Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw4/lora/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,2870,0.6631265853728078,0.7344048019011988,0.4670495249614149,0.5395235474343575,5,5,5,5,55877,9321,,,,,,,,,,,
+lora,T cell,pseudobulk_log1p_cpm,2870,0.371485040719346,0.6900634955326531,0.2527165207639843,0.284212144802611,5,5,5,5,55877,9321,,,,,,,,,,,
+lora,B cell,mean_cp10k,3061,0.2925989610866921,0.565884313340693,0.1608945387708825,0.2929270554715147,5,5,5,5,4890,776,,,,,,,,,,,
+lora,B cell,pseudobulk_log1p_cpm,3061,0.1170765920354445,0.4704332503129004,0.0641456386014538,0.1295598953522298,5,5,5,5,4890,776,,,,,,,,,,,
+lora,Monocyte,mean_cp10k,3017,0.3657364980723787,0.5561945453231222,0.1509583855847481,0.4569352941809483,5,5,5,5,21294,2778,,,,,,,,,,,
+lora,Monocyte,pseudobulk_log1p_cpm,3017,0.1702847466295969,0.6573550923248582,0.0307788419606781,0.2246629357229864,5,5,5,5,21294,2778,,,,,,,,,,,
+lora,NK cell,mean_cp10k,2940,0.4472912287558259,0.6558646674649503,0.2842241710325422,0.3792998523868367,5,5,5,5,12579,1322,,,,,,,,,,,
+lora,NK cell,pseudobulk_log1p_cpm,2940,0.1547172121195283,0.5646910960578172,0.0772087764689645,0.1626466347999063,5,5,5,5,12579,1322,,,,,,,,,,,
+lora,T cell,welch_top50_deg,5498,,,,,5,5,5,5,55877,9321,True,0.0,0.0,0.0,3.0,0.0,3.0,0.0,0.0,1.0,1.0
+lora,B cell,welch_top50_deg,5498,,,,,5,5,5,5,4890,776,True,0.0,,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0
+lora,Monocyte,welch_top50_deg,5498,,,,,5,5,5,5,21294,2778,True,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0
+lora,NK cell,welch_top50_deg,5498,,,,,5,5,5,5,12579,1322,True,0.0,,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0
+lora,DC,welch_top50_deg,5498,,,,,5,5,5,5,1773,375,True,0.0,,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw4/lora/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,1500,5914,150,0.5026666666666667,0.3094352384173148,0.044,0.0361853229624619,0.3393333333333333,0.4293202570172472,0.0853333333333333,0.120899560365235,0.0206666666666666,0.0099763273588096,0.008,0.0941832938789313,0.4234728891894939,0.5987967413223616,0.8785277453953022,2,False,1.0,0.9133333333333332,0.9933333333333332,0.96,33.93333333333333,42.93202570172472,593.0,574.5
+lora,450905_d14,mild,1500,7407,150,0.61,0.4422843256379101,0.0446666666666666,0.0292966113136222,0.1853333333333333,0.2742000810044552,0.1053333333333333,0.1578236803024166,0.0213333333333333,0.0298366410152558,0.0333333333333333,0.0665586607263399,0.3661714594302687,0.330631705821744,0.8736027844299484,2,False,1.0,0.98,1.0,1.0,18.53333333333333,27.420008100445525,496.0,558.0
+lora,7085CA_d0,mild,1500,12585,150,0.4566666666666666,0.2166070719110051,0.0513333333333333,0.0247914183551847,0.3746666666666666,0.5874453714739769,0.0953333333333333,0.1319825188716726,0.0146666666666666,0.0177195073500198,0.0073333333333333,0.0214541120381406,0.5332030194676202,0.8949626862138647,0.8861215630154395,1,True,1.0,0.92,1.0,0.9866666666666668,37.46666666666666,58.74453714739769,596.5,640.0
+lora,7085CA_d7,mild,1500,9515,150,0.5913333333333334,0.521492380451918,0.052,0.0722017866526537,0.1613333333333333,0.1011035207566999,0.1313333333333333,0.2725170782974251,0.0253333333333333,0.019863373620599,0.0386666666666666,0.0128218602207041,0.322771063233491,0.4348078856615509,0.8640947374830064,3,False,1.0,0.9866666666666668,1.0,1.0,16.133333333333333,10.110352075669994,465.0,502.0
+lora,7085CA_d14,mild,1500,11887,150,0.6373333333333333,0.472533019264743,0.0413333333333333,0.0713384369479263,0.1466666666666666,0.162109867922941,0.1013333333333333,0.2427021115504332,0.0353333333333333,0.0185917388744006,0.038,0.0327248254395558,0.3736341661759345,0.3709079832657155,0.8666074096998785,2,False,1.0,0.94,1.0,1.0,14.666666666666666,16.2109867922941,460.5,536.0
