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/aad670c960d24ddf/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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+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1_obs_loo_null,ok
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+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,median_umi_obs,ok
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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/b53e4bba91122698/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,77,11550,11550,100,156.53842142402968,304.7800102720137,187.98792981622253,0.21215037316176566,True,"[11550, 11550]",,,9.1
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+ye2026_sepsis,scored,strict,real_R2,all,sq,77,278382,278423,100,125.00658835260758,215.76695728547273,134.36629344041708,0.10312546321547915,False,"[20000, 20000]",,,72.3
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+ye2026_sepsis,scored,strict,lora,all,l2,77,556805,115500,100,11.177950063882118,13.865239684871941,15.272651978960905,1.52372929329834,False,"[20000, 20000]",,,76.6
+ye2026_sepsis,scored,strict,pairedcal,pc,sq,77,11550,11550,100,172.0130828151481,292.02772259851264,364.28031088420266,1.602031455630008,True,"[11550, 11550]",,,9.2
+ye2026_sepsis,scored,strict,pairedcal,pc,l2,77,11550,11550,100,12.810946348188187,16.51368686778326,18.673144735882858,1.583205292585761,True,"[11550, 11550]",,,9.2
+ye2026_sepsis,scored,strict,pairedcal,all,sq,77,556805,115500,100,128.06679952675734,201.54248753677123,290.5188319239545,2.21096306542998,False,"[20000, 20000]",,,81.6
+ye2026_sepsis,scored,strict,pairedcal,all,l2,77,556805,115500,100,11.079553522554301,13.863212263197791,16.741344050598542,2.0339384441698556,False,"[20000, 20000]",,,81.6
+ye2026_sepsis,scored,strict,scsemi,pc,sq,77,11550,11550,100,121.16917068808908,289.50690092649904,490.3563807993575,2.1931340620335287,True,"[11550, 11550]",,,9.0
+ye2026_sepsis,scored,strict,scsemi,pc,l2,77,11550,11550,100,10.551799144606473,16.35957451600536,21.769033165994003,1.9314166447669785,True,"[11550, 11550]",,,9.0
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+ye2026_sepsis,scored,strict,scsemi,all,l2,77,556805,115500,100,10.158561155000402,13.718481127844314,20.696809626754415,2.9602487000108963,False,"[20000, 20000]",,,76.5
+ye2026_sepsis,scored,strict,raw,pc,sq,77,11550,11550,100,242.09932750874404,263.2005420334426,638.7216575414114,18.796184910040527,True,"[11550, 11550]",,,9.2
+ye2026_sepsis,scored,strict,raw,pc,l2,77,11550,11550,100,14.874212178169154,15.626689923979463,24.720242868641776,13.084813132739079,True,"[11550, 11550]",,,9.2
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+ye2026_sepsis,scored,strict,raw,all,l2,77,556805,115500,100,11.54286214249717,13.707194522217392,20.86282703959388,4.306161560222777,False,"[20000, 20000]",,,77.8
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+ye2026_sepsis,scored,strict,refcal,all,l2,77,556805,115500,100,11.11223704708518,13.839949468601912,17.646809739550978,2.395623761845202,False,"[20000, 20000]",,,79.1

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/ce5c7f9c6a53c0df/support.json

@@ -0,0 +1,81 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "immicro",
+  "design": "healthy_outerfold",
+  "unit": "fold4_n10",
+  "n_pairs": 10,
+  "train_sample_ids": [
+    "HS46",
+    "HS65",
+    "HS25",
+    "HS90",
+    "HS95",
+    "HS56",
+    "HS16",
+    "HS2",
+    "HS63",
+    "HS67"
+  ],
+  "train_donor_ids": [
+    "HS46",
+    "HS65",
+    "HS25",
+    "HS90",
+    "HS95",
+    "HS56",
+    "HS16",
+    "HS2",
+    "HS63",
+    "HS67"
+  ],
+  "test_sample_ids": [
+    "HS8",
+    "HS11",
+    "HS20",
+    "HS27",
+    "HS28",
+    "HS41",
+    "HS45",
+    "HS54",
+    "HS64",
+    "HS70",
+    "HS74",
+    "HS75",
+    "HS76",
+    "HS77",
+    "HS87",
+    "HS88",
+    "HS93",
+    "HS94",
+    "HS97",
+    "HS103",
+    "HS104"
+  ],
+  "test_donor_ids": [
+    "HS8",
+    "HS11",
+    "HS20",
+    "HS27",
+    "HS28",
+    "HS41",
+    "HS45",
+    "HS54",
+    "HS64",
+    "HS70",
+    "HS74",
+    "HS75",
+    "HS76",
+    "HS77",
+    "HS87",
+    "HS88",
+    "HS93",
+    "HS94",
+    "HS97",
+    "HS103",
+    "HS104"
+  ],
+  "excluded_sample_ids": [],
+  "seed": 20261016,
+  "selection_audit": [],
+  "sha256": "71350ef0e193641d9f260d1758377a3de64dc12ad169c130a0293e33711a48ac"
+}

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/fdb12f2696fcecc3/manifest.json

@@ -0,0 +1,562 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "ye2026_sepsis",
+ "design": "scored",
+ "unit": "strict",
+ "written_utc": "2026-10-12T16:02:20.586842+00:00",
+ "command": [
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+  "--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/draw1/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/draw1",
+  "--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/draw1/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/draw1/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/draw1/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": [
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+  "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",
+  "HC13",
+  "HC16",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC19",
+  "IC22",
+  "IC23",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PHC05",
+  "PIC01",
+  "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-S136",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S174",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S77",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Skin-S74",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_samples": 77,
+ "contrast": {
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+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
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+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 57,
+  "n_control_donors": 20
+ },
+ "calls": {
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+   "arms": [
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+    "pairedcal",
+    "scsemi",
+    "raw",
+    "refcal"
+   ],
+   "summary_sha256": "166acaf4ca9da339dbc39a5fea6533c4a08d657668c9e23128220bc832696686",
+   "contrast_csv_sha256": "811cd3b75888db050eb7ffb618fd5fcf55a3a95a02ae05c53773aeceb23eaaf4"
+  }
+ },
+ "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": {
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+  "sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0"
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+ "gene_exclusion": null,
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+ "genes_per_type": {
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+  "NK cell": 3237
+ },
+ "arms": {
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+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ye2026_sepsis/disease/draw1/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/draw1/lora.npz",
+   "npz_sha256": "490db66526025581a6faf86969efbe6d33722e57c87aa9a4bcec8ab31496475c",
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+   "n_generated_cells": 115500,
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+ "observed_cells": {
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+ "params": {
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