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_n40__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/fold1/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/fold1/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": 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_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/fold1/scsemi_n40__raw.npz",
+    "source_sha256": "d977710ce9864cb41013fab14060345956752005f6bb2331159436d5c62b3a5f"
+  },
+  "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": 14000,
+      "Monocyte": 5783,
+      "B cell": 2469,
+      "Other": 1460,
+      "NK cell": 1279,
+      "DC": 509
+    },
+    "aifi_l1": {
+      "T cell": 14000,
+      "Monocyte": 5783,
+      "B cell": 2469,
+      "NK cell": 1279,
+      "Platelet": 760,
+      "Erythrocyte": 600,
+      "DC": 509,
+      "ILC": 94,
+      "Progenitor cell": 6
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 4852,
+      "CD14 monocyte": 4102,
+      "Naive CD4 T cell": 2694,
+      "Memory CD8 T cell": 2269,
+      "gdT": 2008,
+      "Naive B cell": 1096,
+      "CD56dim NK cell": 1030,
+      "CD16 monocyte": 864,
+      "Memory B cell": 863,
+      "Intermediate monocyte": 817,
+      "Platelet": 760,
+      "Naive CD8 T cell": 734,
+      "CD8aa": 715,
+      "Erythrocyte": 600,
+      "cDC2": 458,
+      "Treg": 405,
+      "Plasma cell": 249,
+      "Effector B cell": 202,
+      "CD56bright NK cell": 165,
+      "MAIT": 152,
+      "DN T cell": 102,
+      "ILC": 94,
+      "Proliferating NK cell": 84,
+      "Proliferating T cell": 69,
+      "Transitional B cell": 59,
+      "cDC1": 27,
+      "pDC": 22,
+      "Progenitor cell": 6,
+      "ASDC": 2
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9182638959855426,
+    "mean_l1_mass": 0.9717967510223389,
+    "frac_l2_max_prob_ge_0.5": 0.9698039215686275
+  },
+  "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": "2026-10-08T02:06:43.358192+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_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/fold1/arms/scsemi_n5__raw/deg_top50_lists.csv

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+celltype,source,rank,gene_id
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+NK cell,observed,35,ENSG00000156110
+NK cell,observed,36,ENSG00000115808
+DC,observed,1,ENSG00000086015
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+DC,observed,4,ENSG00000204519
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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/fold1/arms/scsemi_n5__raw/generated_cells.parquet

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