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/fold3/contrast.csv

@@ -0,0 +1,14 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+scsemi__raw,T cell,mean_cp10k,3267,0.03635784167664253,0.4054314090999793,-0.13714311489887304,0.37618023838203085,13,3,13,3,48746,13022,,,,,,,,,,,
+scsemi__raw,T cell,pseudobulk_log1p_cpm,3267,-0.030160970302942038,0.43288100523285106,-0.13960265142868528,0.21428685326583358,13,3,13,3,48746,13022,,,,,,,,,,,
+scsemi__raw,B cell,mean_cp10k,3235,0.1624857581591851,0.28791499229461276,0.04907388296813311,0.4159126025010562,13,3,13,3,20084,2844,,,,,,,,,,,
+scsemi__raw,B cell,pseudobulk_log1p_cpm,3235,0.027415848115578886,0.22618496973249358,-0.03133819456171851,0.25182113150124613,13,3,13,3,20084,2844,,,,,,,,,,,
+scsemi__raw,Monocyte,mean_cp10k,3323,0.09934719947734288,0.42584414362557405,-0.06746492581027583,0.3666554324988477,13,3,13,3,19536,5156,,,,,,,,,,,
+scsemi__raw,Monocyte,pseudobulk_log1p_cpm,3323,0.06832838657944222,0.49229818193386826,-0.09438347074457167,0.29808654017733804,13,3,13,3,19536,5156,,,,,,,,,,,
+scsemi__raw,NK cell,mean_cp10k,3307,0.4088199409821355,0.3851833932466608,0.3203104279082378,0.33954114753673903,13,3,13,2,7787,821,,,,,,,,,,,
+scsemi__raw,NK cell,pseudobulk_log1p_cpm,3307,0.09841533753009564,0.2648524879635766,0.07168428110096443,0.11224281231600854,13,3,13,2,7787,821,,,,,,,,,,,
+scsemi__raw,T cell,welch_top50_deg,5975,,,,,13,3,13,3,48746,13022,True,0,0.0,50,0,97,0,0,0.0,0,0
+scsemi__raw,B cell,welch_top50_deg,5975,,,,,13,3,13,3,20084,2844,True,0,0.0,50,0,122,0,0,0.0,0,0
+scsemi__raw,Monocyte,welch_top50_deg,5975,,,,,13,3,13,3,19536,5156,True,0,0.0,5,7,5,7,0,0.0,0,0
+scsemi__raw,NK cell,welch_top50_deg,5975,,,,,13,3,13,2,7787,821,True,0,0.0,30,10,30,10,0,0.0,0,0
+scsemi__raw,DC,welch_top50_deg,5975,,,,,12,3,12,3,284,396,True,0,0.0,50,3,63,3,0,0.0,0,0

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/fold3/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-S102,adult_sepsis,1500,9512,150,0.7313333333333333,0.47981497056349875,0.18,0.39318755256518084,0.052,0.0053616484440706475,0.0013333333333333333,0.095878889823381,0.0013333333333333333,0.0007359125315391085,0.034,0.02502102607232969,0.615466218110457,0.5809371755543881,0.5189254737687113,9,False,0.9866666666666667,0.11333333333333333,0.9733333333333334,0.24,5.2,0.5361648444070648,1970.0,1646.0
+scsemi__raw,Abd-S103,adult_sepsis,1500,9423,150,0.36866666666666664,0.4813753581661891,0.478,0.14782977820227103,0.066,0.0024408362517245037,0.058,0.04393505253104107,0.0013333333333333333,0.00021224663058473945,0.028,0.3242067282181895,0.8178308394354239,0.6326678068482368,0.6501249244403682,2,False,0.94,0.38666666666666666,0.68,0.44,6.6000000000000005,0.24408362517245036,1971.0,971.0
+scsemi__raw,Abd-S51,adult_sepsis,1500,6865,150,0.31066666666666665,0.25273124544792425,0.08266666666666667,0.269482884195193,0.49066666666666664,0.3551347414420976,0.027333333333333334,0.03670793882010197,0.011333333333333334,0.0014566642388929353,0.07733333333333334,0.08448652585579024,0.4066880310755037,0.49873446759411355,0.5691520351044408,3,False,1.0,0.18666666666666668,0.8133333333333334,0.4266666666666667,49.06666666666666,35.51347414420976,1967.0,1849.0
