chore: update claude-flow v3 init configuration #160
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Re-initialized claude-flow with --force to update agent configs, helpers, settings, and skills for DNA analyzer swarm orchestration. https://claude.ai/code/session_01QJhN7RNDnEHTPRVn9fMM2X
Initial draft from swarm agent covering three-regime gate selection based on El-Hayek, Khanna, and Abboud arXiv papers for dynamic min-cut, hypergraph sparsification, and Gomory-Hu trees. https://claude.ai/code/session_01QJhN7RNDnEHTPRVn9fMM2X
Comprehensive architecture design for the world's fastest DNA analyzer,
produced by a 15-agent hierarchical-mesh swarm. Documents include:
ADR Documents:
- ADR-018: DNA Analyzer Specification & DDD Architecture
- ADR-024: Deployment Architecture & Platform Strategy
- ADR-028: Graph Genome Min-Cut, Neural Intelligence, Vector Search, Security
- ADR-029: Self-Optimizing Nervous System (SONA)
DDD Domain Models:
- Epigenomics, CRISPR Engineering, Population Genomics, Pharmacogenomics
Grounded in three 2025 arXiv papers:
- El-Hayek et al.: Deterministic fully-dynamic min-cut (n^{o(1)} updates)
- Khanna et al.: Near-optimal hypergraph sparsification sketches
- Abboud et al.: Almost-linear-time Gomory-Hu trees
https://claude.ai/code/session_01QJhN7RNDnEHTPRVn9fMM2X
…chmarks, tests - ADR-018 specification: add information-theoretic bounds, TDA, quantum-inspired algorithms - Fix compile errors in ruvector-sparse-inference-wasm (9 errors resolved) - Fix compile error in ruvector-fpga-transformer (BackendSpec::as_ref) - Add HNSW genomic benchmarks (criterion) with real DNA k-mer workloads - Add min-cut genome graph benchmarks - Add real integration tests for core HNSW and min-cut (no mocks) - Add ruvector-dna-bench crate for real genomic data benchmarking https://claude.ai/code/session_01QJhN7RNDnEHTPRVn9fMM2X
ADR SOTA Enhancements (8 ADRs optimized): - ADR-018 DDD: event sourcing, CQRS, saga patterns, hexagonal architecture - ADR-028 Graph Genome: spectral sparsification, persistent homology, graph neural diffusion, expander decomposition - ADR-028 Neural: state space models (Mamba/S4), ring attention, KAN, mixture-of-depths, speculative decoding - ADR-028 Vector Search: DiskANN, RaBitQ, Matryoshka embeddings, ACORN filtered search, learned indexes - ADR-028 Security: post-quantum crypto (Kyber/Dilithium), TFHE, SPDZ MPC, Renyi DP, Plonk/Halo2 - ADR-029 SONA: progressive nets, lottery tickets, hypernetworks, PackNet, MAML meta-learning, NAS - ADR-024 Deployment: WebGPU, WebNN, confidential computing, unikernels, edge TPU, RISC-V RVV - DDD-003 Epigenomics: single-cell multi-omics, TADs, methylation clocks, 4D nucleome Code Quality (compile fixes + optimization): - Fix warnings across ruvector-mincut, ruvllm, sona crates - Optimize workspace Cargo.toml profiles (release, bench, release-with-debug) - Reduce unused imports, dead code, type mismatches Real DNA Benchmarks & Tests (no mocks): - Benchmark suite: HNSW genomic, min-cut graph, attention, delta propagation, quantization - Integration tests: core HNSW, min-cut, delta, SONA adaptation, Flash Attention - Real DNA analysis pipeline example with NCBI public sequences (PhiX174, SARS-CoV-2, E.coli, human mito) - Download script for public benchmark data from NCBI Deliverables: - Comprehensive README with comparison tables, QuickStart, collapsible guides - Security audit report - Performance optimization report https://claude.ai/code/session_01QJhN7RNDnEHTPRVn9fMM2X
Add complete DNA analysis pipeline with 2-bit packed sequence encoding, k-mer extraction, FASTA/FASTQ parsing, k-mer frequency embeddings, genomic vector search, variant calling with coherence gating, and staged pipeline orchestration. Fix ruvector-gnn-wasm native compilation by gating WASM-only bindings behind cfg(target_arch = "wasm32"). Modules: - sequence: 2-bit packed DNA (4x memory reduction), reverse complement - kmer: O(1) sliding window k-mer iterator, canonical forms - fasta: FASTA/FASTQ parser with N-base filtering - embedding: k-mer frequency + random projection to 384-dim vectors - search: brute-force cosine similarity index with taxonomy filtering - variant: SNP detection with isolation-based coherence gating - pipeline: staged parse -> QC -> embed -> search -> call pipeline https://claude.ai/code/session_01QJhN7RNDnEHTPRVn9fMM2X
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Re-initialized claude-flow with --force to update agent configs,
helpers, settings, and skills for DNA analyzer swarm orchestration.
https://claude.ai/code/session_01QJhN7RNDnEHTPRVn9fMM2X