+lora,B85D75_d0,severe,1500,11441,150,0.716,0.7173324010138974,0.05,0.0312035661218424,0.0973333333333333,0.1144130757800891,0.0793333333333333,0.0603968184599248,0.02,0.0165195350056813,0.0373333333333333,0.0601346036185648,0.0824268274917694,0.4453152798334465,0.8656891666514337,3,False,1.0,0.9933333333333332,1.0,1.0,9.733333333333333,11.441307578008916,452.0,347.0
+lora,B85D75_d7,severe,1500,12328,150,0.7046666666666667,0.6435756002595717,0.0666666666666666,0.0644873458792991,0.1273333333333333,0.1374107722258273,0.0513333333333333,0.0420181700194678,0.0233333333333333,0.0277417261518494,0.0266666666666666,0.0847663854639844,0.1451711010166558,0.4045481459575713,0.8708057566460601,1,True,1.0,0.9866666666666668,1.0,0.9933333333333332,12.733333333333333,13.741077222582735,457.0,363.0
+lora,180E1A_d0,severe,1500,7157,150,0.6726666666666666,0.7019700992035769,0.056,0.0413581109403381,0.1313333333333333,0.131759116948442,0.0733333333333333,0.0655302501047925,0.036,0.0132737180382841,0.0306666666666666,0.0461087047645661,0.090342508499837,0.4544373307053366,0.8674781048381301,2,False,1.0,0.9933333333333332,1.0,1.0,13.133333333333333,13.175911694844208,462.0,433.0
+lora,180E1A_d7,severe,1500,10591,150,0.6826666666666666,0.7348692285903126,0.0573333333333333,0.0490982910017939,0.132,0.0906429987725427,0.0806666666666666,0.0828061561703333,0.0193333333333333,0.0104805967330752,0.028,0.0321027287319422,0.1168895603185094,0.5242880319872557,0.8615920786832327,5,False,1.0,0.9933333333333332,1.0,0.9933333333333332,13.2,9.064299877254273,455.5,408.0
+lora,180E1A_d14,severe,1500,12511,150,0.64,0.680840860043162,0.054,0.0514747022620094,0.1566666666666666,0.1227719606746063,0.078,0.0800095915594277,0.034,0.0098313484133962,0.0373333333333333,0.0550715370473982,0.1211773106333093,0.424657551112119,0.8691456202232917,3,False,1.0,0.9866666666666668,1.0,1.0,15.666666666666668,12.277196067460634,458.5,342.0

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw4/lora/score/summary.json

@@ -0,0 +1,751 @@
+{
+  "schema": "paired_ft_scores.v1",
+  "dataset": "giroux2022",
+  "written_utc": "2026-10-15T06:52:52.652114+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/draw4/score",
+    "--arm",
+    "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw4/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/draw4/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/draw4/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",
+    "7085CA_d0",
+    "7085CA_d7",
+    "7085CA_d14",
+    "B85D75_d0",
+    "B85D75_d7",
+    "180E1A_d0",
+    "180E1A_d7",
+    "180E1A_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": 0.2558751106262207,
+      "n_fit_cells": 1500
+    },
+    "r2_control": {
+      "precision": 0.9993333333333333,
+      "coverage": 1.0,
+      "density": 6.356199999999999,
+      "n_query": 1500,
+      "depth_matched": {
+        "precision": 0.9986666666666667,
+        "coverage": 1.0,
+        "density": 6.294933333333334
+      }
+    },
+    "observed_l1_loo_null_mean": 0.4883353341880966
+  },
+  "contrast_definition": {
+    "enabled": true,
+    "rule": "explicit --case-groups / --control-groups",
+    "group_source": "features groups",
+    "case_groups": [
+      "severe"
+    ],
+    "control_groups": [
+      "mild"
+    ],
+    "n_case_donors": 5,
+    "n_control_donors": 5,
+    "n_donors_in_neither": 0,
+    "case": [
+      false,
+      false,
