Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T023822Z-pbisc-yellow-scsemi-blue/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/method_palette_20261013/REPORT.md

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+# PBISC muted yellow/gold and scSemiProfiler blue throughout the current deck
+
+User directive: use yellow/gold-family colors for PBISC and blue-family colors for scSemiProfiler across the entire deck.
+
+## Applied design
+
+The user replaced the earlier red preference with muted yellow/gold. The current 34-slide results review uses PBISC #C5AA4B and scSemiProfiler #2166AC. PBISC raw/calibrated inputs, full fine-tuning, sc-only fine-tuning, gene panels, cross-cohort variants and scratch ablation use distinguishable yellow/ochre shades. scSemi training/inference and modified readout use blue shades; hatch patterns are retained. CIBERSORTx is purple and BayesPrism remains green.
+
+25 scientific figure assets were recolored. Seven assets whose color encodes input data, cell type, cohort or observed abundance remain unchanged. The Figure 1 model blocks/arrows and adaptation box are yellow/gold-family; expression values, detection, bulk and biological categories retain their independent semantic encodings. The conditioning-only diagram keeps its context color.
+
+PBISC win-count labels use dark ink for legibility on yellow; diagram text/arrows use a darker gold. scSemiProfiler remains blue #2166AC.
+
+The policy is explicit per figure (`palette.json`), because the same old RGB denoted different entities in different panels. The current deck builder always applies it. Original 76-slide artifacts remain intact; review variants live in `figures/method_palette_20261013/`.
+
+## Preservation and validation
+
+Native PDF paint colors were edited; plot coordinates, text, numbers, uncertainty geometry, cell images and plotting data were not changed. Marker Form objects and colored hatch patterns were included. Four black pseudobulk-input reconstruction rectangles were scoped individually to avoid recoloring black text or axes. Per-figure receipts verify the serialized files.
+
+Verified: 34-slide PPTX/PDF; 25 recolored assets; seven non-method assets preserved; 86 numerical CSV hashes unchanged; all derived summary numbers and slide text unchanged; all 180 source hashes verified; no old mapped method colors remain. Original source geometry/text and embedded raster payloads pass preservation checks. Whole-deck contact sheets and method-comparison slides were visually inspected.
+
+No training, generation or scoring was started. Only presentation assets were revised. Private versioned archive maintenance records the exact current files, with prior versions preserved.