+scsemi__raw,Abd-S83,adult_sepsis,1500,6209,150,0.25333333333333335,0.3924947656627476,0.06066666666666667,0.16991464003865356,0.496,0.049927524561120956,0.014,0.3013367692059913,0.025333333333333333,0.0009663391850539539,0.15066666666666667,0.0853599613464326,1.071492349814785,0.5160252489243918,0.5407519448180522,8,False,1.0,0.16666666666666666,0.5466666666666666,0.4866666666666667,49.6,4.992752456112096,1973.0,1649.0
+scsemi__raw,HC12,adult_HC,1500,3720,150,0.6433333333333333,0.5456989247311828,0.05333333333333334,0.05725806451612903,0.134,0.14623655913978495,0.11133333333333334,0.2196236559139785,0.024,0.008870967741935484,0.034,0.022311827956989248,0.24890322580645166,0.5323006254835988,0.6355015005169565,9,False,0.96,0.05333333333333334,0.48,0.4266666666666667,13.4,14.623655913978496,1970.0,2457.5
+scsemi__raw,IC22,adult_ICU_ctrl,1500,2107,150,0.8686666666666667,0.16753678215472234,0.11066666666666666,0.01613668723303275,0.006666666666666667,0.722828666350261,0.0,0.019933554817275746,0.006,0.04129093497864262,0.008,0.0322733744660655,1.5913197278911562,1.1255936603700172,0.49432038458103017,16,False,0.98,0.05333333333333334,0.28,0.29333333333333333,0.6666666666666667,72.2828666350261,1969.0,3217.0
+scsemi__raw,PIC01,ped_ICU_ctrl,1500,8345,150,0.6213333333333333,0.647813061713601,0.056666666666666664,0.07070101857399641,0.15933333333333333,0.12055122828040743,0.09333333333333334,0.11024565608148593,0.034666666666666665,0.004313960455362493,0.034666666666666665,0.04637507489514679,0.1382696225284602,0.5079475218536647,0.547579906119057,12,False,0.96,0.08666666666666667,0.4066666666666667,0.28,15.933333333333334,12.055122828040743,1970.0,2157.0
+scsemi__raw,Res-PS02,ped_sepsis,1500,6473,150,0.634,0.5892167464854009,0.15666666666666668,0.33848292909006644,0.019333333333333334,0.012050054070755446,0.050666666666666665,0.05051753437355168,0.0,0.0,0.13933333333333334,0.009732735980225553,0.36363252484679953,0.6592152399467534,0.6123429144959585,10,False,1.0,0.15333333333333332,0.74,0.4,1.9333333333333333,1.2050054070755445,1972.0,1680.0
+scsemi__raw,Res-PS16,ped_sepsis,1500,7403,150,0.658,0.4078076455491017,0.05533333333333333,0.5172227475347831,0.06,0.0009455626097528029,0.013333333333333334,0.017695528839659597,0.06466666666666666,0.00013508037282182898,0.14866666666666667,0.05619343509388086,0.9325032194155523,0.7266430987733835,0.5427230925572364,15,False,1.0,0.20666666666666667,0.82,0.25333333333333335,6.0,0.09455626097528029,1968.0,1895.0
+scsemi__raw,Res-PS21,ped_sepsis,1500,6455,150,0.884,0.2689388071262587,0.086,0.19550735863671573,0.008,0.339426800929512,0.016,0.06893880712625872,0.0013333333333333333,0.002168861347792409,0.004666666666666667,0.12501936483346243,1.2301223857474826,0.3938797964615466,0.5479908057075089,13,False,1.0,0.18,0.7733333333333333,0.4,0.8,33.9426800929512,1971.0,1720.0
+scsemi__raw,Res-S125,adult_sepsis,1500,3975,150,0.5413333333333333,0.510188679245283,0.186,0.24125786163522012,0.19666666666666666,0.14440251572327045,0.02266666666666667,0.0810062893081761,0.007333333333333333,0.0015094339622641509,0.046,0.021635220125786163,0.22719496855345914,0.28988953232584097,0.6238047090274894,5,False,0.9666666666666667,0.07333333333333333,0.5533333333333333,0.44,19.666666666666664,14.440251572327046,1972.5,1933.0
