diff --git a/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/disease_additions.json b/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/disease_additions.json
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index 0000000000000000000000000000000000000000..ca901e99ccafd85d51e46bd574c484bc434a61b1
--- /dev/null
+++ b/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/disease_additions.json
@@ -0,0 +1,1740 @@
+{
+  "schema": "pbisc.expanded-master.disease-additions.v1",
+  "created_at": "2026-10-13T03:41:51.170727+00:00",
+  "snapshot_started_at": "2026-10-13T03:41:43.484116+00:00",
+  "snapshot_scope": "Sepsis draws 0\u20134 and Imperial draw 0 only; each included unit must pass receipt/output hash checks",
+  "other_completed_receipts_for_next_refresh": [],
+  "slides": [
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_strict_sepsis_quality",
+      "title": "Sepsis: exact-five reconstruction across five draws",
+      "section_label": "Fig. 4 update",
+      "figures": [
+        "figures/expanded_master_20261013/disease/strict_sepsis_quality.png"
+      ],
+      "keywords": [],
+      "footnote": "Completed exact-five Sepsis draws. Bars = means; dots = support draws. Five matched methods; no new generation.",
+      "footnote_full": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Precision, coverage and composition are read directly from completed score summaries.\nSources: plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw1-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw2-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw3-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw4-score.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_sepsis_quality.csv",
+      "sources": "plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw1-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw2-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw3-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw4-score.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_sepsis_quality.csv",
+      "notes": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Precision, coverage and composition are read directly from completed score summaries.\nSources: plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw1-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw2-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw3-score.json; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw4-score.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_sepsis_quality.csv",
+      "after_original": 38,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_strict_sepsis_realism",
+      "title": "Sepsis: realism beyond precision and coverage",
+      "section_label": "Fig. 4 update",
+      "figures": [
+        "figures/expanded_master_20261013/disease/strict_sepsis_realism.png"
+      ],
+      "keywords": [],
+      "footnote": "Completed exact-five outputs; raw readout, fixed R1 reference. Real/real control shown. Dots are five support draws.",
+      "footnote_full": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. C2ST uses cached kNN AUROC; MMD uses bandwidth 1; E_N uses the saved PC subsample, squared distance and exact lower bound. No refitting.\nSources: plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/extras/ye2026_sepsis/strict/en.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_sepsis_realism.csv",
+      "sources": "plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/extras/ye2026_sepsis/strict/en.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_sepsis_realism.csv",
+      "notes": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. C2ST uses cached kNN AUROC; MMD uses bandwidth 1; E_N uses the saved PC subsample, squared distance and exact lower bound. No refitting.\nSources: plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/extras/ye2026_sepsis/strict/en.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/extras/ye2026_sepsis/strict/metrics.csv; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/extras/ye2026_sepsis/strict/en.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_sepsis_realism.csv",
+      "after_original": 38,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_strict_ye2026_sepsis_deg",
+      "title": "Sepsis: patient-aware disease-gene agreement",
+      "section_label": "Fig. 4 update",
+      "figures": [
+        "figures/expanded_master_20261013/disease/strict_ye2026_sepsis_deg.png"
+      ],
+      "keywords": [],
+      "footnote": "Completed corrected count-based DEG fits; mean of five support draws.",
+      "footnote_full": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Values are saved FDR-filtered top-50 list overlap counts, not correlations or cell classification accuracy. The recorded method is edgeR/TMM/limma-voom, with donor duplicateCorrelation for Imperial. A donor can contribute to both disease conditions; group donor counts must not be summed as independent people. Historical sample-level Welch metrics are different endpoints.\nSources: plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw1-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw2-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw3-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw4-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/status.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_ye2026_sepsis_deg.csv",
+      "sources": "plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw1-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw2-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw3-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw4-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/status.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_ye2026_sepsis_deg.csv",
