From d84ccc57127572370931fb5fe3197df8e7f8e47d Mon Sep 17 00:00:00 2001
From: JamieLyu <5819016+JamieLyu@users.noreply.github.com>
Date: Thu, 6 Aug 2026 13:21:04 +0900
Subject: [PATCH] =?UTF-8?q?P5=20MoFlow=20run-to-run=20null=20=EC=9E=AC?=
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 =?UTF-8?q?=20gene-set=20=EA=B0=80=EB=93=9C=20=EB=B2=84=EA=B7=B8=20?=
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run1/run2 재적합 완료, 판정 MOFLOW-REPRODUCIBLE (재현성 천장 +0.9999 >>
근접-0 세 쌍 중심화 코사인 |값| 최댓값 0.0118) — REVIEW-GB-2026-07-19b
MAJOR-1 (1) 해소.

recompute_shuffle_delta()가 moflow_scrambled.h5ad에 없는 유전자를 걸러내지
않고 조회해 죽던 버그를, 메인 재현성 천장 루프에 이미 있던 gene-set 교집합
가드와 같은 패턴으로 수정. 봉인 판정 기준(runs/near_zero_pairs_centered)에는
영향 없음 — 이 함수 결과는 §3 대조용 재현 확인일 뿐 판정에 쓰이지 않는다.
---
 .../results/moflow_runtorun_null.json         |  73 ++
 .../results/moflow_runtorun_null.md           |  46 ++
 .../moflow_rr_run1_genes.csv                  | 637 ++++++++++++++++++
 .../moflow_rr_run2_genes.csv                  | 637 ++++++++++++++++++
 .../results/runtime.csv                       |   2 +
 .../p10g_moflow_runtorun_null_audit.py        |   9 +-
 6 files changed, 1401 insertions(+), 3 deletions(-)
 create mode 100644 pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.json
 create mode 100644 pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.md
 create mode 100644 pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run1_genes.csv
 create mode 100644 pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run2_genes.csv

diff --git a/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.json b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.json
new file mode 100644
index 0000000..c439f22
--- /dev/null
+++ b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.json
@@ -0,0 +1,73 @@
+{
+ "design": "MoFlow run-to-run null: identical full-cohort input, ATAC intact, independent re-run only",
+ "audit_genes": 354,
+ "orig_cells": 21878,
+ "sealed_criteria": {
+  "moflow_reproducible": "min-over-runs lower CI(centered ceiling) > max |near-zero pair centered cosine|",
+  "moflow_not_separable": "ceiling CI touches or falls below that threshold, or includes 0"
+ },
+ "near_zero_pairs_raw_excess": {
+  "MultiVelo × MoFlow": -0.012113868549931794,
+  "MoFlow × CRAK-Velo": 0.0026473532780073583,
+  "MoFlow × MultiVeloVAE": 0.0030109183862805367
+ },
+ "near_zero_pairs_centered": {
+  "MultiVelo × MoFlow": -0.01176658645272255,
+  "MoFlow × CRAK-Velo": 0.0019254691433161497,
+  "MoFlow × MultiVeloVAE": 0.0018753123003989458
+ },
+ "runs": [
+  {
+   "run": 1,
+   "n_gene": 354,
+   "n_cell": 21878,
+   "same_cells_as_first_run": null,
+   "centered_ci": [
+    0.9999053180217743,
+    0.9999030828475952,
+    0.9999077335000038
+   ],
+   "raw_median": 0.9997379779815674,
+   "raw_null": 0.36715182662010193,
+   "raw_excess": 0.6325861513614655,
+   "sign_agreement": 0.9983017955668275
+  },
+  {
+   "run": 2,
+   "n_gene": 354,
+   "n_cell": 21878,
+   "same_cells_as_first_run": true,
+   "centered_ci": [
+    0.9999053180217743,
+    0.9999030828475952,
+    0.9999077335000038
+   ],
+   "raw_median": 0.9997379779815674,
+   "raw_null": 0.3673593997955322,
+   "raw_excess": 0.6323785781860352,
+   "sign_agreement": 0.9983017955668275
+  }
+ ],
+ "run1_vs_run2": {
+  "n_gene": 354,
+  "centered_ci": [
+   1.0,
+   1.0,
+   1.0
+  ]
+ },
+ "shuffle_recompute": {
+  "centered_median": 0.11260438710451126,
+  "ci": [
+   0.11122911470010877,
+   0.11391775077208877
+  ],
+  "n_gene": 353
+ },
+ "verdict": "MOFLOW-REPRODUCIBLE (근접-0 쌍은 arm 불안정으로 설명 안 됨)",
+ "verdict_checks": {
+  "min_lower_ci_ceiling": 0.9999030828475952,
+  "near_zero_threshold": 0.01176658645272255,
+  "passes": true
+ }
+}
\ No newline at end of file
diff --git a/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.md b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.md
new file mode 100644
index 0000000..8732c05
--- /dev/null
+++ b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_null.md
@@ -0,0 +1,46 @@
+# MoFlow run-to-run null — 세포·ATAC 고정, 독립 재실행만 반복
+
+> 생성 = `scripts/p10g_moflow_runtorun_null_audit.py` (fit = `scripts/p2_moflow_runtorun_refit.py`).
