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/fold4/per_donor.csv

@@ -0,0 +1,17 @@
+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-PS20,ped_sepsis,1500,7286,150,0.39666666666666667,0.30496843261048584,0.4066666666666667,0.5780949766675817,0.034,0.08770244304144935,0.0013333333333333333,0.007823222618720834,0.15133333333333332,0.0005489980785067252,0.01,0.02086192698325556,0.48496513862201485,0.8183075443274621,0.5686977303509008,6,False,0.94,0.04,0.74,0.18,3.4000000000000004,8.770244304144935,1978.0,1820.0
+scsemi__raw,Abd-PS27,ped_sepsis,1500,9427,150,0.6513333333333333,0.6126021003500584,0.20933333333333334,0.06078285774901877,0.0013333333333333333,0.13196138750397793,0.0026666666666666666,0.010289593720165482,0.0,0.0029701920016972526,0.13533333333333333,0.1813938686750822,0.37456341713517904,0.5444559358148133,0.5548955819065788,2,False,0.9333333333333333,0.18,0.62,0.3333333333333333,0.13333333333333333,13.196138750397793,1976.0,2356.0
+scsemi__raw,Abd-S42,adult_sepsis,1500,6567,150,0.6006666666666667,0.5748439165524593,0.09666666666666666,0.09760925841327851,0.23133333333333334,0.17039744175422566,0.034666666666666665,0.05862646566164154,0.014,0.0016750418760469012,0.02266666666666667,0.0968478757423481,0.19816719963453636,0.28354035879010253,0.6382119656323586,1,True,0.9733333333333334,0.16,0.76,0.2866666666666667,23.133333333333333,17.039744175422566,1976.0,1982.0
+scsemi__raw,Abd-S54,adult_sepsis,1500,7818,150,0.6273333333333333,0.4854182655410591,0.09533333333333334,0.1364799181376311,0.17333333333333334,0.012918905090816066,0.05733333333333333,0.340752110514198,0.025333333333333333,0.0011511895625479663,0.021333333333333333,0.023279611153747763,0.6530232796111537,0.5525001038535718,0.516471997552279,10,False,0.9933333333333333,0.08666666666666667,0.94,0.16,17.333333333333336,1.2918905090816066,1974.0,1933.5
+scsemi__raw,Abd-S98,adult_sepsis,1500,5010,150,0.18266666666666667,0.7477045908183633,0.019333333333333334,0.10958083832335329,0.72,0.019560878243512974,0.005333333333333333,0.11037924151696607,0.03933333333333333,0.0015968063872255488,0.03333333333333333,0.011177644710578843,1.5206626746506988,0.6112521506261259,0.6381786523344748,15,False,0.96,0.18,0.47333333333333333,0.29333333333333333,72.0,1.9560878243512974,1976.0,2016.0
+scsemi__raw,HC16,adult_HC,1500,9614,150,0.5933333333333334,0.511441647597254,0.08,0.05325566881630955,0.092,0.1367796962762638,0.19266666666666668,0.28073642604535054,0.024,0.010609527771999168,0.018,0.007177033492822967,0.26569891130989537,0.4818593323054142,0.6284098702856629,8,False,0.8666666666666667,0.07333333333333333,0.41333333333333333,0.20666666666666667,9.2,13.67796962762638,1974.0,1764.0
+scsemi__raw,IC15,adult_ICU_ctrl,1500,15576,150,0.6006666666666667,0.5791602465331279,0.09666666666666666,0.045839753466872114,0.222,0.278954802259887,0.03866666666666667,0.04840780688238315,0.013333333333333334,0.0104648176682075,0.028666666666666667,0.03717257318952234,0.1504036979969183,0.41354969125033086,0.67941601752062,4,False,0.96,0.19333333333333333,0.6533333333333333,0.28,22.2,27.8954802259887,1976.0,1517.0
+scsemi__raw,PHC02,ped_HC,1500,6519,150,0.588,0.5781561589200798,0.07933333333333334,0.16643657002607762,0.18066666666666667,0.16612977450529223,0.1,0.057984353428439946,0.02266666666666667,0.006749501457278723,0.029333333333333333,0.02454364166283172,0.17420647338548853,0.19148225666934166,0.6489961070400546,8,False,0.88,0.21333333333333335,0.5266666666666666,0.14,18.066666666666666,16.612977450529222,1975.0,1516.0
+scsemi__raw,PIC02,ped_ICU_ctrl,1500,6570,150,0.5053333333333333,0.4786910197869102,0.3486666666666667,0.2785388127853881,0.044,0.14170471841704718,0.023333333333333334,0.036225266362252664,0.066,0.0030441400304414,0.012666666666666666,0.06179604261796043,0.31945205479452055,0.2065727806374711,0.6218467580495344,2,False,0.9933333333333333,0.5333333333333333,0.7333333333333333,0.5666666666666667,4.3999999999999995,14.170471841704718,1977.0,1062.5
+scsemi__raw,Res-PS03,ped_sepsis,1500,5934,150,0.362,0.15267947421638017,0.08933333333333333,0.8156386922817661,0.4573333333333333,0.009605662285136502,0.042,0.014492753623188406,0.006,0.0,0.043333333333333335,0.007583417593528817,1.4526107178968655,1.3250674709710555,0.565834342194383,16,False,0.98,0.08,0.7666666666666667,0.16666666666666666,45.733333333333334,0.9605662285136503,1977.0,1871.0
