Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw2/score/arms/lora/deg_top50_lists.csv

@@ -0,0 +1,64 @@
+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000119508
+T cell,observed,2,ENSG00000177570
+T cell,observed,3,ENSG00000022556
+T cell,observed,4,ENSG00000137968
+T cell,observed,5,ENSG00000173262
+T cell,observed,6,ENSG00000153234
+T cell,observed,7,ENSG00000130413
+T cell,observed,8,ENSG00000165646
+T cell,observed,9,ENSG00000108839
+T cell,observed,10,ENSG00000138722
+T cell,observed,11,ENSG00000166435
+T cell,observed,12,ENSG00000100453
+T cell,observed,13,ENSG00000100450
+T cell,observed,14,ENSG00000137441
+T cell,observed,15,ENSG00000151240
+T cell,observed,16,ENSG00000184368
+T cell,observed,17,ENSG00000184005
+T cell,observed,18,ENSG00000126838
+T cell,observed,19,ENSG00000205336
+T cell,observed,20,ENSG00000124406
+T cell,observed,21,ENSG00000150764
+T cell,observed,22,ENSG00000179104
+T cell,observed,23,ENSG00000135541
+T cell,observed,24,ENSG00000172543
+T cell,observed,25,ENSG00000198380
+T cell,observed,26,ENSG00000111860
+B cell,observed,1,ENSG00000185304
+B cell,observed,2,ENSG00000154721
+B cell,observed,3,ENSG00000164292
+B cell,observed,4,ENSG00000197520
+B cell,observed,5,ENSG00000174469
+B cell,observed,6,ENSG00000177570
+B cell,observed,7,ENSG00000069020
+B cell,observed,8,ENSG00000258484
+B cell,observed,9,ENSG00000125726
+B cell,observed,10,ENSG00000136205
+B cell,observed,11,ENSG00000116741
+B cell,observed,12,ENSG00000153234
+B cell,observed,13,ENSG00000166435
+B cell,observed,14,ENSG00000102221
+B cell,observed,15,ENSG00000135541
+B cell,observed,16,ENSG00000145088
+B cell,observed,17,ENSG00000144802
+B cell,observed,18,ENSG00000155307
+B cell,observed,19,ENSG00000081052
+B cell,observed,20,ENSG00000138031
+B cell,observed,21,ENSG00000082438
+B cell,observed,22,ENSG00000106799
+B cell,observed,23,ENSG00000047346
+B cell,observed,24,ENSG00000163219
+B cell,observed,25,ENSG00000080298
+B cell,observed,26,ENSG00000082805
+B cell,observed,27,ENSG00000131725
+NK cell,observed,1,ENSG00000198848
+NK cell,observed,2,ENSG00000177570
+NK cell,observed,3,ENSG00000022556
+NK cell,observed,4,ENSG00000166435
+NK cell,observed,5,ENSG00000100450
+NK cell,observed,6,ENSG00000139182
+NK cell,observed,7,ENSG00000082805
+NK cell,observed,8,ENSG00000135541
+NK cell,observed,9,ENSG00000136068
+NK cell,observed,10,ENSG00000067369

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw2/score/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
+lora,T cell,mean_cp10k,2872,0.30806212595655197,0.3625775242708975,0.1961302895883202,0.38421475138891836,6,6,6,6,67243,11982,,,,,,,,,,,
+lora,T cell,pseudobulk_log1p_cpm,2872,0.18452857247363613,0.48116424377694494,0.09904651429367538,0.20695889617134333,6,6,6,6,67243,11982,,,,,,,,,,,
+lora,B cell,mean_cp10k,3000,0.12431387870744201,0.3415650846257105,0.08368894040258096,0.13580681721090138,6,6,6,6,10555,890,,,,,,,,,,,
+lora,B cell,pseudobulk_log1p_cpm,3000,0.06750773737053338,0.444312077425732,0.03376212384158388,0.08410385163145427,6,6,6,6,10555,890,,,,,,,,,,,
+lora,Monocyte,mean_cp10k,3030,0.21086226632712277,0.5778525672489366,0.03951403192058372,0.31188196120253325,6,6,6,6,25096,2829,,,,,,,,,,,