+> 신규 격리 산출물이다. `velocity_matrix_audit.*` · `scrambled_null_moflow.md` · `FINDINGS.md` · draft 는 읽기만 하고 건드리지 않는다.
+
+## 0. 무엇을 재는가
+
+층② 세포x유전자 velocity 행렬 감사에서 MoFlow가 낀 근접-0 세 쌍은 method 간 실제 불일치인지 MoFlow 한 arm의 내부 불안정인지 구분되지 않았다(REVIEW-GB-2026-07-19b MAJOR-1). MultiVelo가 이미 가진 재현성 천장(재표본 재적합 대비 +0.826~+0.887)의 대응물을, MoFlow는 세포 bootstrap이 없으므로 **동일 입력 독립 재실행**으로 잰다.
+
+## 1. 근접-0 세 쌍 원값 (재계산 아님, 대조용)
+
+| pair | cell_cos_excess (원값, `velocity_matrix_audit.json`) | 중심화 코사인 (재계산) |
+|---|---|---|
+| MultiVelo × MoFlow | -0.0121 | -0.0118 |
+| MoFlow × CRAK-Velo | +0.0026 | +0.0019 |
+| MoFlow × MultiVeloVAE | +0.0030 | +0.0019 |
+
+## 2. MoFlow 재현성 천장 (원본 vs 독립 재실행)
+
+| run | n_cell | n_gene | 중심화 코사인 [95% CI] | raw 중앙값 | 세포-셔플 null | raw 초과분 | 부호일치 |
+|---|---|---|---|---|---|---|---|
+| 1 | 21878 | 354 | +0.9999 [+0.9999, +0.9999] | +0.9997 | +0.3672 | +0.6326 | 99.8% |
+| 2 | 21878 | 354 | +0.9999 [+0.9999, +0.9999] | +0.9997 | +0.3674 | +0.6324 | 99.8% |
+
+run1 대 run2(원본을 거치지 않은 직접 비교, n_gene=354): 중심화 코사인 +1.0000 [+1.0000, +1.0000]
+
+## 3. 셔플 Δ 재계산 (봉인 수치 재현)
+
+원본×MoFlow-scr 중심화 코사인 재계산 +0.1126 [+0.1112, +0.1139] (n_gene=353) — 봉인 보고 +0.113(`velocity_matrix_audit.md` §6)과 대조.
+
+## 4. 판정 대비 봉인 기준
+
+**MOFLOW-REPRODUCIBLE (근접-0 쌍은 arm 불안정으로 설명 안 됨)**
+
+- 가장 보수적인 run의 lower CI(천장) +0.9999 vs 근접-0 세 쌍 중심화 코사인 |값| 최댓값 0.0118 → True
+
+## 5. 한계
+
+- 재실행 축만 쟀다. MultiVelo 처럼 세포 재표본까지 곱한 이중 축은 MoFlow에 없다(전체 세포 단일 fit 구조이므로 bootstrap 축 자체가 성립하지 않는다).
+- run 수는 2로 적다. 분산 추정의 정밀도는 MultiVelo의 6-refit 천장보다 낮다.
+- 이 감사는 `velo_s`(cell x gene velocity 행렬) 축만 본다. DTW c-s lag(`cs_lag_median`) 축의 재현성 상한은 별도이며 `scrambled_null_moflow.md` §4의 유보가 그대로 유효하다.
