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/draw1/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
+lora,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+lora,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,23
+lora,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,7,50,50
+lora,NK cell,ok,ok,ok,57,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
+lora,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+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,,,,,1,50,50
+pairedcal,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,12,50,50
+pairedcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+pairedcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,46
+scsemi,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,2,50,50
+scsemi,B cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,47
+scsemi,Monocyte,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+scsemi,NK cell,ok,ok,ok,57,20,55,17,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,3,50,50
+scsemi,DC,ok,ok,ok,53,20,56,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,4,50,50
+raw,T cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,5,50,50
+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,,,,,4,50,50
+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,,,,,1,50,50
+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,,,,,4,50,50
+refcal,NK cell,ok,ok,ok,57,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,1,50,50
+refcal,DC,ok,ok,ok,53,20,57,20,edgeR_TMM_limma_voom,edgeR_TMM_limma_voom,,,,,0,50,33

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/draw1/statistics/status.json

@@ -0,0 +1,18 @@
+{
+  "schema": "pbisc.paper.strict-statistics.v1",
+  "support_sha256": "b85d386f59fff3c35b7beb041528403ab3fde9abf06af2bdd0b3b63c1bb8d99f",
+  "bootstrap_unit": "unique_donor_all_visits_and_draws",
+  "bootstrap_replicates": 2000,
+  "draws": [
+    "draw1_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/draw1/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/source_snapshot/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/contrast/ye2026_sepsis/strict/headline.csv

@@ -0,0 +1,6 @@
+dataset,design,unit,arm,label,role,condition,pearson_r,spearman_r,partial_r,broadcast_pearson_r,broadcast_spearman_r,splithalf_r_AB,splithalf_r_AB_sd,splithalf_spearman_AB,sb_reliability,noise_free_ceiling,r_generated_vs_halfB,r_broadcast_vs_halfB,welch_top50,welch_top50_max,welch_top50_chance,welch_top50_broadcast,welch_top50_broadcast_chance,welch_n_sig_obs,welch_n_sig_gen,welch_n_sig_broadcast_per_type,welch_types_scored,limma_top50,limma_top50_max,limma_top50_chance,limma_top50_broadcast,limma_top50_broadcast_chance,limma_n_sig_obs,limma_n_sig_gen,limma_n_sig_broadcast_per_type,limma_types_scored,limma_fbe_top50,limma_fbe_top50_max,limma_fbe_top50_chance,limma_fbe_top50_broadcast,limma_fbe_top50_broadcast_chance,limma_fbe_n_sig_obs,limma_fbe_n_sig_gen,limma_fbe_n_sig_broadcast_per_type,limma_fbe_types_scored,cat50,cat50_chance,cat100,cat100_chance,rbo,rbo_up_down,cat_types,broadcast_cat50,broadcast_cat50_chance,broadcast_cat100,broadcast_cat100_chance,broadcast_rbo,broadcast_rbo_up_down,broadcast_cat_types,repro_pass
+ye2026_sepsis,scored,strict,lora,lora,other,test_raw.npz@a7f4df1f,0.31843175224811415,0.09741989079567198,0.3037006390224007,0.3386821732452143,0.3501254222844883,0.9609285298153744,0.0018336035889258886,0.8393755597740762,0.9799700095896768,0.9899206005587549,0.31647518492087356,0.33802762724643476,29,250,2.390903361477991,18,2.2438976662663683,7438,1259,1469,5,21,250,2.1011182854094086,35,2.2438976662663683,5680,2254,890,5,18,250,6.7050819130957064,31,5.820233101906957,3363,1098,560,5,0.064,0.00632074177989658,0.07,0.01264148355979316,0.12156936344372873,0.07737091533617348,5,0.05600000000000001,0.004487795332532736,0.078,0.008975590665065472,0.06837577991746888,0.07586985059567151,5,True
+ye2026_sepsis,scored,strict,pairedcal,pairedcal,other,test_cal.npz@e1f35eed,0.16762152598604235,0.14295594104702058,0.07306317901026409,0.3326480144206522,0.37653959705274,0.9609285298153744,0.0018336035889258886,0.8393755597740762,0.9799700095896768,0.9899206005587549,0.16911663985241818,0.33279041278644994,10,250,1.9044933221994966,29,2.2438976662663683,7438,1192,2047,5,9,250,1.9668811698149584,37,2.2438976662663683,5680,680,944,5,12,250,7.403031069758388,28,5.847526811553892,3363,752,474,5,0.068,0.0062165244991497,0.06400000000000002,0.0124330489982994,0.12640606288509726,0.08755838292284104,5,0.052000000000000005,0.004487795332532736,0.07999999999999999,0.008975590665065472,0.06470480218822196,0.07373265048041981,5,True
+ye2026_sepsis,scored,strict,scsemi,scsemi,other,test_raw.npz@a7f4df1f,0.31019769204333947,0.21440638829679198,0.28180600331728967,0.3386821732452143,0.3501254222844883,0.9609285298153744,0.0018336035889258886,0.8393755597740762,0.9799700095896768,0.9899206005587549,0.30850004729408265,0.33802762724643476,6,250,4.901164661713413,18,2.2438976662663683,7438,647,1469,5,4,250,6.043134962400005,35,2.2438976662663683,5680,2402,890,5,4,250,50.22749701708349,31,5.820233101906957,3363,488,560,5,0.016,0.013622622736444389,0.018000000000000002,0.027245245472888778,0.03631070400913959,0.03010809973762864,5,0.05600000000000001,0.004487795332532736,0.078,0.008975590665065472,0.06837577991746888,0.07586985059567151,5,True
+ye2026_sepsis,scored,strict,raw,raw,other,conditions_raw.npz@36add186,0.008866251374828589,-0.031298529399549205,-0.07968534454913388,0.3386821732452143,0.3501254222844883,0.9609285298153744,0.0018336035889258886,0.8393755597740762,0.9799700095896768,0.9899206005587549,0.012018598490712459,0.33802762724643476,12,250,2.625601782680223,18,2.2438976662663683,7438,2625,1469,5,8,250,2.2588881014390383,35,2.2438976662663683,5680,3580,890,5,9,250,6.102595375666641,31,5.820233101906957,3363,2316,560,5,0.004,0.0059282134384210945,0.026000000000000002,0.011856426876842189,0.0375476250216929,0.02623586647756364,5,0.05600000000000001,0.004487795332532736,0.078,0.008975590665065472,0.06837577991746888,0.07586985059567151,5,True
+ye2026_sepsis,scored,strict,refcal,refcal,other,conditions_refcal.npz@3886924b,0.17445504500618855,0.12634224478338535,0.10021229815910042,0.25631002819323256,0.21236915264742826,0.9609285298153744,0.0018336035889258886,0.8393755597740762,0.9799700095896768,0.9899206005587549,0.17532095672310294,0.25634277329423494,14,250,2.690379095500738,11,2.2438976662663683,7438,937,1012,5,10,250,2.285926975412703,37,2.2438976662663683,5680,2401,746,5,11,250,11.232278820876664,30,5.919185571835534,3363,412,460,5,0.028000000000000004,0.006339781730670177,0.05200000000000001,0.012679563461340354,0.06494770761818647,0.055654008745213666,5,0.048,0.004487795332532736,0.06999999999999999,0.008975590665065472,0.06783604293472888,0.07132983218525964,5,True