+      false,
+      false,
+      false,
+      true,
+      true,
+      true,
+      true,
+      true
+    ],
+    "ctrl": [
+      true,
+      true,
+      true,
+      true,
+      true,
+      false,
+      false,
+      false,
+      false,
+      false
+    ],
+    "groups": [
+      "mild",
+      "mild",
+      "mild",
+      "mild",
+      "mild",
+      "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": 0,
+        "n_tested": 5182,
+        "n_case_donors": 5,
+        "n_control_donors": 5,
+        "n_cells": 55877,
+        "top_list_size": 0
+      },
+      "B cell": {
+        "n_significant": 0,
+        "n_tested": 4807,
+        "n_case_donors": 5,
+        "n_control_donors": 5,
+        "n_cells": 4890,
+        "top_list_size": 0
+      },
+      "Monocyte": {
+        "n_significant": 1,
+        "n_tested": 5109,
+        "n_case_donors": 5,
+        "n_control_donors": 5,
+        "n_cells": 21294,
+        "top_list_size": 1
+      },
+      "NK cell": {
+        "n_significant": 0,
+        "n_tested": 4929,
+        "n_case_donors": 5,
+        "n_control_donors": 5,
+        "n_cells": 12579,
+        "top_list_size": 0
+      },
+      "DC": {
+        "n_significant": 0,
+        "n_tested": 4638,
+        "n_case_donors": 5,
+        "n_control_donors": 5,
+        "n_cells": 1773,
+        "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": 0.2575259905456889,
+      "comp_l1_obs_loo_null": 0.4883353341880966,
+      "precision": 1.0,
+      "coverage": 0.9693333333333334,
+      "precision_dm": 0.9993333333333333,
+      "coverage_dm": 0.9933333333333333,
+      "pb_r_median": 0.8683118625307109,
+      "pb_top1": 0.2,
+      "mono_pct_gen": 18.519999999999996,
+      "mono_pct_obs": 21.511770225768277,
+      "median_umi_gen": 483.0,
+      "median_umi_obs": 447.0,
+      "contrast_mean_cp10k_r_gen": 0.4421883183219261,
+      "contrast_pseudobulk_log1p_cpm_r_gen": 0.20339089787597897,
+      "contrast_mean_cp10k_r_broadcast": 0.6280870820074911,
+      "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.5956357335570572,
+      "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": 1,
+      "deg_top50_sum_4type": 0,
+      "deg_top50_sum_broadcast": 0,
+      "seconds": 4.7
+    }
+  },
+  "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/draw4/lora.npz",
+      "npz_sha256": "7dc39e3963038c6e4c41d2681b5be1135bce425de1514732c4b91af899249afc",
+      "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/draw4/lora/checkpoint_ft.pt",
+        "checkpoint_sha256": "ccd39f782235579aae57cd576348a44f26f57e5c62d068b5d2554a6e87c68ea4",
+        "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw4/test_raw.npz",
+        "input_condition_sha256": "1339e7631cd54c77bef770b2248bdc2ca560a6dc70e244ed61cd4d38a835bf3f",
+        "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/draw4/test_raw.npz",
+        "sha256": "1339e7631cd54c77bef770b2248bdc2ca560a6dc70e244ed61cd4d38a835bf3f"
+      },
+      "poisson": {
+        "seed": 20260916,
+        "rule": "whole NPZ, rows in NPZ order",
+        "nnz_whole_npz": 3706513,
+        "median_library_whole_npz_panel": 1449.5,
+        "n_rows_whole_npz": 15000
+      },
+      "annotation": {
+        "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+        "zero_padded_model_genes": 0,
+        "label_counts": {
+          "T cell": 9321,
+          "Monocyte": 2778,
+          "NK cell": 1322,
+          "B cell": 776,
+          "Other": 428,
+          "DC": 375
+        },
+        "mean_l2_max_prob": 0.8912148882766565,
