Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/AGENTS.md

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+# Model 8 PBISC-Diffusion paper maintenance
+
+This active Model 8 source and its experiments are part of the
+`pbisc-diffusion` paper. At task start, read
+`../../paper-release-20260928/maintenance/POLICY.md` along with this
+directory's README and applicable parent instructions.
+
+At the end of each related task, follow that policy's versioned update
+workflow for the exact source, experiment, checkpoint, or evidence assets that
+changed. From the release root, use
+`maintenance/update.py prepare --request FILE --id ID`, inspect the prepared
+update, then run `maintenance/update.py publish ID --execute` and
+`maintenance/update.py status` under the policy. Record a no-op or pending
+status when no
+asset changed or publication failed; never describe that as an upload. Do not
+regenerate or alter the frozen 2026-09-28 release, its root manifests, or the
+HF `paper-20260928` revision. Inference assets are location plus receipt by
+default unless the task explicitly needs their payload.
+
+The private dataset must stay private. Include datalake, VAE, or Model 7 assets
+only with exact evidence that they are dependencies of this diffusion paper.
+The parent host GPU safety rules still apply.
+
+## Reuse existing experiments before starting compute
+
+User instruction, 2026-10-13: avoid repeating completed Model 8 experiments.
+Start with `EXPERIMENT_INDEX.md` and query `EXPERIMENT_REUSE_INDEX.jsonl` using
+`scripts/audit_experiment_reuse.py`. A missing output in a new plan directory
+does not establish that an experiment has never been done.
+
+- Before training, generation, or deconvolution, compare existing source
+  receipts: base checkpoint, exact support/test sample and donor IDs, data and
+  condition content, measured genes/masks, validation access, optimization and
+  selection schedule, seed, and implementation/configuration provenance.
+- Registry matches are candidates, not automatic equivalence. Verify payloads
+  and write truthful adoption evidence. Preserve original execution provenance;
+  do not relabel an old artifact as newly executed strict work.
+- Changing a sampling seed or receipt format does not justify retraining an
+  existing model. Reuse verified checkpoints and run only the genuinely changed
+  operation. Missing native receipts call for adoption, not automatic reruns.
+- Record the candidate sources and the exact scientific reason for any new
+  operation before launching it. Unknown provenance requires investigation,
+  not a conclusion that new compute is necessary. Consult newer live receipts
+  when the inventory predates an ongoing campaign.
+- Distinguish existing results, CPU-only statistics/plotting, a new protocol
+  update, and missing data in plans and decks. Never label all four as an empty
+  TODO. Archive/backup copies and tensor-identical models are not independent
+  experimental evidence.
+
+The 2026-10-13 audit and confirmed duplicate-training proof are in
+`plans/paper_figures_strictpairs_20261012/audit_reuse_20261013/`.
+Sepsis deconvolution uses verified historical draw-specific outputs through
+`tools/adopt_deconv_legacy.py` in that plan; its methods must not be rerun as a
+fallback when adoption validation fails. Current expanded evidence master (154 slides, all 142 parent pages represented):
+`presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_expanded_master_20261013_strengthened.pptx`.
+Use its `data/strengthening_20261013/page_map.csv` and source manifest.
+Earlier 142/140/131-slide decks remain preserved source versions, not the current master.
+The 34-slide review is a historical subset, not the master. The approved method palette is
+`presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_color_palette_20261013.md`:
+PBISC LoRA #168FE5, calibrated #59A8DF, raw #C3E2F4; scSemiProfiler #83C6A8;
+BayesPrism #D9B23F and CIBERSORTx #F0D77D. Preserve biological/cohort colours and quantitative heatmap scales.
+Older gold/blue source figures are preserved historical assets; use the final semantic palette derivatives in current decks.
+
+## Current manuscript figure scopes
+
+The user's 2026-10-13 definitions supersede old figure numbers inside the deck and earlier plans:
+Figure 1 overview/corpus statistics; Figure 2 architecture/gene-context ablations on SLE pseudobulk;
+Figure 3 healthy measured bulk–sc paired mismatch, full FT, LoRA ranks and support budgets;
+Figure 4 disease measured-paired quantitative integrity comparisons;
+Figure 5 paired rare-population qualitative recovery; Figure 6 paired adaptation followed by
+bulk-only published-finding reproduction (TODO).
+The authoritative scope and proposed 131-page mapping are in
+`presentations/2026-09-30--paper-summary--r00/data/figure_assignment_20261013/`.
+Read `AUTHOR_SCOPE.md` and `ASSIGNMENT.md` before figure work. Preserve the distinction
+between total-five pairs and five training plus extra validation; rank16 is not universally
+best in existing metrics, and disease comparisons have cohort/endpoint exceptions.
+Existing rare-state quantitative slides do not substitute for paired qualitative panels.
+The scope is now applied in the actual reordered PPTX/PDF, not only in planning documents.
+Use `tools/build_strengthened_master_20261013.py` in the presentation directory. It consumes
+the verified 142-page spec and source-bound strengthening bundles; older builders are preserved historical entry points.
+Figure 2 now includes corpus-validation curves and cost metadata alongside SLE pseudobulk
+benchmarks; these are not paired real-bulk performance panels. Figure 1's recorded PCA
+uses an existing ctx2048 E12 illustration, with endpoint colours revealed by denoising progress,
+not per-step confidence. Display real R2 as a real-cell repeat from the same donors, not new donors.
+Healthy pair-budget panels cover all six types with both Pearson correlation and MAE, including adverse results.
+They use historical n+7 validation access, not total-n. Do not omit NK/DC/Other to make a five-pair claim appear stronger.
+
+The latest strengthening proposal is `data/figure_assignment_20261013/STRENGTHENING_PROPOSAL.md` under the deck.
+Corpus 41,395,184 vs train 33,141,380 is a split difference, not K exclusion; all training cells are covered after top-up.
+Healthy 88.51% is a source-cell share. The remainder includes ACPA+ at-risk and is labelled Disease / at-risk.
+Historical LoRA all means 78–79 training +7 validation, keeping21–22 test/fold. Nested random training subsets and
+outer/inner splits replay exactly. The legacy total-five102-test/draw design differs from strict healthy outer-fold tests.
+Figure5 original-paper targets require author identity: Ye Mono_c06 pediatric pulmonary and Imperial wave2
+steroid-associated monocytes. Ye observed-marker co-detection is a diagnostic, not reproduced cluster identity;
+fine labels were not found in133 audited canonical obs schemas. Existing generic rare-state rules do not substitute
+for those source-defined populations. Giroux/Ji program results are not automatically rare-population evidence.

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/ara/PAPER.md

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+# PBISC-Diffusion / Model 8 research record
+
+Paper-specific record initialized2026-10-13. This scope is Model8 and its manuscript, not the broader parent SBRNA-FM artifact. Trace entries record actions; interpretations remain staged.
+
+- Current evidence: ../presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/
+- Manuscript: /home/sj_server_1/PBISC/paper-release-20260928/manuscript/

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/ara/evidence/README.md

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+# Evidence index
+
+Use the source-bound bundles and QA at ../../presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/. No duplicate experiment payload copied into this artifact.

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/ara/logic/claims.md

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+# Claims
+
+No general biological/model claim is promoted by this presentation-only update.