+scsemi__raw,Res-S136,adult_sepsis,1500,2882,150,0.32066666666666666,0.3650242886884108,0.025333333333333333,0.04996530187369882,0.6,0.4961832061068702,0.005333333333333333,0.034004163775156145,0.010666666666666666,0.004857737682165163,0.038,0.04996530187369882,0.2192514457552625,0.5643591909516315,0.6241872461545281,2,False,0.9933333333333333,0.05333333333333334,0.5666666666666667,0.48,60.0,49.61832061068702,1972.0,3386.0
+scsemi__raw,Res-S149,adult_sepsis,1500,7304,150,0.5686666666666667,0.37089266155531214,0.10133333333333333,0.10282037239868565,0.228,0.40963855421686746,0.034666666666666665,0.06489594742606791,0.012,0.003696604600219058,0.05533333333333333,0.04805585980284775,0.42670974808324197,0.37943529483069355,0.6982306319992936,1,True,0.9533333333333334,0.12,0.5533333333333333,0.31333333333333335,22.8,40.963855421686745,1970.0,2356.0
+scsemi__raw,Skin-S38,adult_sepsis,1500,9976,150,0.574,0.8330994386527666,0.08,0.13572574178027266,0.214,0.00020048115477145148,0.08,0.02475942261427426,0.02,0.00020048115477145148,0.032,0.006014434643143544,0.6296503608660786,0.8341668304791459,0.5909065650789878,15,False,0.9533333333333334,0.08666666666666667,0.5733333333333334,0.23333333333333334,21.4,0.020048115477145148,1971.0,1675.0
+scsemi__raw,Uri-S134,adult_sepsis,1500,9030,150,0.38,0.3501661129568106,0.11533333333333333,0.038981173864894796,0.44733333333333336,0.5069767441860465,0.014666666666666666,0.037541528239202655,0.006666666666666667,0.0035437430786267998,0.036,0.06279069767441861,0.2186179401993356,0.5870901000982757,0.6335703962967585,3,False,1.0,0.17333333333333334,0.5,0.4266666666666667,44.733333333333334,50.697674418604656,1969.0,2577.0
+scsemi__raw,Uri-S20,adult_sepsis,1500,4516,150,0.3233333333333333,0.41054030115146145,0.068,0.0812666076173605,0.25933333333333336,0.3961470327723649,0.004666666666666667,0.03897254207263064,0.037333333333333336,0.001550044286979628,0.30733333333333335,0.07152347209920283,0.5431863005609683,0.36044145076903955,0.5602654819070938,2,False,1.0,0.11333333333333333,0.7066666666666667,0.5333333333333333,25.933333333333337,39.614703277236494,1972.0,4883.5

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/fold3/summary.json

@@ -0,0 +1,501 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-07T03:01:19.978261+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/fold3",
+  "--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/fold3/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-S102",
+  "Abd-S103",
+  "Abd-S51",
+  "Abd-S83",
+  "HC12",
+  "IC22",
+  "PIC01",
+  "Res-PS02",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-S125",
+  "Res-S136",
+  "Res-S149",
+  "Skin-S38",
+  "Uri-S134",
+  "Uri-S20"
+ ],
+ "n_donors": 16,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis",
+  "reference_sha256": "bac12da8a241652cb75100a1b082b2be56806c9bf2fd20ce6f927f19683ea5b8",
+  "features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
+  "n_r1_cells": 2400,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.37217968702316284,
+   "n_fit_cells": 2400
+  },
+  "r2_control": {
+   "precision": 0.9966666666666667,
+   "coverage": 1.0,
+   "density": 2.0915,
+   "n_query": 2400,
+   "depth_matched": {
+    "precision": 0.9970833333333333,
+    "coverage": 1.0,
+    "density": 2.0460833333333333
+   }
+  },
+  "observed_l1_loo_null_mean": 0.5743329400790451
