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/draw0/score/arms/lora/deg_top50_lists.csv

@@ -0,0 +1,4 @@
+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000173262
+B cell,observed,1,ENSG00000197520
+B cell,observed,2,ENSG00000130856

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw0/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,2863,0.3563914715250282,0.4659672798536223,0.2218085591407057,0.3742731766713961,6,5,6,5,59044,10828,,,,,,,,,,,
+lora,T cell,pseudobulk_log1p_cpm,2863,0.15518483081128517,0.5669062142141347,0.07354063271502896,0.16840274801386212,6,5,6,5,59044,10828,,,,,,,,,,,
+lora,B cell,mean_cp10k,3005,0.13206111640016924,0.3989038406365887,0.07395471487893368,0.16333743049040902,6,5,6,5,9139,765,,,,,,,,,,,
+lora,B cell,pseudobulk_log1p_cpm,3005,0.07277531821196102,0.4804240789506083,0.03368313626567538,0.09024218255985579,6,5,6,5,9139,765,,,,,,,,,,,
+lora,Monocyte,mean_cp10k,3028,0.24776423621286625,0.6141260231172326,0.09111033870527305,0.2914396663259063,6,5,6,5,19384,2983,,,,,,,,,,,
+lora,Monocyte,pseudobulk_log1p_cpm,3028,0.118522835737594,0.6247044807439144,0.0369013387558337,0.1440819996894487,6,5,6,5,19384,2983,,,,,,,,,,,
+lora,NK cell,mean_cp10k,2910,0.1012931562128459,0.40486451543783863,0.04717315928029971,0.1447732264968033,6,5,6,5,11027,1009,,,,,,,,,,,
+lora,NK cell,pseudobulk_log1p_cpm,2910,0.0400801728742779,0.47190028654240307,0.011741211541534702,0.06304107476395901,6,5,6,5,11027,1009,,,,,,,,,,,
+lora,T cell,welch_top50_deg,5498,,,,,6,5,6,5,59044,10828,True,0,0.0,1,0,1,0,0,0.0,0,0
+lora,B cell,welch_top50_deg,5498,,,,,6,5,6,5,9139,765,True,0,0.0,2,0,2,0,0,0.0,0,0
+lora,Monocyte,welch_top50_deg,5498,,,,,6,5,6,5,19384,2983,True,0,,0,0,0,0,0,,0,0
+lora,NK cell,welch_top50_deg,5498,,,,,6,5,6,5,11027,1009,True,0,,0,0,0,0,0,,0,0
+lora,DC,welch_top50_deg,5498,,,,,6,5,6,5,1558,372,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/draw0/score/per_donor.csv

