Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/palette.json

@@ -0,0 +1,673 @@
+{
+  "schema": "pbisc.method-palette.v1",
+  "user_directive": "Expanded original 76-slide master; every original slide retained. PBISC muted yellow/gold #C5AA4B family and scSemiProfiler blue #2166AC; biological and planning encodings preserved.",
+  "primary": {
+    "PBISC": "#C5AA4B",
+    "scSemiProfiler": "#2166AC"
+  },
+  "rules": {
+    "fig1b_overview_nature": {
+      "mapping": {
+        "#5B6E8F": "#8F772B",
+        "#E6EAF1": "#F6F0DC",
+        "#A5AFC1": "#DED09B",
+        "#8E6C9E": "#A48A34"
+      },
+      "reason": "PBISC model blocks, model arrows and optional adaptation only; preserve expression, detection, bulk and cell-type encodings.",
+      "source_pdf": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_architecture_nature.pdf"
+    },
+    "sec02_bulk_conditioning": {
+      "mapping": {},
+      "reason": "Orange denotes bulk-conditioning/context, not a method comparison; preserve semantic diagram colors."
+    },
+    "fig1d_corpus": {
+      "mapping": {},
+      "reason": "Cell types and cohort composition, not method colors."
+    },
+    "review_style_20261013_ablation": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#009E73": "#D4BE75",
+        "#332288": "#806A25",
+        "#0072B2": "#B59A50",
+        "#A6CBE3": "#E8DDAE",
+        "#882255": "#978034"
+      },
+      "reason": "PBISC architecture and gene-panel variants; black real-R2 reference retained."
+    },
+    "sec03_panel": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#0072B2": "#B59A50",
+        "#A6CBE3": "#E8DDAE",
+        "#882255": "#978034"
+      },
+      "reason": "PBISC gene panels in yellow/gold shades; scSemi reference line blue."
+    },
+    "review_style_20261013_rank": {
+      "mapping": {
+        "#E07B39": "#806A25",
+        "#D55E00": "#C5AA4B"
+      },
+      "reason": "Full fine-tuning dark gold and LoRA gold; rank markers preserve their shapes."
+    },
+    "fig3_healthy_pairs": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "fig3_healthy_fewpair": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "fig3_healthy_copy": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "fig2_healthy_pairs": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "fig4_disease_fewpair": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "sec09_fewpair_cells": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "sec09_extra_ksens": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "sec09_same_pairs": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "sec04_sle_benchmark": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
+    "review_style_20261013_healthy_composition": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#0072B2": "#2166AC"
+      },
+      "reason": "Two-method paired comparison; this asset already used blue for scSemi."
+    },
+    "sec05_condition_space": {
+      "mapping": {},
+      "reason": "Input-space diagnostic: measured/shift-corrected inputs, no method comparison."
+    },
+    "sec09_time_to_apply": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#F2B48C": "#E5D59C",
+        "#F5D08A": "#67A9CF"
+      },
+      "reason": "PBISC adaptation/generation yellow/gold shades; scSemi training/inference blue shades."
+    },
+    "sec09_cohorts": {
+      "mapping": {},
+      "reason": "Cohort metadata table, no method colors."
+    },
+    "fig4_disease_fivefold": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#8E823C"
+      },
+      "reason": "PBISC LoRA, zero-shot/calibrated and sc-only fine-tuning yellow/gold family; scSemi blue."
+    },
+    "sec09_cat_curves": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#8E823C"
+      },
+      "reason": "PBISC LoRA, zero-shot/calibrated and sc-only fine-tuning yellow/gold family; scSemi blue."
+    },
+    "secS_deconv_disease": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#CC79A7": "#6A51A3"
+      },
+      "reason": "PBISC gold, scSemi blue where present; CIBERSORTx purple and BayesPrism green."
+    },
+    "secS_deconv_composition": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#CC79A7": "#6A51A3"
+      },
+      "reason": "PBISC gold, scSemi blue where present; CIBERSORTx purple and BayesPrism green."
+    },
+    "review_style_20261013_rare_observed": {
+      "mapping": {},
+      "reason": "Observed-frequency heatmap encodes abundance, not a method."
