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/ye2026_sepsis/pooled/headline.csv

@@ -0,0 +1,14 @@
+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
+ye2026_sepsis,pooled,pooled,lora_multik__raw,"LoRA, multi-K",other,conditions_pooled_raw.npz@3b2d8ef2,0.508675501890909,0.38452960672994624,0.4467418313251978,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.5065436677458786,0.3154897236225909,23,250,2.782229231846274,21,2.242290489478891,7946,780,1378,5,27,250,2.9060069436358074,36,2.242290489478891,6015,2596,850,5,33,250,11.541020833171302,32,5.841610666408343,3476,767,500,5,0.084,0.006036845263739264,0.15,0.012073690527478528,0.18472190213892073,0.1463436561791,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,lora_n10__raw,"LoRA, 10 pairs + inner-val",other,conditions_pooled_raw.npz@3b2d8ef2,0.4222959020688887,0.32165025078188414,0.36904669114334154,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.4212800995318027,0.3154897236225909,8,250,2.3541307741805966,21,2.242290489478891,7946,1064,1378,5,10,250,1.6338889057182442,36,2.242290489478891,6015,294,850,5,14,250,7.195569409498819,32,5.841610666408343,3476,494,500,5,0.084,0.006149821677502915,0.10800000000000001,0.01229964335500583,0.1797959542460603,0.1370810002807254,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,lora_n20__raw,"LoRA, 20 pairs + inner-val",other,conditions_pooled_raw.npz@3b2d8ef2,0.3671933060907342,0.3079567223197276,0.29460781187133706,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.36538338526281977,0.3154897236225909,18,250,1.8700926743400883,21,2.242290489478891,7946,749,1378,5,13,250,1.7833901923209083,36,2.242290489478891,6015,1727,850,5,11,250,5.4425744757661905,32,5.841610666408343,3476,373,500,5,0.08399999999999999,0.0060765844770727,0.11000000000000001,0.0121531689541454,0.1617250583596135,0.12101351676229558,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,lora_n40__raw,"LoRA, 40 pairs + inner-val",other,conditions_pooled_raw.npz@3b2d8ef2,0.47588059575028696,0.3849970284900032,0.4020213698715577,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.4737013665272123,0.3154897236225909,22,250,2.1567764382922023,21,2.242290489478891,7946,1180,1378,5,17,250,2.1296371573239057,36,2.242290489478891,6015,2572,850,5,16,250,7.048618352910271,32,5.841610666408343,3476,590,500,5,0.08,0.0060080722827227356,0.128,0.012016144565445471,0.18173597823066776,0.13618447287812058,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,lora_n5__raw,"LoRA, 5 pairs + inner-val",other,conditions_pooled_raw.npz@3b2d8ef2,0.29404452074006043,0.17560305920103123,0.2503210158718151,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.2932837580380448,0.3154897236225909,5,250,1.4605361772666805,21,2.242290489478891,7946,127,1378,5,2,250,0.8174331499544756,36,2.242290489478891,6015,173,850,5,4,250,4.543662773446803,32,5.841610666408343,3476,325,500,5,0.064,0.00620518138795159,0.076,0.01241036277590318,0.12463603882675227,0.09386114568193912,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,lora_recipe__raw,LoRA + recipes,other,conditions_pooled_raw.npz@3b2d8ef2,0.49573986020110955,0.4175895455967523,0.43102640789208446,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.4947044741565998,0.3154897236225909,23,250,2.962490214926574,21,2.242290489478891,7946,764,1378,5,31,250,3.0000277524641117,36,2.242290489478891,6015,2421,850,5,31,250,11.390945004491472,32,5.841610666408343,3476,836,500,5,0.07200000000000001,0.006000055504928223,0.138,0.012000111009856446,0.16100101007942402,0.14353764942973196,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,pseudo_full__cal,sc-only fine-tune (+ calibration),other,conditions_pooled_cal.npz@216c347f,0.29562555618189484,0.22501700190329005,0.19012782309492765,0.27791460488477016,0.2561733145444484,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.29717411790281023,0.27862638169889314,15,250,2.430944268607117,22,2.242290489478891,7946,598,940,5,10,250,2.381722646549528,36,2.242290489478891,6015,1715,686,5,11,250,12.92100748659745,32,5.864154253743737,3476,370,404,5,0.06400000000000002,0.0060254762449752485,0.08399999999999999,0.012050952489950497,0.09698012272806517,0.093519853283306,5,0.05600000000000001,0.004484580978957781,0.078,0.008969161957915563,0.06818082771511619,0.07312162990437765,5,True
+ye2026_sepsis,pooled,pooled,pseudo_full__raw,"sc-only fine-tune, real bulk",other,conditions_pooled_raw.npz@3b2d8ef2,0.14853801746689407,0.09882065376957522,0.037603700704565146,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.15048263259103734,0.3154897236225909,10,250,2.068681856672018,21,2.242290489478891,7946,857,1378,5,12,250,1.4153126789412998,36,2.242290489478891,6015,1738,850,5,12,250,5.920481237516834,32,5.841610666408343,3476,668,500,5,0.04,0.005874893752582625,0.041999999999999996,0.01174978750516525,0.03877344205024693,0.05615334641561245,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,real_full__raw,"Full FT, all training pairs",other,conditions_pooled_raw.npz@3b2d8ef2,0.534366534546327,0.43194654946201383,0.46768653125846193,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.5321590256780235,0.3154897236225909,24,250,2.4690747911501205,21,2.242290489478891,7946,732,1378,5,18,250,2.650429466106818,36,2.242290489478891,6015,2260,850,5,31,250,10.709884695257378,32,5.841610666408343,3476,676,500,5,0.11600000000000002,0.006047998787455289,0.14800000000000002,0.012095997574910578,0.19454372632947767,0.1575090050821027,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,real_lora__raw,"LoRA, all training pairs",lora,conditions_pooled_raw.npz@3b2d8ef2,0.5267612711229187,0.4133769716845018,0.46874787884206276,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.5241068798668347,0.3154897236225909,23,250,1.968642882095894,21,2.242290489478891,7946,617,1378,5,18,250,2.366296324712202,36,2.242290489478891,6015,2178,850,5,25,250,12.493041062643442,32,5.841610666408343,3476,751,500,5,0.10400000000000001,0.006005142373080123,0.136,0.012010284746160246,0.1862726918295739,0.15142035088196826,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,True
+ye2026_sepsis,pooled,pooled,zs__cal,Zero-shot + calibration,zs_cal,conditions_pooled_cal.npz@216c347f,0.12267970089558222,0.13184043745224291,0.03938214909552812,0.27791460488477016,0.2561733145444484,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.12417846066583334,0.27862638169889314,11,250,2.731942935144981,22,2.242290489478891,7946,1227,940,5,11,250,2.476223792531467,36,2.242290489478891,6015,1555,686,5,20,250,9.996570571006874,32,5.864154253743737,3476,863,404,5,0.036,0.006237081746578622,0.052000000000000005,0.012474163493157244,0.07970053891627406,0.06647284189722637,5,0.05600000000000001,0.004484580978957781,0.078,0.008969161957915563,0.06818082771511619,0.07312162990437765,5,True
+ye2026_sepsis,pooled,pooled,zs__pseudo,"Zero-shot, sc pseudobulk input (reference)",other,conditions_pooled_pseudo.npz@ad384538,0.4675925305606039,0.3340365132319549,0.20989887740136498,0.7296018266853084,0.6623267402105322,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,0.46286733618305737,0.7235754964275722,22,250,3.1760070066146633,64,2.2130500703124856,7946,1524,1834,5,33,250,3.1760070066146633,50,2.2130500703124856,6015,4018,936,5,32,250,12.173452947664723,52,5.8420983791792995,3476,953,435,5,0.044,0.006352014013229326,0.10400000000000001,0.012704028026458652,0.14111469662667156,0.09527588731707302,5,0.10400000000000001,0.0044261001406249705,0.134,0.008852200281249941,0.15968914557623096,0.14442137415541886,5,True