+- 판정은 중심화 코사인 기준으로 봉인했다. raw 초과분(§1~2 표)은 대조용으로만 병기한다.
+
+## 산출물
+
+`results/moflow_runtorun_null.json` · `scripts/p10g_moflow_runtorun_null_audit.py` · `scripts/p2_moflow_runtorun_refit.py`
diff --git a/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run1_genes.csv b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run1_genes.csv
new file mode 100644
index 0000000..47cb14c
--- /dev/null
+++ b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run1_genes.csv
@@ -0,0 +1,637 @@
+gene,cs_lag_mean,cs_lag_median
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diff --git a/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run2_genes.csv b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run2_genes.csv
new file mode 100644
index 0000000..47cb14c
--- /dev/null
+++ b/pipeline/hspc-velocity-benchmark/results/moflow_runtorun_refit/moflow_rr_run2_genes.csv
@@ -0,0 +1,637 @@
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diff --git a/pipeline/hspc-velocity-benchmark/results/runtime.csv b/pipeline/hspc-velocity-benchmark/results/runtime.csv
index 9d55567..a0d0c85 100644
--- a/pipeline/hspc-velocity-benchmark/results/runtime.csv
+++ b/pipeline/hspc-velocity-benchmark/results/runtime.csv
@@ -70,3 +70,5 @@ timestamp_utc,method,arm,n_cells,n_genes,wall_sec,peak_mem_mb,commit,note
 2026-07-21T10:41:22+00:00,multivelo_shuffle_seed,shuffle_seed_refit:b0_s303,15315,498,2709.1,11088.0,c8d5bdf,shuffle-draw variability; subsample seed=20260701 shuf_seed=303; njobs=8
 2026-07-21T10:43:45+00:00,multivelo_shuffle_seed,shuffle_seed_refit:b2_s305,15315,499,2731.7,11089.0,c8d5bdf,shuffle-draw variability; subsample seed=20260703 shuf_seed=305; njobs=8
 2026-07-21T10:46:05+00:00,multivelo_shuffle_seed,shuffle_seed_refit:b1_s304,15315,499,2755.9,11075.9,c8d5bdf,shuffle-draw variability; subsample seed=20260702 shuf_seed=304; njobs=8
+2026-08-05T08:49:45+00:00,moflow_runtorun,runtorun_refit:run1,21878,636,6789.1,8047.3,5e35798,ATAC intact independent re-run; gpu=True
+2026-08-06T02:46:43+00:00,moflow_runtorun,runtorun_refit:run2,21878,636,6689.3,8113.0,5e35798,ATAC intact independent re-run; gpu=True
diff --git a/pipeline/hspc-velocity-benchmark/scripts/p10g_moflow_runtorun_null_audit.py b/pipeline/hspc-velocity-benchmark/scripts/p10g_moflow_runtorun_null_audit.py
index b987ec8..47b8ac8 100644
--- a/pipeline/hspc-velocity-benchmark/scripts/p10g_moflow_runtorun_null_audit.py
+++ b/pipeline/hspc-velocity-benchmark/scripts/p10g_moflow_runtorun_null_audit.py
@@ -92,9 +92,12 @@ def recompute_shuffle_delta(genes, A_full, ok_mask):
     p_scr, layer = SCRAMBLED["MoFlow-scr"]
     if not os.path.exists(p_scr):
         return None
-    B = load(p_scr, layer, list(genes))
-    good = ok_mask & np.isfinite(B).all(0) & (np.nanstd(B, 0) > 0)
-    m, lo, hi = boot_ci(centered_cos(A_full[:, good], B[:, good]))
+    scr_genes = set(_names(p_scr, "var"))
+    g = [x for x in genes if x in scr_genes]
+    gmask = np.isin(genes, np.array(g))
+    B = load(p_scr, layer, g)
+    good = ok_mask[gmask] & np.isfinite(B).all(0) & (np.nanstd(B, 0) > 0)
+    m, lo, hi = boot_ci(centered_cos(A_full[:, gmask][:, good], B[:, good]))
     return dict(centered_median=m, ci=[lo, hi], n_gene=int(good.sum()))