Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold1/arms/scsemi__raw/generated_cells.parquet

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paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold1/arms/scsemi__raw/labels/labels.manifest.json

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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": [
+    "T cell",
+    "B cell",
+    "Monocyte",
+    "NK cell",
+    "DC",
+    "Other"
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+  "l2_labels": [
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+    "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": 37500,
+  "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": 1005,
+    "model_genes_missing_from_query_zero_padded": 0,
+    "query_genes_outside_model_dropped": 0,
+    "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/imperial_eskd/fold1/scsemi__raw.npz",
+    "source_sha256": "9d8043a8277ec693e0a368fb8b38a80c777da5dbd69397ccf5aa995a18fea900"
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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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+  "label_counts": {
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+      "B cell": 3663,
+      "DC": 903,
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+      "B cell": 3663,
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+      "Platelet": 185,
+      "ILC": 141,
+      "Erythrocyte": 62,
+      "Progenitor cell": 3
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+    "aifi_l2": {
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+      "Memory CD4 T cell": 6176,
+      "CD56dim NK cell": 4113,
+      "gdT": 3475,
+      "CD16 monocyte": 2259,
+      "CD14 monocyte": 2213,
+      "Naive CD4 T cell": 1962,
+      "Memory B cell": 1685,
+      "Intermediate monocyte": 1196,
+      "Naive B cell": 1172,
+      "Treg": 875,
+      "CD8aa": 709,
+      "cDC2": 704,
+      "CD56bright NK cell": 586,
+      "Plasma cell": 562,
+      "Naive CD8 T cell": 234,
+      "Effector B cell": 188,
+      "Platelet": 185,
+      "Proliferating NK cell": 171,
+      "ILC": 141,
+      "pDC": 129,
+      "MAIT": 111,
+      "DN T cell": 84,
+      "Proliferating T cell": 83,
+      "Erythrocyte": 62,
+      "Transitional B cell": 56,
+      "cDC1": 53,
+      "ASDC": 17,
+      "Progenitor cell": 3
+    }
+  },
+  "confidence": {
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+    "mean_l1_mass": 0.9848452210426331,
+    "frac_l2_max_prob_ge_0.5": 0.9790666666666666
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+  "timings_s": {
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+    "total": 0.5
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+  "versions": {
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+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
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+  "device": "cpu",
+  "created_at_utc": "2026-10-08T04:46:45.252985+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold1/arms/scsemi__raw/labels/labels.parquet

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paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold1/contrast.csv

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+scsemi__raw,Monocyte,mean_cp10k,2919,0.7357718757673274,0.681168905466175,0.597040767738387,0.5401025812970133,18,7,17,7,18012,5668,,,,,,,,,,,
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+scsemi__raw,NK cell,mean_cp10k,2952,0.6104383428911735,0.50894713059556,0.5020398537531338,0.4347369074105965,18,7,18,7,13189,4870,,,,,,,,,,,
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+scsemi__raw,DC,welch_top50_deg,5927,,,,,18,7,18,7,2764,903,True,1,0.018518518518518517,50,5,51,5,6,0.06382978723404255,50,1531