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/fold4/arms/scsemi_n10__raw/generated_cells.parquet

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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/fold4/arms/scsemi_n10__raw/labels/labels.manifest.json

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+{
+  "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/fold4/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/fold4/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": 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": {
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+    "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/fold4/scsemi_n10__raw.npz",
+    "source_sha256": "a30d8f88c856e599a98045a66dadf9f53da47f3e9df67f0399a669311c6d1633"
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+  "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
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+  },
+  "label_counts": {
+    "celltype_l1_pred": {
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+      "Monocyte": 5860,
+      "B cell": 2856,
+      "Other": 1099,
+      "NK cell": 1047,
+      "DC": 513
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+    "aifi_l1": {
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+      "Monocyte": 5860,
+      "B cell": 2856,
+      "NK cell": 1047,
+      "Platelet": 515,
+      "DC": 513,
+      "ILC": 467,
+      "Erythrocyte": 111,
+      "Progenitor cell": 6
+    },
+    "aifi_l2": {
+      "CD14 monocyte": 4234,
+      "Memory CD4 T cell": 3406,
+      "Naive CD4 T cell": 2122,
+      "gdT": 1843,
+      "Memory CD8 T cell": 1694,
+      "CD8aa": 1621,
+      "Naive B cell": 1412,
+      "Treg": 1056,
+      "Memory B cell": 967,
+      "Intermediate monocyte": 925,
+      "CD56dim NK cell": 892,
+      "CD16 monocyte": 701,
+      "Naive CD8 T cell": 638,
+      "Platelet": 515,
+      "ILC": 467,
+      "cDC2": 434,
+      "Transitional B cell": 220,
+      "Effector B cell": 167,
+      "Erythrocyte": 111,
+      "MAIT": 111,
+      "CD56bright NK cell": 99,
+      "DN T cell": 96,
+      "Plasma cell": 90,
+      "Proliferating NK cell": 56,
+      "cDC1": 56,
+      "Proliferating T cell": 38,
+      "pDC": 12,
+      "ASDC": 11,
+      "Progenitor cell": 6
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.880895137205099,
+    "mean_l1_mass": 0.9572027921676636,
+    "frac_l2_max_prob_ge_0.5": 0.920125
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+  "timings_s": {
+    "predict": 0.2,
+    "total": 0.4
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+  "versions": {
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+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-08T02:08:10.450493+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/fold4/arms/scsemi_n10__raw/labels/labels.parquet

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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/fold4/arms/scsemi_n20__raw/deg_top50_lists.csv

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+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000272602
+T cell,observed,2,ENSG00000154451
+T cell,observed,3,ENSG00000100629
+T cell,observed,4,ENSG00000172197
+T cell,observed,5,ENSG00000197044
+T cell,observed,6,ENSG00000150347
+T cell,observed,7,ENSG00000100084
+T cell,observed,8,ENSG00000148154
+T cell,observed,9,ENSG00000119321
+T cell,observed,10,ENSG00000124406
+T cell,observed,11,ENSG00000142065
+T cell,observed,12,ENSG00000122122
+T cell,observed,13,ENSG00000158161
+T cell,observed,14,ENSG00000134318
+T cell,observed,15,ENSG00000118308
+T cell,observed,16,ENSG00000163138
+T cell,observed,17,ENSG00000115365
+T cell,observed,18,ENSG00000185305
+T cell,observed,19,ENSG00000187790
+T cell,observed,20,ENSG00000177463
+T cell,observed,21,ENSG00000083642
+T cell,observed,22,ENSG00000181804
+T cell,observed,23,ENSG00000182504
+T cell,observed,24,ENSG00000197603
+T cell,observed,25,ENSG00000148356
+T cell,observed,26,ENSG00000178974
+T cell,observed,27,ENSG00000197563
+T cell,observed,28,ENSG00000006715
+T cell,observed,29,ENSG00000136813
+T cell,observed,30,ENSG00000132842
+T cell,observed,31,ENSG00000100991
+T cell,observed,32,ENSG00000160654
+T cell,observed,33,ENSG00000165181
+T cell,observed,34,ENSG00000118873
+T cell,observed,35,ENSG00000149806
+B cell,observed,1,ENSG00000182621
+B cell,observed,2,ENSG00000160593
+B cell,observed,3,ENSG00000155749
+Monocyte,observed,1,ENSG00000164659
+NK cell,generated,1,ENSG00000136213
+NK cell,generated,2,ENSG00000084676
+NK cell,generated,3,ENSG00000171552
+NK cell,generated,4,ENSG00000169032
+NK cell,generated,5,ENSG00000169252
+NK cell,generated,6,ENSG00000139687