Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/fold0/per_donor.csv

@@ -0,0 +1,18 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
+scsemi__raw,Abd-PS19,ped_sepsis,1500,7984,150,0.8833333333333333,0.4622995991983968,0.08733333333333333,0.11209919839679358,0.006666666666666667,0.2937124248496994,0.016,0.05586172344689379,0.0013333333333333333,0.0156563126252505,0.005333333333333333,0.06037074148296593,0.842067468269873,0.17976211899936204,0.6496072479379835,6,False,0.88,0.11333333333333333,0.8533333333333334,0.14666666666666667,0.6666666666666667,29.37124248496994,1953.0,2111.0
+scsemi__raw,Abd-PS23,ped_sepsis,1500,4309,150,0.3953333333333333,0.2529589231840334,0.42333333333333334,0.3272220932931075,0.068,0.32142028312833604,0.08533333333333333,0.013460199582269667,0.0,0.002088651659317707,0.028,0.08284984915293572,0.6207175678811789,0.5708838013443897,0.6683017944928925,4,False,0.8466666666666667,0.12666666666666668,0.72,0.18666666666666668,6.800000000000001,32.1420283128336,1950.0,1832.0
+scsemi__raw,Abd-S123,adult_sepsis,1500,6299,150,0.5226666666666666,0.16986823305286552,0.16866666666666666,0.08779171297031275,0.048666666666666664,0.5027782187648833,0.17733333333333334,0.10938244165740593,0.004,0.0007937767899666614,0.07866666666666666,0.1293856167645658,1.0096610043922316,0.7650207172461033,0.5751479904733526,4,False,0.88,0.23333333333333334,0.5733333333333334,0.4066666666666667,4.866666666666666,50.277821876488325,1952.0,2261.0
+scsemi__raw,Abd-S39,adult_sepsis,1500,4291,150,0.338,0.13819622465625728,0.072,0.06152412025168958,0.4086666666666667,0.6933115823817292,0.07333333333333333,0.049638778839431366,0.0033333333333333335,0.0013982754602656724,0.10466666666666667,0.05593101841062689,0.5692898314301251,0.9633289157537908,0.620094640856168,4,False,0.9666666666666667,0.14666666666666667,0.56,0.28,40.86666666666667,69.33115823817292,1951.0,3523.0
+scsemi__raw,Abd-S47,adult_sepsis,1500,7971,150,0.588,0.7027976414502571,0.2826666666666667,0.20474219044034625,0.07266666666666667,0.03224187680341237,0.044,0.019069125580228326,0.011333333333333334,0.0006272738677706687,0.0013333333333333333,0.040521891857985194,0.3079723999498181,0.6288356545294588,0.651998499520915,3,False,0.92,0.10666666666666667,0.7466666666666667,0.31333333333333335,7.2666666666666675,3.224187680341237,1950.0,2030.0
+scsemi__raw,Abd-S66,adult_sepsis,1500,7946,150,0.36866666666666664,0.49295242889504154,0.096,0.23873647118046817,0.4573333333333333,0.03788069468915178,0.043333333333333335,0.18688648376541656,0.0026666666666666666,0.0003775484520513466,0.032,0.04316637301787063,0.8434835137175937,0.47033269157789737,0.6118203530903721,16,False,0.9533333333333334,0.1,0.3933333333333333,0.22666666666666666,45.733333333333334,3.7880694689151775,1949.0,1821.0
+scsemi__raw,HC01,adult_HC,1500,10173,150,0.6606666666666666,0.5901897178806645,0.059333333333333335,0.09938071365378945,0.15133333333333332,0.1862774009633343,0.08066666666666666,0.06772830040302762,0.021333333333333333,0.028408532389658903,0.02666666666666667,0.028015334709525212,0.1668306300992823,0.3550119706716009,0.6613515235636601,6,False,0.7866666666666666,0.1,0.44,0.20666666666666667,15.133333333333333,18.62774009633343,1952.0,2276.0
+scsemi__raw,HC07,adult_HC,1500,9812,150,0.5506666666666666,0.3848348960456584,0.06533333333333333,0.03770892784345699,0.134,0.21962902568283735,0.21666666666666667,0.3080921320831635,0.012666666666666666,0.019262128006522626,0.020666666666666667,0.03047289033836119,0.3869123522217692,0.4991259018586224,0.7332502156066073,2,False,0.84,0.14,0.4266666666666667,0.26666666666666666,13.4,21.962902568283734,1952.0,2035.0
+scsemi__raw,IC23,adult_ICU_ctrl,1500,13774,150,0.9526666666666667,0.42819805430521274,0.046,0.11986351096268331,0.0,0.3843473210396399,0.0,0.024466385944533178,0.0,0.007840859590532889,0.0013333333333333333,0.03528386815739799,1.0489372247229078,0.2960984586998728,0.4699723184698366,10,False,0.7933333333333333,0.17333333333333334,0.98,0.07333333333333333,0.0,38.434732103963995,1951.0,1894.0
+scsemi__raw,PHC03,ped_HC,1500,9638,150,0.5393333333333333,0.6757626063498651,0.26266666666666666,0.17804523760116206,0.08133333333333333,0.055613197758871136,0.09266666666666666,0.07273293214359826,0.016666666666666666,0.011516912222452791,0.007333333333333333,0.006329113924050633,0.27285854603306353,0.5245802286446084,0.6181814069015706,15,False,0.9533333333333334,0.02666666666666667,0.5933333333333334,0.14,8.133333333333333,5.561319775887114,1952.0,1660.5
+scsemi__raw,PIC04,ped_ICU_ctrl,1500,11535,150,0.42733333333333334,0.36341569137407886,0.07133333333333333,0.08253142609449501,0.436,0.4273948851322063,0.02,0.03233636757693975,0.006,0.006501950585175552,0.03933333333333333,0.08781967923710446,0.1450455136540963,0.46601933835481935,0.5283463887230075,12,False,0.9733333333333334,0.36,0.82,0.1,43.6,42.73948851322063,1953.0,1144.0
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+scsemi__raw,Res-S139,adult_sepsis,1500,2657,150,0.4886666666666667,0.3522770041400075,0.078,0.06925103500188182,0.3473333333333333,0.26345502446368085,0.06466666666666666,0.29055325555137373,0.016666666666666666,0.00978547233722243,0.004666666666666667,0.014678208505833647,0.4717962614477481,0.4788067877633468,0.6762125048534721,3,False,0.9466666666666667,0.14,0.4533333333333333,0.16666666666666666,34.733333333333334,26.345502446368087,1952.0,1637.0
+scsemi__raw,Res-S26,adult_sepsis,1500,6036,150,0.744,0.6973161033797217,0.10933333333333334,0.145791915175613,0.058666666666666666,0.023028495692511596,0.08666666666666667,0.11911862160371106,0.0,0.0001656726308813784,0.0013333333333333333,0.0145791915175613,0.16464413518886675,0.608009358576924,0.5622350961550737,4,False,0.6666666666666666,0.06666666666666667,0.5266666666666666,0.20666666666666667,5.866666666666666,2.3028495692511597,1953.0,3953.0
+scsemi__raw,Res-S77,adult_sepsis,1500,7804,150,0.368,0.685033316248078,0.09666666666666666,0.20861096873398258,0.4633333333333333,0.04651460789338801,0.036,0.023193234238851872,0.002,0.0012813941568426447,0.034,0.035366478728856995,0.8606881940885016,0.5993076173488051,0.6570445274898101,11,False,0.9266666666666666,0.06,0.6133333333333333,0.38666666666666666,46.33333333333333,4.651460789338801,1953.0,2095.0
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+scsemi__raw,Uri-S147,adult_sepsis,1500,7529,150,0.5426666666666666,0.5427015539912339,0.24266666666666667,0.20268295922433258,0.13533333333333333,0.18262717492362865,0.04933333333333333,0.031212644441492896,0.007333333333333333,0.004648691725328729,0.02266666666666667,0.036126975693983265,0.12157807588435829,0.28425560234500524,0.594793812167712,2,False,0.8666666666666667,0.09333333333333334,0.6266666666666667,0.25333333333333335,13.533333333333333,18.262717492362864,1951.0,2024.0