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/draw2/contrast/ye2026_sepsis/strict/manifest.json

@@ -0,0 +1,562 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "ye2026_sepsis",
+ "design": "scored",
+ "unit": "strict",
+ "written_utc": "2026-10-12T16:43:43.234189+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/tools/score_strict.py",
+  "--support-manifest",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/protocol/splits/ye2026_sepsis/disease/draw2/support.json",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2",
+  "--action",
+  "all",
+  "--threads",
+  "4",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/lora.npz",
+  "--arm",
+  "pairedcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/pairedcal.npz",
+  "--arm",
+  "scsemi=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/scsemi.npz",
+  "--arm",
+  "raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/raw.npz",
+  "--arm",
+  "refcal=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/global/ye2026_sepsis/refcal.npz"
+ ],
+ "threads": 4,
+ "donors": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Uri-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_samples": 77,
+ "contrast": {
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 57,
+  "n_control_donors": 20
+ },
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/score": {
+   "arms": [
+    "lora",
+    "pairedcal",
+    "scsemi",
+    "raw",
+    "refcal"
+   ],
+   "summary_sha256": "b5d9d1d3a0f5af919c9da94588e0d238c217fb6b6aff3250c21af8c9e25eb3ce",
+   "contrast_csv_sha256": "20b72c34d1e1f5ac6a8ca39ee25c2a55d4230172a50146bc3eff4d7ba85308a5"
+  }
+ },
+ "notes": {
+  "source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores"
+ },
+ "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+ "deg_reference": {
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz",
+  "sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0"
+ },
+ "gene_exclusion": null,
+ "n_genes_disease_scores": 5975,
+ "genes_per_type": {
+  "T cell": 3250,
+  "B cell": 3308,
+  "Monocyte": 3287,
+  "NK cell": 3233
+ },
+ "arms": {
+  "lora": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/score",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/lora.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/lora.npz",
+   "npz_sha256": "ee517a12eea1c5e67a1682caf3a8a6cb72895203214422f9a15ad3db3a950b11",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw2/test_raw.npz",
+   "condition_sha256": "a7f4df1f36bb0f35a331030f36e42e6b1b6fb02de7471eca430bceceb884b82f",
+   "condition_label": "test_raw.npz@a7f4df1f",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw2/test_raw.npz",
+   "condition_key": "bcast:a7f4df1f36bb0f35",
+   "n_generated_cells": 115500,
+   "label": "lora",
+   "seconds": 12.2
+  },
+  "pairedcal": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/score",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/pairedcal.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw2/pairedcal.npz",
+   "npz_sha256": "69c4c71131a0dd07875dee834ff64c0245fb780c22b2933487e259c5cce30c09",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ye2026_sepsis/disease/draw2/test_cal.npz",
+   "condition_sha256": "e1f35eed2826765c6ff9eff20b4939be0fb8670bd1a3b93ccf0a360c268f70b7",
+   "condition_label": "test_cal.npz@e1f35eed",
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