+    },
+    "review_style_20261013_rare_corrected_comparison": {
+      "mapping": {},
+      "reason": "Points encode cohorts; x/y axes explicitly name methods. Preserve cohort color legend."
+    },
+    "review_style_20261013_behcet": {
+      "mapping": {
+        "#0072B2": "#B59A50",
+        "#D55E00": "#C5AA4B"
+      },
+      "reason": "PBISC raw/calibrated and LoRA predictions in yellow/gold family; observed native/depth-matched references black."
+    },
+    "sec05_cells_umap": {
+      "mapping": {},
+      "reason": "UMAP points and legend encode cell types. Preserve images and biological labels."
+    },
+    "sec05_cells_metrics": {
+      "mapping": {
+        "#A6CBE3": "#E8DDAE",
+        "#5E8FB5": "#B59A50"
+      },
+      "reason": "Raw-bulk and pseudobulk-input PBISC reconstructions gold; observed real cells grey. Scope black replacement to four verified rectangles only.",
+      "rectangle_rules": [
+        {
+          "rect": [
+            66.389,
+            247.078,
+            91.925,
+            361.296
+          ],
+          "old": "#1A1A1A",
+          "new": "#C5AA4B"
+        },
+        {
+          "rect": [
+            207.736,
+            98.028,
+            233.272,
+            361.296
+          ],
+          "old": "#1A1A1A",
+          "new": "#C5AA4B"
+        },
+        {
+          "rect": [
+            349.082,
+            217.017,
+            374.618,
+            361.296
+          ],
+          "old": "#1A1A1A",
+          "new": "#C5AA4B"
+        },
+        {
+          "rect": [
+            172.368,
+            8.734,
+            185.568,
+            17.134
+          ],
+          "old": "#1A1A1A",
+          "new": "#C5AA4B"
+        }
+      ]
+    },
+    "sec08_cross_cohort": {
+      "mapping": {
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#44AA99": "#D4BE75",
+        "#117733": "#978034",
+        "#332288": "#665522",
+        "#D55E00": "#C5AA4B"
+      },
+      "reason": "All PBISC adaptation/cohort variants in distinct yellow/gold shades; existing line styles preserved."
+    },
+    "sec08_cross_cohort_steps": {
+      "mapping": {
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#44AA99": "#D4BE75",
+        "#117733": "#978034",
+        "#332288": "#665522",
+        "#D55E00": "#C5AA4B"
+      },
+      "reason": "All PBISC adaptation/cohort variants in distinct yellow/gold shades; existing line styles preserved."
+    },
+    "sec07_no_pretraining": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#882255": "#806A25",
+        "#0072B2": "#B59A50"
+      },
+      "reason": "Pretrained LoRA gold, same-architecture scratch ablation dark gold, zero-shot ochre."
+    },
+    "secA_scsemi_readout": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#F5D08A": "#67A9CF"
+      },
+      "reason": "PBISC gold; official scSemi blue and modified readout pale blue with original hatch."
+    },
+    "figplan_overview": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "figplan_fig1": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "figplan_fig2": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "figplan_fig3": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "figplan_fig4": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "figplan_fig5": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "figplan_fig6": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "figplan_supp": {
+      "mapping": {},
+      "reason": "Planning/status cards retain their original status and figure-category colours; no method-performance encoding.",
+      "semantic_evidence": "Original slide title and planning-card semantics; PNG-only planning asset."
+    },
+    "sec02_backbone_compare": {
+      "mapping": {},
+      "reason": "Orange explicitly means changed from SDD in this comparison table; preserve the stated difference-highlight meaning.",
+      "semantic_evidence": "tools/sec02_backbone.py; visible legend: orange = changed from SDD"
+    },
+    "sec03_width_loss": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#009E73": "#D4BE75",
+        "#332288": "#806A25",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#6F5B1B",
+        "#999933": "#DED09B"
+      },
+      "reason": "PBISC width/context/proportion-hint variants use distinct muted-gold shades; failed-run dash and neutral convergence markers remain intact.",
+      "semantic_evidence": "tools/sec03_width_loss.py uses style.VARIANT; #1F77B4/#FF7F0E unused marker fill remains untouched."
