Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_budget_20261002/pooled/arms/scsemi_n40__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/scsemi_budget_20261002/pooled/arms/scsemi_n40__raw/query.h5ad",
+  "method": "scsemi_n40__raw",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_budget_20261002/pooled/arms/scsemi_n40__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": 123000,
+  "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": "scsemi_n40__raw",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/pooled_scsemi_budget_20261002/scsemi_n40__raw.npz",
+    "source_sha256": "ecf1b42ada44f4a08ce2847fc8ef629d8209a2690fffd7f4426efa7e32cc6017"
+  },
+  "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": 65603,
+      "Monocyte": 26718,
+      "B cell": 15307,
+      "Other": 6799,
+      "NK cell": 6455,
+      "DC": 2118
+    },
+    "aifi_l1": {
+      "T cell": 65603,
+      "Monocyte": 26718,
+      "B cell": 15307,
+      "NK cell": 6455,
+      "Erythrocyte": 2889,
+      "Platelet": 2842,
+      "DC": 2118,
+      "ILC": 1047,
+      "Progenitor cell": 21
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 19785,
+      "CD14 monocyte": 19099,
+      "Naive CD4 T cell": 14408,
+      "gdT": 9242,
+      "Memory CD8 T cell": 9161,
+      "Naive B cell": 6488,
+      "CD56dim NK cell": 5523,
+      "Memory B cell": 5017,
+      "CD16 monocyte": 4274,
+      "CD8aa": 4233,
+      "Naive CD8 T cell": 3621,
+      "Intermediate monocyte": 3345,
+      "Erythrocyte": 2889,
+      "Platelet": 2842,
+      "Treg": 2838,
+      "Plasma cell": 2261,
+      "cDC2": 1834,
+      "MAIT": 1194,
+      "ILC": 1047,
+      "Effector B cell": 860,
+      "CD56bright NK cell": 685,
+      "Transitional B cell": 681,
+      "Proliferating T cell": 599,
+      "DN T cell": 522,
+      "Proliferating NK cell": 247,
+      "cDC1": 176,
+      "pDC": 76,
+      "ASDC": 32,
+      "Progenitor cell": 21
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.912175284003218,
+    "mean_l1_mass": 0.9712412357330322,
+    "frac_l2_max_prob_ge_0.5": 0.9607560975609756
+  },
+  "timings_s": {
+    "predict": 0.8,
+    "total": 1.5
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-08T02:10:19.884565+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_budget_20261002/pooled/arms/scsemi_n40__raw/labels/labels.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a2f89e4547f0c72fb5ba7ce378457bb6bba8ab710384c17db5ba7dadb6760a79
+size 2988130

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_budget_20261002/pooled/arms/scsemi_n5__raw/deg_top50_lists.csv

@@ -0,0 +1,328 @@
+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000123358
+T cell,observed,2,ENSG00000090382
+T cell,observed,3,ENSG00000143333
+T cell,observed,4,ENSG00000109321
+T cell,observed,5,ENSG00000124762
+T cell,observed,6,ENSG00000184113
+T cell,observed,7,ENSG00000144655
+T cell,observed,8,ENSG00000118515
+T cell,observed,9,ENSG00000184557
+T cell,observed,10,ENSG00000162772
