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/draw0/lora/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,1500,5914,150,0.38,0.3094352384173148,0.0133333333333333,0.0361853229624619,0.4633333333333333,0.4293202570172472,0.092,0.120899560365235,0.0246666666666666,0.0099763273588096,0.0266666666666666,0.0941832938789313,0.2385363544132566,0.652432804255913,0.8784872032904227,1,True,1.0,0.9466666666666668,0.98,1.0,46.33333333333333,42.93202570172472,572.0,574.5
+lora,450905_d14,mild,1500,7407,150,0.5646666666666667,0.4422843256379101,0.0313333333333333,0.0292966113136222,0.2046666666666666,0.2742000810044552,0.1233333333333333,0.1578236803024166,0.0313333333333333,0.0298366410152558,0.0446666666666666,0.0665586607263399,0.2518315107330903,0.3927979931719725,0.8739467542084013,1,True,1.0,1.0,1.0,1.0,20.466666666666665,27.420008100445525,543.0,558.0
+lora,2AD75E_d0,mild,1500,7693,150,0.7153333333333334,0.6034056934875861,0.0486666666666666,0.0640842324190822,0.1126666666666666,0.1406473417392434,0.072,0.1594956453919147,0.018,0.0253477187053165,0.0333333333333333,0.0070193682568568,0.2764832098444474,0.3152895182425347,0.8540978238947612,7,False,1.0,0.9866666666666668,0.9933333333333332,0.98,11.266666666666666,14.064734173924348,434.0,532.0
+lora,2AD75E_d7,mild,1500,10499,150,0.726,0.5808172206876845,0.106,0.1437279740927707,0.0633333333333333,0.1027716925421468,0.0573333333333333,0.1471568720830555,0.008,0.0137155919611391,0.0393333333333333,0.0118106486332031,0.3454109280248912,0.3751047669969859,0.8440753409315591,5,False,1.0,0.9666666666666668,1.0,0.8866666666666667,6.333333333333334,10.277169254214687,342.5,443.0
+lora,2AD75E_d14,mild,1500,13692,150,0.718,0.5811422728600643,0.0566666666666666,0.1250365176745544,0.116,0.1419807186678352,0.056,0.1249634823254455,0.0253333333333333,0.0165790242477359,0.028,0.0102979842243645,0.3266281040023371,0.2997120435632864,0.8590343881265933,3,False,1.0,0.9866666666666668,1.0,0.9733333333333334,11.6,14.198071866783524,456.0,428.0
+lora,82CCF5_d0,severe,1500,10125,150,0.6073333333333333,0.5422222222222223,0.0753333333333333,0.1183209876543209,0.178,0.1539753086419753,0.0773333333333333,0.093037037037037,0.0326666666666666,0.0166913580246913,0.0293333333333333,0.075753086419753,0.2102222222222221,0.2014335510446355,0.8597653677916022,4,False,1.0,1.0,0.9933333333333332,1.0,17.8,15.397530864197533,475.0,390.0
+lora,82CCF5_d7,severe,1500,10860,150,0.7346666666666667,0.619060773480663,0.0473333333333333,0.0997237569060773,0.112,0.1415285451197053,0.064,0.0941068139963167,0.0186666666666666,0.0136279926335174,0.0233333333333333,0.03195211786372,0.2412891344383057,0.2587112556016884,0.8737217900707615,1,True,1.0,0.9933333333333332,0.9933333333333332,0.9933333333333332,11.2,14.152854511970531,507.5,497.0
+lora,82CCF5_d14,severe,1500,11056,150,0.7086666666666667,0.6330499276410999,0.0513333333333333,0.101212011577424,0.1246666666666666,0.1136939218523878,0.05,0.0682887120115774,0.0426666666666666,0.0145622286541244,0.0226666666666666,0.0691931982633864,0.2293878437047756,0.3322264186222185,0.8703436480745063,2,False,1.0,0.9933333333333332,1.0,1.0,12.466666666666669,11.369392185238784,525.0,394.0
+lora,0BF51C_d0,severe,1500,6510,150,0.554,0.4012288786482335,0.0106666666666666,0.0167434715821812,0.3673333333333333,0.4609831029185868,0.0133333333333333,0.0772657450076804,0.0086666666666666,0.0061443932411674,0.046,0.0376344086021505,0.3273179723502304,0.5474367391909245,0.8613878314515696,1,True,1.0,0.7333333333333333,0.9933333333333332,0.7733333333333333,36.73333333333333,46.09831029185868,422.0,628.0
+lora,0BF51C_d7,severe,1500,10105,150,0.744,0.612370113805047,0.0366666666666666,0.0570014844136566,0.1313333333333333,0.1607125185551707,0.028,0.0529440870856011,0.0213333333333333,0.0073231073725878,0.0386666666666666,0.1096486887679366,0.291280224311397,0.2744910969706922,0.8573433316267198,4,False,1.0,0.9666666666666668,1.0,0.98,13.133333333333333,16.071251855517072,431.5,509.0
