Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T095445Z-all-width-results/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold2/n40/score/arms/lora/labels/labels.manifest.json

@@ -0,0 +1,156 @@
+{
+  "dataset_id": "GSE314416_ImMicro",
+  "split": "generated",
+  "input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold2/n40/score/arms/lora/query.h5ad",
+  "method": "lora",
+  "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/all_width_results_20261015/immicro/healthy/fold2/n40/score/arms/lora/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": 31500,
+  "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": 1004,
+    "model_genes_missing_from_query_zero_padded": 1,
+    "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"
+  },
+  "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": "lora",
+    "source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/immicro/healthy/fold2/n40/lora.npz",
+    "source_sha256": "aabfbe50388f34fe4b5bc584672d4a929f1133b227fe9fbc3c59b8676d13dad0"
+  },
+  "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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+      "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": 21480,
+      "Monocyte": 4193,
+      "B cell": 2372,
+      "NK cell": 1891,
+      "DC": 1187,
+      "Other": 377
+    },
+    "aifi_l1": {
+      "T cell": 21480,
+      "Monocyte": 4193,
+      "B cell": 2372,
+      "NK cell": 1891,
+      "DC": 1187,
+      "ILC": 300,
+      "Progenitor cell": 42,
+      "Erythrocyte": 33,
+      "Platelet": 2
+    },
+    "aifi_l2": {
+      "Naive CD4 T cell": 5837,
+      "Memory CD4 T cell": 5542,
+      "CD14 monocyte": 2783,
+      "Memory CD8 T cell": 2761,
+      "gdT": 2702,
+      "Naive CD8 T cell": 2145,
+      "Memory B cell": 1997,
+      "CD56dim NK cell": 1032,
+      "Treg": 997,
+      "cDC2": 976,
+      "CD8aa": 825,
+      "CD16 monocyte": 796,
+      "CD56bright NK cell": 727,
+      "Intermediate monocyte": 614,
+      "MAIT": 520,
+      "ILC": 300,
+      "Naive B cell": 206,
+      "Effector B cell": 143,
+      "pDC": 132,
+      "Proliferating NK cell": 132,
+      "DN T cell": 129,
+      "ASDC": 46,
+      "Progenitor cell": 42,
+      "cDC1": 33,
+      "Erythrocyte": 33,
+      "Proliferating T cell": 22,
+      "Plasma cell": 17,
+      "Transitional B cell": 9,
+      "Platelet": 2
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9141204889189629,
+    "mean_l1_mass": 0.9799597263336182,
+    "frac_l2_max_prob_ge_0.5": 0.9729523809523809
+  },
+  "timings_s": {
+    "predict": 0.3,
+    "total": 0.6
+  },
+  "versions": {
+    "scvi-tools": "1.4.1",
+    "torch": "2.11.0+cu130",
+    "anndata": "0.12.19"
+  },
+  "device": "cpu",
+  "created_at_utc": "2026-10-15T09:50:52.171017+00:00"
+}

paper-releases/pbisc-diffusion/updates/20261015T095445Z-all-width-results/diffusion/metadata/NOTE.md

@@ -0,0 +1,5 @@
+# PBISC-diffusion update 20261015T095445Z-all-width-results
+
+All currently matched exact6k trunk x1/x4 results: SLE5sampling seeds, Giroux5support draws, ImMicro9available fold/budget units. Existing generation reused;7missing healthy x1 core scores computed CPU-only.47metric rows, depth-matched coverage and missing disease results explicitly reported.
+
+Payload states are recorded as supplied. Inference locations are pointers, not archived generated outputs.

paper-releases/pbisc-diffusion/updates/20261015T095445Z-all-width-results/diffusion/metadata/inference_locations.json

@@ -0,0 +1,5 @@
+{
+  "locations": [],
+  "project_id": "pbisc-diffusion",
+  "update_id": "20261015T095445Z-all-width-results"
+}

paper-releases/pbisc-diffusion/updates/20261015T095445Z-all-width-results/diffusion/metadata/request.json

@@ -0,0 +1,229 @@
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+  "project_id": "pbisc-diffusion",
+  "summary": "All currently matched exact6k trunk x1/x4 results: SLE5sampling seeds, Giroux5support draws, ImMicro9available fold/budget units. Existing generation reused;7missing healthy x1 core scores computed CPU-only.47metric rows, depth-matched coverage and missing disease results explicitly reported."
+}