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/ji2025_chili/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
+ji2025_chili,pooled,pooled,pseudo_full__cal,sc-only fine-tune (+ calibration),other,conditions_pooled_cal.npz@b0274507,0.24531460669665245,0.18723746240705455,0.21846001880719554,0.20647363470913363,0.11046477190864454,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.9418625156081898,0.9702277814744693,0.2406132386350377,0.20242294662813648,0,250,0.0,1,0.1875091880819335,2850,0,4,5,0,250,0.0,8,1.2188097225325678,3048,0,26,5,0,250,0.0,16,4.098107119434081,1476,0,29,5,0.008,0.008422968037325278,0.03,0.016845936074650555,0.034824738631920815,0.033350756915947494,5,0.044000000000000004,0.004687729702048338,0.06000000000000001,0.009375459404096675,0.0651812341821517,0.04588520713568105,5,True
+ji2025_chili,pooled,pooled,pseudo_full__raw,"sc-only fine-tune, real bulk",other,conditions_pooled_raw.npz@a13338f5,0.15313939481653605,0.10830439978340554,0.11160564331800676,0.2398746224459366,0.11053961855512523,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.9418625156081898,0.9702277814744693,0.15305801437089922,0.23420492618112912,0,250,0.011322463768115942,4,0.7031594553072507,2850,1,15,5,0,250,0.031100944780774173,15,2.343864851024169,3048,2,53,5,0,250,0.3448275862068966,20,7.294825089496429,1476,1,55,5,0.016,0.007963147814400334,0.030000000000000006,0.015926295628800668,0.0436794700737889,0.04089966788561035,5,0.044,0.004687729702048338,0.068,0.009375459404096675,0.06530702120731043,0.04590326003768017,5,True
+ji2025_chili,pooled,pooled,real_lora__raw,"LoRA, all training pairs",lora,conditions_pooled_raw.npz@a13338f5,0.47928798340225065,0.3780190147009437,0.45204372964017614,0.2398746224459366,0.11053961855512523,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.9418625156081898,0.9702277814744693,0.4718551446054381,0.23420492618112912,15,250,0.6811673849535764,4,0.7031594553072507,2850,106,15,5,16,250,1.8208467117236171,15,2.343864851024169,3048,325,53,5,18,250,4.027103083680692,20,7.294825089496429,1476,277,55,5,0.08,0.006973330543930659,0.142,0.013946661087861318,0.10177919374755093,0.10571142614004884,5,0.044,0.004687729702048338,0.068,0.009375459404096675,0.06530702120731043,0.04590326003768017,5,True
+ji2025_chili,pooled,pooled,zs__cal,Zero-shot + calibration,zs_cal,conditions_pooled_cal.npz@b0274507,0.14191696206220386,0.11414897963213883,0.11277544159311834,0.20647363470913363,0.11046477190864454,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.9418625156081898,0.9702277814744693,0.1385527091003339,0.20242294662813648,0,250,0.0,1,0.1875091880819335,2850,0,4,5,0,250,0.016134236850596968,8,1.2188097225325678,3048,1,26,5,0,250,0.0,16,4.098107119434081,1476,0,29,5,0.016,0.007605320844155933,0.032,0.015210641688311866,0.017413304087972134,0.0265789887188132,5,0.044000000000000004,0.004687729702048338,0.06000000000000001,0.009375459404096675,0.0651812341821517,0.04588520713568105,5,True
+ji2025_chili,pooled,pooled,zs__pseudo,"Zero-shot, sc pseudobulk input (reference)",other,conditions_pooled_pseudo.npz@089c6d4f,0.1410924404745027,0.11709687646943748,0.03209825877314353,0.598153432228882,0.5062896473544363,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.9418625156081898,0.9702277814744693,0.13997602077209473,0.5805515803282599,5,250,1.626263041428495,41,2.275975931994845,2850,376,1373,5,3,250,1.7896817233011524,48,2.275975931994845,3048,1429,609,5,8,250,8.864688510555947,46,6.880578457167011,1476,682,575,5,0.008,0.00669069181797943,0.026000000000000002,0.01338138363595886,0.028849372037790682,0.022664970158104557,5,0.23600000000000004,0.004551951863989691,0.29400000000000004,0.009103903727979382,0.14068264582276865,0.18495555001140562,5,True
