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_cv_20261002/fold0/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/ye2026_sepsis/scsemi_cv_20261002/fold0/arms/scsemi__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_cv_20261002/fold0/arms/scsemi__raw/query.h5ad",
+  "method": "scsemi__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_cv_20261002/fold0/arms/scsemi__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__raw",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/scsemi__raw.npz",
+    "source_sha256": "566f8ae0ce1b3fc4d13673754504048a8d427dccec5d8163ced92e5609353a4c"
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+  "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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+      "l2_macro_f1": 0.8500925599737216,
+      "l1_accuracy": 0.9918367346938776,
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+      "pbmc5_other_accuracy": 0.9920886873267826,
+      "pbmc5_other_macro_f1": 0.9812088972148597
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+  "label_counts": {
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+      "Monocyte": 4969,
+      "B cell": 3616,
+      "NK cell": 1662,
+      "Other": 752,
+      "DC": 171
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+    "aifi_l1": {
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+      "Monocyte": 4969,
+      "B cell": 3616,
+      "NK cell": 1662,
+      "Platelet": 385,
+      "Erythrocyte": 297,
+      "DC": 171,
+      "ILC": 68,
+      "Progenitor cell": 2
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+    "aifi_l2": {
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+      "CD14 monocyte": 3997,
+      "Naive CD4 T cell": 3874,
+      "Memory CD8 T cell": 1843,
+      "Naive B cell": 1820,
+      "gdT": 1758,
+      "CD56dim NK cell": 1457,
+      "Memory B cell": 1058,
+      "Naive CD8 T cell": 707,
+      "Treg": 639,
+      "CD8aa": 582,
+      "CD16 monocyte": 528,
+      "Intermediate monocyte": 444,
+      "Plasma cell": 393,
+      "Platelet": 385,
+      "Erythrocyte": 297,
+      "MAIT": 232,
+      "Transitional B cell": 187,
+      "CD56bright NK cell": 177,
+      "Effector B cell": 158,
+      "cDC2": 142,
+      "DN T cell": 96,
+      "ILC": 68,
+      "Proliferating T cell": 36,
+      "Proliferating NK cell": 28,
+      "pDC": 18,
+      "cDC1": 10,
+      "Progenitor cell": 2,
+      "ASDC": 1
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+  },
+  "confidence": {
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+    "mean_l1_mass": 0.986667275428772,
+    "frac_l2_max_prob_ge_0.5": 0.979764705882353
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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"
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+  "device": "cpu",
+  "created_at_utc": "2026-10-07T03:00:24.005799+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_cv_20261002/fold0/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/ye2026_sepsis/scsemi_cv_20261002/fold0/contrast.csv

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+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
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+scsemi__raw,T cell,pseudobulk_log1p_cpm,3276,0.22250303173550698,0.34430236190429087,0.1736502994725982,0.18050369498241478,12,5,12,5,61162,14330,,,,,,,,,,,
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+scsemi__raw,B cell,pseudobulk_log1p_cpm,3261,0.23186073660762874,0.4467015184665126,0.15729198498667732,0.21111662089975505,12,5,12,5,21022,3616,,,,,,,,,,,
+scsemi__raw,Monocyte,mean_cp10k,3260,0.5164619184327888,0.7018160115879556,0.37310885088628604,0.3866309900909363,12,5,12,4,31471,4969,,,,,,,,,,,
+scsemi__raw,Monocyte,pseudobulk_log1p_cpm,3260,0.21455344134479973,0.7631886901658,0.026872170372653378,0.259152845984567,12,5,12,4,31471,4969,,,,,,,,,,,
+scsemi__raw,NK cell,mean_cp10k,3269,0.4392533890379352,0.3607355096498457,0.386723221179161,0.24939606398661499,12,5,12,4,10457,1662,,,,,,,,,,,
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+scsemi__raw,T cell,welch_top50_deg,5975,,,,,12,5,12,5,61162,14330,True,0,0.0,50,0,113,0,0,0.0,0,0
+scsemi__raw,B cell,welch_top50_deg,5975,,,,,12,5,12,5,21022,3616,True,0,0.0,50,0,164,0,0,0.0,0,0
+scsemi__raw,Monocyte,welch_top50_deg,5975,,,,,12,5,12,4,31471,4969,True,0,0.0,50,0,932,0,0,0.0,0,0
+scsemi__raw,NK cell,welch_top50_deg,5975,,,,,12,5,12,4,10457,1662,True,0,0.0,50,0,122,0,0,0.0,0,0
+scsemi__raw,DC,welch_top50_deg,5975,,,,,12,5,10,4,1035,171,True,0,0.0,50,0,152,0,0,0.0,0,0