+lora,0BF51C_d14,severe,1500,11419,150,0.766,0.6330676941938874,0.0326666666666666,0.0796041684911113,0.1153333333333333,0.151589456169542,0.0393333333333333,0.0790787284350643,0.0166666666666666,0.0105088011209387,0.03,0.0461511515894561,0.278180342703681,0.1888911833914119,0.8574648815071223,3,False,1.0,0.9933333333333332,0.9933333333333332,1.0,11.533333333333331,15.1589456169542,405.0,541.0

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/draw0/lora/score/summary.json

@@ -0,0 +1,755 @@
+{
+  "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
+    },
+    "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": {
+      "T cell": {
+        "n_significant": 1,
+        "n_tested": 5216,
+        "n_case_donors": 6,
+        "n_control_donors": 5,
+        "n_cells": 59044,
+        "top_list_size": 1
+      },
+      "B cell": {
+        "n_significant": 2,
+        "n_tested": 4912,
+        "n_case_donors": 6,
+        "n_control_donors": 5,
+        "n_cells": 9139,
+        "top_list_size": 2
+      },
+      "Monocyte": {
+        "n_significant": 0,
+        "n_tested": 5113,
+        "n_case_donors": 6,
+        "n_control_donors": 5,
+        "n_cells": 19384,
+        "top_list_size": 0
+      },
+      "NK cell": {
+        "n_significant": 0,
+        "n_tested": 4891,
+        "n_case_donors": 6,
+        "n_control_donors": 5,
+        "n_cells": 11027,
+        "top_list_size": 0
+      },
+      "DC": {
+        "n_significant": 0,
+        "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": {
+    "lora": {
+      "comp_l1": 0.27423344061351224,
+      "comp_l1_obs_loo_null": 0.348957033732024,
+      "precision": 1.0,
+      "coverage": 0.9606060606060606,
+      "precision_dm": 0.9951515151515151,
+      "coverage_dm": 0.9624242424242424,
+      "pb_r_median": 0.8597653677916022,
+      "pb_top1": 0.36363636363636365,
+      "mono_pct_gen": 18.078787878787875,
+      "mono_pct_obs": 20.64911767480269,
+      "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,
+      "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": 3,
+      "deg_top50_sum_4type": 0,
+      "deg_top50_sum_broadcast": 0,
+      "seconds": 4.8
+    }
+  },
+  "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/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"
+      },
+      "poisson": {
+        "seed": 20260916,
+        "rule": "whole NPZ, rows in NPZ order",
+        "nnz_whole_npz": 3987887,
+        "median_library_whole_npz_panel": 1552.0,
+        "n_rows_whole_npz": 16500
+      },
+      "annotation": {
+        "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+        "zero_padded_model_genes": 0,
+        "label_counts": {
+          "T cell": 10828,
+          "Monocyte": 2983,
+          "NK cell": 1009,
+          "B cell": 765,
+          "Other": 543,
+          "DC": 372
+        },
+        "mean_l2_max_prob": 0.8848754408982668,
+        "predict_seconds": 3.0
+      },
+      "n_donors": 11,
+      "n_generated_cells": 16500,
+      "composition": {
+        "l1_mean": 0.27423344061351224,
+        "l1_median": 0.2764832098444474,
+        "l1_obs_loo_null_mean": 0.348957033732024,
+        "l1_generated_loo_mean_vs_observed_mean": 0.3510940597678522,
+        "composition_top1": 0.09090909090909091,
+        "mean_fraction_generated": {
+          "T cell": 0.656242,
+          "B cell": 0.046364,
+          "Monocyte": 0.180788,
+          "NK cell": 0.061152,
+          "DC": 0.022545,
+          "Other": 0.032909
+        },
+        "mean_fraction_observed": {
+          "T cell": 0.541644,
+          "B cell": 0.079176,
+          "Monocyte": 0.206491,
+          "NK cell": 0.106824,
+          "DC": 0.014938,
+          "Other": 0.050928
+        }
+      },
+      "pseudobulk": {
+        "n_genes": 5563,
+        "r_median": 0.8597653677916022,
+        "r_mean": 0.8626971237249108,
+        "top1": 0.36363636363636365,
+        "n_top1": 4,
+        "own_rank_median": 3.0,
+        "chance_top1": 0.09090909090909091
