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_cv_20261002/fold3/arms/scsemi__raw/deg_top50_lists.csv

@@ -0,0 +1,206 @@
+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000244734
+T cell,observed,2,ENSG00000124762
+T cell,observed,3,ENSG00000232810
+T cell,observed,4,ENSG00000075618
+T cell,observed,5,ENSG00000184545
+T cell,observed,6,ENSG00000168329
+T cell,observed,7,ENSG00000124507
+T cell,observed,8,ENSG00000262655
+T cell,observed,9,ENSG00000159958
+T cell,observed,10,ENSG00000166920
+T cell,observed,11,ENSG00000108852
+T cell,observed,12,ENSG00000174136
+T cell,observed,13,ENSG00000115594
+T cell,observed,14,ENSG00000170456
+T cell,observed,15,ENSG00000134897
+T cell,observed,16,ENSG00000135547
+T cell,observed,17,ENSG00000047365
+T cell,observed,18,ENSG00000158006
+T cell,observed,19,ENSG00000144451
+T cell,observed,20,ENSG00000139835
+T cell,observed,21,ENSG00000182504
+T cell,observed,22,ENSG00000197362
+T cell,observed,23,ENSG00000152683
+T cell,observed,24,ENSG00000181215
+T cell,observed,25,ENSG00000103995
+T cell,observed,26,ENSG00000197520
+T cell,observed,27,ENSG00000145439
+T cell,observed,28,ENSG00000175066
+T cell,observed,29,ENSG00000196739
+T cell,observed,30,ENSG00000116127
+T cell,observed,31,ENSG00000167996
+T cell,observed,32,ENSG00000111961
+T cell,observed,33,ENSG00000162927
+T cell,observed,34,ENSG00000151414
+T cell,observed,35,ENSG00000100629
+T cell,observed,36,ENSG00000005844
+T cell,observed,37,ENSG00000117262
+T cell,observed,38,ENSG00000145819
+T cell,observed,39,ENSG00000095370
+T cell,observed,40,ENSG00000178974
+T cell,observed,41,ENSG00000106799
+T cell,observed,42,ENSG00000196715
+T cell,observed,43,ENSG00000134318
+T cell,observed,44,ENSG00000160654
+T cell,observed,45,ENSG00000204138
+T cell,observed,46,ENSG00000138182
+T cell,observed,47,ENSG00000113761
+T cell,observed,48,ENSG00000160007
+T cell,observed,49,ENSG00000100242
+T cell,observed,50,ENSG00000175455
+B cell,observed,1,ENSG00000162772
+B cell,observed,2,ENSG00000232810
+B cell,observed,3,ENSG00000151090
+B cell,observed,4,ENSG00000124762
+B cell,observed,5,ENSG00000101665
+B cell,observed,6,ENSG00000185304
+B cell,observed,7,ENSG00000180881
+B cell,observed,8,ENSG00000110492
+B cell,observed,9,ENSG00000136052
+B cell,observed,10,ENSG00000108556
+B cell,observed,11,ENSG00000167414
+B cell,observed,12,ENSG00000184500
+B cell,observed,13,ENSG00000104267
+B cell,observed,14,ENSG00000187391
+B cell,observed,15,ENSG00000128016
+B cell,observed,16,ENSG00000011422
+B cell,observed,17,ENSG00000154556
+B cell,observed,18,ENSG00000127074
+B cell,observed,19,ENSG00000158813
+B cell,observed,20,ENSG00000178607
+B cell,observed,21,ENSG00000183019
+B cell,observed,22,ENSG00000176658
+B cell,observed,23,ENSG00000163564
+B cell,observed,24,ENSG00000183579
+B cell,observed,25,ENSG00000135338
+B cell,observed,26,ENSG00000273734
+B cell,observed,27,ENSG00000249992
+B cell,observed,28,ENSG00000197816
+B cell,observed,29,ENSG00000198053
+B cell,observed,30,ENSG00000167723
+B cell,observed,31,ENSG00000170074
+B cell,observed,32,ENSG00000163806
+B cell,observed,33,ENSG00000205517
+B cell,observed,34,ENSG00000171160
+B cell,observed,35,ENSG00000183655
+B cell,observed,36,ENSG00000110723
+B cell,observed,37,ENSG00000174945
+B cell,observed,38,ENSG00000179761
