectory_tsne.png delete mode 100644 src/benchmark/output/plots/umap_kmeans_clusters.png delete mode 100644 src/benchmark/output/results/testset/graph_html_metadata.csv delete mode 100644 src/benchmark/output/results/testset/results_graph_001.json delete mode 100644 src/benchmark/output/results/testset/results_graph_003.json delete mode 100644 src/benchmark/output/results/testset/results_graph_004.json delete mode 100644 src/benchmark/output/results/testset/results_graph_005.json diff --git a/src/benchmark/main.py b/src/benchmark/main.py deleted file mode 100644 index 76acf22..0000000 --- a/src/benchmark/main.py +++ /dev/null @@ -1,47 +0,0 @@ -# This source file is part of the Daneshjou Lab projects -# -# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see AUTHORS.md) -# -# SPDX-License-Identifier: MIT -# - -""" -This script runs the full benchmarking pipeline on a single patient graph. -Intended for validating information extraction, structure, and representation quality. -""" - -import sys -from pathlib import Path -sys.path.append(str(Path(__file__).resolve().parents[1])) # Adds 'src' to sys.path - - -# Local application imports -from benchmark.modules.io_utils import ( - load_graph_from_file, - save_results, - data_display, -) -from benchmark.modules.run_benchmark import run_pipeline -from benchmark.modules.logging_utils import setup_logger - -logger = setup_logger(__name__) - -ORIGINAL_TEXT = ( - "A patient" -) - - -if __name__ == "__main__": - current_graph_path = "/Users/bikia/Documents/Code/DynamicData/webapp/static/graphs/graph_001.json" - graph, ok = load_graph_from_file(current_graph_path) - - if ok: - cfg = { - "reconstruct_params": {"include_nodes": True, "include_edges": True}, - "bertscore": True, - "topology": True, - "trajectory_embedding": True, - } - results = run_pipeline(graph, ORIGINAL_TEXT, cfg) - # data_display(results) - save_results(results, "output/results/results_001.json") diff --git a/src/benchmark/modules/compare_graph_vs_text_clusters.py b/src/benchmark/modules/compare_graph_vs_text_clusters.py index 6c23218..dae1cef 100644 --- a/src/benchmark/modules/compare_graph_vs_text_clusters.py +++ b/src/benchmark/modules/compare_graph_vs_text_clusters.py @@ -4,6 +4,13 @@ # # SPDX-License-Identifier: MIT # + +"""This modules compares the clustering of graph embeddings and text embeddings. +It loads the graph and text embeddings, reduces their dimensions using PCA or UMAP, +clusters them using KMeans, and evaluates the clustering performance using various metrics. +It also visualizes the clusters using t-SNE and generates a summary of the clusters with metadata. +""" + # Standard library imports import json import numpy as np @@ -121,8 +128,15 @@ def plot_tsne(embeddings, labels, method_label): perplexity = min(5, n_samples - 1) tsne = TSNE(n_components=2, perplexity=perplexity, random_state=42) reduced = tsne.fit_transform(embeddings) + + # Convert numeric labels to "Cluster 1", "Cluster 2", etc. + unique_labels = np.unique(labels) + label_map = {label: f"Cluster {i+1}" for i, label in enumerate(unique_labels)} + cluster_labels = [label_map[label] for label in labels] + + # Plot plt.figure(figsize=(8, 6)) - sns.scatterplot(x=reduced[:, 0], y=reduced[:, 1], hue=labels, palette="tab10") + sns.scatterplot(x=reduced[:, 0], y=reduced[:, 1], hue=cluster_labels, palette="tab10") plt.title(f"t-SNE of {method_label} Embeddings") plt.tight_layout() plt.savefig(PLOTS_DIR / f"tsne_{method_label.lower()}.png") @@ -184,10 +198,32 @@ def summarize_cluster_metadata(shared_ids, glabels, label_type="graph"): # Optional: Heatmap of top cancer types cancer_counts = {} + specific_counts = {} for cluster_id, group in joined.groupby("graph_cluster"): - cancer_list = [c for c in "|".join(group["cancers"].dropna().astype(str)).split("|") if c.strip()] + cancer_list = [] + specific_list = [] + for val in group["cancers"].dropna(): + try: + items = eval(val) if isinstance(val, str) and val.startswith("[") else [val] + cancer_list.extend([item.strip() for item in items if item.strip()]) + except: + continue + for val in group["specific_cancers"].dropna(): + try: + items = eval(val) if isinstance(val, str) and val.startswith("[") else [val] + specific_list.extend([item.strip() for item in items if item.strip()]) + except: + continue + for val in group["cancers"].dropna(): + try: + items = eval(val) if isinstance(val, str) and val.startswith("[") else [val] + cancer_list.extend([item.strip() for item in items if item.strip()]) + except Exception as e: + continue counts = Counter(cancer_list) + specific = Counter(specific_list) cancer_counts[cluster_id] = counts + specific_counts[cluster_id] = specific all_cancers = sorted({cancer for counts in cancer_counts.values() for cancer in counts}) heatmap_data = pd.DataFrame(index=sorted(cancer_counts.keys()), columns=all_cancers).fillna(0.0) @@ -205,9 +241,25 @@ def summarize_cluster_metadata(shared_ids, glabels, label_type="graph"): plt.close() print(f"✅ Cancer type heatmap saved to {PLOTS_DIR / f'{label_type}_cancer_type_heatmap.png'}") + # Specific cancer heatmap + all_specifics = sorted({c for s in specific_counts.values() for c in s}) + specific_data = pd.DataFrame(index=sorted(specific_counts.keys()), columns=all_specifics).fillna(0.0) + for cluster_id, counts in specific_counts.items(): + for name, count in counts.items(): + specific_data.at[cluster_id, name] = count / sum(counts.values()) + + plt.figure(figsize=(12, 6)) + sns.heatmap(specific_data, annot=True, fmt=".2f", cmap="OrRd") + plt.title(f"Top Specific Cancers per Cluster ({label_type})") + plt.ylabel("Cluster") + plt.xlabel("Specific Cancer Type") + plt.tight_layout() + plt.savefig(PLOTS_DIR / f"{label_type}_specific_cancer_type_heatmap.png") + plt.close() + print(f"✅ Specific cancer heatmap saved to {PLOTS_DIR / f'{label_type}_specific_cancer_type_heatmap.png'}") + def plot_score_comparison(score_dicts, shared_ids, glabels, tlabels): - summarize_cluster_metadata(shared_ids, glabels, label_type="graph") summarize_cluster_metadata(shared_ids, tlabels, label_type="text") @@ -228,11 +280,14 @@ def plot_score_comparison(score_dicts, shared_ids, glabels, tlabels): output_path = RESULTS_DIR / "cluster_labels_with_metadata.csv" output_df.to_csv(output_path, index=False) print(f"✅ Cluster labels with metadata saved to {output_path}") - metrics = ["Silhouette", "Calinski-Harabasz", "Davies-Bouldin"] + + # Updated metrics (excluding Davies-Bouldin) + metrics = ["Silhouette", "Calinski-Harabasz"] data = [] for label, scores in score_dicts.items(): - for metric, value in zip(metrics, scores): + for metric, value in zip(metrics, scores): # Expecting only 2 values per label data.append({"Metric": metric, "Type": label, "Score": value}) + df = pd.DataFrame(data) plt.figure(figsize=(8, 5)) sns.barplot(x="Metric", y="Score", hue="Type", data=df) @@ -242,8 +297,6 @@ def plot_score_comparison(score_dicts, shared_ids, glabels, tlabels): plt.close() -from sklearn.metrics import