+T cell,observed,11,ENSG00000232810
+T cell,observed,12,ENSG00000134531
+T cell,observed,13,ENSG00000277632
+T cell,observed,14,ENSG00000144290
+T cell,observed,15,ENSG00000112149
+T cell,observed,16,ENSG00000168497
+T cell,observed,17,ENSG00000062524
+T cell,observed,18,ENSG00000163563
+T cell,observed,19,ENSG00000113070
+T cell,observed,20,ENSG00000101162
+T cell,observed,21,ENSG00000168209
+T cell,observed,22,ENSG00000158813
+T cell,observed,23,ENSG00000173114
+T cell,observed,24,ENSG00000127920
+T cell,observed,25,ENSG00000120708
+T cell,observed,26,ENSG00000138166
+T cell,observed,27,ENSG00000168329
+T cell,observed,28,ENSG00000119508
+T cell,observed,29,ENSG00000085265
+T cell,observed,30,ENSG00000275302
+T cell,observed,31,ENSG00000100906
+T cell,observed,32,ENSG00000179388
+T cell,observed,33,ENSG00000108551
+T cell,observed,34,ENSG00000128016
+T cell,observed,35,ENSG00000160789
+T cell,observed,36,ENSG00000100079
+T cell,observed,37,ENSG00000121552
+T cell,observed,38,ENSG00000110848
+T cell,observed,39,ENSG00000150681
+T cell,observed,40,ENSG00000197728
+T cell,observed,41,ENSG00000110077
+T cell,observed,42,ENSG00000115607
+T cell,observed,43,ENSG00000134545
+T cell,observed,44,ENSG00000125968
+T cell,observed,45,ENSG00000091129
+T cell,observed,46,ENSG00000113088
+T cell,observed,47,ENSG00000106066
+T cell,observed,48,ENSG00000130844
+T cell,observed,49,ENSG00000117281
+T cell,observed,50,ENSG00000038427
+T cell,generated,1,ENSG00000111796
+T cell,generated,2,ENSG00000113088
+T cell,generated,3,ENSG00000197540
+T cell,generated,4,ENSG00000109475
+B cell,observed,1,ENSG00000123358
+B cell,observed,2,ENSG00000090382
+B cell,observed,3,ENSG00000184557
+B cell,observed,4,ENSG00000143333
+B cell,observed,5,ENSG00000125968
+B cell,observed,6,ENSG00000124762
+B cell,observed,7,ENSG00000162772
+B cell,observed,8,ENSG00000113088
+B cell,observed,9,ENSG00000066923
+B cell,observed,10,ENSG00000118515
+B cell,observed,11,ENSG00000158050
+B cell,observed,12,ENSG00000119508
+B cell,observed,13,ENSG00000168209
+B cell,observed,14,ENSG00000232810
+B cell,observed,15,ENSG00000168329
+B cell,observed,16,ENSG00000114315
+B cell,observed,17,ENSG00000112149
+B cell,observed,18,ENSG00000137441
+B cell,observed,19,ENSG00000138166
+B cell,observed,20,ENSG00000185022
+B cell,observed,21,ENSG00000090339
+B cell,observed,22,ENSG00000145649
+B cell,observed,23,ENSG00000130844
+B cell,observed,24,ENSG00000150625
+B cell,observed,25,ENSG00000153563
+B cell,observed,26,ENSG00000165949
+B cell,observed,27,ENSG00000180739
+B cell,observed,28,ENSG00000153234
+B cell,observed,29,ENSG00000160654
+B cell,observed,30,ENSG00000143603
+B cell,observed,31,ENSG00000103257
+B cell,observed,32,ENSG00000172673
+B cell,observed,33,ENSG00000110448
+B cell,observed,34,ENSG00000151090
+B cell,observed,35,ENSG00000111796
+B cell,observed,36,ENSG00000173114
+B cell,observed,37,ENSG00000166750
+B cell,observed,38,ENSG00000144655
+B cell,observed,39,ENSG00000172116
+B cell,observed,40,ENSG00000100906