+        "predict_seconds": 3.1
+      },
+      "n_donors": 10,
+      "n_generated_cells": 15000,
+      "composition": {
+        "l1_mean": 0.2575259905456889,
+        "l1_median": 0.23397108212507342,
+        "l1_obs_loo_null_mean": 0.4883353341880966,
+        "l1_generated_loo_mean_vs_observed_mean": 0.4169110929337795,
+        "composition_top1": 0.1,
+        "mean_fraction_generated": {
+          "T cell": 0.6214,
+          "B cell": 0.051733,
+          "Monocyte": 0.1852,
+          "NK cell": 0.088133,
+          "DC": 0.025,
+          "Other": 0.028533
+        },
+        "mean_fraction_observed": {
+          "T cell": 0.544094,
+          "B cell": 0.047144,
+          "Monocyte": 0.215118,
+          "NK cell": 0.125669,
+          "DC": 0.017383,
+          "Other": 0.050593
+        }
+      },
+      "pseudobulk": {
+        "n_genes": 5563,
+        "r_median": 0.8683118625307109,
+        "r_mean": 0.8703664967065722,
+        "top1": 0.2,
+        "n_top1": 2,
+        "own_rank_median": 2.0,
+        "chance_top1": 0.1
+      },
+      "precision_coverage": {
+        "precision": 1.0,
+        "coverage": 0.9693333333333334,
+        "density": 5.388133333333333,
+        "n_query": 1500,
+        "n_reference": 1500
+      },
+      "precision_coverage_depth_matched": {
+        "precision": 0.9993333333333333,
+        "coverage": 0.9933333333333333,
+        "density": 3.3584666666666663,
+        "detected_median_before": {
+          "R1": 252.0,
+          "Q": 170.0
+        },
+        "detected_median_after": {
+          "R1": 170.0,
+          "Q": 170.0
+        }
+      },
+      "monocyte_pct": {
+        "generated_mean_over_donors": 18.519999999999996,
+        "observed_mean_over_donors": 21.511770225768277,
+        "generated_pooled_cells": 18.52
+      },
+      "median_umi_per_cell_scoring_genes": {
+        "generated_pooled": 483.0,
+        "observed_pooled": 447.0,
+        "generated_mean_of_donor_medians": 489.6000061035156,
+        "observed_mean_of_donor_medians": 470.35
+      },
+      "contrast": {
+        "mean_cp10k": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.6631265853728078,
+              "r_broadcast": 0.7344048019011988,
+              "partial_r_generated_given_broadcast": 0.46704952496141494,
+              "r_generated_vs_broadcast": 0.5395235474343575,
+              "n_genes": 2870
+            },
+            "B cell": {
+              "r_generated": 0.2925989610866921,
+              "r_broadcast": 0.565884313340693,
+              "partial_r_generated_given_broadcast": 0.1608945387708825,
+              "r_generated_vs_broadcast": 0.2929270554715147,
+              "n_genes": 3061
+            },
+            "Monocyte": {
+              "r_generated": 0.3657364980723787,
+              "r_broadcast": 0.5561945453231222,
+              "partial_r_generated_given_broadcast": 0.1509583855847481,
+              "r_generated_vs_broadcast": 0.4569352941809483,
+              "n_genes": 3017
+            },
+            "NK cell": {
+              "r_generated": 0.44729122875582594,
+              "r_broadcast": 0.6558646674649503,
+              "partial_r_generated_given_broadcast": 0.28422417103254227,
+              "r_generated_vs_broadcast": 0.3792998523868367,
+              "n_genes": 2940
+            }
+          },
+          "mean_r_generated": 0.4421883183219261,
+          "mean_r_broadcast": 0.6280870820074911,
+          "mean_partial_r": 0.26578165508739693
+        },
+        "pseudobulk_log1p_cpm": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.371485040719346,
