Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold1/per_donor.csv

@@ -0,0 +1,23 @@
+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
+scsemi__raw,HS2,DB2,1500,5144,150,0.704,0.661353032659409,0.08933333333333333,0.05909797822706065,0.088,0.1386080870917574,0.08266666666666667,0.11372472783825817,0.03333333333333333,0.02041213063763608,0.0026666666666666666,0.006804043545878694,0.17160705028512177,0.07059674896297101,0.6789346875242273,6,False,0.7333333333333333,0.2866666666666667,0.8466666666666667,0.6066666666666667,8.799999999999999,13.860808709175739,1978.0,1429.0
+scsemi__raw,HS12,DB2,1500,5035,150,0.708,0.6798411122144985,0.028666666666666667,0.06971201588877855,0.136,0.1529294935451837,0.048666666666666664,0.064746772591857,0.072,0.025223435948361468,0.006666666666666667,0.007547169811320755,0.14987090367428002,0.07455854626908714,0.7302118866098172,4,False,0.6466666666666666,0.17333333333333334,0.9,0.43333333333333335,13.600000000000001,15.29294935451837,1979.0,1550.0
+scsemi__raw,HS16,DB4,1500,4842,150,0.6586666666666666,0.5846757538207352,0.04933333333333333,0.08736059479553904,0.168,0.23048327137546468,0.06266666666666666,0.07166460140437836,0.059333333333333335,0.020859149111937217,0.002,0.004956629491945477,0.22493019413465506,0.1895789331257937,0.6523278732024758,16,False,0.8666666666666667,0.006666666666666667,0.8533333333333334,0.30666666666666664,16.8,23.04832713754647,1979.0,2066.0
+scsemi__raw,HS17,DB6,1500,1753,150,0.7326666666666667,0.7221905305191101,0.086,0.07529948659440959,0.09666666666666666,0.14432401597261837,0.042666666666666665,0.03194523673702225,0.03666666666666667,0.02053622361665716,0.005333333333333333,0.005704506560182544,0.09605704506560185,0.15543768341508316,0.6878142820450631,12,False,0.8066666666666666,0.09333333333333334,0.8533333333333334,0.32,9.666666666666666,14.432401597261837,1980.0,2194.0
+scsemi__raw,HS21,DB1,1500,4748,150,0.674,0.5945661331086773,0.04533333333333334,0.06887110362257792,0.164,0.1941870261162595,0.06133333333333333,0.11141533277169334,0.05533333333333333,0.02401010951979781,0.0,0.0069502948609941025,0.2215141814097164,0.12734556769243,0.6706449219520693,5,False,0.8066666666666666,0.16666666666666666,0.8866666666666667,0.5466666666666666,16.400000000000002,19.41870261162595,1979.5,1849.5
+scsemi__raw,HS35,DB7,1500,1658,150,0.6426666666666667,0.6363088057901085,0.07466666666666667,0.08443908323281062,0.116,0.1513872135102533,0.04133333333333333,0.097708082026538,0.124,0.024728588661037394,0.0013333333333333333,0.005428226779252111,0.21125854443104153,0.02594557967972921,0.6025125926782741,13,False,0.72,0.06,0.9533333333333334,0.24,11.600000000000001,15.13872135102533,1978.0,2204.0
+scsemi__raw,HS36,DB5,1500,4213,150,0.6973333333333334,0.5829575124614289,0.07933333333333334,0.10064087348682649,0.102,0.14573937811535723,0.08,0.15286019463565156,0.030666666666666665,0.015428435793971042,0.010666666666666666,0.0023736055067647755,0.27581422580900394,0.17486337298048768,0.6698301342083479,16,False,0.8,0.02,0.9133333333333333,0.23333333333333334,10.2,14.573937811535723,1977.0,2180.0
+scsemi__raw,HS39,DB6,1500,2056,150,0.5386666666666666,0.6731517509727627,0.044,0.04571984435797665,0.25933333333333336,0.17607003891050585,0.02266666666666667,0.08025291828793775,0.128,0.02091439688715953,0.007333333333333333,0.0038910505836575876,0.3875823605706875,0.10310873840821068,0.6015822509200941,12,False,0.7866666666666666,0.06,0.9933333333333333,0.34,25.933333333333337,17.607003891050585,1981.0,2023.0
