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/giroux2022/scsemi_cv_20261002/fold3/arms/scsemi__raw/labels/labels.manifest.json

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+  "split": "generated",
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+  "method": "scsemi__raw",
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+  "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": [
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+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
+    "Other"
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+  "l2_labels": [
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+    "CD14 monocyte",
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+    "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": 9000,
+  "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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+    "query_genes": 1006,
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+    "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"
+  },
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+  "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/giroux2022/fold3/scsemi__raw.npz",
+    "source_sha256": "737024a0b24c5374c82b6fb70f5ab4db69ade7561ae49f5b0a24166dc1d6bd7f"
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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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+  "label_counts": {
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+      "Monocyte": 1312,
+      "NK cell": 1269,
+      "B cell": 764,
+      "Other": 144,
+      "DC": 53
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+      "NK cell": 1269,
+      "B cell": 764,
+      "Platelet": 83,
+      "Erythrocyte": 57,
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+      "ILC": 4
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+    "aifi_l2": {
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+      "Memory CD4 T cell": 1198,
+      "CD56dim NK cell": 1133,
+      "Intermediate monocyte": 953,
+      "Memory CD8 T cell": 686,
+      "Naive B cell": 498,
+      "Naive CD8 T cell": 488,
+      "MAIT": 459,
+      "gdT": 342,
+      "Transitional B cell": 236,
+      "CD14 monocyte": 191,
+      "CD16 monocyte": 168,
+      "DN T cell": 165,
+      "Proliferating NK cell": 84,
+      "Platelet": 83,
+      "Proliferating T cell": 74,
+      "Erythrocyte": 57,
+      "Naive CD4 T cell": 56,
+      "CD56bright NK cell": 52,
+      "cDC2": 24,
+      "Plasma cell": 18,
+      "pDC": 16,
+      "cDC1": 13,
+      "Effector B cell": 10,
+      "ILC": 4,
+      "Memory B cell": 2
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+  },
+  "confidence": {
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+    "mean_l1_mass": 0.9800799489021301,
+    "frac_l2_max_prob_ge_0.5": 0.9501111111111111
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+  "timings_s": {
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+    "total": 0.2
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+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
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+  "device": "cpu",
+  "created_at_utc": "2026-10-08T01:56:22.578212+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/arms/scsemi__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/giroux2022/scsemi_cv_20261002/fold3/contrast.csv

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paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/per_donor.csv

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