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/draw1/score/arms/lora/deg_top50_lists.csv

@@ -0,0 +1,57 @@
+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000185736
+T cell,observed,2,ENSG00000167414
+T cell,observed,3,ENSG00000168329
+T cell,observed,4,ENSG00000158966
+T cell,observed,5,ENSG00000213366
+T cell,observed,6,ENSG00000173262
+T cell,observed,7,ENSG00000107438
+T cell,observed,8,ENSG00000180644
+T cell,observed,9,ENSG00000047634
+T cell,observed,10,ENSG00000099139
+T cell,observed,11,ENSG00000188001
+T cell,observed,12,ENSG00000189283
+T cell,observed,13,ENSG00000196126
+T cell,observed,14,ENSG00000135362
+T cell,observed,15,ENSG00000100453
+T cell,observed,16,ENSG00000000938
+T cell,observed,17,ENSG00000197872
+T cell,observed,18,ENSG00000145649
+T cell,observed,19,ENSG00000174136
+T cell,observed,20,ENSG00000152969
+T cell,observed,21,ENSG00000147459
+T cell,observed,22,ENSG00000026751
+T cell,observed,23,ENSG00000107796
+T cell,observed,24,ENSG00000103034
+T cell,observed,25,ENSG00000163568
+T cell,observed,26,ENSG00000188848
+T cell,observed,27,ENSG00000143179
+T cell,observed,28,ENSG00000169554
+T cell,observed,29,ENSG00000155629
+T cell,observed,30,ENSG00000124406
+T cell,observed,31,ENSG00000115392
+T cell,observed,32,ENSG00000139116
+T cell,observed,33,ENSG00000198932
+T cell,observed,34,ENSG00000129595
+T cell,observed,35,ENSG00000163191
+T cell,observed,36,ENSG00000173258
+T cell,observed,37,ENSG00000077984
+T cell,observed,38,ENSG00000253293
+T cell,observed,39,ENSG00000101298
+T cell,observed,40,ENSG00000153563
+T cell,observed,41,ENSG00000100342
+T cell,observed,42,ENSG00000116815
+T cell,observed,43,ENSG00000114861
+T cell,observed,44,ENSG00000077713
+T cell,observed,45,ENSG00000136213
+T cell,observed,46,ENSG00000134250
+T cell,observed,47,ENSG00000171316
+T cell,observed,48,ENSG00000172005
+T cell,observed,49,ENSG00000152495
+T cell,observed,50,ENSG00000182568
+T cell,generated,1,ENSG00000109320
+T cell,generated,2,ENSG00000091409
+T cell,generated,3,ENSG00000160255
+all (input bulk),broadcast,1,ENSG00000205189
+all (input bulk),broadcast,2,ENSG00000148516
+all (input bulk),broadcast,3,ENSG00000179833

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw1/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,2916,0.5661891183203449,0.6571144835533105,0.37347750410121766,0.48758164770792883,6,4,6,4,58362,9153,,,,,,,,,,,
+lora,T cell,pseudobulk_log1p_cpm,2916,0.35809644300124593,0.6872156600560435,0.19004003260105057,0.3315556047121546,6,4,6,4,58362,9153,,,,,,,,,,,
+lora,B cell,mean_cp10k,3099,0.12618303770985873,0.3825835491576257,0.08387389938041898,0.12895810943438019,6,4,6,4,6177,596,,,,,,,,,,,
+lora,B cell,pseudobulk_log1p_cpm,3099,0.05998274948702396,0.3771207985959151,0.046529676614197,0.04489832479614293,6,4,6,4,6177,596,,,,,,,,,,,
+lora,Monocyte,mean_cp10k,3045,0.23220526411321746,0.4614533190457718,0.18756781721244029,0.1464867862193682,6,4,6,4,18467,3225,,,,,,,,,,,
+lora,Monocyte,pseudobulk_log1p_cpm,3045,0.15888707137074218,0.5171610414843097,0.11038020981602084,0.12600910368294188,6,4,6,4,18467,3225,,,,,,,,,,,
+lora,NK cell,mean_cp10k,2993,0.21105332143844824,0.5038596937916778,0.11556582530477336,0.22587448409340705,6,4,6,4,9050,969,,,,,,,,,,,
+lora,NK cell,pseudobulk_log1p_cpm,2993,0.1349091122703371,0.5135427805432597,0.08109339032469605,0.128326426953764,6,4,6,4,9050,969,,,,,,,,,,,
+lora,T cell,welch_top50_deg,5498,,,,,6,4,6,4,58362,9153,True,0,0.0,50,3,84,3,0,0.0,3,3
+lora,B cell,welch_top50_deg,5498,,,,,6,4,6,4,6177,596,True,0,,0,0,0,0,0,0.0,3,3
+lora,Monocyte,welch_top50_deg,5498,,,,,6,4,6,4,18467,3225,True,0,,0,0,0,0,0,0.0,3,3
+lora,NK cell,welch_top50_deg,5498,,,,,6,4,6,4,9050,969,True,0,,0,0,0,0,0,0.0,3,3
+lora,DC,welch_top50_deg,5498,,,,,6,4,6,4,1271,368,True,0,,0,0,0,0,0,0.0,3,3

