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/140b5e451aad71b0/summary.json

@@ -0,0 +1,214 @@
+{
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+  "dataset": "immicro",
+  "written_utc": "2026-10-15T09:51:05.154099+00:00",
+  "command": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+    "--dataset",
+    "immicro",
+    "--out",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold2/n5/score",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold2/n5/lora.npz",
+    "--condition",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/immicro/healthy/fold2/n5/test_raw.npz",
+    "--donors",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold2/n5/test_samples.txt",
+    "--threads",
+    "2",
+    "--no-contrast",
+    "--no-deg"
+  ],
+  "arms": [
+    "lora"
+  ],
+  "donors": [
+    "HS9",
+    "HS14",
+    "HS19",
+    "HS24",
+    "HS25",
+    "HS26",
+    "HS32",
+    "HS42",
+    "HS43",
+    "HS50",
+    "HS55",
+    "HS59",
+    "HS67",
+    "HS71",
+    "HS73",
+    "HS80",
+    "HS91",
+    "HS102",
+    "HS105",
+    "HS108",
+    "HS111"
+  ],
+  "n_donors": 21,
+  "reference": {
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+  "per_arm": {
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+      "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold2/n5/lora.npz",
+      "npz_sha256": "9db828f963f7e4f04ede0c3e8d23ecffb5ad522fed0bdb8da3e67b621a265e04",
+      "receipt_verified": true,
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+        "checkpoint_sha256": "f4bcc2b5d2e63c4303a82f0888983f6760bfee883798284adf6773285c97589a",
+        "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/immicro/healthy/fold2/n5/test_raw.npz",
+        "input_condition_sha256": "35792517469285bed0fd17595441952e8f1880f63022e10db66e74dc36cd585f",
+        "seed": 20260928,
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+        "weights": "ema"
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+      "annotation": {
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+      "n_donors": 21,
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+        "mean_fraction_observed": {
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+      "pseudobulk": {
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+        "r_mean": 0.902487202326985,
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+        "n_query": 3150,
+        "n_reference": 3150
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+      "precision_coverage_depth_matched": {
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+        "detected_median_before": {
+          "R1": 362.0,
+          "Q": 278.0
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+        "detected_median_after": {
+          "R1": 278.0,
+          "Q": 278.0
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+      "monocyte_pct": {
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+        "observed_mean_over_donors": 16.087149423201815,
+        "generated_pooled_cells": 15.079365079365079
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+      "median_umi_per_cell_scoring_genes": {
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+        "generated_mean_of_donor_medians": 2593.78564453125,
+        "observed_mean_of_donor_medians": 1985.452380952381
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+      "seconds": 7.0
+    }
+  },
+  "code_sha256": {
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+    "/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",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+  },
+  "seconds": 8.9,
+  "core_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold2/n5/score"
+}

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/5a6e3a8c20108156/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,77,11550,11550,100,156.33239860597934,313.91321211076354,187.8672717617693,0.20011873561518678,True,"[11550, 11550]",,,11.0
+ye2026_sepsis,scored,strict,real_R2,pc,l2,77,11550,11550,100,12.220484208869925,17.082575029185783,13.256128862937324,0.21300397140671262,True,"[11550, 11550]",,,11.0
+ye2026_sepsis,scored,strict,real_R2,all,sq,77,280355,280396,100,125.11261801615271,213.9997871131819,133.9705507611215,0.09965367144609452,False,"[20000, 20000]",,,75.7
+ye2026_sepsis,scored,strict,real_R2,all,l2,77,280355,280396,100,10.953926376895131,14.259640084398834,11.3024236468773,0.1054227016668466,False,"[20000, 20000]",,,75.7
+ye2026_sepsis,scored,strict,lora,pc,sq,77,11550,11550,100,180.29418504770848,301.3731169684684,301.0993775013917,0.9977391651649531,True,"[11550, 11550]",,,11.2
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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/8958d9f6652cbab6/support.json

@@ -0,0 +1,83 @@
+{
+  "schema": "pbisc.paper.strict-support.v1",
+  "cohort": "immicro",
+  "design": "healthy_outerfold",
+  "unit": "fold0_n10",
+  "n_pairs": 10,
+  "train_sample_ids": [
+    "HS40",
+    "HS30",
+    "HS53",
+    "HS39",
+    "HS109",
+    "HS89",
+    "HS78",
+    "HS96",
+    "HS92",
+    "HS100"
+  ],
+  "train_donor_ids": [
+    "HS40",
+    "HS30",
+    "HS53",
+    "HS39",
+    "HS109",
+    "HS89",
+    "HS78",
+    "HS96",
+    "HS92",
+    "HS100"
+  ],
+  "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": "b76459a585604c60e588279b889094c972e621e2aa6c28ecf5aa163ffe5481bf"
+}

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/cb533ff71c691812/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
+pairedcal,lora,-0.07235260149412495,-0.1571164854009622,0.005364094851233999,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1,ok
+raw,lora,0.013994859994439907,-0.08343952279986991,0.10428911865819832,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1,ok
+refcal,lora,-0.079687956564537,-0.16199675404071423,0.0005301419317795674,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1,ok
+scsemi,lora,0.16118112877457516,0.1034467591194355,0.2224905479365334,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1,ok
+pairedcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1_obs_loo_null,ok
+raw,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1_obs_loo_null,ok
+refcal,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1_obs_loo_null,ok
+scsemi,lora,0.0,0.0,0.0,77,77,0,2000,20261012,donor_all_draws_and_visits,comp_l1_obs_loo_null,ok
+pairedcal,lora,-0.21870129870129876,-0.24711038961038967,-0.19306709956709964,77,77,0,2000,20261012,donor_all_draws_and_visits,coverage,ok
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