Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_metrics_overview.csv

@@ -0,0 +1,10 @@
+group,metric,question,compared_against,reference
+Cells,Precision / coverage,Land on real cells? Cover all real cells?,separate observed-cell sample,Kynkäänniemi 2019; Naeem 2020
+Cells,Classifier AUC,Can a classifier tell generated from real cells?,0.5 = indistinguishable,Lopez-Paz & Oquab 2017
+Cells,MMD²,How far apart are the two cell distributions?,real vs real,Gretton 2012
+Cells,E_N,scSemiProfiler's own nearest-neighbour error,within-sample split,Wang 2024
+Composition,Cell-type L1,Right mix of the six scANVI cell types?,other donors' mean (null),—
+Disease,logFC r (Pearson / Spearman),Same case-vs-control change in each cell type?,zero-shot; partial r (vs bulk),Roohani 2024; Viñas Torné 2026
+Disease,Top-50 DEG overlap,Same top disease genes per cell type?,chance; limma-voom check,Li 2026; Squair 2021; Law 2014
+Disease,CAT curve,Same genes at every list length k?,chance = k / 2G,Irizarry 2005
+Cost,GPU time,How long to apply to a new cohort?,"same donors, same GPU",—

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_metrics_overview.json

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+  "operation": "saved-value plotting and label clarification; no scoring or model inference",
+  "new_training": false,
+  "new_inference": false,
+  "new_scoring": false,
+  "values": "same metric table; held-out real cells renamed without R1/R2 shorthand"
+}

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_real_cell_repeat.json

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+{
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+  "sources": [
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+  "new_scoring": false,
+  "definition": "Independent non-overlapping observed-cell draws from the same donors; not independent donors.",
+  "n_donors": 42,
+  "per_donor_per_set": 100,
+  "cell_sets": 2
+}

paper-releases/pbisc-diffusion/updates/20261013T072655Z-enriched-140-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_result.json

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+{
+  "ablation": {
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+    "pdf": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/labels_ablation.pdf",
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+    "provenance": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_ablation.json"
+  },
+  "supplement_replacements": [
+    {
+      "kind": "content",
+      "key": "healthy_labels_within_type_centroids",
+      "after_original": 19,
+      "title": "Composition agreement does not ensure state agreement",
+      "section_label": "Control evidence",
+      "layout": "full",
+      "figures": [
+        "figures/figure_enrichment_20261013/labels_within_type_centroids.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
+      "footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nCentroids and real within-type RMS normalization are previously computed. No new embedding, centroids or annotation are fitted. Six broad types; small Other/DC groups require caution.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/b_type_centroid_shift_l1.csv",
+      "sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/b_type_centroid_shift_l1.csv",
+      "palette": "native"
+    },
+    {
+      "kind": "content",
+      "key": "healthy_labels_detection_and_library",
+      "after_original": 24,
+      "title": "Detection and library size are separate diagnostics",
+      "section_label": "Control evidence",
+      "layout": "full",
+      "figures": [
+        "figures/figure_enrichment_20261013/labels_detection_and_library.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical native-depth diagnostic: sc-derived depth/masks; 10-pair calibration; AIFI overlaps pretraining. One seed.",
+      "footnote_full": "Historical zero-shot input diagnostics, not strict-five LoRA/scSemiProfiler comparison. Final f01 6k 1x E16 EMA; 107 ImMicro donors; 1,500 generated cells/donor; 50 DDIM steps; Bernoulli support; generation seed 20260922 shared across input arms. Native depth and cell count, and the output gene-availability mask, use each donor's sc data. Paired calibration uses 10 paired samples. AIFI alpha uses no paired ImMicro sc expression, but 85 of its 108 reference donors overlap pretraining; this is not evidence of a completely sc-free deployment. Most cell-space metrics use 150 cells/donor and 5,508 common measured genes; PCA50/UMAP fitted only on real R1. Generated counts are Poisson readouts, not observed UMIs. One cohort and one seed; no new uncertainty tests. The source manifest records exact reproduction of the earlier four-arm controls.\n\nObserved counts and the previously computed Poisson readout of generated cells. Whiskers are saved 10th\u201390th cell percentiles, not donor confidence intervals. Scoring-gene libraries are not full-transcriptome UMI totals.\n\nSource files (existing results, read only):\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md\n/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/e_detected_genes.csv",
+      "sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/RESULTS.md; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/e_detected_genes.csv",
+      "palette": "native"
+    }
+  ],
+  "metrics_overview": {
+    "png": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/labels_metrics_overview.png",
+    "pdf": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/labels_metrics_overview.pdf",
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+    "provenance": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/figure_enrichment_20261013/labels_metrics_overview.json"
+  },
+  "control_explanation": {
+    "png": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/figure_enrichment_20261013/labels_real_cell_repeat.png",
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+  },
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+  ]
+}