+ji2025_chili,pooled,pooled,zs__raw,"Zero-shot, real bulk",zs_raw,conditions_pooled_raw.npz@a13338f5,0.08352233208682591,0.06859753090005666,0.03286103285000008,0.2398746224459366,0.11053961855512523,0.8933460729084324,0.003023938509812342,0.7836746479091096,0.9418625156081898,0.9702277814744693,0.08396213323162124,0.23420492618112912,0,250,0.04519232207217312,4,0.7031594553072507,2850,3,15,5,0,250,0.022930520522815866,15,2.343864851024169,3048,2,53,5,1,250,1.8449225675315117,20,7.294825089496429,1476,40,55,5,0.012,0.007807708485973291,0.03,0.015615416971946582,0.015571218945527177,0.021739705321558604,5,0.044,0.004687729702048338,0.068,0.009375459404096675,0.06530702120731043,0.04590326003768017,5,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/ji2025_chili/pooled/manifest.json

@@ -0,0 +1,552 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "ji2025_chili",
+ "design": "pooled",
+ "unit": "pooled",
+ "written_utc": "2026-10-02T06:32:44.053385+00:00",
+ "command": [
+  "tools/contrast_extra.py",
+  "--design",
+  "pooled",
+  "--dataset",
+  "ji2025_chili",
+  "--threads",
+  "4"
+ ],
+ "threads": 4,
+ "donors": [
+  "N064_TOL",
+  "N064_FU1",
+  "N032_AC",
+  "N038_BC",
+  "N038_AC",
+  "N055_AC",
+  "N136_TOL",
+  "N136_FU1",
+  "N138_TOL",
+  "N138_FU1",
+  "N128_BC",
+  "N128_AC",
+  "N129_BC",
+  "N129_AC",
+  "N147_TOL",
+  "N150_BC",
+  "N158_AC",
+  "N159_BC",
+  "N001_TOL",
+  "N001_FU1",
+  "N002_TOL",
+  "N002_FU1",
+  "N005_BC",
+  "N005_AC",
+  "N012_TOL",
+  "N012_FU1",
+  "N018_BC",
+  "N018_AC",
+  "N022_TOL",
+  "N022_FU1",
+  "N035_TOL",
+  "N043_TOL",
+  "N043_FU1"
+ ],
+ "n_samples": 33,
+ "contrast": {
+  "case_groups": [
+   "TOL",
+   "FU1"
+  ],
+  "control_groups": [
+   "BC",
+   "AC"
+  ],
+  "n_case_donors": 18,
+  "n_control_donors": 15
+ },
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled": {
+   "arms": [
+    "pseudo_full__cal",
+    "pseudo_full__raw",
+    "real_lora__raw",
+    "zs__cal",
+    "zs__pseudo",
+    "zs__raw"
+   ],
+   "summary_sha256": "c5affd46bccadfd4ca31a8a75f8b0047e691ca8f1ca3f56a04db53df53e743d9",
+   "contrast_csv_sha256": "210695ecacb2243c2cb2118373d96a5f7708e8b0150784d784dd658d1cbe4124"
+  }
+ },
+ "notes": {
+  "source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores"
+ },
+ "reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
+ "deg_reference": {
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili/deg_reference.npz",
+  "sha256": "4f5eb8c8389ef1308ce3ec44be8be024cedb97de37351d109d9070c818df5a9e"
+ },
+ "gene_exclusion": null,
+ "n_genes_disease_scores": 5752,
+ "genes_per_type": {
+  "T cell": 3021,
+  "B cell": 3245,
+  "Monocyte": 3154,
+  "NK cell": 3051
+ },
+ "arms": {
+  "pseudo_full__cal": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/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/ji2025_chili/pooled/pseudo_full__cal.npz",
+   "npz_sha256": "f08492665ec5c89211a009a0aa0020217e974e045c456c8c794ded36a0996d79",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_cal.npz",
+   "condition_sha256": "b02745073ef16c9a53a1bc7befa99b01126c443cbb34cffc952d44dc525b4c79",
+   "condition_label": "conditions_pooled_cal.npz@b0274507",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_cal.npz",
+   "condition_key": "bcast:b02745073ef16c9a",
+   "n_generated_cells": 49500,
+   "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/ji2025_chili/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/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/ji2025_chili/pooled/pseudo_full__raw.npz",