+      "notes": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Values are saved FDR-filtered top-50 list overlap counts, not correlations or cell classification accuracy. The recorded method is edgeR/TMM/limma-voom, with donor duplicateCorrelation for Imperial. A donor can contribute to both disease conditions; group donor counts must not be summed as independent people. Historical sample-level Welch metrics are different endpoints.\nSources: plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw0/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw1-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw1/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw2-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw2/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw3-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw3/statistics/status.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/ye2026_sepsis-disease-draw4-score.json; plans/paper_figures_strictpairs_20261012/scores/ye2026_sepsis/disease/draw4/statistics/status.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_ye2026_sepsis_deg.csv",
+      "after_original": 40,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_strict_imperial_quality",
+      "title": "Imperial: first completed exact-five comparison",
+      "section_label": "Fig. 4 update",
+      "figures": [
+        "figures/expanded_master_20261013/disease/strict_imperial_draw0_quality.png"
+      ],
+      "keywords": [],
+      "footnote": "One completed support draw (draw 0). Exact five paired samples; all five methods scored. Not the final five-draw comparison.",
+      "footnote_full": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Single-draw evidence is shown separately from the complete Sepsis set. Repeated held-out visits remain linked to actual donor IDs.\nSources: plans/paper_figures_strictpairs_20261012/receipts/imperial_eskd-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/protocol/splits/imperial_eskd/disease/draw0/support.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_imperial_draw0_quality.csv",
+      "sources": "plans/paper_figures_strictpairs_20261012/receipts/imperial_eskd-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/protocol/splits/imperial_eskd/disease/draw0/support.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_imperial_draw0_quality.csv",
+      "notes": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Single-draw evidence is shown separately from the complete Sepsis set. Repeated held-out visits remain linked to actual donor IDs.\nSources: plans/paper_figures_strictpairs_20261012/receipts/imperial_eskd-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/protocol/splits/imperial_eskd/disease/draw0/support.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_imperial_draw0_quality.csv",
+      "after_original": 38,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_strict_imperial_eskd_deg",
+      "title": "Imperial: patient-aware disease-gene agreement",
+      "section_label": "Fig. 4 update",
+      "figures": [
+        "figures/expanded_master_20261013/disease/strict_imperial_eskd_deg.png"
+      ],
+      "keywords": [],
+      "footnote": "Single completed exact-five draw 0; patient-aware DEG fits. Other draws are outside this frozen snapshot.",
+      "footnote_full": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Values are saved FDR-filtered top-50 list overlap counts, not correlations or cell classification accuracy. The recorded method is edgeR/TMM/limma-voom, with donor duplicateCorrelation for Imperial. A donor can contribute to both disease conditions; group donor counts must not be summed as independent people. Historical sample-level Welch metrics are different endpoints.\nSources: plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/imperial_eskd-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/status.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_imperial_eskd_deg.csv",
+      "sources": "plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/imperial_eskd-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/status.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_imperial_eskd_deg.csv",
+      "notes": "Exactly one paired sample from each of five donors, no extra validation, fixed 3000-step LoRA. Only completed score receipts are used. Raw, external-reference calibration, same-pair calibration, scSemiProfiler and LoRA share the recorded held-out targets. Dots are support draws, not independent population replicates. These slides do not certify the unfinished four-cohort campaign. Values are saved FDR-filtered top-50 list overlap counts, not correlations or cell classification accuracy. The recorded method is edgeR/TMM/limma-voom, with donor duplicateCorrelation for Imperial. A donor can contribute to both disease conditions; group donor counts must not be summed as independent people. Historical sample-level Welch metrics are different endpoints.\nSources: plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/donor_deg/donor_deg_summary.csv; plans/paper_figures_strictpairs_20261012/receipts/imperial_eskd-disease-draw0-score.json; plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/status.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/strict_imperial_eskd_deg.csv",
+      "after_original": 40,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_sle_broadcast",
+      "title": "SLE: what is added beyond the bulk broadcast?",
+      "section_label": "Development benchmark",
+      "figures": [
+        "figures/sec04_sle_broadcast.png"
+      ],
+      "keywords": [],
+      "footnote": "Existing SLE pseudobulk development benchmark; bulk broadcast is an explicit comparator. Separate from paired real-bulk validation.",