+B cell,observed,41,ENSG00000099860
+B cell,observed,42,ENSG00000184613
+B cell,observed,43,ENSG00000271503
+B cell,observed,44,ENSG00000115523
+B cell,observed,45,ENSG00000085265
+B cell,observed,46,ENSG00000102245
+B cell,observed,47,ENSG00000120708
+B cell,observed,48,ENSG00000105374
+B cell,observed,49,ENSG00000101665
+B cell,observed,50,ENSG00000184545
+B cell,generated,1,ENSG00000158050
+B cell,generated,2,ENSG00000163682
+B cell,generated,3,ENSG00000109475
+B cell,generated,4,ENSG00000131469
+B cell,generated,5,ENSG00000182899
+B cell,generated,6,ENSG00000143947
+Monocyte,observed,1,ENSG00000087116
+Monocyte,observed,2,ENSG00000159189
+Monocyte,observed,3,ENSG00000115590
+Monocyte,observed,4,ENSG00000166428
+Monocyte,observed,5,ENSG00000173369
+Monocyte,observed,6,ENSG00000115009
+Monocyte,observed,7,ENSG00000113088
+Monocyte,observed,8,ENSG00000108950
+Monocyte,observed,9,ENSG00000123610
+Monocyte,observed,10,ENSG00000100079
+Monocyte,observed,11,ENSG00000146070
+Monocyte,observed,12,ENSG00000179639
+Monocyte,observed,13,ENSG00000145649
+Monocyte,observed,14,ENSG00000180644
+Monocyte,observed,15,ENSG00000137441
+Monocyte,observed,16,ENSG00000115523
+Monocyte,observed,17,ENSG00000153563
+Monocyte,observed,18,ENSG00000111796
+Monocyte,observed,19,ENSG00000100450
+Monocyte,observed,20,ENSG00000134539
+Monocyte,observed,21,ENSG00000073861
+Monocyte,observed,22,ENSG00000184613
+Monocyte,observed,23,ENSG00000163739
+Monocyte,observed,24,ENSG00000147138
+Monocyte,observed,25,ENSG00000139970
+Monocyte,observed,26,ENSG00000129538
+Monocyte,observed,27,ENSG00000155659
+Monocyte,observed,28,ENSG00000172116
+Monocyte,observed,29,ENSG00000013725
+Monocyte,observed,30,ENSG00000163734
+Monocyte,observed,31,ENSG00000180739
+Monocyte,observed,32,ENSG00000153823
+Monocyte,observed,33,ENSG00000163564
+Monocyte,observed,34,ENSG00000120262
+Monocyte,observed,35,ENSG00000198821
+Monocyte,observed,36,ENSG00000152495
+Monocyte,observed,37,ENSG00000183918
+Monocyte,observed,38,ENSG00000160856
+Monocyte,observed,39,ENSG00000081041
+Monocyte,observed,40,ENSG00000257017
+Monocyte,observed,41,ENSG00000120885
+Monocyte,observed,42,ENSG00000186810
+Monocyte,observed,43,ENSG00000172575
+Monocyte,observed,44,ENSG00000101096
+Monocyte,observed,45,ENSG00000168685
+Monocyte,observed,46,ENSG00000115085
+Monocyte,observed,47,ENSG00000100385
+Monocyte,observed,48,ENSG00000163508
+Monocyte,observed,49,ENSG00000205336
+Monocyte,observed,50,ENSG00000198851
+Monocyte,generated,1,ENSG00000147604
+NK cell,observed,1,ENSG00000090382
+NK cell,observed,2,ENSG00000085265
+NK cell,observed,3,ENSG00000123358
+NK cell,observed,4,ENSG00000185215
+NK cell,observed,5,ENSG00000110077
+NK cell,observed,6,ENSG00000038427
+NK cell,observed,7,ENSG00000119535
+NK cell,observed,8,ENSG00000163563
+NK cell,observed,9,ENSG00000197629
+NK cell,observed,10,ENSG00000116701
+NK cell,observed,11,ENSG00000172243
+NK cell,observed,12,ENSG00000121552
+NK cell,observed,13,ENSG00000125538
+NK cell,observed,14,ENSG00000163220