+              "r_broadcast": 0.6900634955326531,
+              "partial_r_generated_given_broadcast": 0.2527165207639843,
+              "r_generated_vs_broadcast": 0.28421214480261103,
+              "n_genes": 2870
+            },
+            "B cell": {
+              "r_generated": 0.11707659203544454,
+              "r_broadcast": 0.4704332503129004,
+              "partial_r_generated_given_broadcast": 0.06414563860145382,
+              "r_generated_vs_broadcast": 0.12955989535222984,
+              "n_genes": 3061
+            },
+            "Monocyte": {
+              "r_generated": 0.17028474662959694,
+              "r_broadcast": 0.6573550923248582,
+              "partial_r_generated_given_broadcast": 0.030778841960678104,
+              "r_generated_vs_broadcast": 0.22466293572298648,
+              "n_genes": 3017
+            },
+            "NK cell": {
+              "r_generated": 0.15471721211952835,
+              "r_broadcast": 0.5646910960578172,
+              "partial_r_generated_given_broadcast": 0.0772087764689645,
+              "r_generated_vs_broadcast": 0.16264663479990635,
+              "n_genes": 2940
+            }
+          },
+          "mean_r_generated": 0.20339089787597897,
+          "mean_r_broadcast": 0.5956357335570572,
+          "mean_partial_r": 0.10621244444877019
+        }
+      },
+      "deg_top50": {
+        "types_scored": [
+          "T cell",
+          "B cell",
+          "Monocyte",
+          "NK cell",
+          "DC"
+        ],
+        "types_not_scored": {},
+        "per_type": {
+          "T cell": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": 0.0,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 3,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 55877,
+            "n_cells_gen": 9321
+          },
+          "B cell": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": null,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 4890,
+            "n_cells_gen": 776
+          },
+          "Monocyte": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": 0.0,
+            "obs_top_list_size": 1,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 21294,
+            "n_cells_gen": 2778
+          },
+          "NK cell": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": null,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 12579,
+            "n_cells_gen": 1322
+          },
+          "DC": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": null,
+            "obs_top_list_size": 0,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 1773,
+            "n_cells_gen": 375
+          }
+        },
+        "sum": 0,
+        "sum_4type": 0,
+        "max": 1,
+        "mean": 0.0,
+        "sum_broadcast": 0,
+        "sum_broadcast_4type": 0,
+        "broadcast_n_significant": 1,
+        "seconds": 0.03
+      },
+      "seconds": 4.7
+    }
+  },
+  "code_sha256": {
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+  },
+  "seconds": 5.4,
+  "gene_exclusion": {
+    "file": "/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",
+    "sha256": "e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de",
+    "n_listed": 196,
+    "n_scoring_genes": 5563,
+    "n_dropped_from_scoring_genes": 65,
+    "n_scoring_genes_kept": 5498,
+    "dropped": [
+      {
+        "gene_id": "ENSG00000124343",
+        "symbol": "XG"
+      },
+      {
+        "gene_id": "ENSG00000183943",
+        "symbol": "PRKX"
+      },
+      {
+        "gene_id": "ENSG00000146938",
+        "symbol": "NLGN4X"
