Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/scratch_recipe/RUN.json

@@ -0,0 +1,145 @@
+{
+ "schema": "pbisc_sdd.ft_intradataset.run.v1",
+ "source_checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+ "source_checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
+ "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz",
+ "condition_npz_sha256": "ce8b61d7dcd3e62b9e63d52189cfb5bba881f87a661384277a7949a629231cb4",
+ "fold": 0,
+ "mode": "full",
+ "trainable": {
+  "mode": "full",
+  "n_trainable": 54185184,
+  "n_total_base": 54185184,
+  "trainable_tensors": 64
+ },
+ "lr": 0.0002,
+ "warmup": 200,
+ "batch_size": 256,
+ "ema_decay": 0.999,
+ "max_steps": 100000,
+ "steps_run": 100000,
+ "eval_every": 1000,
+ "patience": 10,
+ "train_subset": null,
+ "init": "random",
+ "init_seed": 20260627,
+ "n_tensors": 64,
+ "kept_from_checkpoint": [
+  "model_config",
+  "diffusion_config",
+  "gene panel",
+  "value_scaler",
+  "conditioner z-score constants"
+ ],
+ "augmentation": {
+  "multi_k": [],
+  "recipe_frac": 0.5,
+  "recipe_cells_per_step": 128,
+  "recipe_k_grid": [
+   250,
+   500,
+   1000,
+   2000,
+   4000
+  ]
+ },
+ "selected_step": 100000,
+ "selected_inner_val_loss": 0.11552448304636138,
+ "pretrained_inner_val_loss": 1.7818074481827872,
+ "train_rows": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS20",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S156",
+  "Abd-S42",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC05",
+  "HC09",
+  "HC12",
+  "HC13",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC22",
+  "PHC01",
+  "PHC02",
+  "PHC05",
+  "PIC01",
+  "PIC02",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-S125",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S40",
+  "Res-S87",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S46",
+  "Skin-S52",
+  "Skin-S74",
+  "Uri-S134",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "inner_val_rows": [
+  "HC16",
+  "IC19",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S127",
+  "Res-S136",
+  "Skin-S43"
+ ],
+ "test_rows_never_loaded_for_training": [
+  "Abd-PS19",
+  "Abd-PS23",
+  "Abd-S123",
+  "Abd-S39",
+  "Abd-S47",
+  "Abd-S66",
+  "HC01",
+  "HC07",
+  "IC23",
+  "PHC03",
+  "PIC04",
+  "Res-PS25",
+  "Res-S139",
+  "Res-S26",
+  "Res-S77",
+  "Skin-S140",
+  "Uri-S147"
+ ],
+ "max_abs_weight_change": 17.890527725219727,
+ "n_tensors_changed": 64,
+ "seed": 20260927,
+ "wall_seconds": 5158.9,
+ "written_utc": "2026-10-05T04:55:36.833283+00:00",
+ "checkpoint_sha256": "ec6af76e986f2849ebdb24c67e80d81c342e5929805c9b39f0ea502dc701bede",
+ "reload_forward_max_abs_diff": 0.0
+}

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/scratch_recipe/history.json

@@ -0,0 +1,607 @@
+[
+ {
+  "step": 0,
+  "inner_val_loss": 1.7818074481827872,
+  "train_loss": null
+ },
+ {
+  "step": 1000,
+  "inner_val_loss": 0.3565664440393448,
+  "train_loss": 0.23657394684851168,
+  "sec": 51.8
+ },
+ {
+  "step": 2000,
+  "inner_val_loss": 0.18809035207544053,
+  "train_loss": 0.1506139921322465,
+  "sec": 105.7
+ },
+ {
+  "step": 3000,
+  "inner_val_loss": 0.1553954311779567,
+  "train_loss": 0.14628431218862534,
+  "sec": 160.0
+ },
+ {
+  "step": 4000,
+  "inner_val_loss": 0.14902883448771068,