+scsemi__raw,HS44,DB5,1500,3849,150,0.6893333333333334,0.719147830605352,0.05533333333333333,0.06832943621719927,0.15666666666666668,0.15146791374382956,0.043333333333333335,0.03715250714471291,0.04666666666666667,0.019225772928033256,0.008666666666666666,0.004676539360872954,0.08562120031176927,0.14862681044520484,0.6360616003148629,19,False,0.7533333333333333,0.04666666666666667,0.8333333333333334,0.24666666666666667,15.666666666666668,15.146791374382957,1982.0,1852.0
+scsemi__raw,HS46,DB1,1500,4117,150,0.734,0.6315278115132378,0.03333333333333333,0.060480932717998544,0.12533333333333332,0.13990769978139422,0.07333333333333333,0.13577847947534613,0.028666666666666667,0.028175856205975226,0.005333333333333333,0.004129220306048093,0.2083342239494778,0.09434064598251264,0.7424222691167766,6,False,0.8,0.14,0.9066666666666666,0.6266666666666667,12.533333333333333,13.990769978139422,1977.0,1777.0
+scsemi__raw,HS47,DB3,1500,4401,150,0.7113333333333334,0.609634174051352,0.050666666666666665,0.13542376732560782,0.043333333333333335,0.09702340377187003,0.056666666666666664,0.12315382867530107,0.12266666666666666,0.029993183367416496,0.015333333333333332,0.004771642808452625,0.4098686662122245,0.19711610918969746,0.6192262139631188,4,False,0.8333333333333334,0.06,0.9866666666666667,0.4666666666666667,4.333333333333334,9.702340377187003,1977.0,2179.0
+scsemi__raw,HS48,DB5,1500,3855,150,0.7,0.7058365758754864,0.07666666666666666,0.09909208819714656,0.09666666666666666,0.0840466926070039,0.08,0.0874189364461738,0.04133333333333333,0.019974059662775615,0.005333333333333333,0.0036316472114137485,0.07136186770428023,0.1700324236682078,0.6604454392686561,16,False,0.74,0.06666666666666667,0.88,0.37333333333333335,9.666666666666666,8.40466926070039,1980.0,1918.0
+scsemi__raw,HS51,DB3,1500,3803,150,0.6993333333333334,0.7068104128319748,0.098,0.09019195372074677,0.10066666666666667,0.10544307125953195,0.035333333333333335,0.06731527741256903,0.06466666666666666,0.02576912963449908,0.002,0.004470155140678412,0.0934111666228416,0.1561907464595402,0.6840897749620786,2,False,0.6666666666666666,0.05333333333333334,0.9466666666666667,0.54,10.066666666666666,10.544307125953194,1978.0,2114.0
+scsemi__raw,HS56,DB1,1500,4121,150,0.7313333333333333,0.6112594030575104,0.03266666666666666,0.04707595243872846,0.12333333333333334,0.13977190002426595,0.068,0.16743508857073525,0.043333333333333335,0.028391167192429023,0.0013333333333333333,0.006066488716330988,0.2700321928334546,0.16231403810792758,0.7224940327615211,3,False,0.8733333333333333,0.19333333333333333,0.9066666666666666,0.56,12.333333333333334,13.977190002426596,1979.5,1751.0
+scsemi__raw,HS57,DB2,1500,3932,150,0.6606666666666666,0.6584435401831129,0.04066666666666666,0.03128179043743642,0.134,0.18972533062054933,0.108,0.08214649033570702,0.052,0.030010172939979655,0.004666666666666667,0.00839267548321465,0.11890267887419459,0.11862246718002292,0.6577614502016773,1,True,0.9266666666666666,0.17333333333333334,0.9266666666666666,0.6133333333333333,13.4,18.972533062054932,1980.0,1676.5
+scsemi__raw,HS65,DB2,1500,4394,150,0.7173333333333334,0.6096950386891216,0.066,0.10969503868912153,0.07066666666666667,0.16909421939007738,0.06,0.07055075102412381,0.08,0.03413746017296313,0.006,0.006827492034592627,0.3070016689424974,0.1308382928488044,0.6108698443666754,9,False,0.9066666666666666,0.24,0.9933333333333333,0.38666666666666666,7.066666666666667,16.90942193900774,1980.0,1449.5
+scsemi__raw,HS68,DB6,1500,2659,150,0.7306666666666667,0.6938698758931929,0.07333333333333333,0.07070327190673185,0.11733333333333333,0.156825874388868,0.038,0.05039488529522377,0.03933333333333333,0.02181271154569387,0.0013333333333333333,0.006393380970289583,0.11389494797542937,0.10807608449171868,0.6451552862051921,4,False,0.86,0.08666666666666667,0.98,0.41333333333333333,11.733333333333333,15.6825874388868,1977.5,2248.0