+      "footnote_full": "Existing figure omitted from the original 76-slide specification. Retain its gene axis, cell-type units and seed counts. This is a pseudobulk-conditioned benchmark, not a new external real-bulk result.\nSources: presentations/2026-09-30--paper-summary--r00/data/sec04_sle_broadcast.csv; presentations/2026-09-30--paper-summary--r00/tools/sec04_sle_benchmark.py",
+      "sources": "presentations/2026-09-30--paper-summary--r00/data/sec04_sle_broadcast.csv; presentations/2026-09-30--paper-summary--r00/tools/sec04_sle_benchmark.py",
+      "notes": "Existing figure omitted from the original 76-slide specification. Retain its gene axis, cell-type units and seed counts. This is a pseudobulk-conditioned benchmark, not a new external real-bulk result.\nSources: presentations/2026-09-30--paper-summary--r00/data/sec04_sle_broadcast.csv; presentations/2026-09-30--paper-summary--r00/tools/sec04_sle_benchmark.py",
+      "after_original": 43,
+      "palette": "biological",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_influenza_response",
+      "title": "Influenza: response order versus response genes",
+      "section_label": "External diagnostic",
+      "figures": [
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/randolph/out/fig_randolph_celltype_response.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical zero-shot influenza test. Response-strength ordering is recovered; gene-wise agreement remains below the matched bulk broadcast.",
+      "footnote_full": "Generated cells rank monocytes as strongest and T cells as weakest responders, but fail the preregistered gene-wise beyond-broadcast rule. Different arms can have different eligible donor counts; each broadcast matches its arm's donors. Observed-PBMC broadcast is an oracle. No new fitting or cell generation.\nSources: plans/utility_studies_final6k_20260925/randolph/RESULTS.md; plans/utility_studies_final6k_20260925/randolph/MANIFEST.json; plans/utility_studies_final6k_20260925/randolph/out/extended/extended_analysis.json",
+      "sources": "plans/utility_studies_final6k_20260925/randolph/RESULTS.md; plans/utility_studies_final6k_20260925/randolph/MANIFEST.json; plans/utility_studies_final6k_20260925/randolph/out/extended/extended_analysis.json",
+      "notes": "Generated cells rank monocytes as strongest and T cells as weakest responders, but fail the preregistered gene-wise beyond-broadcast rule. Different arms can have different eligible donor counts; each broadcast matches its arm's donors. Observed-PBMC broadcast is an oracle. No new fitting or cell generation.\nSources: plans/utility_studies_final6k_20260925/randolph/RESULTS.md; plans/utility_studies_final6k_20260925/randolph/MANIFEST.json; plans/utility_studies_final6k_20260925/randolph/out/extended/extended_analysis.json",
+      "after_original": 43,
+      "palette": "biological",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_covid_map",
+      "title": "COVID: calibration on a shared real-cell map",
+      "section_label": "External diagnostic",
+      "figures": [
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/figures/fig1_umap_seven_panels_by_label_depth1000.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical 7 COVID / 5 HC samples, common depth. High-resolution reference overview; following detail panels provide readable quantitative results.",
+      "footnote_full": "This is an existing zero-shot input/calibration study, not LoRA/scSemiProfiler. Observed cells define the reference map. Use saved quantitative endpoints rather than interpreting overlap as a performance score. Biological cell-type colors are preserved.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/MANIFEST.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/receipts/receipt_checks.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/prec_cov.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/composition_full_chain.csv",
+      "sources": "plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/MANIFEST.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/receipts/receipt_checks.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/prec_cov.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/composition_full_chain.csv",
+      "notes": "This is an existing zero-shot input/calibration study, not LoRA/scSemiProfiler. Observed cells define the reference map. Use saved quantitative endpoints rather than interpreting overlap as a performance score. Biological cell-type colors are preserved.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/MANIFEST.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/receipts/receipt_checks.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/prec_cov.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/composition_full_chain.csv",
+      "after_original": 43,
+      "palette": "biological",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_covid_direction",
+      "title": "COVID monocytes: direction after depth matching",
+      "section_label": "External diagnostic",
+      "figures": [
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/figures/fig2_covid_hc_monocyte_arrows_depth1000.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical 7 COVID / 5 HC samples, common depth. High-resolution reference overview; following panels separate direction, magnitude and relabeling null.",
+      "footnote_full": "Native-depth and depth-matched results differ. Relabelling-null shares are descriptive; not every directional cosine exceeds its null. No claim of independent significance or completed Figure 6 reproduction.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/MANIFEST.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/receipts/receipt_checks.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv",