+lora,Monocyte,pseudobulk_log1p_cpm,3030,0.07938286231929745,0.5873665894516398,0.0026420234021854194,0.13154169585881811,6,6,6,6,25096,2829,,,,,,,,,,,
+lora,NK cell,mean_cp10k,2903,0.06970372641062719,0.3037611845888768,0.01499186298176658,0.1832429928475508,6,6,6,6,16282,1172,,,,,,,,,,,
+lora,NK cell,pseudobulk_log1p_cpm,2903,-0.01530121322438831,0.3887293796905318,-0.039482287920825636,0.05408038912619831,6,6,6,6,16282,1172,,,,,,,,,,,
+lora,T cell,welch_top50_deg,5498,,,,,6,6,6,6,67243,11982,True,0,0.0,26,0,26,0,0,0.0,0,0
+lora,B cell,welch_top50_deg,5498,,,,,6,6,6,6,10555,890,True,0,0.0,27,0,27,0,0,0.0,0,0
+lora,Monocyte,welch_top50_deg,5498,,,,,6,6,6,6,25096,2829,True,0,,0,0,0,0,0,,0,0
+lora,NK cell,welch_top50_deg,5498,,,,,6,6,6,6,16282,1172,True,0,0.0,10,0,10,0,0,0.0,0,0
+lora,DC,welch_top50_deg,5498,,,,,6,6,6,6,1911,307,True,0,,0,0,0,0,0,,0,0

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw2/score/per_donor.csv

@@ -0,0 +1,13 @@
+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
+lora,7085CA_d0,mild,1500,12585,150,0.38133333333333336,0.21660707191100517,0.043333333333333335,0.024791418355184745,0.4106666666666667,0.5874453714739769,0.106,0.13198251887167262,0.012666666666666666,0.017719507350019866,0.046,0.021454112038140644,0.4156281287246722,0.8990236963821155,0.8857429836399208,1,True,1.0,0.9866666666666667,0.9866666666666667,1.0,41.06666666666667,58.74453714739769,528.5,640.0
+lora,7085CA_d7,mild,1500,9515,150,0.6666666666666666,0.521492380451918,0.030666666666666665,0.0722017866526537,0.12533333333333332,0.10110352075669994,0.116,0.2725170782974251,0.020666666666666667,0.019863373620599055,0.04066666666666666,0.012821860220704152,0.3961043965668242,0.3579081617616235,0.8621034962980838,3,False,1.0,0.9466666666666667,1.0,0.9666666666666667,12.533333333333333,10.110352075669994,444.0,502.0
+lora,7085CA_d14,mild,1500,11887,150,0.6426666666666667,0.472533019264743,0.042666666666666665,0.07133843694792631,0.14466666666666667,0.16210986792294102,0.1,0.24270211155043325,0.02666666666666667,0.018591738874400604,0.043333333333333335,0.032724825439555814,0.37763416617593454,0.29573495877524286,0.8593441428508096,1,True,1.0,0.9466666666666667,1.0,0.9933333333333333,14.466666666666667,16.2109867922941,443.5,536.0
+lora,2AD75E_d0,mild,1500,7693,150,0.708,0.6034056934875861,0.059333333333333335,0.06408423241908229,0.09133333333333334,0.14064734173924348,0.088,0.15949564539191471,0.01,0.025347718705316522,0.043333333333333335,0.007019368256856883,0.28181654317778065,0.26792313410215146,0.8559897593899317,10,False,1.0,0.9533333333333334,1.0,0.9133333333333333,9.133333333333333,14.064734173924348,425.5,532.0
+lora,2AD75E_d7,mild,1500,10499,150,0.7673333333333333,0.5808172206876845,0.068,0.14372797409277074,0.06333333333333334,0.10277169254214687,0.05466666666666667,0.14715687208305553,0.013333333333333334,0.013715591961139155,0.03333333333333333,0.011810648633203162,0.41607759469155803,0.3201835922843184,0.8460067334532199,6,False,1.0,0.92,0.9933333333333333,0.86,6.333333333333334,10.277169254214687,359.0,443.0
+lora,2AD75E_d14,mild,1500,13692,150,0.7053333333333334,0.5811422728600643,0.06666666666666667,0.12503651767455448,0.118,0.14198071866783524,0.06266666666666666,0.12496348232544552,0.020666666666666667,0.016579024247735902,0.02666666666666667,0.010297984224364592,0.2892947706690039,0.24443705257466458,0.8606023072528465,5,False,0.9933333333333333,0.9266666666666666,0.9933333333333333,0.92,11.799999999999999,14.198071866783524,455.0,428.0