+      },
+      "precision_coverage": {
+        "precision": 1.0,
+        "coverage": 0.9606060606060606,
+        "density": 4.652,
+        "n_query": 1650,
+        "n_reference": 1650
+      },
+      "precision_coverage_depth_matched": {
+        "precision": 0.9951515151515151,
+        "coverage": 0.9624242424242424,
+        "density": 2.6673939393939397,
+        "detected_median_before": {
+          "R1": 256.0,
+          "Q": 161.5
+        },
+        "detected_median_after": {
+          "R1": 161.5,
+          "Q": 161.5
+        }
+      },
+      "monocyte_pct": {
+        "generated_mean_over_donors": 18.078787878787875,
+        "observed_mean_over_donors": 20.64911767480269,
+        "generated_pooled_cells": 18.078787878787878
+      },
+      "median_umi_per_cell_scoring_genes": {
+        "generated_pooled": 460.0,
+        "observed_pooled": 483.0,
+        "generated_mean_of_donor_medians": 464.8636474609375,
+        "observed_mean_of_donor_medians": 499.5
+      },
+      "contrast": {
+        "mean_cp10k": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.3563914715250282,
+              "r_broadcast": 0.4659672798536223,
+              "partial_r_generated_given_broadcast": 0.2218085591407057,
+              "r_generated_vs_broadcast": 0.3742731766713961,
+              "n_genes": 2863
+            },
+            "B cell": {
+              "r_generated": 0.13206111640016924,
+              "r_broadcast": 0.3989038406365887,
+              "partial_r_generated_given_broadcast": 0.07395471487893368,
+              "r_generated_vs_broadcast": 0.16333743049040902,
+              "n_genes": 3005
+            },
+            "Monocyte": {
+              "r_generated": 0.24776423621286625,
+              "r_broadcast": 0.6141260231172326,
+              "partial_r_generated_given_broadcast": 0.09111033870527305,
+              "r_generated_vs_broadcast": 0.2914396663259063,
+              "n_genes": 3028
+            },
+            "NK cell": {
+              "r_generated": 0.1012931562128459,
+              "r_broadcast": 0.40486451543783863,
+              "partial_r_generated_given_broadcast": 0.04717315928029971,
+              "r_generated_vs_broadcast": 0.1447732264968033,
+              "n_genes": 2910
+            }
+          },
+          "mean_r_generated": 0.2093774950877274,
+          "mean_r_broadcast": 0.4709654147613206,
+          "mean_partial_r": 0.10851169300130305
+        },
+        "pseudobulk_log1p_cpm": {
+          "per_type": {
+            "T cell": {
+              "r_generated": 0.15518483081128517,
+              "r_broadcast": 0.5669062142141347,
+              "partial_r_generated_given_broadcast": 0.07354063271502896,
+              "r_generated_vs_broadcast": 0.16840274801386212,
+              "n_genes": 2863
+            },
+            "B cell": {
+              "r_generated": 0.07277531821196102,
+              "r_broadcast": 0.4804240789506083,
+              "partial_r_generated_given_broadcast": 0.03368313626567538,
+              "r_generated_vs_broadcast": 0.09024218255985579,
+              "n_genes": 3005
+            },
+            "Monocyte": {
+              "r_generated": 0.118522835737594,
+              "r_broadcast": 0.6247044807439144,
+              "partial_r_generated_given_broadcast": 0.0369013387558337,
+              "r_generated_vs_broadcast": 0.1440819996894487,
+              "n_genes": 3028
+            },
+            "NK cell": {
+              "r_generated": 0.0400801728742779,
+              "r_broadcast": 0.47190028654240307,
+              "partial_r_generated_given_broadcast": 0.011741211541534702,
+              "r_generated_vs_broadcast": 0.06304107476395901,
+              "n_genes": 2910
+            }
+          },
+          "mean_r_generated": 0.09664078940877951,
+          "mean_r_broadcast": 0.5359837651127651,
+          "mean_partial_r": 0.03896657981951819
+        }
+      },