+    },
+    "sec03_width_bench": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#009E73": "#D4BE75",
+        "#332288": "#806A25",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#6F5B1B",
+        "#999933": "#DED09B",
+        "#E69F00": "#2166AC"
+      },
+      "reason": "PBISC architecture/hint variants gold; dashed scSemiProfiler reference blue; cut/Bernoulli/hatch encodings retained.",
+      "semantic_evidence": "tools/sec03_width_bench.py: style.VARIANT arms and style.ARM[scsemi] reference."
+    },
+    "sec01_slide_a": {
+      "mapping": {},
+      "reason": "Composite encodes architecture components, corpus datasets and recipe sizes rather than method identity. Preserve its embedded diagram image.",
+      "semantic_evidence": "tools/sec01_overview.py; PDF has one embedded raster component."
+    },
+    "sec01_fig1a_denoiser": {
+      "mapping": {},
+      "reason": "Detailed denoiser colours distinguish value, support, conditioning and computational components; preserve those component roles rather than map every blue element to a method.",
+      "semantic_evidence": "tools/sec01_overview.py redraws manuscript fig01_architecture.svg component colours."
+    },
+    "sec05_shift_cohorts": {
+      "mapping": {},
+      "reason": "Colours distinguish measured inputs and shift-removed inputs across cohorts; preserve this input-space diagnostic encoding.",
+      "semantic_evidence": "tools/sec05_shift_cohorts.py; legend as measured / shift removed."
+    },
+    "sec06_ft_method": {
+      "mapping": {
+        "#D55E00": "#C5AA4B"
+      },
+      "reason": "PBISC trainable LoRA adaptation components use muted gold; frozen weights, data and other schematic elements remain unchanged.",
+      "semantic_evidence": "tools/sec06_finetune_method.py; trainable LoRA highlight."
+    },
+    "sec06_eval_design": {
+      "mapping": {},
+      "reason": "Neutral donor/sample split table has no method colours.",
+      "semantic_evidence": "tools/sec06_finetune_method.py; no explicit RGB operators in PDF."
+    },
+    "sec04_metrics_overview": {
+      "mapping": {},
+      "reason": "Orange, blue and purple label Cells, Composition and Disease metric categories, not models. Preserve these categories.",
+      "semantic_evidence": "tools/sec04_metrics_overview.py GROUP_COL maps metric-group labels."
+    },
+    "fig2_healthy_cells": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#8E823C"
+      },
+      "reason": "PBISC raw/calibrated, LoRA and sc-only variants use gold shades; neutral real-reference controls remain intact.",
+      "semantic_evidence": "tools/fig23_healthy.py method C palette and corresponding visible legends."
+    },
+    "fig2_healthy_realism": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#8E823C"
+      },
+      "reason": "PBISC raw/calibrated, LoRA and sc-only variants use gold shades; neutral real-reference controls remain intact.",
+      "semantic_evidence": "tools/fig23_healthy.py method C palette and corresponding visible legends."
+    },
+    "fig2_healthy_modes": {
+      "mapping": {
+        "#E07B39": "#806A25",
+        "#D55E00": "#C5AA4B",
+        "#009E73": "#D4BE75",
+        "#CC79A7": "#8E823C",
+        "#0072B2": "#B59A50",
+        "#A6CBE3": "#E8DDAE",
+        "#5E8FB5": "#B59A50"
+      },
+      "reason": "Full FT, LoRA and condition-encoder-only are PBISC adaptation variants; use distinct gold shades.",
+      "semantic_evidence": "tools/fig23_healthy.py; full/LoRA/cond.-encoder method comparison."
+    },
+    "fig2_healthy_rank": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#F3C9A8": "#E8DDAE",
+        "#7A2E00": "#806A25"
+      },
+      "reason": "PBISC LoRA ranks use gold shades; K and recipe line styles remain unchanged.",
+      "semantic_evidence": "tools/fig23_healthy.py; LoRA r4/r16/r64 colour family."