adjusted_rand_score - def main(): print("Loading graph embeddings...") graph_embs = load_graph_embeddings() diff --git a/src/benchmark/modules/visualization_utils.py b/src/benchmark/modules/visualization_utils.py index 4871a00..1101b20 100644 --- a/src/benchmark/modules/visualization_utils.py +++ b/src/benchmark/modules/visualization_utils.py @@ -23,7 +23,7 @@ def plot_bertscore_f1(graph_ids, bertscore_f1, export_path=None): - """Bar plot of BERTScore F1 for each graph, with summary statistics saved to CSV.""" + """Histogram of BERTScore F1 values across all graphs, with summary statistics saved to CSV.""" # Calculate statistics f1_array = np.array(bertscore_f1) stats = { @@ -43,18 +43,17 @@ def plot_bertscore_f1(graph_ids, bertscore_f1, export_path=None): stats_df = pd.DataFrame([stats]) stats_df.to_csv(export_path, index=False) - # Plotting - _, ax = plt.subplots() - sns.barplot(x=graph_ids, y=bertscore_f1, ax=ax) - ax.set_title("BERTScore F1 per Graph") - ax.set_ylabel("F1 Score") - ax.set_ylim(0, 1) - plt.xticks(rotation=45) + # Plotting histogram + plt.figure(figsize=(8, 6)) + sns.histplot(f1_array, bins=20, kde=True) + plt.title("Distribution of BERTScore F1 Scores") + plt.xlabel("F1 Score") + plt.ylabel("Frequency") + plt.xlim(0, 1) plt.tight_layout() - plt.savefig(os.path.join(PLOTS_DIR, "bertscore_f1_barplot.png")) + plt.savefig(os.path.join(PLOTS_DIR, "bertscore_f1_histogram.png")) plt.close() - def plot_tsne_embeddings(embeddings, graph_ids): """2D t-SNE scatterplot for graph embeddings.""" tsne_results = TSNE(n_components=2, perplexity=2, random_state=42).fit_transform( diff --git a/src/benchmark/output/plots/cluster_assignments.csv b/src/benchmark/output/plots/cluster_assignments.csv deleted file mode 100644 index 902c36c..0000000 --- a/src/benchmark/output/plots/cluster_assignments.csv +++ /dev/null @@ -1,77 +0,0 @@ -Graph ID,KMeans Label -results_graph_076,1 -results_graph_037,1 -results_graph_040,0 -results_graph_056,0 -results_graph_001,0 -results_graph_083,1 -results_graph_082,0 -results_graph_057,1 -results_graph_041,0 -results_graph_016,1 -results_graph_061,0 -results_graph_020,0 -results_graph_077,1 -results_graph_011,0 -results_graph_046,1 -results_graph_050,1 -results_graph_007,1 -results_graph_070,1 -results_graph_027,0 -results_graph_031,0 -results_graph_066,1 -results_graph_088,1 -results_graph_067,0 -results_graph_026,1 -results_graph_084,0 -results_graph_006,1 -results_graph_051,0 -results_graph_047,0 -results_graph_010,0 -results_graph_068,1 -results_graph_087,1 -results_graph_029,1 -results_graph_005,0 -results_graph_052,1 -results_graph_044,0 -results_graph_013,0 -results_graph_064,1 -results_graph_033,0 -results_graph_025,0 -results_graph_072,0 -results_graph_009,0 -results_graph_048,0 -results_graph_049,1 -results_graph_008,1 -results_graph_073,0 -results_graph_032,0 -results_graph_065,0 -results_graph_012,0 -results_graph_045,0 -results_graph_053,0 -results_graph_004,0 -results_graph_028,1 -results_graph_069,0 -results_graph_086,1 -results_graph_062,0 -results_graph_035,0 -results_graph_023,0 -results_graph_074,0 -results_graph_058,0 -results_graph_019,0 -results_graph_081,1 -results_graph_039,0 -results_graph_003,0 -results_graph_054,1 -results_graph_042,1 -results_graph_015,0 -results_graph_014,0 -results_graph_043,1 -results_graph_079,1 -results_graph_038,0 -results_graph_080,1 -results_graph_018,0 -results_graph_059,1 -results_graph_075,0 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