+      "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": 1,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 59044,
+            "n_cells_gen": 10828
+          },
+          "B cell": {
+            "deg_scored": true,
+            "top50_overlap": 0,
+            "top50_jaccard": 0.0,
+            "obs_top_list_size": 2,
+            "gen_top_list_size": 0,
+            "top50_overlap_broadcast": 0,
+            "top50_jaccard_broadcast": 0.0,
+            "n_cells_obs": 9139,
+            "n_cells_gen": 765
+          },
+          "Monocyte": {
+            "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": null,
+            "n_cells_obs": 19384,
+            "n_cells_gen": 2983
+          },
+          "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": null,
+            "n_cells_obs": 11027,
+            "n_cells_gen": 1009
+          },
+          "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": null,
+            "n_cells_obs": 1558,
+            "n_cells_gen": 372
+          }
+        },
+        "sum": 0,
+        "sum_4type": 0,
+        "max": 3,
+        "mean": 0.0,
+        "sum_broadcast": 0,
+        "sum_broadcast_4type": 0,
+        "broadcast_n_significant": 0,
+        "seconds": 0.03
+      },
+      "seconds": 4.8
+    }
+  },
+  "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": 5.6,
+  "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/draw0/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/draw0/lora/scoring_support.json

@@ -0,0 +1,47 @@
+{
+  "schema": "pbisc.paper.strict-score-binding.v1",
+  "support_sha256": "074d1cf9ca3951ef1a032239eabb9d3a13f0f9a2030b030dcbe425ac71d46700",
+  "cohort": "giroux2022",
+  "unit": "draw0_n5",
+  "test_sample_ids": [
+    "450905_d0",
+    "450905_d14",
+    "2AD75E_d0",
+    "2AD75E_d7",
+    "2AD75E_d14",
+    "82CCF5_d0",
+    "82CCF5_d7",
+    "82CCF5_d14",
+    "0BF51C_d0",
+    "0BF51C_d7",
+    "0BF51C_d14"
+  ],
+  "test_donor_ids": [
+    "450905",
+    "450905",
+    "2AD75E",
+    "2AD75E",
+    "2AD75E",
+    "82CCF5",
+    "82CCF5",
+    "82CCF5",
+    "0BF51C",
+    "0BF51C",
+    "0BF51C"
+  ],
+  "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/draw0/lora.npz",
+      "npz_sha256": "765845e9a73b40470b9d94fded33c190ccb8d73529f732ae5bc0fc2cea9cda6e",
+      "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/lora.log",
+      "receipt_sha256": "17a7b0046518b021f45c165b7417db8a99744c46965c216135cc7cea4da270d4",
+      "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw0/lora/RUN.json",
+      "source_binding_sha256": "7e86f51744c22136fc19fed11476d33043dc33347f50fa248d96fdbf58eea019",
+      "condition_npz": "/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",
+      "condition_sha256": "f04c5725cf7d20ca4ca26d2ac43352d8c233b9d6c4d7ddc2116e3be4694623a9",
+      "checkpoint_sha256": "1da445cb2d3c86b2672e1b2dfa52e31b444b509108d125a7feb9b7ebf80dc0da",
+      "support_sha256": "074d1cf9ca3951ef1a032239eabb9d3a13f0f9a2030b030dcbe425ac71d46700"
+    }
+  }
+}

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/milestones/20261015T121654Z-x1-nine-core40-deck/DECK_VERIFIED.json

@@ -0,0 +1,13 @@
+{
+  "schema": "pbisc.x1.priority.latest-verified.v1",
+  "status": "automated_pass_visual_pending",
+  "build": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z",
+  "fingerprint": "b8ae611de49cab060dced282cbd96004639cd848c7b028f9bae7c4191295f451",
+  "slides": 169,
+  "verification": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/builds/20261015T120743086141Z/qa/VERIFICATION.json",
+  "outputs": {
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_expanded_master_20261015_x1_priority.pptx": "6f07090814c11c652e0dac53cc5d01616fc2bb73b4f48fe45e797b1328b855a3",
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_expanded_master_20261015_x1_priority.pdf": "2721a3a1eff50081a69a8d19f13c01f2835396803ce9f29cf0afe84205659c0e"
+  },
+  "parent_base": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/x1_priority_20261015/base/BASE_VERIFIED.json"
+}