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/fold1/arms/scsemi_n10__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/fold1/arms/scsemi_n10__raw/query.h5ad",
+  "method": "scsemi_n10__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/fold1/arms/scsemi_n10__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": "scsemi_n10__raw",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold1/scsemi_n10__raw.npz",
+    "source_sha256": "7bda7486f1ff4c3c8a0767338879aa3a187e661706dfab67ea94557ea5d79efd"
+  },
+  "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": 15248,
+      "Monocyte": 5516,
+      "B cell": 2677,
+      "DC": 771,
+      "Other": 675,
+      "NK cell": 613
+    },
+    "aifi_l1": {
+      "T cell": 15248,
+      "Monocyte": 5516,
+      "B cell": 2677,
+      "DC": 771,
+      "NK cell": 613,
+      "Platelet": 407,
+      "Erythrocyte": 214,
+      "ILC": 51,
+      "Progenitor cell": 3
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 4894,
+      "Naive CD4 T cell": 4770,
+      "CD14 monocyte": 4151,
+      "Memory B cell": 1547,
+      "gdT": 1534,
+      "Treg": 1263,
+      "Memory CD8 T cell": 1257,
+      "Naive B cell": 865,
+      "cDC2": 748,
+      "Intermediate monocyte": 736,
+      "CD8aa": 699,
+      "CD16 monocyte": 629,
+      "Naive CD8 T cell": 575,
+      "CD56dim NK cell": 539,
+      "Platelet": 407,
+      "Erythrocyte": 214,
+      "MAIT": 159,
+      "Transitional B cell": 95,
+      "Effector B cell": 92,
+      "DN T cell": 81,
+      "Plasma cell": 78,
+      "CD56bright NK cell": 64,
+      "ILC": 51,
+      "cDC1": 16,
+      "Proliferating T cell": 16,
+      "Proliferating NK cell": 10,
+      "pDC": 5,
+      "Progenitor cell": 3,
+      "ASDC": 2
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9262177331955994,
+    "mean_l1_mass": 0.9831752181053162,
+    "frac_l2_max_prob_ge_0.5": 0.9779607843137255
+  },
+  "timings_s": {
+    "predict": 0.2,
+    "total": 0.4
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-08T02:06:31.720206+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/fold1/arms/scsemi_n10__raw/labels/labels.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:70a7be09aae83958d34f448610bc7dc8ed57e2a6ccbffcbc4cca1c984a3a2764
+size 626425

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/fold1/arms/scsemi_n20__raw/deg_top50_lists.csv

@@ -0,0 +1,51 @@
+celltype,source,rank,gene_id
+B cell,observed,1,ENSG00000141293
+B cell,observed,2,ENSG00000132842
+B cell,observed,3,ENSG00000121895
+Monocyte,observed,1,ENSG00000146070
+NK cell,observed,1,ENSG00000184731
+NK cell,observed,2,ENSG00000145439
+NK cell,observed,3,ENSG00000186532
+NK cell,observed,4,ENSG00000163590
+NK cell,observed,5,ENSG00000059145
+NK cell,observed,6,ENSG00000145730
+NK cell,observed,7,ENSG00000088812
+NK cell,observed,8,ENSG00000198420
+NK cell,observed,9,ENSG00000008869
+NK cell,observed,10,ENSG00000006459
+NK cell,observed,11,ENSG00000188177
+NK cell,observed,12,ENSG00000115339
+NK cell,observed,13,ENSG00000139324
+NK cell,observed,14,ENSG00000148019
+NK cell,observed,15,ENSG00000070961
+NK cell,observed,16,ENSG00000118308
+NK cell,observed,17,ENSG00000177189
+NK cell,observed,18,ENSG00000006831
+NK cell,observed,19,ENSG00000108306
+NK cell,observed,20,ENSG00000118922
+NK cell,observed,21,ENSG00000121940
+NK cell,observed,22,ENSG00000147133
+NK cell,observed,23,ENSG00000256771
+NK cell,observed,24,ENSG00000033867
+NK cell,observed,25,ENSG00000100242
+NK cell,observed,26,ENSG00000126773
+NK cell,observed,27,ENSG00000168918
+NK cell,observed,28,ENSG00000198646
+NK cell,observed,29,ENSG00000162695
+NK cell,observed,30,ENSG00000123124
+NK cell,observed,31,ENSG00000156639
+NK cell,observed,32,ENSG00000188641
+NK cell,observed,33,ENSG00000083168
+NK cell,observed,34,ENSG00000124406
+NK cell,observed,35,ENSG00000156110
+NK cell,observed,36,ENSG00000115808
+DC,observed,1,ENSG00000086015
+DC,observed,2,ENSG00000160588
+DC,observed,3,ENSG00000149218
+DC,observed,4,ENSG00000204519
+DC,observed,5,ENSG00000174928
+all (input bulk),broadcast,1,ENSG00000159189
+all (input bulk),broadcast,2,ENSG00000173369
+all (input bulk),broadcast,3,ENSG00000173372
+all (input bulk),broadcast,4,ENSG00000187837
+all (input bulk),broadcast,5,ENSG00000068024

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/fold1/arms/scsemi_n20__raw/generated_cells.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2a3446354bbf5ee51c00cc4e14c8e747243a4736115d263432caa3e07839bfd2
+size 195142