Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/fold4/summary.json

@@ -0,0 +1,817 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "immicro",
+ "written_utc": "2026-10-01T14:03:37.444970+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",
+  "immicro",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/fold4",
+  "--threads",
+  "8",
+  "--arm",
+  "lora_r4_n5__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r4_n5__raw.npz",
+  "--arm",
+  "lora_r64_n5__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r64_n5__raw.npz",
+  "--arm",
+  "lora_r4_n20__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r4_n20__raw.npz",
+  "--arm",
+  "lora_r64_n20__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r64_n20__raw.npz",
+  "--arm",
+  "lora_r4__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r4__raw.npz",
+  "--arm",
+  "lora_r64__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r64__raw.npz"
+ ],
+ "arms": [
+  "lora_r4_n5__raw",
+  "lora_r64_n5__raw",
+  "lora_r4_n20__raw",
+  "lora_r64_n20__raw",
+  "lora_r4__raw",
+  "lora_r64__raw"
+ ],
+ "donors": [
+  "HS8",
+  "HS11",
+  "HS20",
+  "HS27",
+  "HS28",
+  "HS41",
+  "HS45",
+  "HS54",
+  "HS64",
+  "HS70",
+  "HS74",
+  "HS75",
+  "HS76",
+  "HS77",
+  "HS87",
+  "HS88",
+  "HS93",
+  "HS94",
+  "HS97",
+  "HS103",
+  "HS104"
+ ],
+ "n_donors": 21,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/immicro",
+  "reference_sha256": "c5e2547be3ec3b12cb0c0b404a49e14a046ae59d40be70427f98f083a76bce17",
+  "features_sha256": "735255066ce7ebbac13a1fdfd058e26f31edd60314cc02fd589b0a292dbbc838",
+  "n_r1_cells": 3150,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.2925134599208832,
+   "n_fit_cells": 3150
+  },
+  "r2_control": {
+   "precision": 0.9946031746031746,
+   "coverage": 1.0,
+   "density": 2.7306349206349205,
+   "n_query": 3150,
+   "depth_matched": {
+    "precision": 0.9949206349206349,
+    "coverage": 1.0,
+    "density": 2.684730158730159
+   }
+  },
+  "observed_l1_loo_null_mean": 0.13719637503029242
+ },
+ "contrast_definition": {
+  "enabled": false,
+  "reason": "dataset immicro has no group contrast (use --groups-csv / --case-groups)"
+ },
+ "deg_definition": {
+  "enabled": false,
+  "reason": "contrast off"
+ },
+ "headline": {
+  "lora_r4_n5__raw": {
+   "comp_l1": 0.12617652194755763,
+   "comp_l1_obs_loo_null": 0.13719637503029242,
+   "precision": 0.9895238095238095,
+   "coverage": 0.9307936507936508,
+   "precision_dm": 0.9917460317460317,
+   "coverage_dm": 0.9857142857142858,
+   "pb_r_median": 0.9033487562192769,
+   "pb_top1": 0.09523809523809523,
+   "mono_pct_gen": 13.339682539682537,
+   "mono_pct_obs": 14.664491120050386,
+   "median_umi_gen": 2654.0,
+   "median_umi_obs": 1973.0,
+   "seconds": 6.9
+  },
+  "lora_r64_n5__raw": {
+   "comp_l1": 0.15415134575922032,
+   "comp_l1_obs_loo_null": 0.13719637503029242,
+   "precision": 0.9920634920634921,
+   "coverage": 0.9584126984126984,
+   "precision_dm": 0.9936507936507937,
+   "coverage_dm": 0.9926984126984127,
+   "pb_r_median": 0.9048270726167733,
+   "pb_top1": 0.09523809523809523,
+   "mono_pct_gen": 11.4984126984127,
+   "mono_pct_obs": 14.664491120050386,
+   "median_umi_gen": 2683.0,
+   "median_umi_obs": 1973.0,
+   "seconds": 6.5
+  },
+  "lora_r4_n20__raw": {
+   "comp_l1": 0.1367051579486552,
+   "comp_l1_obs_loo_null": 0.13719637503029242,
+   "precision": 0.9863492063492063,
+   "coverage": 0.8885714285714286,
+   "precision_dm": 0.9936507936507937,
+   "coverage_dm": 0.9831746031746031,
+   "pb_r_median": 0.899567662593431,
+   "pb_top1": 0.047619047619047616,
+   "mono_pct_gen": 11.266666666666666,
+   "mono_pct_obs": 14.664491120050386,
+   "median_umi_gen": 2539.0,
+   "median_umi_obs": 1973.0,
+   "seconds": 6.8
+  },
+  "lora_r64_n20__raw": {
+   "comp_l1": 0.16384442171014588,
+   "comp_l1_obs_loo_null": 0.13719637503029242,
+   "precision": 0.9838095238095238,
+   "coverage": 0.926984126984127,
+   "precision_dm": 0.9888888888888889,
+   "coverage_dm": 0.9911111111111112,
+   "pb_r_median": 0.9025921876265389,
+   "pb_top1": 0.09523809523809523,
+   "mono_pct_gen": 9.730158730158731,
+   "mono_pct_obs": 14.664491120050386,
+   "median_umi_gen": 2495.0,
+   "median_umi_obs": 1973.0,
+   "seconds": 6.5
+  },
+  "lora_r4__raw": {
+   "comp_l1": 0.15837196804341017,
+   "comp_l1_obs_loo_null": 0.13719637503029242,
+   "precision": 0.986031746031746,
+   "coverage": 0.8644444444444445,
+   "precision_dm": 0.9901587301587301,
+   "coverage_dm": 0.9809523809523809,
+   "pb_r_median": 0.8986802838141615,
+   "pb_top1": 0.09523809523809523,
+   "mono_pct_gen": 10.695238095238095,
+   "mono_pct_obs": 14.664491120050386,
+   "median_umi_gen": 2358.5,
+   "median_umi_obs": 1973.0,
+   "seconds": 6.6
+  },
+  "lora_r64__raw": {
+   "comp_l1": 0.1422339117529488,
+   "comp_l1_obs_loo_null": 0.13719637503029242,
+   "precision": 0.9898412698412699,
+   "coverage": 0.946031746031746,
+   "precision_dm": 0.9917460317460317,
+   "coverage_dm": 0.9904761904761905,
+   "pb_r_median": 0.9010059643345039,
+   "pb_top1": 0.09523809523809523,
+   "mono_pct_gen": 10.936507936507937,
+   "mono_pct_obs": 14.664491120050386,
+   "median_umi_gen": 2153.0,
+   "median_umi_obs": 1973.0,
+   "seconds": 6.4
+  }
+ },
+ "per_arm": {
+  "lora_r4_n5__raw": {
+   "arm": "lora_r4_n5__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r4_n5__raw.npz",
+   "npz_sha256": "1893fe0c3b662bb30e5a0772948d5e78f73d81ff6ba12976071fce881344288f",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r4_n5/checkpoint_ft.pt",
+    "checkpoint_sha256": "a8cf27352ec91effa93c97f9b7113ca987f5588318c45b71176b1fbc96029c6f",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fold4/test_raw.npz",
+    "input_condition_sha256": "9e0a41119111a870b011b94fad6a53480b59eac0a709c61f0f314f74d8f201b8",
+    "seed": 20260927,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 9255640,
+    "median_library_whole_npz_panel": 2656.0,
+    "n_rows_whole_npz": 31500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 22016,
+     "Monocyte": 4202,
+     "B cell": 2557,
+     "NK cell": 1676,
+     "DC": 805,
+     "Other": 244
+    },
+    "mean_l2_max_prob": 0.912580408738719,
+    "predict_seconds": 3.1
+   },
+   "n_donors": 21,
+   "n_generated_cells": 31500,
+   "composition": {
+    "l1_mean": 0.12617652194755763,
+    "l1_median": 0.12366463773807193,
+    "l1_obs_loo_null_mean": 0.13719637503029242,
