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/reference/deg_reference.npz

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paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/reference/deg_reference_manifest.json

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+ "schema": "paired_ft_deg_reference.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-13T12:29:41.203820+00:00",
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+  "built_from": "existing cache"
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+}

paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/reference/reference.npz

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paper-releases/pbisc-diffusion/updates/20261013T124345Z-trunk4x-lora-sepsis-launch/diffusion/dataset/server_1/model8/plans/trunk4x_lora_sepsis_20261013/reference/reference_manifest.json

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+{
+ "schema": "paired_ft_scoring_reference.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-10-13T12:29:25.321243+00:00",
+ "reference_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/reference/reference.npz",
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+ "features": {
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+  "keys": {
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+   "donor_ids": "donor_ids",
+   "groups": "groups",
+   "pseudo": "pseudo_raw_sum"
+  }
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+ "cells": {
+  "source": "datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/evaluation_data/ye2026_sepsis",
+  "inputs_sha256": {
+   "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/evaluation_data/ye2026_sepsis/cells_panel6k.npz": "6147311e108b7d69d4d476af6161c18f0ed38375a2de776ac9910140d2c232f3",
+   "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/trunk4x_lora_sepsis_20261013/evaluation_data/ye2026_sepsis/cells_obs.parquet": "f21b34faaa06d3ba71f2538ec7367836879d59a5c44a820ad8e6ad90bffd4eb7"
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+  "n_cells": 610713,
+  "key_rule": "library_id+barcode"
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+ "labels": {
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+  "mean_l2_max_prob": 0.9297739861708457,
+  "predict_seconds": 16.2,
+  "command": [
+   "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py",
+   "--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",
+   "--query",
+   "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/observed_labels/query.h5ad",
+   "--out-dir",
+   "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ye2026_sepsis/observed_labels/labels",
+   "--method-name",
+   "observed_ye2026_sepsis",
+   "--dataset-id",
+   "Ye2026_sepsis",
+   "--split",
+   "observed",
+   "--sample-id-col",
+   "sample_id",
+   "--batch-key-col",
+   "batch_key",
+   "--batch-prefix",
+   "Ye2026_sepsis_",
+   "--seed",
+   "20260916",
+   "--device",
+   "cpu",
+   "--num-threads",
+   "8",
+   "--eval-batch-size",
+   "2048",
+   "--allow-missing-genes"
+  ],
+  "sha256": "ab27c027a75b7cd47ec8267d4b33bfe41e8cb6ab64190a3592db1cffa2a73ea7",
+  "reused_frozen_observed_labels": true
+ },
+ "annotator_run": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1",
+ "n_donors": 85,
+ "samples_without_cells": [],
+ "gene_sets": {
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+  "scoring": 4243,
+  "query": 1006,
+  "dropped_annotation_genes": [],
+  "model_genes_missing_from_query": 0
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+ "reference_rule": {
+  "n_sub": 150,
+  "seed": 20260925,
+  "rule": "per donor: canonical order = sort by cell key; permutation from default_rng([20260925, sha256(donor)[:8] as uint64 LE]); R1 = first min(150, n//2), R2 = next same number"
+ },
+ "n_ref": {
+  "min": 150,
+  "median": 150.0,
+  "total": 12750
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+ "checks": {
+  "panel_sums_equal_features_pseudobulk": {
+   "n_samples_checked": 85,
+   "n_mismatch": 0
+  }
+ },
+ "seconds": 20.6
+}