Archive 4 checkpoints (1-4)

.gitattributes

@@ -258,3 +258,4 @@ paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-pale
 paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-palette-142/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_expanded_master_20261013_celltypes_palette.pptx filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-palette-142/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/figures/final_palette_20261013/fig2_covid_hc_monocyte_arrows_depth1000.pdf filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261013T094815Z-all-celltypes-final-palette-142/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/figures/final_palette_20261013/native/gene_length_input.pdf filter=lfs diff=lfs merge=lfs -text
+paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_expanded_master_20261013_strengthened.pdf filter=lfs diff=lfs merge=lfs -text

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/ara/trace/pm_reasoning_log.yaml

@@ -0,0 +1,6 @@
+entries:
+- date: '2026-10-13'
+  provenance: ai-executed
+  note: Recorded source/audit actions without promoting universal superiority or rare-population
+    identity claims. No existing paper-specific ARA found; parent artifact covers
+    broader models and was left unchanged.

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/ara/trace/sessions/2026-10-13_001.yaml

@@ -0,0 +1,25 @@
+id: 2026-10-13_001
+date: '2026-10-13'
+summary: Expanded142 to154slides with corpus/split audit, saved adaptation and disease
+  metrics, and original-paper rare-target observed diagnostics.
+ai_actions:
+- provenance: ai-executed
+  action: Created12source-bound panels, verified154PPTX/PDF pages and retained142parent/76original
+    pages.
+- provenance: ai-executed
+  action: Replayed fixed outer/inner folds and20nested random training subsets.
+- provenance: ai-executed
+  action: Streamed five genes from observed Ye cells and audited133canonical obs schemas
+    for fine labels.
+user_directions:
+- provenance: user
+  direction: Separate Healthy/Disease condition detail, explain corpus/train/K, directly
+    visualize adaptation, add reference-backed disease metrics and reproduce paper-reported
+    paired rare populations.
+evidence:
+- ../presentations/2026-09-30--paper-summary--r00/data/strengthening_20261013/manifest.json
+open_threads:
+- Complete existing strict donor-aware disease analyses and CIs.
+- Retrieve/validate original rare-cluster identities before generated population recovery.
+- Figure6 remains a separate bulk-only replication TODO.
+claims_touched: []

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/ara/trace/sessions/session_index.yaml

@@ -0,0 +1,9 @@
+sessions:
+- id: 2026-10-13_001
+  date: '2026-10-13'
+  summary: Expanded142 to154slides with corpus/split audit, saved adaptation and disease
+    metrics, and original-paper rare-target observed diagnostics.
+  turn_count: 1
+  events_count: 3
+  claims_touched: []
+  open_threads: 3

paper-releases/pbisc-diffusion/updates/20261013T115045Z-figure-strengthening-154/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_expanded_master_20261013_strengthened.pdf

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:851cbb902519dbf0bf9a48cf141aa0d8ef7c793f512064118965584faa81ebf5
+size 20760146