+    "l1_generated_loo_mean_vs_observed_mean": 0.15290803393074245,
+    "composition_top1": 0.23809523809523808,
+    "mean_fraction_generated": {
+     "T cell": 0.698921,
+     "B cell": 0.081175,
+     "Monocyte": 0.133397,
+     "NK cell": 0.053206,
+     "DC": 0.025556,
+     "Other": 0.007746
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.668001,
+     "B cell": 0.081749,
+     "Monocyte": 0.146645,
+     "NK cell": 0.07743,
+     "DC": 0.020687,
+     "Other": 0.005487
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.9033487562192769,
+    "r_mean": 0.9040099361880947,
+    "top1": 0.09523809523809523,
+    "n_top1": 2,
+    "own_rank_median": 9.0,
+    "chance_top1": 0.047619047619047616
+   },
+   "precision_coverage": {
+    "precision": 0.9895238095238095,
+    "coverage": 0.9307936507936508,
+    "density": 2.659873015873016,
+    "n_query": 3150,
+    "n_reference": 3150
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9917460317460317,
+    "coverage": 0.9857142857142858,
+    "density": 3.9605396825396824,
+    "detected_median_before": {
+     "R1": 359.0,
+     "Q": 280.0
+    },
+    "detected_median_after": {
+     "R1": 280.0,
+     "Q": 280.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 13.339682539682537,
+    "observed_mean_over_donors": 14.664491120050386,
+    "generated_pooled_cells": 13.33968253968254
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2654.0,
+    "observed_pooled": 1973.0,
+    "generated_mean_of_donor_medians": 2649.428466796875,
+    "observed_mean_of_donor_medians": 2012.3095238095239
+   },
+   "seconds": 6.9
+  },
+  "lora_r64_n5__raw": {
+   "arm": "lora_r64_n5__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r64_n5__raw.npz",
+   "npz_sha256": "f90a31d95e455ac435e2d00680cfbb8254d73d9446354225ea63978e22130ac3",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r64_n5/checkpoint_ft.pt",
+    "checkpoint_sha256": "06ab029c7f3e9e6f80f05e06a68ffd37178e5f700a42dd8cf89aedcb9b058be6",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fold4/test_raw.npz",
+    "input_condition_sha256": "9e0a41119111a870b011b94fad6a53480b59eac0a709c61f0f314f74d8f201b8",
+    "seed": 20260927,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 9197162,
+    "median_library_whole_npz_panel": 2685.0,
+    "n_rows_whole_npz": 31500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 22376,
+     "Monocyte": 3622,
+     "B cell": 2789,
+     "NK cell": 1664,
+     "DC": 805,
+     "Other": 244
+    },
+    "mean_l2_max_prob": 0.9199535644778184,
+    "predict_seconds": 3.1
+   },
+   "n_donors": 21,
+   "n_generated_cells": 31500,
+   "composition": {
+    "l1_mean": 0.15415134575922032,
+    "l1_median": 0.1404272091544818,
+    "l1_obs_loo_null_mean": 0.13719637503029242,
+    "l1_generated_loo_mean_vs_observed_mean": 0.16811973924707677,
+    "composition_top1": 0.14285714285714285,
+    "mean_fraction_generated": {
+     "T cell": 0.710349,
+     "B cell": 0.08854,
+     "Monocyte": 0.114984,
+     "NK cell": 0.052825,
+     "DC": 0.025556,
+     "Other": 0.007746
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.668001,
+     "B cell": 0.081749,
+     "Monocyte": 0.146645,
+     "NK cell": 0.07743,
+     "DC": 0.020687,
+     "Other": 0.005487
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.9048270726167733,
+    "r_mean": 0.9047514066723689,
+    "top1": 0.09523809523809523,
+    "n_top1": 2,
+    "own_rank_median": 9.0,
+    "chance_top1": 0.047619047619047616
+   },
+   "precision_coverage": {
+    "precision": 0.9920634920634921,
+    "coverage": 0.9584126984126984,
+    "density": 2.6686666666666667,
+    "n_query": 3150,
+    "n_reference": 3150
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9936507936507937,
+    "coverage": 0.9926984126984127,
+    "density": 3.9938095238095235,
+    "detected_median_before": {
+     "R1": 359.0,
+     "Q": 280.0
+    },
+    "detected_median_after": {
+     "R1": 280.0,
+     "Q": 280.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 11.4984126984127,
+    "observed_mean_over_donors": 14.664491120050386,
+    "generated_pooled_cells": 11.498412698412698
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2683.0,
+    "observed_pooled": 1973.0,
+    "generated_mean_of_donor_medians": 2681.02392578125,
+    "observed_mean_of_donor_medians": 2012.3095238095239
+   },
+   "seconds": 6.5
+  },
+  "lora_r4_n20__raw": {
+   "arm": "lora_r4_n20__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r4_n20__raw.npz",
+   "npz_sha256": "a9a8ae835b3cc1d6e0d1d3c6481892113c86aa90a8016d0876004a00ac41a4e1",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r4_n20/checkpoint_ft.pt",
+    "checkpoint_sha256": "a33c1fc223961103633fd1411853d5949fb25a0863c12f75fc6204bf421de3c2",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fold4/test_raw.npz",
+    "input_condition_sha256": "9e0a41119111a870b011b94fad6a53480b59eac0a709c61f0f314f74d8f201b8",
+    "seed": 20260927,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 8717245,
+    "median_library_whole_npz_panel": 2540.0,
+    "n_rows_whole_npz": 31500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 22403,
+     "Monocyte": 3549,
+     "B cell": 2448,
+     "NK cell": 1901,
+     "DC": 847,
+     "Other": 352
+    },
+    "mean_l2_max_prob": 0.9048634717904386,
+    "predict_seconds": 3.3
+   },
+   "n_donors": 21,
+   "n_generated_cells": 31500,
+   "composition": {
+    "l1_mean": 0.1367051579486552,
+    "l1_median": 0.1187886262418637,
+    "l1_obs_loo_null_mean": 0.13719637503029242,
+    "l1_generated_loo_mean_vs_observed_mean": 0.17077834201769648,
+    "composition_top1": 0.2857142857142857,
+    "mean_fraction_generated": {
+     "T cell": 0.711206,
+     "B cell": 0.077714,
+     "Monocyte": 0.112667,
+     "NK cell": 0.060349,
+     "DC": 0.026889,
+     "Other": 0.011175
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.668001,
+     "B cell": 0.081749,
+     "Monocyte": 0.146645,
+     "NK cell": 0.07743,
+     "DC": 0.020687,
+     "Other": 0.005487
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.899567662593431,
+    "r_mean": 0.8987719756043385,
+    "top1": 0.047619047619047616,
+    "n_top1": 1,
+    "own_rank_median": 10.0,
+    "chance_top1": 0.047619047619047616
+   },
+   "precision_coverage": {
+    "precision": 0.9863492063492063,
+    "coverage": 0.8885714285714286,
+    "density": 2.42584126984127,
+    "n_query": 3150,