+scsemi__raw,HS72,DB4,1500,4520,150,0.746,0.7331858407079646,0.058,0.08517699115044247,0.10733333333333334,0.11438053097345133,0.034666666666666665,0.0418141592920354,0.048,0.01836283185840708,0.006,0.007079646017699115,0.08490265486725666,0.20149714056663054,0.670079046520797,21,False,0.8,0.03333333333333333,0.84,0.37333333333333335,10.733333333333334,11.438053097345133,1978.0,1974.0
+scsemi__raw,HS84,DB3,1500,3090,150,0.6146666666666667,0.6702265372168285,0.13066666666666665,0.04692556634304207,0.13333333333333333,0.17184466019417477,0.07266666666666667,0.08608414239482201,0.043333333333333335,0.020711974110032363,0.005333333333333333,0.004207119741100324,0.2149773462783171,0.0881265446567977,0.708828279575057,2,False,0.7933333333333333,0.1,0.8533333333333334,0.7,13.333333333333334,17.184466019417478,1978.0,2083.0
+scsemi__raw,HS92,DB7,1500,2115,150,0.702,0.5810874704491725,0.1,0.11678486997635934,0.07,0.05484633569739953,0.08666666666666667,0.23356973995271868,0.037333333333333336,0.007565011820330969,0.004,0.006146572104018913,0.3316690307328605,0.3791565281986444,0.6200623512157214,16,False,0.8066666666666666,0.08,0.8733333333333333,0.36,7.000000000000001,5.484633569739953,1980.0,1976.0
+scsemi__raw,HS96,DB7,1500,1801,150,0.7173333333333334,0.5147140477512493,0.08933333333333333,0.06885063853414769,0.12266666666666666,0.25818989450305385,0.046,0.10716268739589117,0.022,0.04553026096612993,0.0026666666666666666,0.00555247084952804,0.44620396076253943,0.29377781550504867,0.6707938028939086,15,False,0.8466666666666667,0.08,0.88,0.26,12.266666666666666,25.818989450305384,1977.0,2252.0
+scsemi__raw,HS109,DB5,1500,4265,150,0.6893333333333334,0.6801875732708089,0.092,0.04126611957796014,0.09533333333333334,0.17327080890973037,0.06,0.06424384525205158,0.056666666666666664,0.03610785463071512,0.006666666666666667,0.00492379835873388,0.16436264165689723,0.1364133017609488,0.6110602278119237,18,False,0.7933333333333333,0.006666666666666667,0.9733333333333334,0.25333333333333335,9.533333333333333,17.327080890973036,1979.5,2074.0

paper-releases/pbisc-diffusion/updates/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold1/summary.json

@@ -0,0 +1,208 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "immicro",
+ "written_utc": "2026-10-05T12:05:34.815594+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/scsemi_cv_20261002/fold1",
+  "--threads",
+  "8",
+  "--arm",
+  "scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold1/scsemi__raw.npz"
+ ],
+ "arms": [
+  "scsemi__raw"
+ ],
+ "donors": [
+  "HS2",
+  "HS12",
+  "HS16",
+  "HS17",
+  "HS21",
+  "HS35",
+  "HS36",
+  "HS39",
+  "HS44",
+  "HS46",
+  "HS47",
+  "HS48",
+  "HS51",
+  "HS56",
+  "HS57",
+  "HS65",
+  "HS68",
+  "HS72",
+  "HS84",
+  "HS92",
+  "HS96",
+  "HS109"
+ ],
+ "n_donors": 22,
+ "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": 3300,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.29773756861686707,
+   "n_fit_cells": 3300
+  },
+  "r2_control": {
+   "precision": 0.9954545454545455,
+   "coverage": 1.0,
+   "density": 2.5628484848484847,
+   "n_query": 3300,
+   "depth_matched": {
+    "precision": 0.9942424242424243,
+    "coverage": 1.0,
+    "density": 2.5162121212121216
+   }
+  },
+  "observed_l1_loo_null_mean": 0.1502983690725227
+ },
+ "contrast_definition": {
+  "enabled": false,
+  "reason": "dataset immicro has no group contrast (use --groups-csv / --case-groups)"
+ },
+ "deg_definition": {
+  "enabled": false,
+  "reason": "contrast off"
+ },
+ "headline": {
+  "scsemi__raw": {
+   "comp_l1": 0.2117808524138249,
+   "comp_l1_obs_loo_null": 0.1502983690725227,
+   "precision": 0.7984848484848485,
