Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/ablation_extra_donor.csv

@@ -0,0 +1,10 @@
+set,coverage_k10,precision_k10,c2st_knn_auc,c2st_rf_auc,mmd2_sum,coverage_dm,EN_all,comp_r_mean4,pb_top1_n,donor_sd_ratio
+real_R2,1.0,0.9969,0.5687,0.8103,0.0025,1.0,0.0336,,,
+zs__raw,0.1808,0.8788,0.9899,0.9988,0.3464,0.1612,4.432,0.61,7.0,0.9244
+lora_n5__raw,0.8098,0.9922,0.9185,0.9582,0.0722,0.9224,1.1891,0.7009,4.0,0.6561
+scratch_n5__raw,0.798,0.9906,0.911,0.9584,0.0694,0.9145,1.2063,0.1709,1.0,0.2815
+real_lora__raw,0.8584,0.9859,0.8817,0.942,0.052,0.9553,1.172,0.7707,8.0,0.7366
+real_full__raw,0.8714,0.9784,0.8803,0.9305,0.0501,0.9502,1.1777,0.7527,6.0,0.662
+scratch_full__raw,0.862,0.9898,0.8858,0.9426,0.0561,0.9435,1.082,0.6794,4.0,0.6257
+lora_recipe__raw,0.8663,0.9875,0.8874,0.9453,0.054,0.9541,1.1809,0.8048,6.0,0.6695
+scratch_recipe__raw,0.8776,0.9902,0.8883,0.9403,0.0665,0.951,1.1352,0.7692,4.0,0.7244

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_recipe__raw/labels/labels.manifest.json

@@ -0,0 +1,156 @@
+{
+  "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/fold0_scratch_20261005/arms/scratch_recipe__raw/query.h5ad",
+  "method": "scratch_recipe__raw",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_recipe__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": "scratch_recipe__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/scratch_recipe__raw.npz",
+    "source_sha256": "c3eb533e26c970fcdb2fe782fffd5c6901972426b42cbc3e00f5b1115d307ebd"
+  },
+  "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": 13815,
+      "B cell": 5051,
+      "Monocyte": 3598,
+      "NK cell": 2184,
+      "Other": 742,
+      "DC": 110
+    },
+    "aifi_l1": {
+      "T cell": 13815,
+      "B cell": 5051,
+      "Monocyte": 3598,
+      "NK cell": 2184,
+      "Platelet": 328,
+      "Erythrocyte": 295,
+      "DC": 110,
+      "ILC": 85,
+      "Progenitor cell": 34
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 3961,
+      "CD14 monocyte": 2720,
+      "Naive B cell": 2602,
+      "Naive CD4 T cell": 2368,
+      "Memory CD8 T cell": 2299,
+      "CD56dim NK cell": 1804,
+      "gdT": 1566,
+      "Naive CD8 T cell": 1479,
+      "Memory B cell": 911,
+      "Transitional B cell": 856,
+      "CD8aa": 753,
+      "Effector B cell": 519,
+      "Treg": 471,
+      "DN T cell": 468,
+      "CD16 monocyte": 463,
+      "Intermediate monocyte": 415,
+      "MAIT": 352,
+      "Platelet": 328,
+      "Erythrocyte": 295,
+      "CD56bright NK cell": 193,
+      "Proliferating NK cell": 187,
+      "Plasma cell": 163,
+      "Proliferating T cell": 98,
+      "cDC2": 87,
+      "ILC": 85,
+      "Progenitor cell": 34,
+      "pDC": 18,
+      "ASDC": 4,
+      "cDC1": 1
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9275101350171894,
+    "mean_l1_mass": 0.9856195449829102,
+    "frac_l2_max_prob_ge_0.5": 0.9763529411764705
+  },
+  "timings_s": {
+    "predict": 0.2,
+    "total": 0.5
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-05T04:58:54.009796+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_recipe__raw/labels/labels.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:0a2e2e13b9c5f5695f0dd2cb736d09dcbd2f56051c46ca4a17c98a406fc08a08
+size 599614

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_recipe__raw/predict_scanvi.log

@@ -0,0 +1,84 @@
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+INFO     Found 100.0% reference vars in query data.                             
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+{
+  "method": "scratch_recipe__raw",
+  "n_cells": 25500,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 13815,
+      "B cell": 5051,
+      "Monocyte": 3598,
+      "NK cell": 2184,
+      "Other": 742,
+      "DC": 110
+    },
+    "aifi_l1": {
+      "T cell": 13815,
+      "B cell": 5051,
+      "Monocyte": 3598,
+      "NK cell": 2184,
+      "Platelet": 328,
+      "Erythrocyte": 295,
+      "DC": 110,
+      "ILC": 85,
+      "Progenitor cell": 34
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 3961,
+      "CD14 monocyte": 2720,
+      "Naive B cell": 2602,
+      "Naive CD4 T cell": 2368,
+      "Memory CD8 T cell": 2299,
+      "CD56dim NK cell": 1804,
+      "gdT": 1566,
+      "Naive CD8 T cell": 1479,
+      "Memory B cell": 911,
+      "Transitional B cell": 856,
+      "CD8aa": 753,
+      "Effector B cell": 519,
+      "Treg": 471,
+      "DN T cell": 468,
+      "CD16 monocyte": 463,
+      "Intermediate monocyte": 415,
+      "MAIT": 352,
+      "Platelet": 328,
+      "Erythrocyte": 295,
+      "CD56bright NK cell": 193,
+      "Proliferating NK cell": 187,
+      "Plasma cell": 163,
+      "Proliferating T cell": 98,
+      "cDC2": 87,
+      "ILC": 85,
+      "Progenitor cell": 34,
+      "pDC": 18,
+      "ASDC": 4,
+      "cDC1": 1
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9275101350171894,
+    "mean_l1_mass": 0.9856195449829102,
+    "frac_l2_max_prob_ge_0.5": 0.9763529411764705
+  },
+  "timings_s": {
+    "predict": 0.2,
+    "total": 0.5
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0_scratch_20261005/arms/scratch_recipe__raw/labels/labels.parquet
+
+--- stderr ---
+Seed set to 20260916