+    "n_reference": 3150
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9936507936507937,
+    "coverage": 0.9831746031746031,
+    "density": 4.006253968253968,
+    "detected_median_before": {
+     "R1": 359.0,
+     "Q": 266.0
+    },
+    "detected_median_after": {
+     "R1": 266.0,
+     "Q": 266.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 11.266666666666666,
+    "observed_mean_over_donors": 14.664491120050386,
+    "generated_pooled_cells": 11.266666666666666
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2539.0,
+    "observed_pooled": 1973.0,
+    "generated_mean_of_donor_medians": 2538.238037109375,
+    "observed_mean_of_donor_medians": 2012.3095238095239
+   },
+   "seconds": 6.8
+  },
+  "lora_r64_n20__raw": {
+   "arm": "lora_r64_n20__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r64_n20__raw.npz",
+   "npz_sha256": "d0f3076a25baab3b095ad1c7ffc172a2714f11963b8f7939caf4ab6d11579361",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r64_n20/checkpoint_ft.pt",
+    "checkpoint_sha256": "4e775f3e00180ec400c3e3c8a8773123f3f3ecb0b8e128b355053b21fb042a03",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fold4/test_raw.npz",
+    "input_condition_sha256": "9e0a41119111a870b011b94fad6a53480b59eac0a709c61f0f314f74d8f201b8",
+    "seed": 20260927,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 8793748,
+    "median_library_whole_npz_panel": 2496.0,
+    "n_rows_whole_npz": 31500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 22831,
+     "Monocyte": 3065,
+     "B cell": 2576,
+     "NK cell": 1910,
+     "DC": 738,
+     "Other": 380
+    },
+    "mean_l2_max_prob": 0.9074481198238948,
+    "predict_seconds": 3.1
+   },
+   "n_donors": 21,
+   "n_generated_cells": 31500,
+   "composition": {
+    "l1_mean": 0.16384442171014588,
+    "l1_median": 0.1603039014373717,
+    "l1_obs_loo_null_mean": 0.13719637503029242,
+    "l1_generated_loo_mean_vs_observed_mean": 0.1883061275093223,
+    "composition_top1": 0.14285714285714285,
+    "mean_fraction_generated": {
+     "T cell": 0.724794,
+     "B cell": 0.081778,
+     "Monocyte": 0.097302,
+     "NK cell": 0.060635,
+     "DC": 0.023429,
+     "Other": 0.012063
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.668001,
+     "B cell": 0.081749,
+     "Monocyte": 0.146645,
+     "NK cell": 0.07743,
+     "DC": 0.020687,
+     "Other": 0.005487
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.9025921876265389,
+    "r_mean": 0.9025767686667773,
+    "top1": 0.09523809523809523,
+    "n_top1": 2,
+    "own_rank_median": 9.0,
+    "chance_top1": 0.047619047619047616
+   },
+   "precision_coverage": {
+    "precision": 0.9838095238095238,
+    "coverage": 0.926984126984127,
+    "density": 2.329428571428571,
+    "n_query": 3150,
+    "n_reference": 3150
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9888888888888889,
+    "coverage": 0.9911111111111112,
+    "density": 3.401396825396825,
+    "detected_median_before": {
+     "R1": 359.0,
+     "Q": 270.0
+    },
+    "detected_median_after": {
+     "R1": 270.0,
+     "Q": 270.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 9.730158730158731,
+    "observed_mean_over_donors": 14.664491120050386,
+    "generated_pooled_cells": 9.730158730158731
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2495.0,
+    "observed_pooled": 1973.0,
+    "generated_mean_of_donor_medians": 2501.6904296875,
+    "observed_mean_of_donor_medians": 2012.3095238095239
+   },
+   "seconds": 6.5
+  },
+  "lora_r4__raw": {
+   "arm": "lora_r4__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r4__raw.npz",
+   "npz_sha256": "3d48dfff1fb12bfae637f76797177f33fe9ecb49d2dfec13bf019fd779bb5e52",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r4/checkpoint_ft.pt",
+    "checkpoint_sha256": "951a3994ff2b7a5350cfd97a08a7ef939a4e8f13397c5184e2366c1c75ed091b",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fold4/test_raw.npz",
+    "input_condition_sha256": "9e0a41119111a870b011b94fad6a53480b59eac0a709c61f0f314f74d8f201b8",
+    "seed": 20260927,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 8617726,
+    "median_library_whole_npz_panel": 2359.0,
+    "n_rows_whole_npz": 31500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 22893,
+     "Monocyte": 3369,
+     "B cell": 2499,
+     "NK cell": 1585,
+     "DC": 775,
+     "Other": 379
+    },
+    "mean_l2_max_prob": 0.9059603853263553,
+    "predict_seconds": 3.2
+   },
+   "n_donors": 21,
+   "n_generated_cells": 31500,
+   "composition": {
+    "l1_mean": 0.15837196804341017,
+    "l1_median": 0.16047055152508002,
+    "l1_obs_loo_null_mean": 0.13719637503029242,
+    "l1_generated_loo_mean_vs_observed_mean": 0.18707460494727804,
+    "composition_top1": 0.09523809523809523,
+    "mean_fraction_generated": {
+     "T cell": 0.726762,
+     "B cell": 0.079333,
+     "Monocyte": 0.106952,
+     "NK cell": 0.050317,
+     "DC": 0.024603,
+     "Other": 0.012032
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.668001,
+     "B cell": 0.081749,
+     "Monocyte": 0.146645,
+     "NK cell": 0.07743,
+     "DC": 0.020687,
+     "Other": 0.005487
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.8986802838141615,
+    "r_mean": 0.8977280956772405,
+    "top1": 0.09523809523809523,
+    "n_top1": 2,
+    "own_rank_median": 10.0,
+    "chance_top1": 0.047619047619047616
+   },
+   "precision_coverage": {
+    "precision": 0.986031746031746,
+    "coverage": 0.8644444444444445,
+    "density": 2.1077142857142857,
+    "n_query": 3150,
+    "n_reference": 3150
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9901587301587301,
+    "coverage": 0.9809523809523809,
+    "density": 3.2963809523809524,
+    "detected_median_before": {
+     "R1": 359.0,
+     "Q": 264.0
+    },
+    "detected_median_after": {
+     "R1": 264.0,
+     "Q": 264.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 10.695238095238095,
+    "observed_mean_over_donors": 14.664491120050386,
+    "generated_pooled_cells": 10.695238095238095
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2358.5,
+    "observed_pooled": 1973.0,
+    "generated_mean_of_donor_medians": 2357.928466796875,
+    "observed_mean_of_donor_medians": 2012.3095238095239
+   },
+   "seconds": 6.6
+  },
+  "lora_r64__raw": {
+   "arm": "lora_r64__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold4/lora_r64__raw.npz",