+  "train_loss": 0.1444334934055805,
+  "sec": 214.3
+ },
+ {
+  "step": 5000,
+  "inner_val_loss": 0.14669094766889298,
+  "train_loss": 0.14294497397542,
+  "sec": 268.6
+ },
+ {
+  "step": 6000,
+  "inner_val_loss": 0.1455851016300065,
+  "train_loss": 0.14243612357974053,
+  "sec": 323.1
+ },
+ {
+  "step": 7000,
+  "inner_val_loss": 0.14491481014660426,
+  "train_loss": 0.14117006593197584,
+  "sec": 377.6
+ },
+ {
+  "step": 8000,
+  "inner_val_loss": 0.14447699167898723,
+  "train_loss": 0.14068242178857326,
+  "sec": 431.8
+ },
+ {
+  "step": 9000,
+  "inner_val_loss": 0.14404520179544175,
+  "train_loss": 0.14056443486362696,
+  "sec": 486.1
+ },
+ {
+  "step": 10000,
+  "inner_val_loss": 0.1436258437378066,
+  "train_loss": 0.14013562431931495,
+  "sec": 540.0
+ },
+ {
+  "step": 11000,
+  "inner_val_loss": 0.14326513345752442,
+  "train_loss": 0.13906350637227297,
+  "sec": 594.5
+ },
+ {
+  "step": 12000,
+  "inner_val_loss": 0.14289738237857819,
+  "train_loss": 0.13862412328273058,
+  "sec": 648.4
+ },
+ {
+  "step": 13000,
+  "inner_val_loss": 0.1424849501677922,
+  "train_loss": 0.13836256685107948,
+  "sec": 702.7
+ },
+ {
+  "step": 14000,
+  "inner_val_loss": 0.14201795416218893,
+  "train_loss": 0.13761741138994693,
+  "sec": 756.3
+ },
+ {
+  "step": 15000,
+  "inner_val_loss": 0.14145703188010625,
+  "train_loss": 0.13709825225174427,
+  "sec": 810.9
+ },
+ {
+  "step": 16000,
+  "inner_val_loss": 0.1406149630035673,
+  "train_loss": 0.13679010706394912,
+  "sec": 864.7
+ },
+ {
+  "step": 17000,
+  "inner_val_loss": 0.13945734820195607,
+  "train_loss": 0.13463101560622454,
+  "sec": 918.9
+ },
+ {
+  "step": 18000,
+  "inner_val_loss": 0.13814055813210352,
+  "train_loss": 0.13389788818359374,
+  "sec": 968.4
+ },
+ {
+  "step": 19000,
+  "inner_val_loss": 0.13687613819326674,
+  "train_loss": 0.13257296388596296,
+  "sec": 1016.6
+ },
+ {
+  "step": 20000,
+  "inner_val_loss": 0.1356198095849582,
+  "train_loss": 0.13116567225009204,
+  "sec": 1064.3
+ },
+ {
+  "step": 21000,
+  "inner_val_loss": 0.13444291001984052,
+  "train_loss": 0.12992072887718678,
+  "sec": 1112.5
+ },
+ {
+  "step": 22000,
+  "inner_val_loss": 0.13335069428597177,
+  "train_loss": 0.12928874226659537,
+  "sec": 1160.5
+ },
+ {
+  "step": 23000,
+  "inner_val_loss": 0.13236748480371066,
+  "train_loss": 0.1280067993402481,
+  "sec": 1208.2
+ },
+ {
+  "step": 24000,
+  "inner_val_loss": 0.13149938306638173,
+  "train_loss": 0.12716022816300393,
+  "sec": 1257.2
+ },
+ {
+  "step": 25000,
+  "inner_val_loss": 0.13063780378018106,
+  "train_loss": 0.12640594418346882,
+  "sec": 1305.3
+ },
+ {
+  "step": 26000,
+  "inner_val_loss": 0.1298088010932718,
+  "train_loss": 0.12530799473822116,
+  "sec": 1356.3
+ },
+ {
+  "step": 27000,
+  "inner_val_loss": 0.12905310413667134,
+  "train_loss": 0.12482245367020368,
+  "sec": 1405.3
+ },
+ {
+  "step": 28000,
+  "inner_val_loss": 0.1283388180392129,
+  "train_loss": 0.1241136982217431,
+  "sec": 1453.4
+ },
+ {
+  "step": 29000,
+  "inner_val_loss": 0.12769334656851633,
+  "train_loss": 0.12331638681143522,
+  "sec": 1501.3
+ },
+ {
+  "step": 30000,
+  "inner_val_loss": 0.1271361352077552,
+  "train_loss": 0.12272434643656015,
+  "sec": 1549.1
+ },
+ {
+  "step": 31000,