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw1/score/per_donor.csv

@@ -0,0 +1,11 @@
+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,450905_d0,mild,1500,5914,150,0.33466666666666667,0.30943523841731485,0.016666666666666666,0.036185322962461956,0.5093333333333333,0.4293202570172472,0.08533333333333333,0.12089956036523504,0.032,0.009976327358809604,0.022,0.09418329387893135,0.2545363544132567,0.6721216782161549,0.8745946459221489,1,True,1.0,0.9666666666666667,0.9933333333333333,1.0,50.93333333333333,42.93202570172472,582.5,574.5
+lora,450905_d14,mild,1500,7407,150,0.5253333333333333,0.4422843256379101,0.029333333333333333,0.02929661131362225,0.2693333333333333,0.27420008100445525,0.09533333333333334,0.15782368030241664,0.02666666666666667,0.02983664101525584,0.054,0.06655866072633995,0.1661714594302687,0.4172767195297901,0.8683588070494046,1,True,1.0,0.9533333333333334,1.0,0.98,26.93333333333333,27.420008100445525,482.5,558.0
+lora,0B943B_d0,mild,1500,11344,150,0.5486666666666666,0.6220028208744711,0.028,0.08312764456981664,0.27266666666666667,0.12588152327221439,0.06666666666666667,0.11865303244005641,0.04066666666666666,0.023977433004231313,0.043333333333333335,0.026357545839210156,0.36090032910202174,0.27288152831947954,0.8533928930687678,7,False,1.0,0.96,0.9866666666666667,0.9933333333333333,27.266666666666666,12.588152327221438,474.5,539.0
+lora,0B943B_d14,mild,1500,15650,150,0.488,0.5652396166134185,0.102,0.11175718849840256,0.216,0.17086261980830672,0.11,0.09789137380191694,0.024666666666666667,0.009968051118210863,0.059333333333333335,0.04428115015974441,0.17399361022364213,0.1514797576931834,0.8703283904454833,1,True,1.0,0.98,0.9933333333333333,1.0,21.6,17.08626198083067,499.0,461.0
+lora,180E1A_d0,severe,1500,7157,150,0.7326666666666667,0.7019700992035769,0.034,0.04135811094033813,0.12,0.13175911694844208,0.052,0.0655302501047925,0.021333333333333333,0.013273718038284197,0.04,0.04610870476456616,0.07751236551627783,0.37947485892421606,0.8567296619077492,1,True,1.0,1.0,1.0,1.0,12.0,13.175911694844208,403.0,433.0
+lora,180E1A_d7,severe,1500,10591,150,0.7606666666666667,0.7348692285903126,0.03933333333333333,0.04909829100179398,0.08666666666666667,0.09064299877254273,0.056,0.08280615617033331,0.02266666666666667,0.010480596733075253,0.034666666666666665,0.03210272873194221,0.08109489188934003,0.4452731176976873,0.8557970744308521,5,False,1.0,1.0,1.0,1.0,8.666666666666668,9.064299877254273,403.0,408.0
+lora,180E1A_d14,severe,1500,12511,150,0.7313333333333333,0.680840860043162,0.036,0.05147470226200943,0.12933333333333333,0.12277196067460634,0.043333333333333335,0.0800095915594277,0.02,0.009831348413396212,0.04,0.05507153704739829,0.13444499507100413,0.33721638060338627,0.8589010576928573,2,False,1.0,0.98,1.0,0.9933333333333333,12.933333333333334,12.277196067460634,389.5,342.0
+lora,0BF51C_d0,severe,1500,6510,150,0.5446666666666666,0.4012288786482335,0.03,0.01674347158218126,0.29133333333333333,0.4609831029185868,0.066,0.07726574500768049,0.021333333333333333,0.006144393241167435,0.04666666666666667,0.03763440860215054,0.36183102918586785,0.5375551894092265,0.8737430778138352,1,True,1.0,0.68,1.0,0.6733333333333333,29.133333333333333,46.09831029185868,432.0,628.0
+lora,0BF51C_d7,severe,1500,10105,150,0.7173333333333334,0.612370113805047,0.04066666666666666,0.05700148441365661,0.12933333333333333,0.1607125185551707,0.03266666666666666,0.05294408708560119,0.016666666666666666,0.0073231073725878275,0.06333333333333334,0.10964868876793667,0.22861355764473038,0.18080737356645343,0.8500915173892076,6,False,1.0,0.9066666666666666,1.0,0.98,12.933333333333334,16.071251855517072,342.0,509.0
+lora,0BF51C_d14,severe,1500,11419,150,0.7186666666666667,0.6330676941938874,0.04133333333333333,0.07960416849111131,0.126,0.151589456169542,0.03866666666666667,0.07907872843506436,0.019333333333333334,0.010508801120938787,0.056,0.04615115158945617,0.20854470619143528,0.15136085081896566,0.8545213598922642,3,False,1.0,0.92,1.0,0.9666666666666667,12.6,15.1589456169542,354.0,541.0