+      },
+      {
+        "gene_id": "ENSG00000130021",
+        "symbol": "PUDP"
+      },
+      {
+        "gene_id": "ENSG00000101846",
+        "symbol": "STS"
+      },
+      {
+        "gene_id": "ENSG00000011201",
+        "symbol": "ANOS1"
+      },
+      {
+        "gene_id": "ENSG00000177138",
+        "symbol": "FAM9B"
+      },
+      {
+        "gene_id": "ENSG00000101849",
+        "symbol": "TBL1X"
+      },
+      {
+        "gene_id": "ENSG00000146950",
+        "symbol": "SHROOM2"
+      },
+      {
+        "gene_id": "ENSG00000182287",
+        "symbol": "AP1S2"
+      },
+      {
+        "gene_id": "ENSG00000047230",
+        "symbol": "CTPS2"
+      },
+      {
+        "gene_id": "ENSG00000086712",
+        "symbol": "TXLNG"
+      },
+      {
+        "gene_id": "ENSG00000188158",
+        "symbol": "NHS"
+      },
+      {
+        "gene_id": "ENSG00000177324",
+        "symbol": "BEND2"
+      },
+      {
+        "gene_id": "ENSG00000086717",
+        "symbol": "PPEF1"
+      },
+      {
+        "gene_id": "ENSG00000149970",
+        "symbol": "CNKSR2"
+      },
+      {
+        "gene_id": "ENSG00000102174",
+        "symbol": "PHEX"
+      },
+      {
+        "gene_id": "ENSG00000165186",
+        "symbol": "PTCHD1"
+      },
+      {
+        "gene_id": "ENSG00000169306",
+        "symbol": "IL1RAPL1"
+      },
+      {
+        "gene_id": "ENSG00000147036",
+        "symbol": "LANCL3"
+      },
+      {
+        "gene_id": "ENSG00000047597",
+        "symbol": "XK"
+      },
+      {
+        "gene_id": "ENSG00000180182",
+        "symbol": "MED14"
+      },
+      {
+        "gene_id": "ENSG00000183690",
+        "symbol": "EFHC2"
+      },
+      {
+        "gene_id": "ENSG00000147050",
+        "symbol": "KDM6A"
+      },
+      {
+        "gene_id": "ENSG00000147117",
+        "symbol": "ZNF157"
+      },
+      {
+        "gene_id": "ENSG00000102265",
+        "symbol": "TIMP1"
+      },
+      {
+        "gene_id": "ENSG00000158423",
+        "symbol": "RIBC1"
+      },
+      {
+        "gene_id": "ENSG00000155659",
+        "symbol": "VSIG4"
+      },
+      {
+        "gene_id": "ENSG00000204165",
+        "symbol": "CXorf65"
+      },
+      {
+        "gene_id": "ENSG00000204131",
+        "symbol": "NHSL2"
+      },
+      {
+        "gene_id": "ENSG00000078589",
+        "symbol": "P2RY10"
+      },
+      {
+        "gene_id": "ENSG00000147138",
+        "symbol": "GPR174"
+      },
+      {
+        "gene_id": "ENSG00000198157",
+        "symbol": "HMGN5"
+      },
+      {
+        "gene_id": "ENSG00000147180",
+        "symbol": "ZNF711"
+      },
+      {
+        "gene_id": "ENSG00000124429",
+        "symbol": "POF1B"
+      },
+      {
+        "gene_id": "ENSG00000126733",
+        "symbol": "DACH2"
+      },
+      {
+        "gene_id": "ENSG00000102290",
+        "symbol": "PCDH11X"
+      },
+      {
+        "gene_id": "ENSG00000102362",
+        "symbol": "SYTL4"
+      },
+      {
+        "gene_id": "ENSG00000182489",
+        "symbol": "XKRX"
+      },
+      {
+        "gene_id": "ENSG00000166432",
+        "symbol": "ZMAT1"
+      },
+      {
+        "gene_id": "ENSG00000189108",
+        "symbol": "IL1RAPL2"
+      },
+      {
+        "gene_id": "ENSG00000198088",
+        "symbol": "NUP62CL"
+      },
+      {
+        "gene_id": "ENSG00000147234",
+        "symbol": "FRMPD3"
+      },
+      {
+        "gene_id": "ENSG00000080561",
+        "symbol": "MID2"
+      },
+      {
+        "gene_id": "ENSG00000197565",
+        "symbol": "COL4A6"
+      },
+      {