+  "inner_val_loss": 0.12655053287744522,
+  "train_loss": 0.1218122222572565,
+  "sec": 1596.9
+ },
+ {
+  "step": 32000,
+  "inner_val_loss": 0.1259957796760968,
+  "train_loss": 0.12150617586821318,
+  "sec": 1645.0
+ },
+ {
+  "step": 33000,
+  "inner_val_loss": 0.12550453948123114,
+  "train_loss": 0.12136621098220349,
+  "sec": 1692.3
+ },
+ {
+  "step": 34000,
+  "inner_val_loss": 0.12503466914807046,
+  "train_loss": 0.12034468111395837,
+  "sec": 1740.9
+ },
+ {
+  "step": 35000,
+  "inner_val_loss": 0.12453154580933708,
+  "train_loss": 0.11964633052796125,
+  "sec": 1789.1
+ },
+ {
+  "step": 36000,
+  "inner_val_loss": 0.12411893638116973,
+  "train_loss": 0.1198335874453187,
+  "sec": 1838.0
+ },
+ {
+  "step": 37000,
+  "inner_val_loss": 0.12369576575500625,
+  "train_loss": 0.1190081579387188,
+  "sec": 1888.6
+ },
+ {
+  "step": 38000,
+  "inner_val_loss": 0.12328357568808965,
+  "train_loss": 0.1184410906136036,
+  "sec": 1941.7
+ },
+ {
+  "step": 39000,
+  "inner_val_loss": 0.1229555250278541,
+  "train_loss": 0.1183831441551447,
+  "sec": 1995.1
+ },
+ {
+  "step": 40000,
+  "inner_val_loss": 0.12264086731842586,
+  "train_loss": 0.11756622228771448,
+  "sec": 2047.8
+ },
+ {
+  "step": 41000,
+  "inner_val_loss": 0.12231136858463287,
+  "train_loss": 0.11750146259367467,
+  "sec": 2096.1
+ },
+ {
+  "step": 42000,
+  "inner_val_loss": 0.12199339696339198,
+  "train_loss": 0.11734486290067435,
+  "sec": 2143.3
+ },
+ {
+  "step": 43000,
+  "inner_val_loss": 0.12166188337973186,
+  "train_loss": 0.11693619984388351,
+  "sec": 2191.3
+ },
+ {
+  "step": 44000,
+  "inner_val_loss": 0.12137471565178462,
+  "train_loss": 0.11676418705284596,
+  "sec": 2239.7
+ },
+ {
+  "step": 45000,
+  "inner_val_loss": 0.12109518317239625,
+  "train_loss": 0.11592690517753362,
+  "sec": 2287.7
+ },
+ {
+  "step": 46000,
+  "inner_val_loss": 0.1208101739840848,
+  "train_loss": 0.11594655752927065,
+  "sec": 2336.5
+ },
+ {
+  "step": 47000,
+  "inner_val_loss": 0.12056576939565795,
+  "train_loss": 0.11573552632331849,
+  "sec": 2384.3
+ },
+ {
+  "step": 48000,
+  "inner_val_loss": 0.12033451295324735,
+  "train_loss": 0.11539365667104722,
+  "sec": 2432.4
+ },
+ {
+  "step": 49000,
+  "inner_val_loss": 0.12017713114619255,
+  "train_loss": 0.11569693789631129,
+  "sec": 2481.0
+ },
+ {
+  "step": 50000,
+  "inner_val_loss": 0.11996427338038172,
+  "train_loss": 0.11512865433841944,
+  "sec": 2529.1
+ },
+ {
+  "step": 51000,
+  "inner_val_loss": 0.11976227749671255,
+  "train_loss": 0.11463018821924925,
+  "sec": 2577.4
+ },
+ {
+  "step": 52000,
+  "inner_val_loss": 0.11955207320196289,
+  "train_loss": 0.11439854905754328,
+  "sec": 2625.2
+ },
+ {
+  "step": 53000,
+  "inner_val_loss": 0.11934312699096543,
+  "train_loss": 0.11389919279515744,
+  "sec": 2673.4
+ },
+ {
+  "step": 54000,
+  "inner_val_loss": 0.11915863305330276,
+  "train_loss": 0.11378780456632376,
+  "sec": 2721.5
+ },
+ {
+  "step": 55000,
+  "inner_val_loss": 0.11899566171424729,
+  "train_loss": 0.11385539833456278,
+  "sec": 2769.7
+ },
+ {
+  "step": 56000,
+  "inner_val_loss": 0.1188232648585524,
+  "train_loss": 0.1134542827680707,
+  "sec": 2817.9
+ },
+ {
+  "step": 57000,
+  "inner_val_loss": 0.11864239190305982,
+  "train_loss": 0.11318401571363211,