@@ -0,0 +1,12 @@
+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,1500,5914,150,0.38,0.30943523841731485,0.013333333333333334,0.036185322962461956,0.4633333333333333,0.4293202570172472,0.092,0.12089956036523504,0.024666666666666667,0.009976327358809604,0.02666666666666667,0.09418329387893135,0.23853635441325668,0.652432804255913,0.8784872032904227,1,True,1.0,0.9466666666666667,0.98,1.0,46.33333333333333,42.93202570172472,572.0,574.5
+lora,450905_d14,mild,1500,7407,150,0.5646666666666667,0.4422843256379101,0.03133333333333333,0.02929661131362225,0.20466666666666666,0.27420008100445525,0.12333333333333334,0.15782368030241664,0.03133333333333333,0.02983664101525584,0.04466666666666667,0.06655866072633995,0.2518315107330903,0.3927979931719725,0.8739467542084013,1,True,1.0,1.0,1.0,1.0,20.466666666666665,27.420008100445525,543.0,558.0
+lora,2AD75E_d0,mild,1500,7693,150,0.7153333333333334,0.6034056934875861,0.048666666666666664,0.06408423241908229,0.11266666666666666,0.14064734173924348,0.072,0.15949564539191471,0.018,0.025347718705316522,0.03333333333333333,0.007019368256856883,0.2764832098444474,0.3152895182425347,0.8540978238947612,7,False,1.0,0.9866666666666667,0.9933333333333333,0.98,11.266666666666666,14.064734173924348,434.0,532.0
+lora,2AD75E_d7,mild,1500,10499,150,0.726,0.5808172206876845,0.106,0.14372797409277074,0.06333333333333334,0.10277169254214687,0.05733333333333333,0.14715687208305553,0.008,0.013715591961139155,0.03933333333333333,0.011810648633203162,0.34541092802489126,0.37510476699698597,0.8440753409315591,5,False,1.0,0.9666666666666667,1.0,0.8866666666666667,6.333333333333334,10.277169254214687,342.5,443.0
+lora,2AD75E_d14,mild,1500,13692,150,0.718,0.5811422728600643,0.056666666666666664,0.12503651767455448,0.116,0.14198071866783524,0.056,0.12496348232544552,0.025333333333333333,0.016579024247735902,0.028,0.010297984224364592,0.3266281040023371,0.29971204356328646,0.8590343881265933,3,False,1.0,0.9866666666666667,1.0,0.9733333333333334,11.600000000000001,14.198071866783524,456.0,428.0
+lora,82CCF5_d0,severe,1500,10125,150,0.6073333333333333,0.5422222222222223,0.07533333333333334,0.11832098765432099,0.178,0.1539753086419753,0.07733333333333334,0.09303703703703704,0.03266666666666666,0.016691358024691356,0.029333333333333333,0.07575308641975309,0.2102222222222221,0.20143355104463556,0.8597653677916022,4,False,1.0,1.0,0.9933333333333333,1.0,17.8,15.397530864197531,475.0,390.0
+lora,82CCF5_d7,severe,1500,10860,150,0.7346666666666667,0.619060773480663,0.04733333333333333,0.09972375690607735,0.112,0.14152854511970533,0.064,0.09410681399631676,0.018666666666666668,0.013627992633517496,0.023333333333333334,0.03195211786372008,0.2412891344383057,0.25871125560168845,0.8737217900707615,1,True,1.0,0.9933333333333333,0.9933333333333333,0.9933333333333333,11.200000000000001,14.152854511970533,507.5,497.0
+lora,82CCF5_d14,severe,1500,11056,150,0.7086666666666667,0.6330499276410999,0.051333333333333335,0.10121201157742403,0.12466666666666666,0.11369392185238784,0.05,0.06828871201157742,0.042666666666666665,0.014562228654124458,0.02266666666666667,0.0691931982633864,0.2293878437047756,0.3322264186222185,0.8703436480745063,2,False,1.0,0.9933333333333333,1.0,1.0,12.466666666666667,11.369392185238784,525.0,394.0
+lora,0BF51C_d0,severe,1500,6510,150,0.554,0.4012288786482335,0.010666666666666666,0.01674347158218126,0.36733333333333335,0.4609831029185868,0.013333333333333334,0.07726574500768049,0.008666666666666666,0.006144393241167435,0.046,0.03763440860215054,0.32731797235023047,0.5474367391909245,0.8613878314515696,1,True,1.0,0.7333333333333333,0.9933333333333333,0.7733333333333333,36.733333333333334,46.09831029185868,422.0,628.0
+lora,0BF51C_d7,severe,1500,10105,150,0.744,0.612370113805047,0.03666666666666667,0.05700148441365661,0.13133333333333333,0.1607125185551707,0.028,0.05294408708560119,0.021333333333333333,0.0073231073725878275,0.03866666666666667,0.10964868876793667,0.291280224311397,0.2744910969706922,0.8573433316267198,4,False,1.0,0.9666666666666667,1.0,0.98,13.133333333333333,16.071251855517072,431.5,509.0
+lora,0BF51C_d14,severe,1500,11419,150,0.766,0.6330676941938874,0.03266666666666666,0.07960416849111131,0.11533333333333333,0.151589456169542,0.03933333333333333,0.07907872843506436,0.016666666666666666,0.010508801120938787,0.03,0.04615115158945617,0.278180342703681,0.18889118339141198,0.8574648815071223,3,False,1.0,0.9933333333333333,0.9933333333333333,1.0,11.533333333333333,15.1589456169542,405.0,541.0