+scsemi__raw,Res-S127,adult_sepsis,1500,2869,150,0.37266666666666665,0.28302544440571625,0.09266666666666666,0.08051585918438481,0.45,0.5137678633670268,0.038,0.06099686301847333,0.012666666666666666,0.006273963053328686,0.034,0.05542000697107006,0.21636946671314047,0.7286070088209968,0.6215658230201944,2,False,0.9933333333333333,0.14666666666666667,0.6933333333333334,0.43333333333333335,45.0,51.376786336702686,1975.0,2020.0
+scsemi__raw,Res-S164,adult_sepsis,1500,6275,150,0.5733333333333334,0.5641434262948207,0.078,0.0796812749003984,0.14533333333333334,0.21529880478087648,0.09466666666666666,0.08366533864541832,0.07266666666666667,0.020239043824701194,0.036,0.03697211155378486,0.14523771580345285,0.2706143531207481,0.5942846358427757,5,False,0.9,0.17333333333333334,0.72,0.2733333333333333,14.533333333333335,21.529880478087648,1974.0,2196.0
+scsemi__raw,Res-S166,adult_sepsis,1500,6119,150,0.5313333333333333,0.29874162444843927,0.11133333333333334,0.20934793266873672,0.23266666666666666,0.3784932178460533,0.03,0.07991501879392057,0.014666666666666666,0.002941657133518549,0.08,0.030560549109331592,0.5875123386174211,0.4559951768035859,0.6940170398473481,5,False,0.9066666666666666,0.15333333333333332,0.5733333333333334,0.26666666666666666,23.266666666666666,37.84932178460533,1976.0,2014.0
+scsemi__raw,Res-S87,adult_sepsis,1500,3841,150,0.9133333333333333,0.3967716740432179,0.004,0.01900546732621713,0.008,0.4712314501431919,0.05,0.058318146316063524,0.004,0.014579536579015881,0.020666666666666667,0.040093725592293676,1.0331233185802307,0.6418650409196258,0.5517202607967837,3,False,0.98,0.32,0.68,0.49333333333333335,0.8,47.12314501431919,1976.0,1793.0
+scsemi__raw,Skin-S43,adult_sepsis,1500,7439,150,0.43,0.7525205000672134,0.07533333333333334,0.07554778868127436,0.344,0.05135098803602635,0.024666666666666667,0.015459067078908456,0.004,0.0016131200430165346,0.122,0.10350853609356096,0.6454699108303088,0.6767931457041653,0.6630083340069838,5,False,1.0,0.19333333333333333,0.6866666666666666,0.4,34.4,5.135098803602635,1975.0,2254.0
+scsemi__raw,Uri-S93,adult_sepsis,1500,8007,150,0.4093333333333333,0.5157986761583614,0.086,0.3058573747970526,0.3466666666666667,0.08742350443362058,0.012666666666666666,0.04421131509928812,0.002,0.0012489072061945797,0.14333333333333334,0.0454602223054827,0.7157347321094044,0.29301554302897825,0.6214479580213371,2,False,1.0,0.12,0.7333333333333333,0.4866666666666667,34.66666666666667,8.742350443362058,1975.5,4595.0

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/fold4/summary.json

@@ -0,0 +1,501 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-07T03:01:41.409404+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/fold4",
+  "--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/fold4/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-PS20",
+  "Abd-PS27",
+  "Abd-S42",
+  "Abd-S54",
+  "Abd-S98",
+  "HC16",
+  "IC15",
+  "PHC02",
+  "PIC02",
+  "Res-PS03",
+  "Res-S127",
+  "Res-S164",
+  "Res-S166",
+  "Res-S87",
+  "Skin-S43",
+  "Uri-S93"
+ ],
+ "n_donors": 16,
+ "reference": {
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+  "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
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+ "contrast_definition": {
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+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
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+   "ped_sepsis"
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+  "n_case_donors": 12,
+  "n_control_donors": 4,
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+  "groups": [
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis"
+  ]
+ },
+ "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",
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+ "per_arm": {
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+ },
+ "seconds": 11.4
+}

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/pooled/arms/scsemi__raw/deg_top50_lists.csv

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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/pooled/arms/scsemi__raw/generated_cells.parquet

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