+  "sec": 2865.7
+ },
+ {
+  "step": 58000,
+  "inner_val_loss": 0.1185429213302476,
+  "train_loss": 0.11359425082802772,
+  "sec": 2913.2
+ },
+ {
+  "step": 59000,
+  "inner_val_loss": 0.11839618693505015,
+  "train_loss": 0.11313988484442233,
+  "sec": 2961.3
+ },
+ {
+  "step": 60000,
+  "inner_val_loss": 0.11825216827648026,
+  "train_loss": 0.11259610421210528,
+  "sec": 3010.2
+ },
+ {
+  "step": 61000,
+  "inner_val_loss": 0.11812599216188703,
+  "train_loss": 0.11263373418152332,
+  "sec": 3058.9
+ },
+ {
+  "step": 62000,
+  "inner_val_loss": 0.11800212572727885,
+  "train_loss": 0.1125659332871437,
+  "sec": 3106.7
+ },
+ {
+  "step": 63000,
+  "inner_val_loss": 0.11787135207227298,
+  "train_loss": 0.11211149560660123,
+  "sec": 3155.3
+ },
+ {
+  "step": 64000,
+  "inner_val_loss": 0.11774909868836403,
+  "train_loss": 0.11232676993310452,
+  "sec": 3203.8
+ },
+ {
+  "step": 65000,
+  "inner_val_loss": 0.1176729505615575,
+  "train_loss": 0.11190619633346796,
+  "sec": 3252.4
+ },
+ {
+  "step": 66000,
+  "inner_val_loss": 0.11762262135744095,
+  "train_loss": 0.11272756592184305,
+  "sec": 3301.9
+ },
+ {
+  "step": 67000,
+  "inner_val_loss": 0.11745793265955788,
+  "train_loss": 0.11180350236594677,
+  "sec": 3355.9
+ },
+ {
+  "step": 68000,
+  "inner_val_loss": 0.11734392121434212,
+  "train_loss": 0.11138260732591153,
+  "sec": 3409.6
+ },
+ {
+  "step": 69000,
+  "inner_val_loss": 0.11725425933088575,
+  "train_loss": 0.11217197719216347,
+  "sec": 3463.5
+ },
+ {
+  "step": 70000,
+  "inner_val_loss": 0.1171950234898499,
+  "train_loss": 0.11184576016664505,
+  "sec": 3517.7
+ },
+ {
+  "step": 71000,
+  "inner_val_loss": 0.11713129760963577,
+  "train_loss": 0.11151032032072544,
+  "sec": 3572.0
+ },
+ {
+  "step": 72000,
+  "inner_val_loss": 0.11701717014823641,
+  "train_loss": 0.1111701887100935,
+  "sec": 3626.2
+ },
+ {
+  "step": 73000,
+  "inner_val_loss": 0.11690119015319007,
+  "train_loss": 0.11108873553574085,
+  "sec": 3680.4
+ },
+ {
+  "step": 74000,
+  "inner_val_loss": 0.11677923213158335,
+  "train_loss": 0.11098147592693568,
+  "sec": 3734.7
+ },
+ {
+  "step": 75000,
+  "inner_val_loss": 0.11668967242751803,
+  "train_loss": 0.11078576864302159,
+  "sec": 3788.8
+ },
+ {
+  "step": 76000,
+  "inner_val_loss": 0.11660533451608249,
+  "train_loss": 0.11109650626033545,
+  "sec": 3842.9
+ },
+ {
+  "step": 77000,
+  "inner_val_loss": 0.11655187553593091,
+  "train_loss": 0.11119181018322706,
+  "sec": 3896.9
+ },
+ {
+  "step": 78000,
+  "inner_val_loss": 0.1164993489427226,
+  "train_loss": 0.11097149375081063,
+  "sec": 3951.2
+ },
+ {
+  "step": 79000,
+  "inner_val_loss": 0.1164369492658547,
+  "train_loss": 0.11051307631283999,
+  "sec": 4005.5
+ },
+ {
+  "step": 80000,
+  "inner_val_loss": 0.11639945687992233,
+  "train_loss": 0.11075366619974375,
+  "sec": 4062.9
+ },
+ {
+  "step": 81000,
+  "inner_val_loss": 0.11637057097894805,
+  "train_loss": 0.11078128405660391,
+  "sec": 4120.3
+ },
+ {
+  "step": 82000,
+  "inner_val_loss": 0.11633819820625442,
+  "train_loss": 0.11060621506720782,
+  "sec": 4176.3
+ },
+ {
+  "step": 83000,
+  "inner_val_loss": 0.11626615109188217,
+  "train_loss": 0.11025107654184103,
+  "sec": 4232.3
+ },
+ {
+  "step": 84000,
+  "inner_val_loss": 0.1162030350949083,