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw0/score/summary.json

@@ -0,0 +1,754 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "giroux2022",
+ "written_utc": "2026-10-15T06:52:25.110343+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/draw0/score",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/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/draw0/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/draw0/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",
+  "2AD75E_d0",
+  "2AD75E_d7",
+  "2AD75E_d14",
+  "82CCF5_d0",
+  "82CCF5_d7",
+  "82CCF5_d14",
+  "0BF51C_d0",
+  "0BF51C_d7",
+  "0BF51C_d14"
+ ],
+ "n_donors": 11,
+ "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": 1650,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.2656761705875397,
+   "n_fit_cells": 1650
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+  "r2_control": {
+   "precision": 0.9987878787878788,
+   "coverage": 1.0,
+   "density": 5.159575757575757,
+   "n_query": 1650,
+   "depth_matched": {
+    "precision": 0.9981818181818182,
+    "coverage": 1.0,
+    "density": 5.011030303030303
+   }
+  },
+  "observed_l1_loo_null_mean": 0.348957033732024
+ },
+ "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": 5,
+  "n_donors_in_neither": 0,
+  "case": [
+   false,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   true,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "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": {
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+    "n_significant": 1,
+    "n_tested": 5216,
+    "n_case_donors": 6,
+    "n_control_donors": 5,
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+    "top_list_size": 1
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+   "B cell": {
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+    "n_tested": 4912,
+    "n_case_donors": 6,
+    "n_control_donors": 5,
+    "n_cells": 9139,
+    "top_list_size": 2
+   },
+   "Monocyte": {
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+    "n_tested": 5113,
+    "n_case_donors": 6,
+    "n_control_donors": 5,
+    "n_cells": 19384,
+    "top_list_size": 0
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+   "NK cell": {
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+    "n_case_donors": 6,
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+    "top_list_size": 0
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+   "DC": {
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+    "n_tested": 4635,
+    "n_case_donors": 6,
+    "n_control_donors": 5,
+    "n_cells": 1558,
+    "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": {
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+   "precision": 1.0,
+   "coverage": 0.9606060606060606,
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+   "coverage_dm": 0.9624242424242424,
+   "pb_r_median": 0.8597653677916022,
+   "pb_top1": 0.36363636363636365,
+   "mono_pct_gen": 18.078787878787875,
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+   "median_umi_gen": 460.0,
+   "median_umi_obs": 483.0,
+   "contrast_mean_cp10k_r_gen": 0.2093774950877274,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.09664078940877951,
+   "contrast_mean_cp10k_r_broadcast": 0.4709654147613206,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5359837651127651,
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+   "deg_top50_B": 0,
+   "deg_top50_Mono": 0,
+   "deg_top50_NK": 0,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 0,
+   "deg_top50_max": 3,
+   "deg_top50_sum_4type": 0,
+   "deg_top50_sum_broadcast": 0,
+   "seconds": 4.8
+  }
+ },
+ "per_arm": {
+  "lora": {
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+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/lora.npz",
+   "npz_sha256": "765845e9a73b40470b9d94fded33c190ccb8d73529f732ae5bc0fc2cea9cda6e",
+   "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/draw0/lora/checkpoint_ft.pt",
+    "checkpoint_sha256": "1da445cb2d3c86b2672e1b2dfa52e31b444b509108d125a7feb9b7ebf80dc0da",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw0/test_raw.npz",
+    "input_condition_sha256": "f04c5725cf7d20ca4ca26d2ac43352d8c233b9d6c4d7ddc2116e3be4694623a9",
+    "seed": 20260928,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw0/test_raw.npz",
+    "sha256": "f04c5725cf7d20ca4ca26d2ac43352d8c233b9d6c4d7ddc2116e3be4694623a9"
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+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 3987887,
+    "median_library_whole_npz_panel": 1552.0,
+    "n_rows_whole_npz": 16500
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+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 0,
+    "label_counts": {
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+     "Monocyte": 2983,
+     "NK cell": 1009,
+     "B cell": 765,
+     "Other": 543,
+     "DC": 372
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+    "mean_l2_max_prob": 0.8848754408982668,
+    "predict_seconds": 3.0
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+   "n_donors": 11,
+   "n_generated_cells": 16500,
+   "composition": {
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+    "l1_median": 0.2764832098444474,
+    "l1_obs_loo_null_mean": 0.348957033732024,
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+ }
+}