+   "coverage": 0.10121212121212121,
+   "precision_dm": 0.9081818181818182,
+   "coverage_dm": 0.41818181818181815,
+   "pb_r_median": 0.665137786738502,
+   "pb_top1": 0.045454545454545456,
+   "mono_pct_gen": 11.93939393939394,
+   "mono_pct_obs": 15.179849365920914,
+   "median_umi_gen": 1979.0,
+   "median_umi_obs": 1887.0,
+   "seconds": 7.7
+  }
+ },
+ "per_arm": {
+  "scsemi__raw": {
+   "arm": "scsemi__raw",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fold1/scsemi__raw.npz",
+   "npz_sha256": "1f3ef507bcf047eb0be7f722aeaa67415bf3d32cc3c18f2bf9ec29e27847e922",
+   "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/data/immicro/fold1/test_raw.npz",
+    "input_condition_sha256": "f64c30e0d9cd130f95402573ee1b53826b57447fb3d7e8de727481c86f243d9d",
+    "seed": 20260927,
+    "steps": null,
+    "support_readout": "upstream (values <= 10 normalized units zeroed by fast_semi)",
+    "weights": null
+   },
+   "condition_for_broadcast": null,
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 4134387,
+    "median_library_whole_npz_panel": 1979.0,
+    "n_rows_whole_npz": 33000
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 22799,
+     "Monocyte": 3940,
+     "B cell": 2240,
+     "NK cell": 1957,
+     "DC": 1898,
+     "Other": 166
+    },
+    "mean_l2_max_prob": 0.9206276106504779,
+    "predict_seconds": 4.1
+   },
+   "n_donors": 22,
+   "n_generated_cells": 33000,
+   "composition": {
+    "l1_mean": 0.2117808524138249,
+    "l1_median": 0.20979638419025964,
+    "l1_obs_loo_null_mean": 0.1502983690725227,
+    "l1_generated_loo_mean_vs_observed_mean": 0.1991221538354961,
+    "composition_top1": 0.09090909090909091,
+    "mean_fraction_generated": {
+     "T cell": 0.690879,
+     "B cell": 0.067879,
+     "Monocyte": 0.119394,
+     "NK cell": 0.059303,
+     "DC": 0.057515,
+     "Other": 0.00503
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.648212,
+     "B cell": 0.075565,
+     "Monocyte": 0.151798,
+     "NK cell": 0.094479,
+     "DC": 0.024449,
+     "Other": 0.005497
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5508,
+    "r_median": 0.665137786738502,
+    "r_mean": 0.6615094658326517,
+    "top1": 0.045454545454545456,
+    "n_top1": 1,
+    "own_rank_median": 10.5,
+    "chance_top1": 0.045454545454545456
+   },
+   "precision_coverage": {
+    "precision": 0.7984848484848485,
+    "coverage": 0.10121212121212121,
+    "density": 0.23478787878787877,
+    "n_query": 3300,
+    "n_reference": 3300
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9081818181818182,
+    "coverage": 0.41818181818181815,
+    "density": 0.8363939393939394,
+    "detected_median_before": {
+     "R1": 356.0,
+     "Q": 121.0
+    },
+    "detected_median_after": {
+     "R1": 121.0,
+     "Q": 121.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 11.93939393939394,
+    "observed_mean_over_donors": 15.179849365920914,
+    "generated_pooled_cells": 11.93939393939394
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 1979.0,
+    "observed_pooled": 1887.0,
+    "generated_mean_of_donor_medians": 1978.8636474609375,
+    "observed_mean_of_donor_medians": 1946.340909090909
+   },
+   "seconds": 7.7
+  }
+ },
+ "code_sha256": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+ },
+ "seconds": 9.3
+}

paper-releases/pbisc-diffusion/updates/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold2/README.md

@@ -0,0 +1,60 @@
+# score_ft.py output: immicro, 21 scored donors
+
+Arms: scsemi__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 21 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) (3150 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 0.9943, coverage 1.0000.