+B cell,observed,39,ENSG00000196586
+B cell,observed,40,ENSG00000182489
+B cell,observed,41,ENSG00000107338
+B cell,observed,42,ENSG00000270629
+B cell,observed,43,ENSG00000166743
+B cell,observed,44,ENSG00000271447
+B cell,observed,45,ENSG00000135931
+B cell,observed,46,ENSG00000163126
+B cell,observed,47,ENSG00000151067
+B cell,observed,48,ENSG00000157578
+B cell,observed,49,ENSG00000091436
+B cell,observed,50,ENSG00000221955
+Monocyte,observed,1,ENSG00000111186
+Monocyte,observed,2,ENSG00000124191
+Monocyte,observed,3,ENSG00000214954
+Monocyte,observed,4,ENSG00000136492
+Monocyte,observed,5,ENSG00000188641
+Monocyte,generated,1,ENSG00000135404
+Monocyte,generated,2,ENSG00000159388
+Monocyte,generated,3,ENSG00000142541
+Monocyte,generated,4,ENSG00000122406
+Monocyte,generated,5,ENSG00000109475
+Monocyte,generated,6,ENSG00000089009
+Monocyte,generated,7,ENSG00000197958
+NK cell,observed,1,ENSG00000125266
+NK cell,observed,2,ENSG00000196735
+NK cell,observed,3,ENSG00000054793
+NK cell,observed,4,ENSG00000023445
+NK cell,observed,5,ENSG00000145439
+NK cell,observed,6,ENSG00000125885
+NK cell,observed,7,ENSG00000173930
+NK cell,observed,8,ENSG00000076770
+NK cell,observed,9,ENSG00000011258
+NK cell,observed,10,ENSG00000177932
+NK cell,observed,11,ENSG00000162676
+NK cell,observed,12,ENSG00000142197
+NK cell,observed,13,ENSG00000077157
+NK cell,observed,14,ENSG00000178177
+NK cell,observed,15,ENSG00000054654
+NK cell,observed,16,ENSG00000188641
+NK cell,observed,17,ENSG00000135677
+NK cell,observed,18,ENSG00000186174
+NK cell,observed,19,ENSG00000121940
+NK cell,observed,20,ENSG00000082068
+NK cell,observed,21,ENSG00000213079
+NK cell,observed,22,ENSG00000197299
+NK cell,observed,23,ENSG00000135365
+NK cell,observed,24,ENSG00000196663
+NK cell,observed,25,ENSG00000100523
+NK cell,observed,26,ENSG00000115942
+NK cell,observed,27,ENSG00000011114
+NK cell,observed,28,ENSG00000185883
+NK cell,observed,29,ENSG00000115085
+NK cell,observed,30,ENSG00000157869
+NK cell,generated,1,ENSG00000198695
+NK cell,generated,2,ENSG00000164483
+NK cell,generated,3,ENSG00000265681
+NK cell,generated,4,ENSG00000082701
+NK cell,generated,5,ENSG00000101335
+NK cell,generated,6,ENSG00000168497
+NK cell,generated,7,ENSG00000115904
+NK cell,generated,8,ENSG00000197756
+NK cell,generated,9,ENSG00000168028
+NK cell,generated,10,ENSG00000177600
+DC,observed,1,ENSG00000107317
+DC,observed,2,ENSG00000104918
+DC,observed,3,ENSG00000083544
+DC,observed,4,ENSG00000106952
+DC,observed,5,ENSG00000050405
+DC,observed,6,ENSG00000058866
+DC,observed,7,ENSG00000058673
+DC,observed,8,ENSG00000183323
+DC,observed,9,ENSG00000187474
+DC,observed,10,ENSG00000196911
+DC,observed,11,ENSG00000089177
+DC,observed,12,ENSG00000178971
+DC,observed,13,ENSG00000142459
+DC,observed,14,ENSG00000105325
+DC,observed,15,ENSG00000184220
+DC,observed,16,ENSG00000146433
+DC,observed,17,ENSG00000168781
+DC,observed,18,ENSG00000181450
+DC,observed,19,ENSG00000111846
+DC,observed,20,ENSG00000118762
+DC,observed,21,ENSG00000186409
+DC,observed,22,ENSG00000159459
+DC,observed,23,ENSG00000184719
+DC,observed,24,ENSG00000197283
+DC,observed,25,ENSG00000111271
+DC,observed,26,ENSG00000148019
+DC,observed,27,ENSG00000151881
+DC,observed,28,ENSG00000275740
+DC,observed,29,ENSG00000197050
+DC,observed,30,ENSG00000141337