+NK cell,observed,15,ENSG00000169429
+NK cell,observed,16,ENSG00000100079
+NK cell,observed,17,ENSG00000144655
+NK cell,observed,18,ENSG00000109321
+NK cell,observed,19,ENSG00000120708
+NK cell,observed,20,ENSG00000241399
+NK cell,observed,21,ENSG00000143333
+NK cell,observed,22,ENSG00000197249
+NK cell,observed,23,ENSG00000143546
+NK cell,observed,24,ENSG00000101336
+NK cell,observed,25,ENSG00000168497
+NK cell,observed,26,ENSG00000277632
+NK cell,observed,27,ENSG00000160789
+NK cell,observed,28,ENSG00000126759
+NK cell,observed,29,ENSG00000171051
+NK cell,observed,30,ENSG00000232810
+NK cell,observed,31,ENSG00000131042
+NK cell,observed,32,ENSG00000197467
+NK cell,observed,33,ENSG00000187164
+NK cell,observed,34,ENSG00000120594
+NK cell,observed,35,ENSG00000160593
+NK cell,observed,36,ENSG00000197766
+NK cell,observed,37,ENSG00000275302
+NK cell,observed,38,ENSG00000189292
+NK cell,observed,39,ENSG00000122877
+NK cell,observed,40,ENSG00000184731
+NK cell,observed,41,ENSG00000165061
+NK cell,observed,42,ENSG00000163694
+NK cell,observed,43,ENSG00000106066
+NK cell,observed,44,ENSG00000127920
+NK cell,observed,45,ENSG00000119508
+NK cell,observed,46,ENSG00000162444
+NK cell,observed,47,ENSG00000204472
+NK cell,observed,48,ENSG00000111275
+NK cell,observed,49,ENSG00000186407
+NK cell,observed,50,ENSG00000166592
+DC,observed,1,ENSG00000179639
+DC,observed,2,ENSG00000168685
+DC,observed,3,ENSG00000100721
+DC,observed,4,ENSG00000163606
+DC,observed,5,ENSG00000008517
+DC,observed,6,ENSG00000158481
+DC,observed,7,ENSG00000138449
+DC,observed,8,ENSG00000081059
+DC,observed,9,ENSG00000155974
+DC,observed,10,ENSG00000184709
+DC,observed,11,ENSG00000167286
+DC,observed,12,ENSG00000271503
+DC,observed,13,ENSG00000107317
+DC,observed,14,ENSG00000138795
+DC,observed,15,ENSG00000139970
+DC,observed,16,ENSG00000160654
+DC,observed,17,ENSG00000109099
+DC,observed,18,ENSG00000112182
+DC,observed,19,ENSG00000156313
+DC,observed,20,ENSG00000153823
+DC,observed,21,ENSG00000167644
+DC,observed,22,ENSG00000132514
+DC,observed,23,ENSG00000186854
+DC,observed,24,ENSG00000152315
+DC,observed,25,ENSG00000136111
+DC,observed,26,ENSG00000149131
+DC,observed,27,ENSG00000134326
+DC,observed,28,ENSG00000113263
+DC,observed,29,ENSG00000157657
+DC,observed,30,ENSG00000118961
+DC,observed,31,ENSG00000141337
+DC,observed,32,ENSG00000102174
+DC,observed,33,ENSG00000172954
+DC,observed,34,ENSG00000106952
+DC,observed,35,ENSG00000127152
+DC,observed,36,ENSG00000110448
+DC,observed,37,ENSG00000125257
+DC,observed,38,ENSG00000198851
+DC,observed,39,ENSG00000062524
+DC,observed,40,ENSG00000013725
+DC,observed,41,ENSG00000171408
+DC,observed,42,ENSG00000177409
+DC,observed,43,ENSG00000172116
+DC,observed,44,ENSG00000179152
+DC,observed,45,ENSG00000162869
+DC,observed,46,ENSG00000035664
+DC,observed,47,ENSG00000153563
+DC,observed,48,ENSG00000127920
+DC,observed,49,ENSG00000162654
+DC,observed,50,ENSG00000075223
+DC,generated,1,ENSG00000163931
+DC,generated,2,ENSG00000025708
+DC,generated,3,ENSG00000163131