+   "npz_sha256": "8420289f7cd8b6850c735f01566e23368e25e807b7b804d644dc125b4e193869",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_r64/checkpoint_ft.pt",
+    "checkpoint_sha256": "3905c4cfc2cb2f54af3b211a41022a569d9f5d2742099c6a7430d3555c9aa2f0",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fold4/test_raw.npz",
+    "input_condition_sha256": "9e0a41119111a870b011b94fad6a53480b59eac0a709c61f0f314f74d8f201b8",
+    "seed": 20260927,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 8525860,
+    "median_library_whole_npz_panel": 2154.0,
+    "n_rows_whole_npz": 31500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 22686,
+     "Monocyte": 3445,
+     "B cell": 2542,
+     "NK cell": 1933,
+     "DC": 627,
+     "Other": 267
+    },
+    "mean_l2_max_prob": 0.9053968789530179,
+    "predict_seconds": 3.1
+   },
+   "n_donors": 21,
+   "n_generated_cells": 31500,
+   "composition": {
+    "l1_mean": 0.1422339117529488,
+    "l1_median": 0.12485179002040439,
+    "l1_obs_loo_null_mean": 0.13719637503029242,
+    "l1_generated_loo_mean_vs_observed_mean": 0.17213063521098476,
+    "composition_top1": 0.14285714285714285,
+    "mean_fraction_generated": {
+     "T cell": 0.72019,
+     "B cell": 0.080698,
+     "Monocyte": 0.109365,
+     "NK cell": 0.061365,
+     "DC": 0.019905,
+     "Other": 0.008476
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.668001,
+     "B cell": 0.081749,
+     "Monocyte": 0.146645,
+     "NK cell": 0.07743,
+     "DC": 0.020687,
+     "Other": 0.005487
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.9010059643345039,
+    "r_mean": 0.8995039873094622,
+    "top1": 0.09523809523809523,
+    "n_top1": 2,
+    "own_rank_median": 9.0,
+    "chance_top1": 0.047619047619047616
+   },
+   "precision_coverage": {
+    "precision": 0.9898412698412699,
+    "coverage": 0.946031746031746,
+    "density": 1.9775555555555555,
+    "n_query": 3150,
+    "n_reference": 3150
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9917460317460317,
+    "coverage": 0.9904761904761905,
+    "density": 2.901936507936508,
+    "detected_median_before": {
+     "R1": 359.0,
+     "Q": 261.0
+    },
+    "detected_median_after": {
+     "R1": 261.0,
+     "Q": 261.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 10.936507936507937,
+    "observed_mean_over_donors": 14.664491120050386,
+    "generated_pooled_cells": 10.936507936507937
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2153.0,
+    "observed_pooled": 1973.0,
+    "generated_mean_of_donor_medians": 2146.666748046875,
+    "observed_mean_of_donor_medians": 2012.3095238095239
+   },
+   "seconds": 6.4
+  }
+ },
+ "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": 44.9
+}

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/pooled/README.md

@@ -0,0 +1,60 @@
+# score_ft.py output: immicro, 107 scored donors
+
+Arms: lora_r4_n5__raw, lora_r64_n5__raw, lora_r4_n20__raw, lora_r64_n20__raw, lora_r4__raw, lora_r64__raw.  Every arm is scored on the same donors against the same observed reference.
+
+## Inputs and fixed contracts
+- Observed reference: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/immicro/reference.npz` (sha c5e2547be3ec), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro;
+  observed cells sum exactly to the features pseudobulk of every donor. Observed labels: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/labels/observed_immicro/labels.parquet.
+- Generated cells: `generated_counts` read out once with Poisson(seed 20260916) over the **whole NPZ in row order**
+  (`poisson_readout.poisson_integerise`), then the scored donors' rows. These integer counts are used for labels, embedding,
+  depth and the contrast. Pseudobulk uses the summed `generated_counts` (rates), as `score_generated.py`.
+- Labels: frozen f01common scANVI (`predict_scanvi.py`, CPU, zero query epochs), six-type gate ['T cell', 'B cell', 'Monocyte', 'NK cell', 'DC', 'Other']; query genes =
+  the 1,006-gene annotation list minus genes the dataset's sc assay did not measure in every sample (1004 genes).
+- Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (5508 genes).
+
+## Definitions
+1. **Composition**: fraction of each donor's cells per six-type label (all generated cells; all observed QC cells).
+   `comp_l1` = sum over the six labels of |generated - observed| (immicro_common.l1). `comp_l1_obs_loo_null` = L1 of the
+   donor's observed composition to the mean of the *other scored donors'* observed compositions. `composition_top1` =
+   fraction of donors whose generated composition is closest (L1) to their own observed composition.
+2. **Pseudobulk**: `pb_r` = Pearson r of CPM-log1p(summed generated_counts) vs CPM-log1p(observed pseudobulk) on the scoring
+   genes (evaluate_realbulk.cpm_log1p / paired_r). `pb_top1` = the donor's generated pseudobulk is closest (Pearson) to its own
+   observed pseudobulk among the 107 scored donors (immicro_common.retrieval = evaluate_realbulk.top1 arithmetic).
+3. **Precision / coverage / density** (stage_b_embed.py functions): per-cell CP10K over the scoring genes + log1p; PCA-50
+   (randomized, random_state 20260925) and k = 10 real-real k-NN balls fitted on **R1 of the scored donors only**.
+   Reference rule (independent of fold and arm): per donor, cells in canonical order (library_id+barcode), one
+   permutation from `default_rng([20260925, uint64(sha256(donor)[:8])])`; R1 = first n, R2 = next n,
+   n = min(150, n_cells // 2) (16050 R1 cells here). Generated query: per donor n cells (the donor's R1 size),
+   without replacement, `default_rng([20260926, same key])`. Precision = fraction of generated cells inside any R1 ball
+   (Kynkaanniemi 2019); coverage = fraction of R1 cells whose ball holds a generated cell; density = Naeem 2020.
+   Per-donor precision = that donor's generated cells; per-donor coverage = that donor's R1 cells (the pooled values are
+   their n-weighted means; plain means when every donor has 150 reference cells). R2 (held-out real cells of the same donors) is the
+   perfect-generator control: precision 0.9634, coverage 0.9999.
+   **Depth matched**: stage_b_embed depth matching run pairwise (R1 vs this arm): per donor and within-donor rank of detected
+   genes, both cells are thinned by UMI sampling without replacement to the smaller detected-gene count; PCA kept from
+   un-thinned R1, radii recomputed on thinned R1; fresh rng(20260929) per arm. R2 control: precision
+   0.9635, coverage 0.9997.