+DC,observed,31,ENSG00000156313
+DC,observed,32,ENSG00000105576
+DC,observed,33,ENSG00000261609
+DC,observed,34,ENSG00000133317
+DC,observed,35,ENSG00000186854
+DC,observed,36,ENSG00000139618
+DC,observed,37,ENSG00000108423
+DC,observed,38,ENSG00000140006
+DC,observed,39,ENSG00000186376
+DC,observed,40,ENSG00000126262
+DC,observed,41,ENSG00000118420
+DC,observed,42,ENSG00000196236
+DC,observed,43,ENSG00000127152
+DC,observed,44,ENSG00000255639
+DC,observed,45,ENSG00000121964
+DC,observed,46,ENSG00000198689
+DC,observed,47,ENSG00000153982
+DC,observed,48,ENSG00000106692
+DC,observed,49,ENSG00000104381
+DC,observed,50,ENSG00000188452
+DC,generated,1,ENSG00000160888
+DC,generated,2,ENSG00000125148
+DC,generated,3,ENSG00000169554

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/fold3/arms/scsemi__raw/generated_cells.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:77deb0c95bf5ff29eb48cc7be133c3d5ae1b5d8eb5d5b5527693034bbc569461
+size 184818

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002/fold3/arms/scsemi__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_cv_20261002/fold3/arms/scsemi__raw/query.h5ad",
+  "method": "scsemi__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_cv_20261002/fold3/arms/scsemi__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": 24000,
+  "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__raw",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold3/scsemi__raw.npz",
+    "source_sha256": "25343f6e9e69df4251439c64ff71b7bd4f54cdbc318b41d12ad45c5cc401f4a4"
+  },
+  "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": 13022,
+      "Monocyte": 5156,
+      "B cell": 2844,
+      "Other": 1761,
+      "NK cell": 821,
+      "DC": 396
+    },
+    "aifi_l1": {
+      "T cell": 13022,
+      "Monocyte": 5156,
+      "B cell": 2844,
+      "Erythrocyte": 1125,
+      "NK cell": 821,
+      "Platelet": 525,
+      "DC": 396,
+      "ILC": 107,
+      "Progenitor cell": 4
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 4074,
+      "CD14 monocyte": 3483,
+      "Naive CD4 T cell": 3465,
+      "gdT": 2058,
+      "Memory CD8 T cell": 1682,
+      "Naive B cell": 1131,
+      "CD16 monocyte": 1125,
+      "Erythrocyte": 1125,
+      "Memory B cell": 1032,
+      "CD56dim NK cell": 727,
+      "CD8aa": 599,
+      "Intermediate monocyte": 548,
+      "Platelet": 525,
+      "Treg": 481,
+      "Plasma cell": 475,
+      "Naive CD8 T cell": 466,
+      "cDC2": 312,
+      "Effector B cell": 142,
+      "ILC": 107,
+      "CD56bright NK cell": 86,
+      "MAIT": 85,
+      "Transitional B cell": 64,
+      "cDC1": 62,
+      "Proliferating T cell": 59,
+      "DN T cell": 53,
+      "pDC": 19,
+      "Proliferating NK cell": 8,
+      "Progenitor cell": 4,
+      "ASDC": 3
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9243828023057431,
+    "mean_l1_mass": 0.97833651304245,
+    "frac_l2_max_prob_ge_0.5": 0.973
+  },
+  "timings_s": {
+    "predict": 0.4,
+    "total": 0.7
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-07T03:01:17.116675+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_cv_20261002/fold3/arms/scsemi__raw/labels/labels.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c87b627699997a06618cfb9b4e80898ed5852375154cea8f30894e6eca415356
+size 600985