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/fold2/arms/scsemi__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/giroux2022/scsemi_cv_20261002/fold2/arms/scsemi__raw/labels/labels.manifest.json

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+  "dataset_id": "Giroux2022",
+  "split": "generated",
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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": 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",
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+  "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"
+  },
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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",
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+    "source_sha256": "219d7e8499c90e2478d4d58cc803e167860ed8e10599450a9ea29939e8347d51"
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+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
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+    "held_out_summary": {
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+      "Monocyte": 1419,
+      "NK cell": 997,
+      "B cell": 526,
+      "Other": 165,
+      "DC": 55
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+      "NK cell": 997,
+      "B cell": 526,
+      "Platelet": 132,
+      "DC": 55,
+      "Erythrocyte": 17,
+      "ILC": 16
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+    "aifi_l2": {
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+      "Intermediate monocyte": 1175,
+      "Memory CD4 T cell": 883,
+      "MAIT": 824,
+      "CD56dim NK cell": 814,
+      "Proliferating T cell": 582,
+      "Memory CD8 T cell": 507,
+      "Naive CD8 T cell": 391,
+      "gdT": 327,
+      "Naive B cell": 325,
+      "Transitional B cell": 182,
+      "DN T cell": 172,
+      "CD16 monocyte": 132,
+      "Platelet": 132,
+      "Proliferating NK cell": 123,
+      "CD14 monocyte": 112,
+      "Naive CD4 T cell": 83,
+      "CD56bright NK cell": 60,
+      "pDC": 37,
+      "Erythrocyte": 17,
+      "cDC2": 16,
+      "ILC": 16,
+      "Effector B cell": 16,
+      "Plasma cell": 3,
+      "cDC1": 2
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+  "confidence": {
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+    "mean_l1_mass": 0.9854244589805603,
+    "frac_l2_max_prob_ge_0.5": 0.9307777777777778
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+  "timings_s": {
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+    "total": 0.2
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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": "2026-10-08T01:56:09.407758+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/fold2/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/fold2/contrast.csv

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+scsemi__raw,NK cell,mean_cp10k,2879,0.2889500654676106,0.33439641097445927,0.2535462264867015,0.15856283855560205,3,3,3,3,6830,997,,,,,,,,,,,
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+scsemi__raw,B cell,welch_top50_deg,5563,,,,,3,3,3,3,5174,526,True,0,,0,0,0,0,0,0.0,1,1
+scsemi__raw,Monocyte,welch_top50_deg,5563,,,,,3,3,3,3,7544,1419,True,0,0.0,5,0,5,0,1,0.2,1,1
+scsemi__raw,NK cell,welch_top50_deg,5563,,,,,3,3,3,3,6830,997,True,0,0.0,3,0,3,0,0,0.0,1,1
+scsemi__raw,DC,welch_top50_deg,5563,,,,,3,3,3,3,895,55,True,0,,0,0,0,0,0,0.0,1,1