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/fold0/summary.json

@@ -0,0 +1,505 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-07T03:00:25.201731+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",
+  "ye2026_sepsis",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/fold0",
+  "--threads",
+  "8",
+  "--arm",
+  "scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/scsemi__raw.npz",
+  "--case-groups",
+  "adult_sepsis,ped_sepsis",
+  "--control-groups",
+  "adult_HC,adult_ICU_ctrl,ped_HC,ped_ICU_ctrl"
+ ],
+ "arms": [
+  "scsemi__raw"
+ ],
+ "donors": [
+  "Abd-PS19",
+  "Abd-PS23",
+  "Abd-S123",
+  "Abd-S39",
+  "Abd-S47",
+  "Abd-S66",
+  "HC01",
+  "HC07",
+  "IC23",
+  "PHC03",
+  "PIC04",
+  "Res-PS25",
+  "Res-S139",
+  "Res-S26",
+  "Res-S77",
+  "Skin-S140",
+  "Uri-S147"
+ ],
+ "n_donors": 17,
+ "reference": {
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+  "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+  "features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
+  "n_r1_cells": 2550,
+  "pca": {
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+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
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+  "control_groups": [
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+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 12,
+  "n_control_donors": 5,
+  "n_donors_in_neither": 0,
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+  "ctrl": [
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+   true,
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+   true,
+   false,
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+  "groups": [
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_HC",
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis"
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+ "deg_definition": {
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+  "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
+  "functions": [
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+   "top_deg_genes",
+   "jaccard"
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+  "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
+  "top_n": 50,
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paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/fold1/arms/scsemi__raw/generated_cells.parquet

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