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/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/pooled/headline.csv

@@ -0,0 +1,7 @@
+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
+giroux2022,pooled,pooled,pseudo_full__cal,sc-only fine-tune (+ calibration),other,conditions_pooled_cal.npz@7ad270e1,0.3441273714068387,0.20432479390870267,0.17515529453855735,0.5643395657145305,0.4710110292358014,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.33827076939519085,0.5496662519642362,0,101,0.0,2,0.09755311535340801,337,0,5,5,2,157,0.05861244019138756,16,0.4583768053300474,1123,4,15,5,1,155,0.13026979333299857,12,0.6226895399028884,620,2,12,5,0.05600000000000001,0.007222715529187905,0.062,0.01444543105837581,0.05820538760567712,0.059948030559418906,5,0.12,0.004897943725432538,0.12799999999999997,0.009795887450865076,0.16800414521732945,0.1398341507325511,5,True
+giroux2022,pooled,pooled,pseudo_full__raw,"sc-only fine-tune, real bulk",other,conditions_pooled_raw.npz@1370617c,0.398147551245955,0.3547944561891905,0.3194546947956906,0.5752659929360795,0.4958964592770665,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.39037524076970687,0.5605251826360979,0,101,0.0,5,0.15608498456545283,337,0,8,5,0,157,0.012470611748988834,16,0.3361429905753681,1123,2,11,5,0,155,0.02610966057441253,12,0.46703603072378436,620,1,9,5,0.036,0.006581005279131111,0.039999999999999994,0.013162010558262221,0.05939438145089043,0.056308149319016496,5,0.128,0.004897943725432538,0.13399999999999998,0.009795887450865076,0.16975308975867145,0.14127058542196963,5,True
+giroux2022,pooled,pooled,real_lora__raw,"LoRA, all training pairs",lora,conditions_pooled_raw.npz@1370617c,0.46094848304079133,0.37861361939512955,0.3230347269696575,0.5752659929360795,0.4958964592770665,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.45091776143261264,0.5605251826360979,5,101,0.6546216286986122,5,0.15608498456545283,337,77,8,5,4,157,1.455390366687081,16,0.3361429905753681,1123,977,11,5,7,155,1.6972165648336728,12,0.46703603072378436,620,119,9,5,0.052000000000000005,0.0077162250260124675,0.05800000000000001,0.015432450052024935,0.08606966945889905,0.07671637155618719,5,0.128,0.004897943725432538,0.13399999999999998,0.009795887450865076,0.16975308975867145,0.14127058542196963,5,True
+giroux2022,pooled,pooled,zs__cal,Zero-shot + calibration,zs_cal,conditions_pooled_cal.npz@7ad270e1,0.26862025176520443,0.16882835772931584,0.13339193412452294,0.5643395657145305,0.4710110292358014,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.2654828565096056,0.5496662519642362,0,101,0.012903225806451613,2,0.09755311535340801,337,1,5,5,0,157,0.10023336438456146,16,0.4583768053300474,1123,7,15,5,0,155,0.21168501270110077,12,0.6226895399028884,620,5,12,5,0.008,0.007798695693819401,0.022,0.015597391387638802,0.020084192992015935,0.025333955783953765,5,0.12,0.004897943725432538,0.12799999999999997,0.009795887450865076,0.16800414521732945,0.1398341507325511,5,True
+giroux2022,pooled,pooled,zs__pseudo,"Zero-shot, sc pseudobulk input (reference)",other,conditions_pooled_pseudo.npz@e35caf80,0.40995286106415924,0.32888473065692236,0.14426653827662855,0.7202428536715684,0.6744101540595969,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.40131859838315426,0.7026482550909734,3,101,0.763280879476918,27,0.971595235018782,337,77,220,5,2,157,1.3276813877618736,36,1.5219153050385095,1123,180,391,5,8,155,4.6459845776282815,28,2.6835482168110505,620,260,346,5,0.032,0.008427023125330689,0.05,0.016854046250661378,0.04740755642802233,0.05535355058373574,5,0.164,0.004878882064456874,0.192,0.009757764128913748,0.2698858281302703,0.21619106669662855,5,True
+giroux2022,pooled,pooled,zs__raw,"Zero-shot, real bulk",zs_raw,conditions_pooled_raw.npz@1370617c,0.33402890838128363,0.2232208443948936,0.19038234933406017,0.5752659929360795,0.4958964592770665,0.8963310768143463,0.0008479133641406827,0.7850129413304465,0.9441432653258389,0.9714956476546757,0.32858721008573893,0.5605251826360979,1,101,0.05946717411988582,5,0.15608498456545283,337,5,8,5,0,157,0.023786869647954328,16,0.3361429905753681,1123,2,11,5,1,155,1.0732617825478301,12,0.46703603072378436,620,46,9,5,0.02,0.006627976180322459,0.026000000000000002,0.013255952360644918,0.027743383947820676,0.026290107718369614,5,0.128,0.004897943725432538,0.13399999999999998,0.009795887450865076,0.16975308975867145,0.14127058542196963,5,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/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/pooled/manifest.json

