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/fold2/arms/scsemi_n40__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/fold2/arms/scsemi_n5__raw/deg_top50_lists.csv

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+celltype,source,rank,gene_id
+Monocyte,observed,1,ENSG00000170298
+Monocyte,generated,1,ENSG00000185950
+NK cell,observed,1,ENSG00000120594
+NK cell,observed,2,ENSG00000198948
+NK cell,observed,3,ENSG00000134369
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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/fold2/arms/scsemi_n5__raw/generated_cells.parquet

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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/fold2/arms/scsemi_n5__raw/query.h5ad",
+  "method": "scsemi_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/scsemi_budget_20261002/fold2/arms/scsemi_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": 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",
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+  "gene_space": {
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+    "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_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/fold2/scsemi_n5__raw.npz",
+    "source_sha256": "73fe6bc98974e3977f4472c5ac65c7bd1d3a5cbaac409d414dbda560e3ef96ca"
+  },
+  "model": {
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+    "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": {
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+      "pbmc5_other_macro_f1": 0.9812088972148597
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+      "Monocyte": 5238,
+      "B cell": 3234,
+      "NK cell": 1470,
+      "Other": 884,
+      "DC": 586
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+      "Monocyte": 5238,
+      "B cell": 3234,
+      "NK cell": 1470,
+      "DC": 586,
+      "Platelet": 391,
+      "Erythrocyte": 383,
+      "ILC": 110
+    },
+    "aifi_l2": {
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+      "Memory CD4 T cell": 3583,
+      "Naive CD4 T cell": 2248,
+      "Memory CD8 T cell": 1833,
+      "CD8aa": 1662,
+      "Naive B cell": 1567,
+      "gdT": 1379,
+      "CD56dim NK cell": 1289,
+      "Memory B cell": 1168,
+      "Naive CD8 T cell": 855,
+      "CD16 monocyte": 727,
+      "Intermediate monocyte": 725,
+      "cDC2": 488,
+      "Platelet": 391,
+      "Erythrocyte": 383,
+      "Treg": 332,
+      "MAIT": 322,
+      "DN T cell": 278,
+      "Effector B cell": 249,
+      "Plasma cell": 156,
+      "ILC": 110,
+      "CD56bright NK cell": 104,
+      "Proliferating T cell": 96,
+      "Transitional B cell": 94,
+      "Proliferating NK cell": 77,
+      "cDC1": 72,
+      "pDC": 21,
+      "ASDC": 5
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+  },
+  "confidence": {
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+    "mean_l1_mass": 0.9706875085830688,
+    "frac_l2_max_prob_ge_0.5": 0.9613333333333334
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+  "timings_s": {
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+    "total": 0.4
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+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-08T02:06:58.899364+00:00"
+}