+lora,82CCF5_d0,severe,1500,10125,150,0.63,0.5422222222222223,0.092,0.11832098765432099,0.174,0.1539753086419753,0.056,0.09303703703703704,0.017333333333333333,0.016691358024691356,0.030666666666666665,0.07575308641975309,0.2168888888888888,0.23874194415185002,0.8624872048857414,5,False,1.0,0.96,1.0,0.9866666666666667,17.4,15.397530864197531,497.5,390.0
+lora,82CCF5_d7,severe,1500,10860,150,0.712,0.619060773480663,0.05266666666666667,0.09972375690607735,0.11466666666666667,0.14152854511970533,0.06,0.09410681399631676,0.02666666666666667,0.013627992633517496,0.034,0.03195211786372008,0.21605156537753217,0.26485931945363844,0.8765659034678561,1,True,1.0,0.9733333333333334,0.9866666666666667,0.9933333333333333,11.466666666666667,14.152854511970533,506.0,497.0
+lora,82CCF5_d14,severe,1500,11056,150,0.7133333333333334,0.6330499276410999,0.051333333333333335,0.10121201157742403,0.13933333333333334,0.11369392185238784,0.04466666666666667,0.06828871201157742,0.028666666666666667,0.014562228654124458,0.02266666666666667,0.0691931982633864,0.24005451037144238,0.36985318969456304,0.8674824684211488,2,False,1.0,0.9866666666666667,1.0,0.9933333333333333,13.933333333333334,11.369392185238784,509.0,394.0
+lora,0BF51C_d0,severe,1500,6510,150,0.5613333333333334,0.4012288786482335,0.014,0.01674347158218126,0.26866666666666666,0.4609831029185868,0.015333333333333332,0.07726574500768049,0.004,0.006144393241167435,0.13666666666666666,0.03763440860215054,0.5182734254992319,0.5709498030244532,0.865819781401572,1,True,0.9866666666666667,0.8133333333333334,0.98,0.8666666666666667,26.866666666666667,46.09831029185868,320.0,628.0
+lora,0BF51C_d7,severe,1500,10105,150,0.7466666666666667,0.612370113805047,0.034666666666666665,0.05700148441365661,0.126,0.1607125185551707,0.034666666666666665,0.05294408708560119,0.014,0.0073231073725878275,0.044,0.10964868876793667,0.2819468909780637,0.3232914310644849,0.8601670475845816,4,False,1.0,0.94,0.9933333333333333,0.98,12.6,16.071251855517072,409.0,509.0
+lora,0BF51C_d14,severe,1500,11419,150,0.7533333333333333,0.6330676941938874,0.038,0.07960416849111131,0.11,0.151589456169542,0.043333333333333335,0.07907872843506436,0.01,0.010508801120938787,0.04533333333333334,0.04615115158945617,0.24053127827889187,0.23769151748520465,0.8576870519879147,3,False,1.0,0.9333333333333333,0.9933333333333333,0.98,11.0,15.1589456169542,395.0,541.0

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw2/score/summary.json

@@ -0,0 +1,758 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "giroux2022",
+ "written_utc": "2026-10-15T06:52:38.744721+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",
+  "giroux2022",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw2/score",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw2/lora.npz",
+  "--condition",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw2/test_raw.npz",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw2/test_samples.txt",
+  "--threads",
+  "2",
+  "--case-groups",
+  "severe",
+  "--control-groups",
+  "mild",
+  "--exclude-genes",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv"
