Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/1d92198fc737dbd3/en.csv

@@ -0,0 +1,25 @@
+dataset,design,unit,set,cellset,distance,n_samples,n_cells_real,n_cells_gen,n_pcs,lb,ub,dif_mean,en,lb_exact,lb_queries,n_representative_rows,en_reps_at_lb,seconds
+ye2026_sepsis,scored,strict,real_R2,pc,sq,77,11550,11550,100,155.32008011762113,303.9220499913664,186.61799435077495,0.21061574257558666,True,"[11550, 11550]",,,9.0
+ye2026_sepsis,scored,strict,real_R2,pc,l2,77,11550,11550,100,12.178810018847406,16.753866389829323,13.211688573886514,0.22576302263515666,True,"[11550, 11550]",,,9.0
+ye2026_sepsis,scored,strict,real_R2,all,sq,77,278163,278206,100,124.84538832369427,212.60118286469827,133.1926883839539,0.09511964541964639,False,"[20000, 20000]",,,69.7
+ye2026_sepsis,scored,strict,real_R2,all,l2,77,278163,278206,100,10.940921579647604,14.221208488346894,11.268509226075158,0.099865546991879,False,"[20000, 20000]",,,69.7
+ye2026_sepsis,scored,strict,lora,pc,sq,77,11550,11550,100,180.21349560953746,291.693835306077,313.0455597789041,1.1915290582263076,True,"[11550, 11550]",,,10.3
+ye2026_sepsis,scored,strict,lora,pc,l2,77,11550,11550,100,13.123882646561027,16.433265117520456,17.19440081262105,1.2299932696748506,True,"[11550, 11550]",,,10.3
+ye2026_sepsis,scored,strict,lora,all,sq,77,556369,115500,100,129.69894767633915,203.63697206298346,234.4022085546405,1.4160949220224808,False,"[20000, 20000]",,,78.2
+ye2026_sepsis,scored,strict,lora,all,l2,77,556369,115500,100,11.152021790793624,13.960268989630523,14.987399298188157,1.3657549481338553,False,"[20000, 20000]",,,78.2
+ye2026_sepsis,scored,strict,pairedcal,pc,sq,77,11550,11550,100,170.13702264948495,291.8239790535891,335.1318850696812,1.3558960409221925,True,"[11550, 11550]",,,10.4
+ye2026_sepsis,scored,strict,pairedcal,pc,l2,77,11550,11550,100,12.744515415218817,16.432085208148784,17.897020667959897,1.3972631142113638,True,"[11550, 11550]",,,10.4
+ye2026_sepsis,scored,strict,pairedcal,all,sq,77,556369,115500,100,126.72078097501976,203.24346334695457,269.25852173664305,1.8626861519153952,False,"[20000, 20000]",,,78.9
+ye2026_sepsis,scored,strict,pairedcal,all,l2,77,556369,115500,100,11.022591433100587,13.945620220560288,16.11713380008328,1.7428984582153828,False,"[20000, 20000]",,,78.9
+ye2026_sepsis,scored,strict,scsemi,pc,sq,77,11550,11550,100,107.209641237541,291.2741336480139,514.7949250875819,2.214361273662199,True,"[11550, 11550]",,,10.6
+ye2026_sepsis,scored,strict,scsemi,pc,l2,77,11550,11550,100,9.653977441850694,16.315830992912154,22.190366456280028,1.8818169625526908,True,"[11550, 11550]",,,10.6
+ye2026_sepsis,scored,strict,scsemi,all,sq,77,556369,115500,100,107.3593312376781,200.71838437696047,520.3030632748291,4.4231782366202905,False,"[20000, 20000]",,,80.3
+ye2026_sepsis,scored,strict,scsemi,all,l2,77,556369,115500,100,9.903122243581464,13.828137366380352,22.20000585524359,3.1329519064103235,False,"[20000, 20000]",,,80.3
+ye2026_sepsis,scored,strict,raw,pc,sq,77,11550,11550,100,240.3375652262957,262.94177394197783,637.8380426307511,17.5852418637721,True,"[11550, 11550]",,,9.3
+ye2026_sepsis,scored,strict,raw,pc,l2,77,11550,11550,100,14.815050931679941,15.524208241657343,24.69271216853248,13.928730759564912,True,"[11550, 11550]",,,9.3
+ye2026_sepsis,scored,strict,raw,all,sq,77,556369,115500,100,139.41956067885096,199.14992134175915,445.43708922277676,5.123316269107326,False,"[20000, 20000]",,,78.4
+ye2026_sepsis,scored,strict,raw,all,l2,77,556369,115500,100,11.46763082127734,13.79458152879272,20.844537828416726,4.029697310241542,False,"[20000, 20000]",,,78.4
+ye2026_sepsis,scored,strict,refcal,pc,sq,77,11550,11550,100,176.10486733926115,288.79607224114665,390.776689178156,1.9049563098184876,True,"[11550, 11550]",,,10.7
+ye2026_sepsis,scored,strict,refcal,pc,l2,77,11550,11550,100,12.971645489788566,16.321835306222102,19.39620735451776,1.917671002763807,True,"[11550, 11550]",,,10.7
+ye2026_sepsis,scored,strict,refcal,all,sq,77,556369,115500,100,127.60733127998876,202.70084430086254,316.29326753975994,2.5126795733650393,False,"[20000, 20000]",,,81.3
+ye2026_sepsis,scored,strict,refcal,all,l2,77,556369,115500,100,11.061867071942823,13.921343656651164,17.501631580423226,2.252078070132979,False,"[20000, 20000]",,,81.3