+        "gene_id": "ENSG00000072315",
+        "symbol": "TRPC5"
+      },
+      {
+        "gene_id": "ENSG00000187823",
+        "symbol": "RTL4"
+      },
+      {
+        "gene_id": "ENSG00000125675",
+        "symbol": "GRIA3"
+      },
+      {
+        "gene_id": "ENSG00000183918",
+        "symbol": "SH2D1A"
+      },
+      {
+        "gene_id": "ENSG00000056277",
+        "symbol": "ZNF280C"
+      },
+      {
+        "gene_id": "ENSG00000171004",
+        "symbol": "HS6ST2"
+      },
+      {
+        "gene_id": "ENSG00000170965",
+        "symbol": "PLAC1"
+      },
+      {
+        "gene_id": "ENSG00000022267",
+        "symbol": "FHL1"
+      },
+      {
+        "gene_id": "ENSG00000102245",
+        "symbol": "CD40LG"
+      },
+      {
+        "gene_id": "ENSG00000129682",
+        "symbol": "FGF13"
+      },
+      {
+        "gene_id": "ENSG00000155966",
+        "symbol": "AFF2"
+      },
+      {
+        "gene_id": "ENSG00000011677",
+        "symbol": "GABRA3"
+      },
+      {
+        "gene_id": "ENSG00000183837",
+        "symbol": "PNMA3"
+      },
+      {
+        "gene_id": "ENSG00000067646",
+        "symbol": "ZFY"
+      },
+      {
+        "gene_id": "ENSG00000099715",
+        "symbol": "PCDH11Y"
+      },
+      {
+        "gene_id": "ENSG00000114374",
+        "symbol": "USP9Y"
+      },
+      {
+        "gene_id": "ENSG00000067048",
+        "symbol": "DDX3Y"
+      },
+      {
+        "gene_id": "ENSG00000183878",
+        "symbol": "UTY"
+      },
+      {
+        "gene_id": "ENSG00000165246",
+        "symbol": "NLGN4Y"
+      },
+      {
+        "gene_id": "ENSG00000012817",
+        "symbol": "KDM5D"
+      }
+    ],
+    "applies_to": "group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene"
+  },
+  "core_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw4/score"
+}

paper-releases/pbisc-diffusion/updates/20261015T121654Z-x1-nine-core40-deck/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/x1_priority_completion_20261015/evaluation/units/giroux2022/disease/draw4/lora/scoring_support.json

@@ -0,0 +1,45 @@
+{
+  "schema": "pbisc.paper.strict-score-binding.v1",
+  "support_sha256": "df74fb20effc23b7784248bf76e32951803075e492251168f3d5f83dfdec81ea",
+  "cohort": "giroux2022",
+  "unit": "draw4_n5",
+  "test_sample_ids": [
+    "450905_d0",
+    "450905_d14",
+    "7085CA_d0",
+    "7085CA_d7",
+    "7085CA_d14",
+    "B85D75_d0",
+    "B85D75_d7",
+    "180E1A_d0",
+    "180E1A_d7",
+    "180E1A_d14"
+  ],
+  "test_donor_ids": [
+    "450905",
+    "450905",
+    "7085CA",
+    "7085CA",
+    "7085CA",
+    "B85D75",
+    "B85D75",
+    "180E1A",
+    "180E1A",
+    "180E1A"
+  ],
+  "arm_bindings": {
+    "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/draw4/lora.npz",
+      "npz_sha256": "7dc39e3963038c6e4c41d2681b5be1135bce425de1514732c4b91af899249afc",
+      "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw4/lora.log",
+      "receipt_sha256": "986e4876a6b229da8e23539f432e50c6dd5f6f3d69a45c7d52f13add9aa53149",
+      "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw4/lora/RUN.json",
+      "source_binding_sha256": "237e2b577cc2fd6f634a0eb4681896c6b3fdcd4157e0406ed1818193a76f773b",
+      "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw4/test_raw.npz",
+      "condition_sha256": "1339e7631cd54c77bef770b2248bdc2ca560a6dc70e244ed61cd4d38a835bf3f",
+      "checkpoint_sha256": "ccd39f782235579aae57cd576348a44f26f57e5c62d068b5d2554a6e87c68ea4",
+      "support_sha256": "df74fb20effc23b7784248bf76e32951803075e492251168f3d5f83dfdec81ea"
+    }
+  }
+}