+    },
+    "fig3_time_days": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC"
+      },
+      "reason": "PBISC adaptation/sampling time gold; scSemiProfiler time blue; day reference lines remain neutral.",
+      "semantic_evidence": "tools/fig3_time_days.py method bars and legend."
+    },
+    "sec04_sle_per_celltype": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC"
+      },
+      "reason": "PBISC gold and scSemiProfiler blue within each cell type; cell-type names and neutral single-seed/error marks unchanged.",
+      "semantic_evidence": "tools/sec04_sle_benchmark.py method palette; visible PBISC 6k / scSemiProfiler legend."
+    },
+    "fig4_disease_variants": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E07B39": "#806A25"
+      },
+      "reason": "PBISC LoRA ranks, K/recipe variants gold and full FT dark gold.",
+      "semantic_evidence": "tools/fig4_disease.py variant methods; no cohort colour mapping."
+    },
+    "sec08_pairs_signal": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#5E8FB5": "#B59A50",
+        "#DDCC77": "#DAC990"
+      },
+      "reason": "PBISC paired/unpaired/calibrated/length-corrected inputs use gold shades, scSemiProfiler blue; black pseudobulk oracle and grey cohort-mean references remain neutral.",
+      "semantic_evidence": "tools/sec08_pairs_needed.py method arms and source-input controls."
+    },
+    "sec08_pairs_realism": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#5E8FB5": "#B59A50",
+        "#DDCC77": "#DAC990"
+      },
+      "reason": "PBISC paired/unpaired/calibrated/length-corrected inputs use gold shades, scSemiProfiler blue; black pseudobulk oracle and grey cohort-mean references remain neutral.",
+      "semantic_evidence": "tools/sec08_pairs_needed.py method arms and source-input controls."
+    },
+    "fig5_rare_fraction": {
+      "mapping": {
+        "#F6DCC8": "#F6F0DC"
+      },
+      "reason": "Reuse palette-only rerender of the original saved-CSV plot: FEW/POOL methods use gold/blue while the original local COH cohort colours are unchanged. Numerical table must equal the original exactly. Recolour only the LoRA within-twofold background band to pale gold.",
+      "semantic_evidence": "tools/fig5_rare_states.py: COH[ji2025_chili] and FEW[scsemi5] both #E69F00.",
+      "source_pdf": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fraction.pdf",
+      "precolored_source_png": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fraction.png",
+      "precolored_proof": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/PROVENANCE.json",
+      "precolored_builder": "tools/expanded_legacy_rare.py:build"
+    },
+    "fig5_rare_donors": {
+      "mapping": {},
+      "reason": "Reuse palette-only rerender of the original saved-CSV plot: FEW/POOL methods use gold/blue while the original local COH cohort colours are unchanged. Numerical table must equal the original exactly.",
+      "semantic_evidence": "tools/fig5_rare_states.py: cohort scatter and FEW method bars share orange.",
+      "source_pdf": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_donors.pdf",
+      "precolored_source_png": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_donors.png",
+      "precolored_proof": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/PROVENANCE.json",
+      "precolored_builder": "tools/expanded_legacy_rare.py:build"
+    },
+    "fig5_rare_fivefold": {
+      "mapping": {
+        "#F6DCC8": "#F6F0DC"
+      },
+      "reason": "Reuse palette-only rerender of the original saved-CSV plot: FEW/POOL methods use gold/blue while the original local COH cohort colours are unchanged. Numerical table must equal the original exactly. Recolour only the LoRA within-twofold background band to pale gold.",
+      "semantic_evidence": "tools/fig5_rare_states.py scatter COH palette; LoRA acceptable-error band #F6DCC8.",
+      "source_pdf": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fivefold.pdf",
+      "precolored_source_png": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fivefold.png",
+      "precolored_proof": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/legacy_rare/PROVENANCE.json",
+      "precolored_builder": "tools/expanded_legacy_rare.py:build"
+    },
+    "sec05_behcet_direction": {
+      "mapping": {
+        "#A6CBE3": "#E8DDAE",
+        "#5E8FB5": "#B59A50"
+      },
+      "reason": "Raw-bulk PBISC predictions use gold shades. Preserve black pseudobulk-input oracle and grey observed reference; case/control and common-depth semantics unchanged.",
+      "semantic_evidence": "tools/sec05_behcet_direction.py ARMS and RAW_EDGE; neutral oracle/observed policy retained."