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/9c6b09a8513fc664/support.json

@@ -0,0 +1,103 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "immicro",
+  "design": "healthy_outerfold",
+  "unit": "fold0_n20",
+  "n_pairs": 20,
+  "train_sample_ids": [
+    "HS40",
+    "HS30",
+    "HS53",
+    "HS39",
+    "HS109",
+    "HS89",
+    "HS78",
+    "HS96",
+    "HS92",
+    "HS100",
+    "HS35",
+    "HS55",
+    "HS50",
+    "HS63",
+    "HS57",
+    "HS62",
+    "HS105",
+    "HS67",
+    "HS1",
+    "HS41"
+  ],
+  "train_donor_ids": [
+    "HS40",
+    "HS30",
+    "HS53",
+    "HS39",
+    "HS109",
+    "HS89",
+    "HS78",
+    "HS96",
+    "HS92",
+    "HS100",
+    "HS35",
+    "HS55",
+    "HS50",
+    "HS63",
+    "HS57",
+    "HS62",
+    "HS105",
+    "HS67",
+    "HS1",
+    "HS41"
+  ],
+  "test_sample_ids": [
+    "HS3",
+    "HS6",
+    "HS7",
+    "HS13",
+    "HS18",
+    "HS31",
+    "HS34",
+    "HS37",
+    "HS38",
+    "HS52",
+    "HS58",
+    "HS60",
+    "HS66",
+    "HS81",
+    "HS82",
+    "HS83",
+    "HS85",
+    "HS86",
+    "HS95",
+    "HS98",
+    "HS101",
+    "HS107"
+  ],
+  "test_donor_ids": [
+    "HS3",
+    "HS6",
+    "HS7",
+    "HS13",
+    "HS18",
+    "HS31",
+    "HS34",
+    "HS37",
+    "HS38",
+    "HS52",
+    "HS58",
+    "HS60",
+    "HS66",
+    "HS81",
+    "HS82",
+    "HS83",
+    "HS85",
+    "HS86",
+    "HS95",
+    "HS98",
+    "HS101",
+    "HS107"
+  ],
+  "excluded_sample_ids": [],
+  "seed": 20261012,
+  "selection_audit": [],
+  "sha256": "52b20ff9322e8bf850bd0092fb61a1ad1bdbf6304ddd2b7b654ef90fe8009e7e"
+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/c0acc57677b6e5fc/status.json

@@ -0,0 +1,23 @@
+{
+  "schema": "pbisc.paper.strict-statistics.v1",
+  "support_sha256": "074d1cf9ca3951ef1a032239eabb9d3a13f0f9a2030b030dcbe425ac71d46700",
+  "bootstrap_unit": "unique_donor_all_visits_and_draws",
+  "bootstrap_replicates": 2000,
+  "draws": [
+    "draw0_n5"
+  ],
+  "disease_deg": {
+    "status": "ok",
+    "method": "donor_condition_pseudobulk_limma_duplicateCorrelation_if_repeated_condition",
+    "n_genes_kept": 5498,
+    "rows": 5,
+    "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/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw0/lora/statistics/donor_deg/donor_deg_summary.csv"
+  },
+  "inter_method_bootstrap": {
+    "status": "not_applicable",
+    "reason": "Only one arm in this isolated evaluation",
+    "combined_comparisons": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/AGGREGATES.json"
+  }
+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/sources/ebbedde56881ab1e/manifest.json

@@ -0,0 +1,153 @@
+{
+ "schema": "paired_ft_extra_metrics.v1",
+ "dataset": "ye2026_sepsis",
+ "design": "scored",
+ "unit": "strict",
+ "written_utc": "2026-10-12T18:04:09.686278+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/draw4/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/draw4",
+  "--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/draw4/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/draw4/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/draw4/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-S103",
+  "Abd-S120",
+  "Abd-S123",
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+  "Abd-S42",
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+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S66",
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+  "HC01",
+  "HC05",
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+  "HC09",
+  "HC12",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC01",
+  "PIC02",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S136",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S77",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S52",
+  "Skin-S74",
+  "Uri-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_samples": 77,
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/score": {
+   "arms": [
+    "lora",
+    "pairedcal",
+    "scsemi",
+    "raw",
+    "refcal"
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+   "summary_sha256": "c2620874b8a5fde37fb43676abf8b92bf73dc8e7a69906be761cefda8101c950"
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+ "n_representative_rows": null,
+ "fetched_from_server2": [],
+ "code_sha256": {
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+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da"
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+}