+DC,generated,4,ENSG00000038427
+DC,generated,5,ENSG00000197746
+DC,generated,6,ENSG00000204472
+DC,generated,7,ENSG00000103490
+DC,generated,8,ENSG00000090382
+DC,generated,9,ENSG00000101439
+DC,generated,10,ENSG00000163682
+DC,generated,11,ENSG00000109475
+DC,generated,12,ENSG00000164587
+DC,generated,13,ENSG00000177600
+DC,generated,14,ENSG00000182899
+DC,generated,15,ENSG00000138326
+DC,generated,16,ENSG00000110700
+all (input bulk),broadcast,1,ENSG00000244734
+all (input bulk),broadcast,2,ENSG00000188536
+all (input bulk),broadcast,3,ENSG00000087116
+all (input bulk),broadcast,4,ENSG00000158578
+all (input bulk),broadcast,5,ENSG00000206172
+all (input bulk),broadcast,6,ENSG00000115590
+all (input bulk),broadcast,7,ENSG00000159189
+all (input bulk),broadcast,8,ENSG00000108950
+all (input bulk),broadcast,9,ENSG00000004939
+all (input bulk),broadcast,10,ENSG00000100985
+all (input bulk),broadcast,11,ENSG00000173369
+all (input bulk),broadcast,12,ENSG00000179639
+all (input bulk),broadcast,13,ENSG00000133742
+all (input bulk),broadcast,14,ENSG00000257017
+all (input bulk),broadcast,15,ENSG00000125740
+all (input bulk),broadcast,16,ENSG00000223609
+all (input bulk),broadcast,17,ENSG00000129538
+all (input bulk),broadcast,18,ENSG00000169385
+all (input bulk),broadcast,19,ENSG00000162551
+all (input bulk),broadcast,20,ENSG00000155659
+all (input bulk),broadcast,21,ENSG00000169429
+all (input bulk),broadcast,22,ENSG00000173372
+all (input bulk),broadcast,23,ENSG00000123610
+all (input bulk),broadcast,24,ENSG00000138772
+all (input bulk),broadcast,25,ENSG00000276085
+all (input bulk),broadcast,26,ENSG00000132170
+all (input bulk),broadcast,27,ENSG00000137869
+all (input bulk),broadcast,28,ENSG00000184792
+all (input bulk),broadcast,29,ENSG00000118520
+all (input bulk),broadcast,30,ENSG00000170298
+all (input bulk),broadcast,31,ENSG00000162747
+all (input bulk),broadcast,32,ENSG00000120885
+all (input bulk),broadcast,33,ENSG00000177606
+all (input bulk),broadcast,34,ENSG00000153234
+all (input bulk),broadcast,35,ENSG00000182885
+all (input bulk),broadcast,36,ENSG00000078053
+all (input bulk),broadcast,37,ENSG00000165682
+all (input bulk),broadcast,38,ENSG00000042062
+all (input bulk),broadcast,39,ENSG00000115414
+all (input bulk),broadcast,40,ENSG00000144290
+all (input bulk),broadcast,41,ENSG00000166428
+all (input bulk),broadcast,42,ENSG00000079215
+all (input bulk),broadcast,43,ENSG00000100079
+all (input bulk),broadcast,44,ENSG00000198336
+all (input bulk),broadcast,45,ENSG00000165949
+all (input bulk),broadcast,46,ENSG00000163221
+all (input bulk),broadcast,47,ENSG00000105610
+all (input bulk),broadcast,48,ENSG00000117281
+all (input bulk),broadcast,49,ENSG00000167100
+all (input bulk),broadcast,50,ENSG00000166947

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_budget_20261002/pooled/arms/scsemi_n5__raw/generated_cells.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0b5b7e86b450c50816fb3a955b790cf7be629b0fa1d80bce573b1100e8eb2a74
+size 963774