+4. **Monocyte %** = 100 x Monocyte fraction (all cells) per donor; **median UMI per cell** = median over cells of the
+   Poisson-read (generated) / observed counts summed over the scoring genes (per donor, and pooled).
+5. **Group contrast** (T, B, Monocyte, NK): not computed (dataset immicro has no group contrast (use --groups-csv / --case-groups)).
+   Genes per type = scoring genes detected (count > 0) in >= 1 % of the scored donors' observed
+   cells of that type. Primary statistic `mean_cp10k`: per-cell CP10K over the scoring genes; per donor the mean over its
+   cells of the type (donors with >= 1 such cell); group mean = mean over the group's donors (donor-balanced);
+   logFC = log2(case mean + 1) - log2(control mean + 1). Secondary `pseudobulk_log1p_cpm`: the SLE benchmark evaluator's
+   statistic (donor x type summed counts, log1p CPM over the scoring genes, mean case - mean control;
+   evaluate_generated_vs_truth.group_log_fold_change). Both are computed on the generated cells (their frozen labels) and on
+   the observed cells; `r_generated` = Pearson r of the two logFC vectors. Broadcast baseline `r_broadcast`: the same
+   observed vector against the logFC of the input bulk (condition NPZ `bulk_counts` of the arm, scoring genes, per-donor
+   CP10K resp. log1p CPM, group means). `partial_r_generated_given_broadcast`: r of the OLS residuals of observed and
+   generated logFC on the bulk logFC (residual_specificity.py).
+6. **Top-50 DEG overlap** (contrast.csv rows `statistic = welch_top50_deg`; summary `deg_top50`): not computed (contrast off).
+
+## Files
+- `per_donor.csv`: one row per arm x donor (all per-donor quantities above).
+- `summary.json`: per arm the donor means / pooled values, provenance (NPZ sha, receipt check, generation metadata,
+  Poisson nnz of the whole NPZ, annotation contract), and the reference block (PCA, R2 control).
+- `contrast.csv`: per arm x cell type x statistic (`mean_cp10k`, `pseudobulk_log1p_cpm`: logFC r; `welch_top50_deg`:
+  top-50 DEG overlap, T / B / Monocyte / NK / DC; columns of the other kind are empty).
+- `arms/<arm>/labels/` (predict_scanvi.py labels + manifest), `arms/<arm>/generated_cells.parquet` (NPZ row, donor, label,
+  UMI on the scoring genes, P/C subsample flag), `arms/<arm>/deg_top50_lists.csv` (observed, generated and broadcast
+  top-50 gene lists, Ensembl ids, rank order).

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/pooled/summary.json

@@ -0,0 +1,903 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "immicro",
+ "written_utc": "2026-10-01T14:07:41.936813+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",
+  "immicro",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/lora_rank_20261001/pooled",
+  "--threads",
+  "8",
+  "--arm",
+  "lora_r4_n5__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r4_n5__raw.npz",
+  "--arm",
+  "lora_r64_n5__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r64_n5__raw.npz",
+  "--arm",
+  "lora_r4_n20__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r4_n20__raw.npz",
+  "--arm",
+  "lora_r64_n20__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r64_n20__raw.npz",
+  "--arm",
+  "lora_r4__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r4__raw.npz",
+  "--arm",
+  "lora_r64__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r64__raw.npz"
+ ],
+ "arms": [
+  "lora_r4_n5__raw",
+  "lora_r64_n5__raw",
+  "lora_r4_n20__raw",
+  "lora_r64_n20__raw",
+  "lora_r4__raw",
+  "lora_r64__raw"
+ ],
+ "donors": [
+  "HS1",
+  "HS2",
+  "HS3",
+  "HS4",
+  "HS6",
+  "HS7",
+  "HS8",
+  "HS9",
+  "HS10",
+  "HS11",
+  "HS12",
+  "HS13",
+  "HS14",
+  "HS15",
+  "HS16",
+  "HS17",
+  "HS18",
+  "HS19",
+  "HS20",
+  "HS21",
+  "HS23",
+  "HS24",
+  "HS25",
+  "HS26",
+  "HS27",
+  "HS28",
+  "HS29",
+  "HS30",
+  "HS31",
+  "HS32",
+  "HS34",
+  "HS35",
+  "HS36",
+  "HS37",
+  "HS38",
+  "HS39",
+  "HS40",
+  "HS41",
+  "HS42",
+  "HS43",
+  "HS44",
+  "HS45",
+  "HS46",
+  "HS47",
+  "HS48",
+  "HS49",
+  "HS50",
+  "HS51",
+  "HS52",
+  "HS53",
+  "HS54",
+  "HS55",
+  "HS56",
+  "HS57",
+  "HS58",
+  "HS59",
+  "HS60",
+  "HS61",
+  "HS62",
+  "HS63",
+  "HS64",
+  "HS65",
+  "HS66",
+  "HS67",
+  "HS68",
+  "HS69",
+  "HS70",
+  "HS71",
+  "HS72",
+  "HS73",
+  "HS74",
+  "HS75",
+  "HS76",
+  "HS77",
+  "HS78",
+  "HS79",
+  "HS80",
+  "HS81",
+  "HS82",
+  "HS83",
+  "HS84",
+  "HS85",
+  "HS86",
+  "HS87",
+  "HS88",
+  "HS89",
+  "HS90",
+  "HS91",
+  "HS92",
+  "HS93",
+  "HS94",
+  "HS95",
+  "HS96",
+  "HS97",
+  "HS98",
+  "HS100",
+  "HS101",
+  "HS102",
+  "HS103",
+  "HS104",
+  "HS105",
+  "HS106",
+  "HS107",
+  "HS108",
+  "HS109",
+  "HS110",
+  "HS111"
+ ],
+ "n_donors": 107,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/immicro",
+  "reference_sha256": "c5e2547be3ec3b12cb0c0b404a49e14a046ae59d40be70427f98f083a76bce17",
+  "features_sha256": "735255066ce7ebbac13a1fdfd058e26f31edd60314cc02fd589b0a292dbbc838",
+  "n_r1_cells": 16050,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.28717318177223206,
+   "n_fit_cells": 16050
+  },
+  "r2_control": {
+   "precision": 0.9634267912772586,
+   "coverage": 0.9999376947040498,
+   "density": 1.3859065420560748,
+   "n_query": 16050,
+   "depth_matched": {
+    "precision": 0.9634890965732087,
+    "coverage": 0.9996884735202493,
+    "density": 1.3669096573208723
+   }
+  },
+  "observed_l1_loo_null_mean": 0.1606372707722086
+ },
+ "contrast_definition": {
+  "enabled": false,
+  "reason": "dataset immicro has no group contrast (use --groups-csv / --case-groups)"
+ },
+ "deg_definition": {
+  "enabled": false,
+  "reason": "contrast off"
+ },
+ "headline": {
+  "lora_r4_n5__raw": {
+   "comp_l1": 0.16221250387191163,
+   "comp_l1_obs_loo_null": 0.1606372707722086,
+   "precision": 0.9368847352024922,
+   "coverage": 0.7890965732087227,
+   "precision_dm": 0.9652336448598131,
+   "coverage_dm": 0.9526479750778816,
+   "pb_r_median": 0.9023670557055304,
+   "pb_top1": 0.028037383177570093,
+   "mono_pct_gen": 15.129595015576319,
+   "mono_pct_obs": 16.6538380766508,
+   "median_umi_gen": 2564.0,
+   "median_umi_obs": 1961.0,
+   "seconds": 21.7
+  },
+  "lora_r64_n5__raw": {
+   "comp_l1": 0.17651083150222252,
