Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/healthy/observed_only_order.csv

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paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/healthy/result.json

@@ -0,0 +1,540 @@
+{
+  "schema": "pbisc.strengthening.healthy.v1",
+  "slides": [
+    {
+      "kind": "content",
+      "title": "Adaptation recovers the observed cell mixture",
+      "figures": [
+        "figures/strengthening_20261013/healthy/same_donors_composition.png"
+      ],
+      "layout": "full",
+      "keywords": [],
+      "section": "Figure 3",
+      "deck_group": "Figure 3",
+      "section_label": "Fig. 3 \u00b7 Adaptation",
+      "footnote": "Same 107 held-out donors in every row. Full FT / LoRA use raw measured bulk; colours identify cell types.",
+      "footnote_full": "Same 107 ImMicro healthy donors, pooled five-fold held-out predictions and six frozen broad cell types. Every donor and type retained; display order uses observed monocyte fraction only. Each generated arm has 1500 cells/sample; observed fractions use all available scored observed cells. Full FT and LoRA consume the raw measured-bulk input, as does raw zero-shot. Input calibration is a separate comparator. Adaptation improves generated-cell composition; it does not change the measured bulk or establish that every transcriptional mismatch disappears. Historical training has 78\u201379 train plus 7 inner-validation pairs/fold. No new training, inference, annotation, or scoring; this reuses saved donor metrics.",
+      "sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/per_donor.csv"
+    },
+    {
+      "kind": "content",
+      "title": "Adaptation: mixture error and expression agreement",
+      "figures": [
+        "figures/strengthening_20261013/healthy/same_donors_output_recovery.png"
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+      "layout": "full",
+      "keywords": [],
+      "section": "Figure 3",
+      "deck_group": "Figure 3",
+      "section_label": "Fig. 3 \u00b7 Adaptation",
+      "footnote": "107 matched donors; lines connect the same person. Gene-expression r is a donor pseudobulk Pearson correlation.",
+      "footnote_full": "Same 107 ImMicro healthy donors, pooled five-fold held-out predictions and six frozen broad cell types. Every donor and type retained; display order uses observed monocyte fraction only. Each generated arm has 1500 cells/sample; observed fractions use all available scored observed cells. Full FT and LoRA consume the raw measured-bulk input, as does raw zero-shot. Input calibration is a separate comparator. Adaptation improves generated-cell composition; it does not change the measured bulk or establish that every transcriptional mismatch disappears. Historical training has 78\u201379 train plus 7 inner-validation pairs/fold. No new training, inference, annotation, or scoring; this reuses saved donor metrics. Error = sum across six types of absolute fraction differences. Expression r is saved pb_r, the per-donor Pearson correlation of log1p-CPM(summed generated expression rates) versus log1p-CPM(observed pseudobulk) on the same 5,508 scorer genes; not cell-wise correspondence. Lines are not diffusion trajectories. No significance tests.",
+      "sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/per_donor.csv"
+    },
+    {
+      "kind": "content",
+      "title": "What does \u201call pairs\u201d actually mean?",
+      "figures": [
+        "figures/strengthening_20261013/healthy/fixed_test_split.png"
+      ],
+      "layout": "full",
+      "keywords": [],
+      "section": "Figure 3",
+      "deck_group": "Figure 3",
+      "section_label": "Fig. 3 \u00b7 Adaptation",
+      "footnote": "Random, nested training subsets; the test fold stays fixed. \u201cAll\u201d = all available training pairs in that fold.",
+      "footnote_full": "Historical ImMicro CV, not strict total-support experiment. Outer group-stratified donor folds and inner validation use seed 20260927. Saved training subsets use fold-specific seeds 1000, 1001, 1002, 1003, 1004. Within each fold one random permutation yields nested 5/10/20/40 training subsets; exact replay matches all 20 saved subset memberships. Every budget has identical held-out test donors (22,22,21,21,21), and seven validation donors. All uses78,78,79,79,79 training donors. Each of107 donors contributes one held-out prediction to the pooled metric. With n20,58\u201359 remaining training-pool donors are unused, not moved into the test fold. The separate legacy healthy five-draw comparison uses 5 support+0 validation,102 test/draw. The newer strict healthy support campaign instead keeps outer-fold held-out tests and has no extra validation; do not conflate these two total-five designs. No training/test overlap or membership changes were introduced.",
+      "sources": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/per_donor.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/PREPARE.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/prepare_dataset.py; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_sdd.py; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json"
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paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/healthy/split_audit.csv

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paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/healthy/summary.csv

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