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/ASSET_MAP.json

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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/VERIFICATION.json

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+      "proof": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/method_palette_20261013/secA_scsemi_readout.palette.json",
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+    {
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+      "proof": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/method_palette_20261013/sec04_sle_benchmark.palette.json",
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+  "preserved_assets": [
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+    "figures/fig1d_corpus.png",
+    "figures/sec05_condition_space.png",
+    "figures/sec09_cohorts.png",
+    "figures/review_style_20261013_rare_observed.png",
+    "figures/review_style_20261013_rare_corrected_comparison.png",
+    "figures/sec05_cells_umap.png"
+  ]
+}

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/palette.json

@@ -0,0 +1,307 @@
+{
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+  "user_directive": "PBISC muted yellow/gold family; scSemiProfiler blue family throughout current results review",
+  "primary": {
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+    "scSemiProfiler": "#2166AC"
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+    "sec02_bulk_conditioning": {
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+      "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."
+    },
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+    },
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+        "#E69F00": "#2166AC",
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+        "#882255": "#978034"
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+      "reason": "PBISC gene panels in yellow/gold shades; scSemi reference line blue."
+    },
+    "review_style_20261013_rank": {
+      "mapping": {
+        "#E07B39": "#806A25",
+        "#D55E00": "#C5AA4B"
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+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
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+      "reason": "PBISC and its raw/calibrated inputs in yellow/gold shades; scSemi blue. Neutral reference/errorbar styles retained."
+    },
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+        "#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": {
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+        "#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": {
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+        "#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."
+    },
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+      "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"
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+      "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"
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+      "reason": "PBISC LoRA, zero-shot/calibrated and sc-only fine-tuning yellow/gold family; scSemi blue."
+    },
+    "secS_deconv_disease": {
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+        "#D55E00": "#C5AA4B",
+        "#E69F00": "#2166AC",
+        "#CC79A7": "#6A51A3"
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+      "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."
+    },
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+      "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"
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+      "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"
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+      "reason": "Raw-bulk and pseudobulk-input PBISC reconstructions gold; observed real cells grey. Scope black replacement to four verified rectangles only.",
+      "rectangle_rules": [
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+            247.078,
+            91.925,
+            361.296
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+          "old": "#1A1A1A",
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+            98.028,
+            233.272,
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+            374.618,
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+            8.734,
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+            17.134
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+        "#0072B2": "#B59A50",
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+        "#117733": "#978034",
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+        "#D55E00": "#C5AA4B"
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+      "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": {
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+        "#D55E00": "#C5AA4B",
+        "#882255": "#806A25",
+        "#0072B2": "#B59A50"
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+      "reason": "Pretrained LoRA gold, same-architecture scratch ablation dark gold, zero-shot ochre."
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+        "#E69F00": "#2166AC",
+        "#F5D08A": "#67A9CF"
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+      "reason": "PBISC gold; official scSemi blue and modified readout pale blue with original hatch."
+    }
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+  "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."
+}