+   **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
+   0.9930, coverage 1.0000.
+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/20261005T121346Z-scsemi-cv-budget-interim/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/fold2/per_donor.csv

@@ -0,0 +1,22 @@
+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
+scsemi__raw,HS9,DB3,1500,3942,150,0.628,0.6958396752917301,0.07466666666666667,0.028665651953323185,0.154,0.18670725520040587,0.036,0.049974632166412986,0.094,0.03373921867072552,0.013333333333333334,0.0050735667174023336,0.2290431253170979,0.21913370255585363,0.6276668420888267,2,False,0.9,0.06666666666666667,0.9933333333333333,0.5666666666666667,15.4,18.670725520040587,1960.0,2389.0
+scsemi__raw,HS14,DB3,1500,4235,150,0.6673333333333333,0.6517119244391971,0.034666666666666665,0.06517119244391972,0.17933333333333334,0.20306965761511217,0.068,0.04250295159386069,0.05,0.0332939787485242,0.0006666666666666666,0.004250295159386069,0.11564895710350262,0.159891466999795,0.688775491728134,4,False,0.7666666666666667,0.1,0.9066666666666666,0.5466666666666666,17.933333333333334,20.30696576151122,1961.0,2164.0
+scsemi__raw,HS19,DB5,1500,4133,150,0.72,0.5971449310428261,0.086,0.1454149528187757,0.09466666666666666,0.14686668279699977,0.05733333333333333,0.09145898862811518,0.03933333333333333,0.014275344785869828,0.0026666666666666666,0.004839099927413501,0.2958261150092749,0.14291883168588088,0.6585380690964877,19,False,0.76,0.02,0.9133333333333333,0.15333333333333332,9.466666666666667,14.686668279699976,1960.0,1955.0
+scsemi__raw,HS24,DB6,1500,1670,150,0.6773333333333333,0.5365269461077844,0.08333333333333333,0.07005988023952096,0.11,0.17664670658682635,0.09133333333333334,0.19401197604790418,0.032,0.017964071856287425,0.006,0.004790419161676647,0.3386506986027944,0.2194523355229991,0.6925952403295599,5,False,0.7666666666666667,0.07333333333333333,0.8866666666666667,0.3933333333333333,11.0,17.664670658682635,1959.0,2073.5
+scsemi__raw,HS25,DB6,1500,1800,150,0.632,0.4872222222222222,0.144,0.095,0.166,0.30333333333333334,0.025333333333333333,0.08444444444444445,0.03266666666666666,0.026111111111111113,0.0,0.0038888888888888888,0.40066666666666667,0.345557515096265,0.6556753682121974,11,False,0.86,0.08666666666666667,0.8666666666666667,0.3,16.6,30.333333333333336,1960.0,2173.0
+scsemi__raw,HS26,DB2,1500,3606,150,0.7453333333333333,0.651414309484193,0.03266666666666666,0.054076539101497505,0.12066666666666667,0.16167498613422074,0.06,0.09678313921242374,0.03933333333333333,0.02689961175818081,0.002,0.009151414309484194,0.21270549084858564,0.0667480048970103,0.7025575196380167,3,False,0.8133333333333334,0.24,0.86,0.42,12.066666666666666,16.167498613422072,1959.0,1454.5
+scsemi__raw,HS32,DB6,1500,1818,150,0.7193333333333334,0.7128712871287128,0.07933333333333334,0.07535753575357536,0.12,0.13036303630363036,0.03666666666666667,0.06050605060506051,0.043333333333333335,0.019251925192519254,0.0013333333333333333,0.0016501650165016502,0.06903850385038512,0.175285741287662,0.6672482992471955,6,False,0.7733333333333333,0.09333333333333334,0.9333333333333333,0.32666666666666666,12.0,13.036303630363037,1962.0,2078.5