+   "comp_l1_obs_loo_null": 0.1606372707722086,
+   "precision": 0.9455451713395638,
+   "coverage": 0.8472897196261682,
+   "precision_dm": 0.971214953271028,
+   "coverage_dm": 0.9844859813084113,
+   "pb_r_median": 0.9035992444051067,
+   "pb_top1": 0.018691588785046728,
+   "mono_pct_gen": 14.333956386292835,
+   "mono_pct_obs": 16.6538380766508,
+   "median_umi_gen": 2705.0,
+   "median_umi_obs": 1961.0,
+   "seconds": 20.7
+  },
+  "lora_r4_n20__raw": {
+   "comp_l1": 0.17095159865002751,
+   "comp_l1_obs_loo_null": 0.1606372707722086,
+   "precision": 0.9247352024922119,
+   "coverage": 0.7149532710280374,
+   "precision_dm": 0.9585046728971962,
+   "coverage_dm": 0.9494080996884735,
+   "pb_r_median": 0.8993883672634128,
+   "pb_top1": 0.018691588785046728,
+   "mono_pct_gen": 13.89595015576324,
+   "mono_pct_obs": 16.6538380766508,
+   "median_umi_gen": 2395.0,
+   "median_umi_obs": 1961.0,
+   "seconds": 20.9
+  },
+  "lora_r64_n20__raw": {
+   "comp_l1": 0.1716537920789307,
+   "comp_l1_obs_loo_null": 0.1606372707722086,
+   "precision": 0.9052959501557633,
+   "coverage": 0.7937071651090343,
+   "precision_dm": 0.9477881619937695,
+   "coverage_dm": 0.974828660436137,
+   "pb_r_median": 0.8986129241189431,
+   "pb_top1": 0.018691588785046728,
+   "mono_pct_gen": 13.456697819314641,
+   "mono_pct_obs": 16.6538380766508,
+   "median_umi_gen": 2202.0,
+   "median_umi_obs": 1961.0,
+   "seconds": 22.9
+  },
+  "lora_r4__raw": {
+   "comp_l1": 0.18577808236758375,
+   "comp_l1_obs_loo_null": 0.1606372707722086,
+   "precision": 0.9333333333333333,
+   "coverage": 0.7123364485981308,
+   "precision_dm": 0.9621183800623053,
+   "coverage_dm": 0.94398753894081,
+   "pb_r_median": 0.8991863255707665,
+   "pb_top1": 0.037383177570093455,
+   "mono_pct_gen": 12.668535825545172,
+   "mono_pct_obs": 16.6538380766508,
+   "median_umi_gen": 2345.0,
+   "median_umi_obs": 1961.0,
+   "seconds": 20.3
+  },
+  "lora_r64__raw": {
+   "comp_l1": 0.1609507558094419,
+   "comp_l1_obs_loo_null": 0.1606372707722086,
+   "precision": 0.9044236760124611,
+   "coverage": 0.8158878504672897,
+   "precision_dm": 0.9530218068535825,
+   "coverage_dm": 0.9682866043613707,
+   "pb_r_median": 0.8995201341884855,
+   "pb_top1": 0.037383177570093455,
+   "mono_pct_gen": 13.087227414330215,
+   "mono_pct_obs": 16.6538380766508,
+   "median_umi_gen": 2127.0,
+   "median_umi_obs": 1961.0,
+   "seconds": 20.6
+  }
+ },
+ "per_arm": {
+  "lora_r4_n5__raw": {
+   "arm": "lora_r4_n5__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r4_n5__raw.npz",
+   "npz_sha256": "df017f58fb0ff0aab2e4cbbfedca905a98cb63019a9ef2e1f57f64e97da9b17c",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/conditions_pooled_raw.npz",
+    "input_condition_sha256": "0cf3f9750bb8b48a787720f344559c0f05bacddd14c68e314c7f9fda7f43820f",
+    "seed": null,
+    "steps": null,
+    "support_readout": null,
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 46659233,
+    "median_library_whole_npz_panel": 2565.0,
+    "n_rows_whole_npz": 160500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 108946,
+     "Monocyte": 24283,
+     "B cell": 12007,
+     "NK cell": 9155,
+     "DC": 4605,
+     "Other": 1504
+    },
+    "mean_l2_max_prob": 0.9134699904019958,
+    "predict_seconds": 5.5
+   },
+   "n_donors": 107,
+   "n_generated_cells": 160500,
+   "composition": {
+    "l1_mean": 0.16221250387191163,
+    "l1_median": 0.1483597499495866,
+    "l1_obs_loo_null_mean": 0.1606372707722086,
+    "l1_generated_loo_mean_vs_observed_mean": 0.1749799320050974,
+    "composition_top1": 0.04672897196261682,
+    "mean_fraction_generated": {
+     "T cell": 0.678791,
+     "B cell": 0.07481,
+     "Monocyte": 0.151296,
+     "NK cell": 0.05704,
+     "DC": 0.028692,
+     "Other": 0.009371
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.639048,
+     "B cell": 0.074796,
+     "Monocyte": 0.166538,
+     "NK cell": 0.091197,
+     "DC": 0.022818,
+     "Other": 0.005602
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.9023670557055304,
+    "r_mean": 0.9016019392485752,
+    "top1": 0.028037383177570093,
+    "n_top1": 3,
+    "own_rank_median": 38.0,
+    "chance_top1": 0.009345794392523364
+   },
+   "precision_coverage": {
+    "precision": 0.9368847352024922,
+    "coverage": 0.7890965732087227,
+    "density": 1.3228847352024922,
+    "n_query": 16050,
+    "n_reference": 16050
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9652336448598131,
+    "coverage": 0.9526479750778816,
+    "density": 2.474747663551402,
+    "detected_median_before": {
+     "R1": 362.0,
+     "Q": 278.0
+    },
+    "detected_median_after": {
+     "R1": 278.0,
+     "Q": 278.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 15.129595015576319,
+    "observed_mean_over_donors": 16.6538380766508,
+    "generated_pooled_cells": 15.129595015576324
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2564.0,
+    "observed_pooled": 1961.0,
+    "generated_mean_of_donor_medians": 2568.775634765625,
+    "observed_mean_of_donor_medians": 1997.7429906542056
+   },
+   "seconds": 21.7
+  },
+  "lora_r64_n5__raw": {
+   "arm": "lora_r64_n5__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r64_n5__raw.npz",
+   "npz_sha256": "f6e6647c428df40fcab53d666c06729ae7ae3a19ed1b44467dd387429f95f38f",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/conditions_pooled_raw.npz",
+    "input_condition_sha256": "0cf3f9750bb8b48a787720f344559c0f05bacddd14c68e314c7f9fda7f43820f",
+    "seed": null,
+    "steps": null,
+    "support_readout": null,
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 46754794,
+    "median_library_whole_npz_panel": 2706.0,
+    "n_rows_whole_npz": 160500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 109346,
+     "Monocyte": 23006,
+     "B cell": 12413,
+     "NK cell": 9252,
+     "DC": 5072,
+     "Other": 1411
+    },
+    "mean_l2_max_prob": 0.9178839904776429,
+    "predict_seconds": 5.1
+   },
+   "n_donors": 107,
+   "n_generated_cells": 160500,
+   "composition": {
+    "l1_mean": 0.17651083150222252,
+    "l1_median": 0.16385760517799355,
+    "l1_obs_loo_null_mean": 0.1606372707722086,
+    "l1_generated_loo_mean_vs_observed_mean": 0.17874222654546573,