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "adult_sepsis",
+   "ped_sepsis"
+  ],
+  "control_groups": [
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_HC",
+   "ped_ICU_ctrl"
+  ],
+  "n_case_donors": 13,
+  "n_control_donors": 3,
+  "n_donors_in_neither": 0,
+  "case": [
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_HC",
+   "adult_ICU_ctrl",
+   "ped_ICU_ctrl",
+   "ped_sepsis",
+   "ped_sepsis",
+   "ped_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis",
+   "adult_sepsis"
+  ]
+ },
+ "deg_definition": {
+  "enabled": true,
+  "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": [
+   "welch_bh_deg",
+   "top_deg_genes",
+   "jaccard"
+  ],
+  "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,
+  "fdr": 0.05,
+  "n_genes": 5975,
+  "types": [
+   "T cell",
+   "B cell",
+   "Monocyte",
+   "NK cell",
+   "DC"
+  ],
+  "aggregates_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",
+  "aggregates_sha256": "9886ea64da90b1db6a07984d5d61d7dab04ee0beee7d4094ee3672316c2691d0",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
+  "observed": {
+   "T cell": {
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+    "n_tested": 5638,
+    "n_case_donors": 13,
+    "n_control_donors": 3,
+    "n_cells": 48746,
+    "top_list_size": 50
+   },
+   "B cell": {
+    "n_significant": 122,
+    "n_tested": 5474,
+    "n_case_donors": 13,
+    "n_control_donors": 3,
+    "n_cells": 20084,
+    "top_list_size": 50
+   },
+   "Monocyte": {
+    "n_significant": 5,
+    "n_tested": 5518,
+    "n_case_donors": 13,
+    "n_control_donors": 3,
+    "n_cells": 19536,
+    "top_list_size": 5
+   },
+   "NK cell": {
+    "n_significant": 30,
+    "n_tested": 5250,
+    "n_case_donors": 13,
+    "n_control_donors": 3,
+    "n_cells": 7787,
+    "top_list_size": 30
+   },
+   "DC": {
+    "n_significant": 63,
+    "n_tested": 4453,
+    "n_case_donors": 12,
+    "n_control_donors": 3,
+    "n_cells": 284,
+    "top_list_size": 50
+   }
+  },
+  "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
+ },
+ "headline": {
+  "scsemi__raw": {
+   "comp_l1": 0.6050524317931512,
+   "comp_l1_obs_loo_null": 0.5743329400790451,
+   "precision": 0.9808333333333333,
+   "coverage": 0.13791666666666666,
+   "precision_dm": 0.6229166666666667,
+   "coverage_dm": 0.37958333333333333,
+   "pb_r_median": 0.5800293000917143,
+   "pb_top1": 0.0625,
+   "mono_pct_gen": 21.48333333333333,
+   "mono_pct_obs": 23.17782597649799,
+   "median_umi_gen": 1970.0,
+   "median_umi_obs": 1947.0,
+   "contrast_mean_cp10k_r_gen": 0.1767526850738265,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.04099965048054367,
+   "contrast_mean_cp10k_r_broadcast": 0.3760934845667067,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.3540541612156974,
+   "deg_top50_T": 0,
+   "deg_top50_B": 0,
+   "deg_top50_Mono": 0,
+   "deg_top50_NK": 0,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 0,
+   "deg_top50_max": 185,
+   "deg_top50_sum_4type": 0,
+   "deg_top50_sum_broadcast": 0,
+   "seconds": 11.1
+  }
+ },
+ "per_arm": {
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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/fold4/arms/scsemi__raw/deg_top50_lists.csv

@@ -0,0 +1,49 @@
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