+scsemi__raw,HS42,DB1,1500,4312,150,0.7126666666666667,0.700139146567718,0.051333333333333335,0.034786641929499075,0.10133333333333333,0.18320964749536178,0.02666666666666667,0.04336734693877551,0.08933333333333333,0.029684601113172542,0.018666666666666668,0.008812615955473098,0.19715398886827457,0.21942995273286833,0.619211198461224,3,False,0.88,0.11333333333333333,1.0,0.43333333333333335,10.133333333333333,18.320964749536177,1960.0,1957.5
+scsemi__raw,HS43,DB5,1500,4357,150,0.742,0.6584806059215056,0.04933333333333333,0.071149873766353,0.11466666666666667,0.13839798026164793,0.04533333333333334,0.11223318797337617,0.046,0.017443194858847832,0.0026666666666666666,0.0022951572182694515,0.22489541733608756,0.07565424537391977,0.6925626564771565,15,False,0.6466666666666666,0.04,0.8533333333333334,0.31333333333333335,11.466666666666667,13.839798026164793,1961.0,2180.0
+scsemi__raw,HS50,DB5,1500,4299,150,0.6846666666666666,0.6882996045591998,0.08066666666666666,0.08211211909746452,0.11533333333333333,0.11979530123284485,0.06266666666666666,0.09211444521981857,0.05333333333333334,0.013258897418004187,0.0033333333333333335,0.004419632472668062,0.08014887183065832,0.13366808876281203,0.6019009122949366,18,False,0.7333333333333333,0.02666666666666667,0.9666666666666667,0.13333333333333333,11.533333333333333,11.979530123284485,1960.0,2077.0
+scsemi__raw,HS55,DB1,1500,4574,150,0.714,0.6228683865325755,0.03866666666666667,0.04241364232619152,0.16533333333333333,0.22431132487975514,0.042666666666666665,0.08439003060778312,0.034666666666666665,0.019676432006996064,0.004666666666666667,0.006340183646698732,0.2122436962541903,0.13515857006071533,0.6911529130811549,4,False,0.7333333333333333,0.10666666666666667,0.8133333333333334,0.5866666666666667,16.53333333333333,22.431132487975514,1960.0,1849.0
+scsemi__raw,HS59,DB4,1500,4268,150,0.6573333333333333,0.5796626054358013,0.12466666666666666,0.06115276476101218,0.138,0.21860356138706655,0.017333333333333333,0.11879100281162137,0.052,0.016166822867853797,0.010666666666666666,0.005623242736644799,0.36412246173070917,0.15002703659666403,0.5818680114993207,19,False,0.7933333333333333,0.03333333333333333,1.0,0.14,13.8,21.860356138706656,1961.0,2091.5
+scsemi__raw,HS67,DB2,1500,3971,150,0.6293333333333333,0.6293125157391085,0.10133333333333333,0.1095441954167716,0.116,0.13925963233442457,0.06333333333333334,0.09393099974817426,0.08533333333333333,0.018886930244270964,0.004666666666666667,0.009065726517250064,0.1329344413665743,0.07524880687029788,0.6882538578000257,6,False,0.84,0.22666666666666666,0.8866666666666667,0.5066666666666667,11.600000000000001,13.925963233442456,1959.0,1563.0
+scsemi__raw,HS71,DB4,1500,4400,150,0.6733333333333333,0.571590909090909,0.03666666666666667,0.08863636363636364,0.07933333333333334,0.10477272727272727,0.11133333333333334,0.21409090909090908,0.088,0.017045454545454544,0.011333333333333334,0.003863636363636364,0.36033333333333334,0.2521739433710278,0.6175663376204797,18,False,0.8066666666666666,0.06,0.92,0.26,7.933333333333334,10.477272727272727,1957.0,1825.0