@@ -0,0 +1,549 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "giroux2022",
+ "design": "pooled",
+ "unit": "pooled",
+ "written_utc": "2026-10-02T06:29:33.854789+00:00",
+ "command": [
+  "tools/contrast_extra.py",
+  "--design",
+  "pooled",
+  "--dataset",
+  "giroux2022",
+  "--threads",
+  "4"
+ ],
+ "threads": 4,
+ "donors": [
+  "450905_d0",
+  "450905_d14",
+  "0B943B_d0",
+  "0B943B_d14",
+  "7085CA_d0",
+  "7085CA_d7",
+  "7085CA_d14",
+  "2AD75E_d0",
+  "2AD75E_d7",
+  "2AD75E_d14",
+  "B85D75_d0",
+  "B85D75_d7",
+  "180E1A_d0",
+  "180E1A_d7",
+  "180E1A_d14",
+  "82CCF5_d0",
+  "82CCF5_d7",
+  "82CCF5_d14",
+  "BAAF62_d0",
+  "BAAF62_d7",
+  "BAAF62_d14",
+  "0BF51C_d0",
+  "0BF51C_d7",
+  "0BF51C_d14"
+ ],
+ "n_samples": 24,
+ "contrast": {
+  "case_groups": [
+   "severe"
+  ],
+  "control_groups": [
+   "mild"
+  ],
+  "n_case_donors": 11,
+  "n_control_donors": 13
+ },
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled": {
+   "arms": [
+    "pseudo_full__cal",
+    "pseudo_full__raw",
+    "real_lora__raw",
+    "zs__cal",
+    "zs__pseudo",
+    "zs__raw"
+   ],
+   "summary_sha256": "5deaaf60370f4868e02859ed4bc06dfab29227ed25397e153efe74ae62e7f709",
+   "contrast_csv_sha256": "f412a4eebae8ce832a0cd8bdc39eb61c695a129331dbedb0e58228023b355691"
+  }
+ },
+ "notes": {
+  "source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex"
+ },
+ "reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
+ "deg_reference": {
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022/deg_reference.npz",
+  "sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e"
+ },
+ "gene_exclusion": {
+  "file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv",
+  "sha256": "e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de",
+  "n_listed": 196,
+  "n_scoring_genes": 5563,
+  "n_dropped_from_scoring_genes": 65,
+  "n_scoring_genes_kept": 5498,
+  "applies_to": "group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene"
+ },
+ "n_genes_disease_scores": 5498,
+ "genes_per_type": {
+  "T cell": 2886,
+  "B cell": 3030,
+  "Monocyte": 3034,
+  "NK cell": 2931
+ },
+ "arms": {
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+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/pseudo_full__cal.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/pseudo_full__cal.npz",
+   "npz_sha256": "1cb066b8b215d043b7fbea1b599c2a91665b8112f84ca5f99bec9501fe507dd0",
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+   "condition_sha256": "7ad270e1b7bd1b5b9b76826877c5ba53fa833a0040c39c11297726f053059b55",
+   "condition_label": "conditions_pooled_cal.npz@7ad270e1",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/conditions_pooled_cal.npz",
+   "condition_key": "bcast:7ad270e1b7bd1b5b",
+   "n_generated_cells": 36000,
+   "label": "sc-only fine-tune (+ calibration)",
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+  "pseudo_full__raw": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/pseudo_full__raw.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/pseudo_full__raw.npz",
+   "npz_sha256": "bdf276aa524d415d810d0243e493918d41d192bcd2ae375fa111f7f7b72cd593",
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+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/conditions_pooled_raw.npz",
+   "condition_sha256": "1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015",
+   "condition_label": "conditions_pooled_raw.npz@1370617c",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/conditions_pooled_raw.npz",
+   "condition_key": "bcast:1370617c5149f307",
+   "n_generated_cells": 36000,
+   "label": "sc-only fine-tune, real bulk",
+   "seconds": 4.5
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+  "real_lora__raw": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/real_lora__raw.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/real_lora__raw.npz",
+   "npz_sha256": "611240c58872f308e8f96569e0897ffd1ebae4550e80eec3c4da568dccb418c6",
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+   "condition_sha256": "1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015",
+   "condition_label": "conditions_pooled_raw.npz@1370617c",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/conditions_pooled_raw.npz",
+   "condition_key": "bcast:1370617c5149f307",
+   "n_generated_cells": 36000,
+   "label": "LoRA, all training pairs",
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+  "zs__cal": {
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+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/zs__cal.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/zs__cal.npz",
+   "npz_sha256": "9b9cf5b00d101dad348a236bcc45c78623a022308b401640f2af4c979d3b8198",
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+   "condition_sha256": "7ad270e1b7bd1b5b9b76826877c5ba53fa833a0040c39c11297726f053059b55",
+   "condition_label": "conditions_pooled_cal.npz@7ad270e1",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/conditions_pooled_cal.npz",
+   "condition_key": "bcast:7ad270e1b7bd1b5b",
+   "n_generated_cells": 36000,
+   "label": "Zero-shot + calibration",
+   "seconds": 3.9
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+  "zs__pseudo": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/zs__pseudo.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/zs__pseudo.npz",
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+   "condition_sha256": "e35caf80738a4e67787f14193fc315213a9298a23a7e371dc557b95ce183695b",
+   "condition_label": "conditions_pooled_pseudo.npz@e35caf80",
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+   "condition_key": "bcast:e35caf80738a4e67",
+   "n_generated_cells": 36000,
+   "label": "Zero-shot, sc pseudobulk input (reference)",
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+  "zs__raw": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/zs__raw.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/zs__raw.npz",
+   "npz_sha256": "e92e868907eac71a40eb3bac10bb45bdcf44e881ba5869a04bdf695ab62e8aa8",
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+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/conditions_pooled_raw.npz",
+   "condition_sha256": "1370617c5149f3073a520c74683a65ad36dc1052c53ce56df6fe9e9d2a868015",
+   "condition_label": "conditions_pooled_raw.npz@1370617c",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled/conditions_pooled_raw.npz",
+   "condition_key": "bcast:1370617c5149f307",
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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/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/pooled/rbo.csv

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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/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/scsemi_cv_20261002/pooled/cat.csv

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