+  "train_loss": 0.1103127064332366,
+  "sec": 4289.5
+ },
+ {
+  "step": 85000,
+  "inner_val_loss": 0.11617253454668182,
+  "train_loss": 0.11035401468724013,
+  "sec": 4347.5
+ },
+ {
+  "step": 86000,
+  "inner_val_loss": 0.11612480985266822,
+  "train_loss": 0.11009867207705974,
+  "sec": 4404.9
+ },
+ {
+  "step": 87000,
+  "inner_val_loss": 0.11608896510941642,
+  "train_loss": 0.11011939832568168,
+  "sec": 4462.3
+ },
+ {
+  "step": 88000,
+  "inner_val_loss": 0.1160595566034317,
+  "train_loss": 0.10968328523635865,
+  "sec": 4515.0
+ },
+ {
+  "step": 89000,
+  "inner_val_loss": 0.11600882400359426,
+  "train_loss": 0.10995694989711047,
+  "sec": 4568.8
+ },
+ {
+  "step": 90000,
+  "inner_val_loss": 0.1159409513430936,
+  "train_loss": 0.10983642309904099,
+  "sec": 4620.8
+ },
+ {
+  "step": 91000,
+  "inner_val_loss": 0.11589380194033895,
+  "train_loss": 0.10962704634666443,
+  "sec": 4671.5
+ },
+ {
+  "step": 92000,
+  "inner_val_loss": 0.11587068491748401,
+  "train_loss": 0.1096884953007102,
+  "sec": 4725.9
+ },
+ {
+  "step": 93000,
+  "inner_val_loss": 0.11584750456469399,
+  "train_loss": 0.10959102140367032,
+  "sec": 4780.3
+ },
+ {
+  "step": 94000,
+  "inner_val_loss": 0.1158138055886541,
+  "train_loss": 0.10969828441739082,
+  "sec": 4835.0
+ },
+ {
+  "step": 95000,
+  "inner_val_loss": 0.11573344841599464,
+  "train_loss": 0.1095349226295948,
+  "sec": 4889.0
+ },
+ {
+  "step": 96000,
+  "inner_val_loss": 0.11569187896592277,
+  "train_loss": 0.10992172940075398,
+  "sec": 4941.4
+ },
+ {
+  "step": 97000,
+  "inner_val_loss": 0.1156567255301135,
+  "train_loss": 0.10961186796426774,
+  "sec": 4993.7
+ },
+ {
+  "step": 98000,
+  "inner_val_loss": 0.1156395822763443,
+  "train_loss": 0.10927521008998156,
+  "sec": 5047.9
+ },
+ {
+  "step": 99000,
+  "inner_val_loss": 0.11558818870357104,
+  "train_loss": 0.1092970443740487,
+  "sec": 5101.7
+ },
+ {
+  "step": 100000,
+  "inner_val_loss": 0.11552448304636138,
+  "train_loss": 0.10885347930341958,
+  "sec": 5156.0
+ }
+]

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_n5__raw/labels/labels.manifest.json

@@ -0,0 +1,156 @@
+{
+  "dataset_id": "Ye2026_sepsis",
+  "split": "generated",
+  "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_n5__raw/query.h5ad",
+  "method": "scratch_n5__raw",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_n5__raw/labels/labels.parquet",
+  "training_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/reference/aifi_reference_f01common.h5ad",
+  "target_truth_used_for_fitting": false,
+  "classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
+  "labels": [
+    "T cell",
+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
+    "Other"
+  ],
+  "l2_labels": [
+    "ASDC",
+    "CD14 monocyte",
+    "CD16 monocyte",
+    "CD56bright NK cell",
+    "CD56dim NK cell",
+    "CD8aa",
+    "DN T cell",
+    "Effector B cell",
+    "Erythrocyte",
+    "ILC",
+    "Intermediate monocyte",
+    "MAIT",
+    "Memory B cell",
+    "Memory CD4 T cell",
+    "Memory CD8 T cell",
+    "Naive B cell",
+    "Naive CD4 T cell",
+    "Naive CD8 T cell",
+    "Plasma cell",
+    "Platelet",
+    "Progenitor cell",
+    "Proliferating NK cell",
+    "Proliferating T cell",
+    "Transitional B cell",