+    },
+    "sec10_paired_subset_cohorts": {
+      "mapping": {},
+      "reason": "Planning readiness is encoded by pale/outlined bulk-only segments, paired-QC passes, excluded hatches and DC-enriched hatches; preserve all status colours.",
+      "semantic_evidence": "tools/sec10_paired_subset_cohorts.py C_BO/C_BO_EDGE and explicit PLANNED legend."
+    },
+    "sec09_extra_fewpair": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#8E823C"
+      },
+      "reason": "PBISC reconstruction variants gold, scSemiProfiler blue; real-real and pseudobulk-input reference guides remain neutral.",
+      "semantic_evidence": "tools/sec09_extra_metrics.py / saved metric legends; #1F77B4 unpainted error-cap fill unchanged."
+    },
+    "sec09_extra_fivefold": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#CC79A7": "#8E823C"
+      },
+      "reason": "PBISC reconstruction variants gold, scSemiProfiler blue; real-real and pseudobulk-input reference guides remain neutral.",
+      "semantic_evidence": "tools/sec09_extra_metrics.py / saved metric legends; #1F77B4 unpainted error-cap fill unchanged."
+    },
+    "sec09_scsemi_representative": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC"
+      },
+      "reason": "PBISC LoRA gold, scSemiProfiler blue; representative-copy null remains neutral.",
+      "semantic_evidence": "tools/sec09_scsemi_representative.py method legend."
+    },
+    "sec07_ft_modes": {
+      "mapping": {
+        "#E07B39": "#806A25",
+        "#D55E00": "#C5AA4B",
+        "#009E73": "#D4BE75",
+        "#CC79A7": "#8E823C",
+        "#0072B2": "#B59A50",
+        "#A6CBE3": "#E8DDAE",
+        "#5E8FB5": "#B59A50"
+      },
+      "reason": "All displayed adaptation/input modes belong to PBISC and use distinct gold shades; marker shape retains pooled-versus-fold0 meaning.",
+      "semantic_evidence": "tools/sec07_ft_modes.py ARMS and RAW_EDGE."
+    },
+    "sec07_rank_sweep": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#F2AE7B": "#E8DDAE",
+        "#6E2E00": "#806A25"
+      },
+      "reason": "PBISC LoRA r4/r16/r64 use pale/primary/dark gold; ranks retain their labels and line markers.",
+      "semantic_evidence": "tools/sec07_rank_sweep.py three-rank method palette."
+    },
+    "sec07_k_aug": {
+      "mapping": {
+        "#D55E00": "#C5AA4B"
+      },
+      "reason": "PBISC K/recipe augmentation variants use muted gold; neutral point/interval geometry unchanged.",
+      "semantic_evidence": "tools/sec07_k_aug.py same-model variant comparison."
+    },
+    "sec08_cross_scratch": {
+      "mapping": {
+        "#A6CBE3": "#E8DDAE",
+        "#0072B2": "#B59A50",
+        "#44AA99": "#D4BE75",
+        "#117733": "#978034",
+        "#332288": "#665522",
+        "#D55E00": "#C5AA4B",
+        "#882255": "#806A25"
+      },
+      "reason": "All methods are PBISC architecture/adaptation controls; pretrained, zero-shot, calibration and scratch variants use gold shades.",
+      "semantic_evidence": "tools/sec08_cross_scratch.py calibration/LoRA/full/scratch/own-cohort methods."
+    },
+    "secS_scratch_rare_states": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#882255": "#806A25",
+        "#0072B2": "#B59A50",
+        "#44AA99": "#D4BE75",
+        "#332288": "#665522"
+      },
+      "reason": "PBISC pretrained/scratch and cross-cohort adaptations use distinct gold shades; markers and acceptable-error grey band retained.",
+      "semantic_evidence": "tools/secS_scratch_rare_states.py SCRATCH and cross-cohort plot definitions."