+    "composition_top1": 0.037383177570093455,
+    "mean_fraction_generated": {
+     "T cell": 0.681283,
+     "B cell": 0.07734,
+     "Monocyte": 0.14334,
+     "NK cell": 0.057645,
+     "DC": 0.031601,
+     "Other": 0.008791
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.639048,
+     "B cell": 0.074796,
+     "Monocyte": 0.166538,
+     "NK cell": 0.091197,
+     "DC": 0.022818,
+     "Other": 0.005602
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.9035992444051067,
+    "r_mean": 0.9029075368816832,
+    "top1": 0.018691588785046728,
+    "n_top1": 2,
+    "own_rank_median": 37.0,
+    "chance_top1": 0.009345794392523364
+   },
+   "precision_coverage": {
+    "precision": 0.9455451713395638,
+    "coverage": 0.8472897196261682,
+    "density": 1.4329781931464174,
+    "n_query": 16050,
+    "n_reference": 16050
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.971214953271028,
+    "coverage": 0.9844859813084113,
+    "density": 2.664915887850467,
+    "detected_median_before": {
+     "R1": 362.0,
+     "Q": 279.0
+    },
+    "detected_median_after": {
+     "R1": 279.0,
+     "Q": 279.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 14.333956386292835,
+    "observed_mean_over_donors": 16.6538380766508,
+    "generated_pooled_cells": 14.333956386292835
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2705.0,
+    "observed_pooled": 1961.0,
+    "generated_mean_of_donor_medians": 2705.004638671875,
+    "observed_mean_of_donor_medians": 1997.7429906542056
+   },
+   "seconds": 20.7
+  },
+  "lora_r4_n20__raw": {
+   "arm": "lora_r4_n20__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r4_n20__raw.npz",
+   "npz_sha256": "3248e87480288587b85b61fabd3f422a62e9cb4f36ad7ad2c484bcbd51e879fb",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/conditions_pooled_raw.npz",
+    "input_condition_sha256": "0cf3f9750bb8b48a787720f344559c0f05bacddd14c68e314c7f9fda7f43820f",
+    "seed": null,
+    "steps": null,
+    "support_readout": null,
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 44489338,
+    "median_library_whole_npz_panel": 2396.0,
+    "n_rows_whole_npz": 160500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 111761,
+     "Monocyte": 22303,
+     "B cell": 10980,
+     "NK cell": 8816,
+     "DC": 4673,
+     "Other": 1967
+    },
+    "mean_l2_max_prob": 0.9057040899698608,
+    "predict_seconds": 5.3
+   },
+   "n_donors": 107,
+   "n_generated_cells": 160500,
+   "composition": {
+    "l1_mean": 0.17095159865002751,
+    "l1_median": 0.1613466848733121,
+    "l1_obs_loo_null_mean": 0.1606372707722086,
+    "l1_generated_loo_mean_vs_observed_mean": 0.19082712487518372,
+    "composition_top1": 0.06542056074766354,
+    "mean_fraction_generated": {
+     "T cell": 0.69633,
+     "B cell": 0.068411,
+     "Monocyte": 0.13896,
+     "NK cell": 0.054928,
+     "DC": 0.029115,
+     "Other": 0.012255
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.639048,
+     "B cell": 0.074796,
+     "Monocyte": 0.166538,
+     "NK cell": 0.091197,
+     "DC": 0.022818,
+     "Other": 0.005602
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.8993883672634128,
+    "r_mean": 0.8991506163101812,
+    "top1": 0.018691588785046728,
+    "n_top1": 2,
+    "own_rank_median": 40.0,
+    "chance_top1": 0.009345794392523364
+   },
+   "precision_coverage": {
+    "precision": 0.9247352024922119,
+    "coverage": 0.7149532710280374,
+    "density": 1.1891651090342679,
+    "n_query": 16050,
+    "n_reference": 16050
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9585046728971962,
+    "coverage": 0.9494080996884735,
+    "density": 2.4306168224299065,
+    "detected_median_before": {
+     "R1": 362.0,
+     "Q": 267.0
+    },
+    "detected_median_after": {
+     "R1": 267.0,
+     "Q": 267.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 13.89595015576324,
+    "observed_mean_over_donors": 16.6538380766508,
+    "generated_pooled_cells": 13.89595015576324
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2395.0,
+    "observed_pooled": 1961.0,
+    "generated_mean_of_donor_medians": 2417.09814453125,
+    "observed_mean_of_donor_medians": 1997.7429906542056
+   },
+   "seconds": 20.9
+  },
+  "lora_r64_n20__raw": {
+   "arm": "lora_r64_n20__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r64_n20__raw.npz",
+   "npz_sha256": "c9db19ebbb963a107f998c9de6808b26bfa80a715424ca22545776d9b379838b",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/conditions_pooled_raw.npz",
+    "input_condition_sha256": "0cf3f9750bb8b48a787720f344559c0f05bacddd14c68e314c7f9fda7f43820f",
+    "seed": null,
+    "steps": null,
+    "support_readout": null,
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 43607483,
+    "median_library_whole_npz_panel": 2204.0,
+    "n_rows_whole_npz": 160500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 111919,
+     "Monocyte": 21598,
+     "B cell": 11737,
+     "NK cell": 9741,
+     "DC": 3943,
+     "Other": 1562
+    },
+    "mean_l2_max_prob": 0.9050131363359939,
+    "predict_seconds": 5.1
+   },
+   "n_donors": 107,
+   "n_generated_cells": 160500,
+   "composition": {
+    "l1_mean": 0.1716537920789307,
+    "l1_median": 0.15651419031719538,
+    "l1_obs_loo_null_mean": 0.1606372707722086,
+    "l1_generated_loo_mean_vs_observed_mean": 0.18555222457386747,
+    "composition_top1": 0.09345794392523364,
+    "mean_fraction_generated": {
+     "T cell": 0.697315,
+     "B cell": 0.073128,
+     "Monocyte": 0.134567,
+     "NK cell": 0.060692,
+     "DC": 0.024567,
+     "Other": 0.009732
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.639048,
+     "B cell": 0.074796,
+     "Monocyte": 0.166538,
+     "NK cell": 0.091197,
+     "DC": 0.022818,
+     "Other": 0.005602
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.8986129241189431,
+    "r_mean": 0.897475919901528,
+    "top1": 0.018691588785046728,
+    "n_top1": 2,
+    "own_rank_median": 39.0,
+    "chance_top1": 0.009345794392523364
+   },
+   "precision_coverage": {
+    "precision": 0.9052959501557633,
+    "coverage": 0.7937071651090343,
+    "density": 0.9868224299065421,
+    "n_query": 16050,
+    "n_reference": 16050