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw1/score/summary.json

@@ -0,0 +1,750 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "giroux2022",
+ "written_utc": "2026-10-15T06:52:31.675476+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/draw1/score",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw1/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/draw1/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/draw1/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": [
+  "450905_d0",
+  "450905_d14",
+  "0B943B_d0",
+  "0B943B_d14",
+  "180E1A_d0",
+  "180E1A_d7",
+  "180E1A_d14",
+  "0BF51C_d0",
+  "0BF51C_d7",
+  "0BF51C_d14"
+ ],
+ "n_donors": 10,
+ "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": 1500,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.25688883662223816,
+   "n_fit_cells": 1500
+  },
+  "r2_control": {
+   "precision": 1.0,
+   "coverage": 1.0,
+   "density": 6.064666666666667,
+   "n_query": 1500,
+   "depth_matched": {
+    "precision": 0.9993333333333333,
+    "coverage": 1.0,
+    "density": 6.024133333333333
+   }
+  },
+  "observed_l1_loo_null_mean": 0.3545447454778543
+ },
+ "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": 4,
+  "n_donors_in_neither": 0,
+  "case": [
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "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": 84,
+    "n_tested": 5224,
+    "n_case_donors": 6,
+    "n_control_donors": 4,
+    "n_cells": 58362,
+    "top_list_size": 50
+   },
+   "B cell": {
+    "n_significant": 0,
+    "n_tested": 4886,
+    "n_case_donors": 6,
+    "n_control_donors": 4,
+    "n_cells": 6177,
+    "top_list_size": 0
+   },
+   "Monocyte": {
+    "n_significant": 0,
+    "n_tested": 5098,
+    "n_case_donors": 6,
+    "n_control_donors": 4,
+    "n_cells": 18467,
+    "top_list_size": 0
+   },
+   "NK cell": {
+    "n_significant": 0,
+    "n_tested": 4876,
+    "n_case_donors": 6,
+    "n_control_donors": 4,
+    "n_cells": 9050,
+    "top_list_size": 0
+   },
+   "DC": {
+    "n_significant": 0,
+    "n_tested": 4578,
+    "n_case_donors": 6,
+    "n_control_donors": 4,
+    "n_cells": 1271,
+    "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": 0.20476432986678444,
+   "comp_l1_obs_loo_null": 0.3545447454778543,
+   "precision": 1.0,
+   "coverage": 0.9346666666666666,
+   "precision_dm": 0.9973333333333333,
+   "coverage_dm": 0.9586666666666667,
+   "pb_r_median": 0.8578153598003033,
+   "pb_top1": 0.5,
+   "mono_pct_gen": 21.5,
+   "mono_pct_obs": 21.18723635141114,
+   "median_umi_gen": 427.0,
+   "median_umi_obs": 482.0,
+   "contrast_mean_cp10k_r_gen": 0.28390768539546735,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.1779688440323373,
+   "contrast_mean_cp10k_r_broadcast": 0.5012527613870964,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.523760070169882,
+   "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": 50,
+   "deg_top50_sum_4type": 0,
+   "deg_top50_sum_broadcast": 0,
+   "seconds": 4.5
+  }
+ },
+ "per_arm": {
+  "lora": {
+   "arm": "lora",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw1/lora.npz",
+   "npz_sha256": "23c22a3ecafc54d6a746016ef7c1c55ff6ec6fcb6df8f81d0cca50e86a2830c3",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw1/lora/checkpoint_ft.pt",
+    "checkpoint_sha256": "0492c0d21a4a15193013661d303b3ffa49f744c69d62330ee4eec3f6bf012a78",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw1/test_raw.npz",
+    "input_condition_sha256": "935e890f67fc789b9ecf47b5c90157bfe0a1983d6ffdb1ea2d198b6de9767f47",
+    "seed": 20260928,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
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