+    },
+    "sec10_other_tissues": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#882255": "#806A25"
+      },
+      "reason": "Saved PBISC pretrained-versus-scratch evidence uses gold/dark gold; next-step planning text and table status remain unchanged.",
+      "semantic_evidence": "tools/sec10_other_tissues.py PRE and SCRATCH evidence columns."
+    },
+    "sec04_sle_broadcast": {
+      "mapping": {
+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC"
+      },
+      "reason": "PBISC gold and scSemi blue; bulk-broadcast comparator grey."
+    },
+    "fig_randolph_celltype_response": {
+      "mapping": {
+        "#2A78D6": "#E8DDAE",
+        "#EB6834": "#B59A50",
+        "#1BAF7A": "#978034",
+        "#EDA100": "#806A25"
+      },
+      "reason": "All four coloured arms are PBISC input variants: raw, reference-calibrated, paired-calibrated and pseudobulk. Observed and bulk-broadcast controls stay neutral.",
+      "rgb_tolerance": 5.1e-07
+    }
+  },
+  "reference_policy": "Biological/cohort colors and neutral observed/oracle diagnostic references are separate encodings, not model identity.",
+  "unused_fill_policy": "Matplotlib #1F77B4 fill on neutral errorbar caps is not painted; preserve.",
+  "preserve_geometry_text_data": true,
+  "contrast_note": "Dark ink on PBISC yellow win-count bars; model text/arrows use a darker gold. scSemi colors stay unchanged.",
+  "base_policy": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/method_palette_20261013/palette.json",
+    "sha256": "a94e734ef7e35a2cb09f63acb81eb48b0c2edaccd3743caf3002cf8f8314d07d",
+    "rules_preserved_exactly": 32
+  },
+  "expanded_master_coverage": {
+    "source_spec": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/slides_spec.json",
+    "source_spec_sha256": "6b8fa055e20a3379ce2e50ca19dbbe285d81e4e95d2c42597e236945b8b2bc23",
+    "original_slides": 76,
+    "original_unique_assets": 66,
+    "covered_original_assets": 66,
+    "new_explicit_rules": 40,
+    "total_rules": 72,
+    "precolored_legacy_assets": [
+      "fig5_rare_fraction",
+      "fig5_rare_donors",
+      "fig5_rare_fivefold"
+    ]
+  },
+  "precolored_rule_contract": "Run tools/expanded_legacy_rare.py:build first. Use precolored_source_png and source_pdf even when mapping is empty; require the exact-table-equality PROVENANCE.json. The method and cohort palettes are separated by the original plotting routine, not spatial RGB rewriting."
+}

paper-releases/pbisc-diffusion/updates/20261013T034842Z-expanded-131-slide-master/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/palette_preflight.json

@@ -0,0 +1,247 @@
+[
+  {
+    "asset": "fig1b_overview_nature",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript/figures/fig01_architecture_nature.pdf"
+  },
+  {
+    "asset": "review_style_20261013_ablation",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/review_style_20261013_ablation.pdf"
+  },
+  {
+    "asset": "sec03_panel",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec03_panel.pdf"
+  },
+  {
+    "asset": "review_style_20261013_rank",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/review_style_20261013_rank.pdf"
+  },
+  {
+    "asset": "fig3_healthy_pairs",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig3_healthy_pairs.pdf"
+  },
+  {
+    "asset": "fig3_healthy_fewpair",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig3_healthy_fewpair.pdf"
+  },
+  {
+    "asset": "fig3_healthy_copy",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig3_healthy_copy.pdf"
+  },
+  {
+    "asset": "fig2_healthy_pairs",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig2_healthy_pairs.pdf"
+  },
+  {
+    "asset": "fig4_disease_fewpair",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig4_disease_fewpair.pdf"
+  },
+  {
+    "asset": "sec09_fewpair_cells",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fewpair_cells.pdf"
+  },
+  {
+    "asset": "sec09_extra_ksens",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_extra_ksens.pdf"
+  },
+  {
+    "asset": "sec09_same_pairs",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_same_pairs.pdf"
+  },
+  {
+    "asset": "sec04_sle_benchmark",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec04_sle_benchmark.pdf"
+  },
+  {
+    "asset": "review_style_20261013_healthy_composition",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/review_style_20261013_healthy_composition.pdf"