+scsemi__raw,HS73,DB2,1500,4209,150,0.6866666666666666,0.5915894511760513,0.03,0.07531480161558565,0.06933333333333333,0.10667617011166548,0.09866666666666667,0.20076027559990497,0.10933333333333334,0.020669992872416252,0.006,0.004989308624376337,0.36950249465431223,0.20049581863710342,0.6811712508349199,5,False,0.8333333333333334,0.25333333333333335,0.7933333333333333,0.4866666666666667,6.933333333333333,10.667617011166548,1961.0,1262.0
+scsemi__raw,HS80,DB3,1500,4301,150,0.718,0.6842594745408045,0.076,0.10578935131364799,0.12933333333333333,0.14415252266914672,0.04066666666666666,0.04022320390606836,0.03266666666666666,0.02022785398744478,0.0033333333333333335,0.0053475935828877,0.09324560179803142,0.17490600337816709,0.701780525542308,1,True,0.7733333333333333,0.08666666666666667,0.92,0.46,12.933333333333334,14.415252266914672,1959.0,2305.0
+scsemi__raw,HS91,DB6,1500,2568,150,0.6933333333333334,0.6320093457943925,0.035333333333333335,0.04361370716510903,0.13533333333333333,0.16277258566978192,0.06133333333333333,0.12694704049844235,0.06866666666666667,0.027258566978193146,0.006,0.007398753894080997,0.20546417445482873,0.07086378418681896,0.6818517820973876,9,False,0.7733333333333333,0.12,0.9066666666666666,0.34,13.533333333333333,16.27725856697819,1963.0,2112.0
+scsemi__raw,HS102,DB7,1500,1983,150,0.6433333333333333,0.6283408976298538,0.10666666666666667,0.10791729702471003,0.12933333333333333,0.17397881996974282,0.062,0.06454866364094806,0.056666666666666664,0.017650025214321734,0.002,0.007564296520423601,0.10801815431164898,0.09620470130285476,0.6788039667930504,14,False,0.8333333333333334,0.04,0.88,0.23333333333333334,12.933333333333334,17.39788199697428,1963.0,2275.0
+scsemi__raw,HS105,DB4,1500,4489,150,0.6986666666666667,0.6277567386945868,0.034,0.08977500556916908,0.12733333333333333,0.13967476052572955,0.052,0.12007128536422365,0.08333333333333333,0.01826687458231232,0.004666666666666667,0.0044553352639786145,0.2723754362515779,0.057123881603879864,0.6776833291729408,16,False,0.7666666666666667,0.02666666666666667,0.84,0.3466666666666667,12.733333333333333,13.967476052572955,1962.0,2019.0
+scsemi__raw,HS108,DB7,1500,1868,150,0.6513333333333333,0.5931477516059958,0.04466666666666667,0.08832976445396146,0.11933333333333333,0.08618843683083512,0.12133333333333333,0.20235546038543897,0.058666666666666666,0.023554603854389723,0.004666666666666667,0.006423982869379015,0.25288508208422555,0.23296810385252853,0.6303883000224011,15,False,0.8133333333333334,0.06666666666666667,0.8533333333333334,0.29333333333333333,11.933333333333334,8.618843683083512,1962.0,2026.0
+scsemi__raw,HS111,DB1,1500,4787,150,0.7026666666666667,0.6772508878211824,0.07933333333333334,0.09024441194902862,0.11066666666666666,0.12784625026112387,0.044,0.077501566743263,0.062,0.02360559849592647,0.0013333333333333333,0.003551284729475663,0.12762036069911564,0.13162224432642336,0.6500527311017898,6,False,0.84,0.13333333333333333,0.9333333333333333,0.5333333333333333,11.066666666666666,12.784625026112387,1959.5,1865.0