+ ],
+ "arms": [
+  "lora"
+ ],
+ "donors": [
+  "7085CA_d0",
+  "7085CA_d7",
+  "7085CA_d14",
+  "2AD75E_d0",
+  "2AD75E_d7",
+  "2AD75E_d14",
+  "82CCF5_d0",
+  "82CCF5_d7",
+  "82CCF5_d14",
+  "0BF51C_d0",
+  "0BF51C_d7",
+  "0BF51C_d14"
+ ],
+ "n_donors": 12,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
+  "reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
+  "features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
+  "n_r1_cells": 1800,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.26048365235328674,
+   "n_fit_cells": 1800
+  },
+  "r2_control": {
+   "precision": 0.9988888888888889,
+   "coverage": 1.0,
+   "density": 4.929388888888889,
+   "n_query": 1800,
+   "depth_matched": {
+    "precision": 0.9994444444444445,
+    "coverage": 1.0,
+    "density": 4.851277777777778
+   }
+  },
+  "observed_l1_loo_null_mean": 0.36588315006285926
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "severe"
+  ],
+  "control_groups": [
+   "mild"
+  ],
+  "n_case_donors": 6,
+  "n_control_donors": 6,
+  "n_donors_in_neither": 0,
+  "case": [
+   false,
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   true,
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "mild",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "severe",
+   "severe"
+  ]
+ },
+ "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": 5498,
+  "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/giroux2022/deg_reference.npz",
+  "aggregates_sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
+  "observed": {
+   "T cell": {
+    "n_significant": 26,
+    "n_tested": 5225,
+    "n_case_donors": 6,
+    "n_control_donors": 6,
+    "n_cells": 67243,
+    "top_list_size": 26
+   },
+   "B cell": {
+    "n_significant": 27,
+    "n_tested": 4949,
+    "n_case_donors": 6,
+    "n_control_donors": 6,
+    "n_cells": 10555,
+    "top_list_size": 27
+   },
+   "Monocyte": {
+    "n_significant": 0,
+    "n_tested": 5151,
+    "n_case_donors": 6,
+    "n_control_donors": 6,
+    "n_cells": 25096,
+    "top_list_size": 0
+   },
+   "NK cell": {
+    "n_significant": 10,
+    "n_tested": 4963,
+    "n_case_donors": 6,
+    "n_control_donors": 6,
+    "n_cells": 16282,
+    "top_list_size": 10
+   },
+   "DC": {
+    "n_significant": 0,
+    "n_tested": 4691,
+    "n_case_donors": 6,
+    "n_control_donors": 6,
+    "n_cells": 1911,
+    "top_list_size": 0
+   }
+  },
+  "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": {
+  "lora": {
+   "comp_l1": 0.32419184661665207,
+   "comp_l1_obs_loo_null": 0.36588315006285926,
+   "precision": 0.9983333333333333,
+   "coverage": 0.9405555555555556,
+   "precision_dm": 0.9938888888888889,
+   "coverage_dm": 0.9544444444444444,
+   "pb_r_median": 0.8613529017754651,
+   "pb_top1": 0.3333333333333333,
+   "mono_pct_gen": 15.716666666666665,
+   "mono_pct_obs": 20.154511386335095,
+   "median_umi_gen": 438.0,
+   "median_umi_obs": 495.0,
+   "contrast_mean_cp10k_r_gen": 0.17823549935043598,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.07902948973476966,
+   "contrast_mean_cp10k_r_broadcast": 0.39643909018360535,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.4753930725862121,
+   "deg_top50_T": 0,
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