Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/donor_bootstrap_2000.csv

@@ -0,0 +1,113 @@
+arm,baseline,estimate,ci_low,ci_high,n_donors,n_paired_samples,n_excluded_nonfinite_pairs,n_boot,seed,bootstrap_unit,metric,status
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paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/donor_deg/donor_deg_summary.csv

@@ -0,0 +1,26 @@
+arm,celltype,status,observed_status,generated_status,n_case_donors_observed,n_control_donors_observed,n_case_donors_generated,n_control_donors_generated,method_observed,method_generated,reason_observed,reason_generated,reason_fit,reason_population,top50_overlap_count,observed_top50_size,generated_top50_size
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+lora,Monocyte,ok,ok,ok,57,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+lora,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,21
+lora,DC,ok,ok,ok,53,20,50,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+pairedcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+pairedcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,1
+pairedcal,Monocyte,ok,ok,ok,57,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+pairedcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,32
+pairedcal,DC,ok,ok,ok,53,20,54,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+scsemi,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,17
+scsemi,Monocyte,ok,ok,ok,57,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,6,50,50
+scsemi,NK cell,ok,ok,ok,57,20,52,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,12
+scsemi,DC,ok,ok,ok,53,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+raw,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+raw,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50
+raw,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+raw,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+raw,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+refcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+refcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0
+refcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+refcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+refcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,19

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/source_snapshot/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/status.json

@@ -0,0 +1,18 @@
+{
+  "schema": "pbisc.paper.strict-statistics.v1",
+  "support_sha256": "e72d06f5f4f5c10cf7fff8edaee1493e18c67dc4bbf65793eae6c984120cc4d2",
+  "bootstrap_unit": "unique_donor_all_visits_and_draws",
+  "bootstrap_replicates": 2000,
+  "draws": [
+    "draw4_n5"
+  ],
+  "disease_deg": {
+    "status": "ok",
+    "method": "donor_condition_pseudobulk_limma_duplicateCorrelation_if_repeated_condition",
+    "n_genes_kept": 5975,
+    "rows": 25,
+    "n_pending": 0,
+    "n_not_estimable": 0,
+    "summary_csv": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/donor_deg/donor_deg_summary.csv"
+  }
+}

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/disease_metrics/strict_sepsis_donor_deg_by_type.csv

@@ -0,0 +1,126 @@
+arm,celltype,status,observed_status,generated_status,n_case_donors_observed,n_control_donors_observed,n_case_donors_generated,n_control_donors_generated,method_observed,method_generated,reason_observed,reason_generated,reason_fit,reason_population,top50_overlap_count,observed_top50_size,generated_top50_size,draw
+lora,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,7,50,50,0
+lora,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,7,50,50,0
+lora,Monocyte,ok,ok,ok,57,20,53,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50,0
+lora,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0,0
+lora,DC,ok,ok,ok,54,20,34,16,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0,0
+pairedcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50,0
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+pairedcal,Monocyte,ok,ok,ok,57,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,18,0
+pairedcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,26,0
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+scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50,0
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+scsemi,Monocyte,ok,ok,ok,57,20,47,19,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,2,0
+scsemi,NK cell,ok,ok,ok,57,20,42,15,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50,0
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+raw,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50,0
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+refcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50,0
+refcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50,0
+refcal,DC,ok,ok,ok,54,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,15,0
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+pairedcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50,1
+pairedcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50,1
+pairedcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,12,50,50,1
+pairedcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50,1
+pairedcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,46,1
+scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50,1
+scsemi,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,47,1
+scsemi,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50,1
+scsemi,NK cell,ok,ok,ok,57,20,55,17,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50,1
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+raw,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50,1
+raw,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50,1
+raw,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50,1
+raw,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0,1
+refcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50,1
+refcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0,1
+refcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50,1
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+refcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,33,1
+lora,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,10,50,50,2
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+lora,Monocyte,ok,ok,ok,57,20,55,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,26,2
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+lora,DC,ok,ok,ok,53,20,35,19,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0,2
+pairedcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50,2
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+scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50,3
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+scsemi,NK cell,ok,ok,ok,57,20,56,19,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,7,50,50,3
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+raw,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,50,4
+raw,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50,4
+raw,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50,4
+raw,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0,4
+refcal,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50,4
+refcal,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,0,4
+refcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50,4
+refcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50,4
+refcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,19,4