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/mismatch_per_donor_errors.csv

@@ -0,0 +1,108 @@
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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/mismatch_result.json

@@ -0,0 +1,172 @@
+{
+  "schema": "pbisc.figure-enrichment.expression-mismatch.v1",
+  "slides": [
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "mismatch_expression_values",
+      "role": "f3_expression_mismatch",
+      "title": "Same-person RNA assays give different expression values",
+      "section_label": "Fig. 3 \u00b7 Input expression",
+      "figures": [
+        "figures/figure_enrichment_20261013/mismatch_expression_values.png"
+      ],
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+      "footnote": "107 paired donors; all 5,508 shared final-model genes. log1p CPM on the same gene axis. Saved calibration uses 10 other-pool pairs.",
+      "footnote_full": "ImMicro, 107 unique paired healthy donors. All 5508 final-model panel genes measured by both assays in every donor are included; the other 492 model genes are excluded by availability, never filled as measured zeros. Each assay row is separately normalized to 1e6 over the same 5508 genes and transformed by natural log(1+CPM). Axes are gene-expression profiles, not cell-type counts, learned embeddings or PCA. Observed pseudobulk is the sum of the donor's measured single-cell UMI counts. The saved calibrated condition uses the historical gene-wise multiplier from exactly 10 other-pool paired donors, with the evaluated donor's whole sc pool excluded. It is a paired-information diagnostic, not zero-shot deployment, LoRA output or the current strict-five budget. Source condition hashes and raw/pseudobulk normalization are verified. The full-expression distances reproduce the old saved analysis within its rounded CSV precision. Assay differences can include cell capture, pool/batch, depth and assay chemistry; this plot does not attribute them to one mechanism or treat scRNA-seq as noise-free truth. No individual genes or donors were chosen for a favorable example. The plots describe 107 biological donors; donor\u2013gene points are not independent replicates.",
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+      "title": "Paired calibration reduces same-donor expression error",
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+      "footnote": "Each line = one donor. Error averages all 5,508 genes; no nearest-neighbor score. Ten-pair, other-pool calibration is diagnostic.",
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