+  },
+  {
+    "asset": "sec09_time_to_apply",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_time_to_apply.pdf"
+  },
+  {
+    "asset": "fig4_disease_fivefold",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig4_disease_fivefold.pdf"
+  },
+  {
+    "asset": "sec09_cat_curves",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_cat_curves.pdf"
+  },
+  {
+    "asset": "secS_deconv_disease",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_deconv_disease.pdf"
+  },
+  {
+    "asset": "secS_deconv_composition",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_deconv_composition.pdf"
+  },
+  {
+    "asset": "review_style_20261013_behcet",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/review_style_20261013_behcet.pdf"
+  },
+  {
+    "asset": "sec05_cells_metrics",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec05_cells_metrics.pdf"
+  },
+  {
+    "asset": "sec08_cross_cohort",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec08_cross_cohort.pdf"
+  },
+  {
+    "asset": "sec08_cross_cohort_steps",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec08_cross_cohort_steps.pdf"
+  },
+  {
+    "asset": "sec07_no_pretraining",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec07_no_pretraining.pdf"
+  },
+  {
+    "asset": "secA_scsemi_readout",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secA_scsemi_readout.pdf"
+  },
+  {
+    "asset": "sec03_width_loss",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec03_width_loss.pdf"
+  },
+  {
+    "asset": "sec03_width_bench",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec03_width_bench.pdf"
+  },
+  {
+    "asset": "sec06_ft_method",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec06_ft_method.pdf"
+  },
+  {
+    "asset": "fig2_healthy_cells",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig2_healthy_cells.pdf"
+  },
+  {
+    "asset": "fig2_healthy_realism",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig2_healthy_realism.pdf"
+  },
+  {
+    "asset": "fig2_healthy_modes",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig2_healthy_modes.pdf"
+  },
+  {
+    "asset": "fig2_healthy_rank",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig2_healthy_rank.pdf"
+  },
+  {
+    "asset": "fig3_time_days",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig3_time_days.pdf"
+  },
+  {
+    "asset": "sec04_sle_per_celltype",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec04_sle_per_celltype.pdf"
+  },
+  {
+    "asset": "fig4_disease_variants",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/fig4_disease_variants.pdf"
+  },
+  {
+    "asset": "sec08_pairs_signal",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec08_pairs_signal.pdf"
+  },
+  {
+    "asset": "sec08_pairs_realism",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec08_pairs_realism.pdf"
+  },
+  {
+    "asset": "fig5_rare_fraction",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fraction.pdf"
+  },
+  {
+    "asset": "fig5_rare_fivefold",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/expanded_master_20261013/legacy_rare/fig5_rare_fivefold.pdf"
+  },
+  {
+    "asset": "sec05_behcet_direction",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec05_behcet_direction.pdf"
+  },
+  {
+    "asset": "sec09_extra_fewpair",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_extra_fewpair.pdf"
+  },
+  {
+    "asset": "sec09_extra_fivefold",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_extra_fivefold.pdf"
+  },
+  {
+    "asset": "sec09_scsemi_representative",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_scsemi_representative.pdf"
+  },
+  {
+    "asset": "sec07_ft_modes",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec07_ft_modes.pdf"
+  },
+  {
+    "asset": "sec07_rank_sweep",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec07_rank_sweep.pdf"
+  },
+  {
+    "asset": "sec07_k_aug",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec07_k_aug.pdf"
+  },
+  {
+    "asset": "sec08_cross_scratch",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec08_cross_scratch.pdf"
+  },
+  {
+    "asset": "secS_scratch_rare_states",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/secS_scratch_rare_states.pdf"
+  },
+  {
+    "asset": "sec10_other_tissues",
+    "status": "pass",
+    "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec10_other_tissues.pdf"
+  }
+]