+   "npz_sha256": "db34b340fcaf2148d88cbdb6eaadc63c24412f410b29e586ef17ee3416d2a81c",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_raw.npz",
+   "condition_sha256": "a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007",
+   "condition_label": "conditions_pooled_raw.npz@a13338f5",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_raw.npz",
+   "condition_key": "bcast:a13338f530600178",
+   "n_generated_cells": 49500,
+   "label": "sc-only fine-tune, real bulk",
+   "seconds": 4.9
+  },
+  "real_lora__raw": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/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/ji2025_chili/pooled/real_lora__raw.npz",
+   "npz_sha256": "b98fc5dd4c125330ffb1738aade5d22d0bd62beaff2252ef45fc27354d88d2ec",
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+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_raw.npz",
+   "condition_sha256": "a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007",
+   "condition_label": "conditions_pooled_raw.npz@a13338f5",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_raw.npz",
+   "condition_key": "bcast:a13338f530600178",
+   "n_generated_cells": 49500,
+   "label": "LoRA, all training pairs",
+   "seconds": 5.5
+  },
+  "zs__cal": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/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/ji2025_chili/pooled/zs__cal.npz",
+   "npz_sha256": "3ca94764962699d8c024a6eb41819f43c2bf495e31474c680c207e128323cda6",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_cal.npz",
+   "condition_sha256": "b02745073ef16c9a53a1bc7befa99b01126c443cbb34cffc952d44dc525b4c79",
+   "condition_label": "conditions_pooled_cal.npz@b0274507",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_cal.npz",
+   "condition_key": "bcast:b02745073ef16c9a",
+   "n_generated_cells": 49500,
+   "label": "Zero-shot + calibration",
+   "seconds": 5.7
+  },
+  "zs__pseudo": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/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/ji2025_chili/pooled/zs__pseudo.npz",
+   "npz_sha256": "4f4c7d22825de87e484e8ba3a3b8625d06be4b160fe4e1a39f4d7cf634d8f2e3",
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+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_pseudo.npz",
+   "condition_sha256": "089c6d4f328f65deb73b241d2af56486080abd47009d0bae660526bd3ae2269b",
+   "condition_label": "conditions_pooled_pseudo.npz@089c6d4f",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_pseudo.npz",
+   "condition_key": "bcast:089c6d4f328f65de",
+   "n_generated_cells": 49500,
+   "label": "Zero-shot, sc pseudobulk input (reference)",
+   "seconds": 5.6
+  },
+  "zs__raw": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/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/ji2025_chili/pooled/zs__raw.npz",
+   "npz_sha256": "712efc06eb4b08d4b98baf039819cf1962e4b029ec4669fb403befb4e1e5611f",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_raw.npz",
+   "condition_sha256": "a13338f530600178689cf085a337667882704cc2bbe48b04ac9a60c9a1fac007",
+   "condition_label": "conditions_pooled_raw.npz@a13338f5",
+   "condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ji2025_chili/pooled/conditions_pooled_raw.npz",
+   "condition_key": "bcast:a13338f530600178",
+   "n_generated_cells": 49500,
+   "label": "Zero-shot, real bulk",
+   "seconds": 5.6
+  }
+ },
+ "observed_cells": {
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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/ji2025_chili/scsemi_cv_20261002/pooled/cat.csv

@@ -0,0 +1,61 @@
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