Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/current_f01/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": "current_f01",
+  "n_cells": 115500,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 67207,
+      "B cell": 23874,
+      "Monocyte": 12985,
+      "NK cell": 7848,
+      "Other": 3153,
+      "DC": 433
+    },
+    "aifi_l1": {
+      "T cell": 67207,
+      "B cell": 23874,
+      "Monocyte": 12985,
+      "NK cell": 7848,
+      "Platelet": 2150,
+      "Erythrocyte": 620,
+      "DC": 433,
+      "ILC": 214,
+      "Progenitor cell": 169
+    },
+    "aifi_l2": {
+      "Memory CD4 T cell": 16792,
+      "Naive B cell": 14543,
+      "Naive CD8 T cell": 11219,
+      "Memory CD8 T cell": 11094,
+      "Naive CD4 T cell": 10122,
+      "CD14 monocyte": 9469,
+      "gdT": 8286,
+      "CD56dim NK cell": 5915,
+      "Memory B cell": 5806,
+      "DN T cell": 3425,
+      "CD8aa": 2911,
+      "Platelet": 2150,
+      "Treg": 2149,
+      "Intermediate monocyte": 2119,
+      "Transitional B cell": 1606,
+      "CD16 monocyte": 1397,
+      "Effector B cell": 1280,
+      "Proliferating NK cell": 1048,
+      "CD56bright NK cell": 885,
+      "MAIT": 715,
+      "Plasma cell": 639,
+      "Erythrocyte": 620,
+      "Proliferating T cell": 494,
+      "cDC2": 357,
+      "ILC": 214,
+      "Progenitor cell": 169,
+      "pDC": 55,
+      "cDC1": 16,
+      "ASDC": 5
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.918184873602865,
+    "mean_l1_mass": 0.9870825409889221,
+    "frac_l2_max_prob_ge_0.5": 0.9733593073593073
+  },
+  "timings_s": {
+    "predict": 2.0,
+    "total": 3.1
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/current_f01/labels/labels.parquet
+
+--- stderr ---
+Seed set to 20260916

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/scsemi/deg_top50_lists.csv

@@ -0,0 +1,341 @@
+celltype,source,rank,gene_id
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paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/scsemi/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/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/scsemi/query.h5ad",
+  "method": "scsemi",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/scsemi/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": 115500,
+  "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",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/projected/draw0/scsemi.npz",
+    "source_sha256": "cb522927436fe1d0b8f95f01d84a6a13831e36a6392c11e19077a549aa017cb9"
+  },
+  "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": 84091,
+      "B cell": 9555,
+      "Monocyte": 8068,
+      "NK cell": 5017,
+      "Other": 4522,
+      "DC": 4247
+    },
+    "aifi_l1": {
+      "T cell": 84091,
+      "B cell": 9555,
+      "Monocyte": 8068,
+      "NK cell": 5017,
+      "DC": 4247,
+      "Platelet": 2241,
+      "Erythrocyte": 1682,
+      "ILC": 582,
+      "Progenitor cell": 17
+    },
+    "aifi_l2": {
+      "Naive CD4 T cell": 32923,
+      "Memory CD4 T cell": 17230,
+      "gdT": 13350,
+      "Memory CD8 T cell": 7149,
+      "CD14 monocyte": 5844,
+      "Memory B cell": 5701,
+      "CD8aa": 4969,
+      "CD56dim NK cell": 3985,
+      "Naive CD8 T cell": 3755,
+      "Treg": 3526,
+      "Naive B cell": 3069,
+      "cDC2": 3039,
+      "Platelet": 2241,
+      "Erythrocyte": 1682,
+      "cDC1": 1192,
+      "CD16 monocyte": 1170,
+      "Intermediate monocyte": 1054,
+      "CD56bright NK cell": 753,
+      "DN T cell": 693,
+      "ILC": 582,
+      "MAIT": 395,
+      "Transitional B cell": 291,
+      "Proliferating NK cell": 279,
+      "Effector B cell": 269,
+      "Plasma cell": 225,
+      "Proliferating T cell": 101,
+      "Progenitor cell": 17,
+      "ASDC": 11,
+      "pDC": 5
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.8893785940873159,
+    "mean_l1_mass": 0.9608671069145203,
+    "frac_l2_max_prob_ge_0.5": 0.9485454545454546
+  },
+  "timings_s": {
+    "predict": 1.8,
+    "total": 2.9
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-13T12:36:50.938063+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/scsemi/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": "scsemi",
+  "n_cells": 115500,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 84091,
+      "B cell": 9555,
+      "Monocyte": 8068,
+      "NK cell": 5017,
+      "Other": 4522,
+      "DC": 4247
+    },
+    "aifi_l1": {
+      "T cell": 84091,
+      "B cell": 9555,
+      "Monocyte": 8068,
+      "NK cell": 5017,
+      "DC": 4247,
+      "Platelet": 2241,
+      "Erythrocyte": 1682,
+      "ILC": 582,
+      "Progenitor cell": 17
+    },
+    "aifi_l2": {
+      "Naive CD4 T cell": 32923,
+      "Memory CD4 T cell": 17230,
+      "gdT": 13350,
+      "Memory CD8 T cell": 7149,
+      "CD14 monocyte": 5844,
+      "Memory B cell": 5701,
+      "CD8aa": 4969,
+      "CD56dim NK cell": 3985,
+      "Naive CD8 T cell": 3755,
+      "Treg": 3526,
+      "Naive B cell": 3069,
+      "cDC2": 3039,
+      "Platelet": 2241,
+      "Erythrocyte": 1682,
+      "cDC1": 1192,
+      "CD16 monocyte": 1170,
+      "Intermediate monocyte": 1054,
+      "CD56bright NK cell": 753,
+      "DN T cell": 693,
+      "ILC": 582,
+      "MAIT": 395,
+      "Transitional B cell": 291,
+      "Proliferating NK cell": 279,
+      "Effector B cell": 269,
+      "Plasma cell": 225,
+      "Proliferating T cell": 101,
+      "Progenitor cell": 17,
+      "ASDC": 11,
+      "pDC": 5
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.8893785940873159,
+    "mean_l1_mass": 0.9608671069145203,
+    "frac_l2_max_prob_ge_0.5": 0.9485454545454546
+  },
+  "timings_s": {
+    "predict": 1.8,
+    "total": 2.9
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/baseline_check/draw0/arms/scsemi/labels/labels.parquet
+
+--- stderr ---
+Seed set to 20260916