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9477881619937695,
+    "coverage": 0.974828660436137,
+    "density": 2.035470404984424,
+    "detected_median_before": {
+     "R1": 362.0,
+     "Q": 262.0
+    },
+    "detected_median_after": {
+     "R1": 262.0,
+     "Q": 262.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 13.456697819314641,
+    "observed_mean_over_donors": 16.6538380766508,
+    "generated_pooled_cells": 13.456697819314641
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2202.0,
+    "observed_pooled": 1961.0,
+    "generated_mean_of_donor_medians": 2215.299072265625,
+    "observed_mean_of_donor_medians": 1997.7429906542056
+   },
+   "seconds": 22.9
+  },
+  "lora_r4__raw": {
+   "arm": "lora_r4__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r4__raw.npz",
+   "npz_sha256": "af9b693654a375d851ce7724b20705be2f7a10d182a132981be99d705b8d260b",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/conditions_pooled_raw.npz",
+    "input_condition_sha256": "0cf3f9750bb8b48a787720f344559c0f05bacddd14c68e314c7f9fda7f43820f",
+    "seed": null,
+    "steps": null,
+    "support_readout": null,
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 44009544,
+    "median_library_whole_npz_panel": 2346.0,
+    "n_rows_whole_npz": 160500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 114070,
+     "Monocyte": 20333,
+     "B cell": 11331,
+     "NK cell": 8485,
+     "DC": 4220,
+     "Other": 2061
+    },
+    "mean_l2_max_prob": 0.9077228844303208,
+    "predict_seconds": 4.9
+   },
+   "n_donors": 107,
+   "n_generated_cells": 160500,
+   "composition": {
+    "l1_mean": 0.18577808236758375,
+    "l1_median": 0.17226517794836013,
+    "l1_obs_loo_null_mean": 0.1606372707722086,
+    "l1_generated_loo_mean_vs_observed_mean": 0.20713929069284534,
+    "composition_top1": 0.037383177570093455,
+    "mean_fraction_generated": {
+     "T cell": 0.710717,
+     "B cell": 0.070598,
+     "Monocyte": 0.126685,
+     "NK cell": 0.052866,
+     "DC": 0.026293,
+     "Other": 0.012841
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.639048,
+     "B cell": 0.074796,
+     "Monocyte": 0.166538,
+     "NK cell": 0.091197,
+     "DC": 0.022818,
+     "Other": 0.005602
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.8991863255707665,
+    "r_mean": 0.8983075543948178,
+    "top1": 0.037383177570093455,
+    "n_top1": 4,
+    "own_rank_median": 44.0,
+    "chance_top1": 0.009345794392523364
+   },
+   "precision_coverage": {
+    "precision": 0.9333333333333333,
+    "coverage": 0.7123364485981308,
+    "density": 1.1389096573208723,
+    "n_query": 16050,
+    "n_reference": 16050
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9621183800623053,
+    "coverage": 0.94398753894081,
+    "density": 2.3741931464174457,
+    "detected_median_before": {
+     "R1": 362.0,
+     "Q": 265.0
+    },
+    "detected_median_after": {
+     "R1": 265.0,
+     "Q": 265.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 12.668535825545172,
+    "observed_mean_over_donors": 16.6538380766508,
+    "generated_pooled_cells": 12.668535825545172
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2345.0,
+    "observed_pooled": 1961.0,
+    "generated_mean_of_donor_medians": 2347.8505859375,
+    "observed_mean_of_donor_medians": 1997.7429906542056
+   },
+   "seconds": 20.3
+  },
+  "lora_r64__raw": {
+   "arm": "lora_r64__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/lora_r64__raw.npz",
+   "npz_sha256": "8384bb9330228af0b3f89836e3f1e3b61d22c76caf23efbb731eb9a4cea942bc",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": null,
+    "checkpoint_sha256": null,
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/pooled_lora_rank_20261001/conditions_pooled_raw.npz",
+    "input_condition_sha256": "0cf3f9750bb8b48a787720f344559c0f05bacddd14c68e314c7f9fda7f43820f",
+    "seed": null,
+    "steps": null,
+    "support_readout": null,
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 43748567,
+    "median_library_whole_npz_panel": 2129.0,
+    "n_rows_whole_npz": 160500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 112418,
+     "Monocyte": 21005,
+     "B cell": 11800,
+     "NK cell": 10274,
+     "DC": 3551,
+     "Other": 1452
+    },
+    "mean_l2_max_prob": 0.9041194169456342,
+    "predict_seconds": 5.1
+   },
+   "n_donors": 107,
+   "n_generated_cells": 160500,
+   "composition": {
+    "l1_mean": 0.1609507558094419,
+    "l1_median": 0.15192730276745148,
+    "l1_obs_loo_null_mean": 0.1606372707722086,
+    "l1_generated_loo_mean_vs_observed_mean": 0.1868260781276386,
+    "composition_top1": 0.07476635514018691,
+    "mean_fraction_generated": {
+     "T cell": 0.700424,
+     "B cell": 0.07352,
+     "Monocyte": 0.130872,
+     "NK cell": 0.064012,
+     "DC": 0.022125,
+     "Other": 0.009047
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.639048,
+     "B cell": 0.074796,
+     "Monocyte": 0.166538,
+     "NK cell": 0.091197,
+     "DC": 0.022818,
+     "Other": 0.005602
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.8995201341884855,
+    "r_mean": 0.8990336906420392,
+    "top1": 0.037383177570093455,
+    "n_top1": 4,
+    "own_rank_median": 34.0,
+    "chance_top1": 0.009345794392523364
+   },
+   "precision_coverage": {
+    "precision": 0.9044236760124611,
+    "coverage": 0.8158878504672897,
+    "density": 0.9126355140186917,
+    "n_query": 16050,
+    "n_reference": 16050
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9530218068535825,
+    "coverage": 0.9682866043613707,
+    "density": 1.870803738317757,
+    "detected_median_before": {
+     "R1": 362.0,
+     "Q": 263.0
+    },
+    "detected_median_after": {
+     "R1": 263.0,
+     "Q": 263.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 13.087227414330215,
+    "observed_mean_over_donors": 16.6538380766508,
+    "generated_pooled_cells": 13.087227414330219
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 2127.0,
+    "observed_pooled": 1961.0,
+    "generated_mean_of_donor_medians": 2126.387939453125,
+    "observed_mean_of_donor_medians": 1997.7429906542056
+   },
+   "seconds": 20.6
+  }
+ },
+ "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": 153.2
+}