+ye2026_sepsis,pooled,pooled,zs__raw,"Zero-shot, real bulk",zs_raw,conditions_pooled_raw.npz@3b2d8ef2,-0.011802666469938336,-0.06281054931133792,-0.09476408639430833,0.31594581626202867,0.33159165418518455,0.9601843706820047,0.0017672040992177348,0.8464325241032679,0.9795648732264725,0.9897135650028939,-0.008889992586226199,0.3154897236225909,9,250,2.7305875416010466,21,2.242290489478891,7946,2661,1378,5,12,250,2.3657264694708195,36,2.242290489478891,6015,3654,850,5,12,250,7.67177546533644,32,5.841610666408343,3476,2343,500,5,0.004,0.00588216862796774,0.022,0.01176433725593548,0.024355325130830142,0.026198833987569038,5,0.048,0.004484580978957781,0.072,0.008969161957915563,0.07020130125867027,0.07613669392963093,5,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/ye2026_sepsis/pooled/manifest.json

@@ -0,0 +1,1013 @@
+{
+ "schema": "paired_ft_contrast_extra.v1",
+ "dataset": "ye2026_sepsis",
+ "design": "pooled",
+ "unit": "pooled",
+ "written_utc": "2026-10-02T06:42:46.708062+00:00",
+ "command": [
+  "tools/contrast_extra.py",
+  "--design",
+  "pooled",
+  "--dataset",
+  "ye2026_sepsis",
+  "--threads",
+  "4"
+ ],
+ "threads": 4,
+ "donors": [
+  "Abd-PS04",
+  "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",
+  "HC12",
+  "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-S164",
+  "Res-S166",
+  "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-S134",
+  "Uri-S147",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "n_samples": 82,
+ "contrast": {
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 61,
+  "n_control_donors": 21
+ },
+ "calls": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg": {
+   "arms": [
+    "lora_multik__raw",
+    "lora_n10__raw",
+    "lora_n20__raw",
+    "lora_n40__raw",
+    "lora_n5__raw",
+    "lora_recipe__raw",
+    "pseudo_full__cal",
+    "pseudo_full__raw",
+    "real_full__raw",
+    "real_lora__raw",
+    "zs__cal",
+    "zs__pseudo",
+    "zs__raw"
+   ],
+   "summary_sha256": "43274799eaee87239b511cfd1e9569c17e432b2f2cbadfcb569c49d09f5f6485",
+   "contrast_csv_sha256": "dcd4ce1976a653f5f469f679f2ccb48252393163248fa9685de15d79819c0fa9"
+  }
+ },
+ "notes": {
+  "source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores",
+  "contrast_also_checked_against": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled"
+ },
+ "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+ "deg_reference": {
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/deg_reference.npz",
+  "sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0"
+ },
+ "gene_exclusion": null,
+ "n_genes_disease_scores": 5975,
+ "genes_per_type": {
+  "T cell": 3258,
+  "B cell": 3310,
+  "Monocyte": 3289,
+  "NK cell": 3240
+ },
+ "arms": {
+  "lora_multik__raw": {
+   "call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/pooled/lora_multik__raw.npz",
+   "npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/_fetch_tmp/generated/ye2026_sepsis/pooled/lora_multik__raw.npz",
+   "npz_sha256": "d593a49d1f24d7032dd1d33df6d1f804f07c53c0db91c7d3099c67c8890921b3",
+   "receipt_verified": true,
+   "condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/pooled/conditions_pooled_raw.npz",
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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/ye2026_sepsis/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/ye2026_sepsis/scsemi_cv_20261002/pooled/cat.csv

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