+    "Treg",
+    "cDC1",
+    "cDC2",
+    "gdT",
+    "pDC"
+  ],
+  "n_cells": 25500,
+  "n_genes": 1005,
+  "note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
+  "label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
+  "query_train_epochs": 0,
+  "confidence_threshold": 0.0,
+  "subset": false,
+  "evaluator_aligned": true,
+  "gene_space": {
+    "join_key": "ensembl_id",
+    "model_genes": 1005,
+    "query_genes": 1006,
+    "model_genes_missing_from_query_zero_padded": 0,
+    "query_genes_outside_model_dropped": 1,
+    "rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
+  },
+  "readout": null,
+  "query_build": {
+    "kind": "generated_npz",
+    "poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
+    "readout": "poisson",
+    "seed": 20260916,
+    "set": "scratch_n5__raw",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/scratch_n5__raw.npz",
+    "source_sha256": "80c0222cf055b0890f405f39525b0642e521b19018c9d43ce677255e5614cb10"
+  },
+  "model": {
+    "scanvi_model_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_model",
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "model_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/MODEL_MANIFEST.json",
+    "held_out_summary": {
+      "l2_accuracy": 0.8692869740488788,
+      "l2_macro_f1": 0.8500925599737216,
+      "l1_accuracy": 0.9918367346938776,
+      "l1_macro_f1": 0.9715232379009036,
+      "pbmc5_other_accuracy": 0.9920886873267826,
+      "pbmc5_other_macro_f1": 0.9812088972148597
+    }
+  },
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 13611,
+      "Monocyte": 6241,
+      "B cell": 2910,
+      "NK cell": 2046,
+      "Other": 644,
+      "DC": 48
+    },
+    "aifi_l1": {
+      "T cell": 13611,
+      "Monocyte": 6241,
+      "B cell": 2910,
+      "NK cell": 2046,
+      "Platelet": 449,
+      "Erythrocyte": 152,
+      "DC": 48,
+      "ILC": 28,
+      "Progenitor cell": 15
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 4744,
+      "CD14 monocyte": 4075,
+      "Memory CD8 T cell": 2591,
+      "Naive CD4 T cell": 1965,
+      "gdT": 1858,
+      "CD56dim NK cell": 1742,
+      "CD16 monocyte": 1680,
+      "Naive B cell": 1070,
+      "Naive CD8 T cell": 868,
+      "Treg": 732,
+      "Effector B cell": 676,
+      "Memory B cell": 632,
+      "Intermediate monocyte": 486,
+      "Platelet": 449,
+      "Transitional B cell": 376,
+      "CD8aa": 331,
+      "DN T cell": 278,
+      "CD56bright NK cell": 158,
+      "Plasma cell": 156,
+      "Erythrocyte": 152,
+      "Proliferating NK cell": 146,
+      "Proliferating T cell": 135,
+      "MAIT": 109,
+      "cDC2": 36,
+      "ILC": 28,
+      "Progenitor cell": 15,
+      "pDC": 6,
+      "cDC1": 5,
+      "ASDC": 1
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9442637594838937,
+    "mean_l1_mass": 0.98914635181427,
+    "frac_l2_max_prob_ge_0.5": 0.9855294117647059
+  },
+  "timings_s": {
+    "predict": 0.2,
+    "total": 0.5
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-05T04:58:47.073982+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_n5__raw/labels/labels.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e27a709cdef015afc96cc23b9c0b3b27081253eb956b37eabe060ce7727cfafa
+size 573498