+      "sources": "plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/MANIFEST.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/receipts/receipt_checks.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv",
+      "notes": "Native-depth and depth-matched results differ. Relabelling-null shares are descriptive; not every directional cosine exceeds its null. No claim of independent significance or completed Figure 6 reproduction.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/MANIFEST.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/receipts/receipt_checks.json; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv",
+      "after_original": 43,
+      "palette": "biological",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_covid_monocyte_direction_detail",
+      "title": "COVID monocytes: direction, magnitude and null",
+      "section_label": "External diagnostic",
+      "figures": [
+        "figures/expanded_master_20261013/disease/covid_monocyte_direction_detail.png"
+      ],
+      "keywords": [],
+      "footnote": "Readable detail of the retained COVID overview. Existing 7 COVID / 5 HC paired samples; native and depth-matched results stay separate.",
+      "footnote_full": "Every saved arm is retained, including the held-out real-cell reference, raw, TPM, both reference calibrations, paired calibration and own-sc-pseudobulk conditions. Cosine and length ratio use the recorded PCA-50 disease displacement; they are not read from the 2D UMAP. Relabeling-null share is the existing descriptive fraction of label permutations whose cosine is at least the observed one, not a newly fitted p-value or proof of biological reproduction. The full original depth-matched spatial overview remains in the deck. Only native UMAP coordinates were persisted in embedding_native_cells.parquet; these detail panels use saved numeric displacement tables instead of refitting depth-matched UMAP.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_monocyte_direction_detail.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md",
+      "sources": "plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_monocyte_direction_detail.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md",
+      "notes": "Every saved arm is retained, including the held-out real-cell reference, raw, TPM, both reference calibrations, paired calibration and own-sc-pseudobulk conditions. Cosine and length ratio use the recorded PCA-50 disease displacement; they are not read from the 2D UMAP. Relabeling-null share is the existing descriptive fraction of label permutations whose cosine is at least the observed one, not a newly fitted p-value or proof of biological reproduction. The full original depth-matched spatial overview remains in the deck. Only native UMAP coordinates were persisted in embedding_native_cells.parquet; these detail panels use saved numeric displacement tables instead of refitting depth-matched UMAP.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_monocyte_direction_detail.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md",
+      "after_original": 43,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_covid_cd14_direction_detail",
+      "title": "COVID CD14 monocytes: direction, magnitude and null",
+      "section_label": "External diagnostic",
+      "figures": [
+        "figures/expanded_master_20261013/disease/covid_cd14_direction_detail.png"
+      ],
+      "keywords": [],
+      "footnote": "Readable detail of the retained COVID overview. Existing 7 COVID / 5 HC paired samples; native and depth-matched results stay separate.",
+      "footnote_full": "Every saved arm is retained, including the held-out real-cell reference, raw, TPM, both reference calibrations, paired calibration and own-sc-pseudobulk conditions. Cosine and length ratio use the recorded PCA-50 disease displacement; they are not read from the 2D UMAP. Relabeling-null share is the existing descriptive fraction of label permutations whose cosine is at least the observed one, not a newly fitted p-value or proof of biological reproduction. The full original depth-matched spatial overview remains in the deck. Only native UMAP coordinates were persisted in embedding_native_cells.parquet; these detail panels use saved numeric displacement tables instead of refitting depth-matched UMAP.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_cd14_direction_detail.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md",
+      "sources": "plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_cd14_direction_detail.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md",
+      "notes": "Every saved arm is retained, including the held-out real-cell reference, raw, TPM, both reference calibrations, paired calibration and own-sc-pseudobulk conditions. Cosine and length ratio use the recorded PCA-50 disease displacement; they are not read from the 2D UMAP. Relabeling-null share is the existing descriptive fraction of label permutations whose cosine is at least the observed one, not a newly fitted p-value or proof of biological reproduction. The full original depth-matched spatial overview remains in the deck. Only native UMAP coordinates were persisted in embedding_native_cells.parquet; these detail panels use saved numeric displacement tables instead of refitting depth-matched UMAP.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_cd14_direction_detail.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/placement/tables/displacement_relabel_null.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md",
+      "after_original": 43,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_covid_endpoints",
+      "title": "COVID: biological endpoints give a mixed verdict",
+      "section_label": "External diagnostic",
+      "figures": [
+        "figures/expanded_master_20261013/disease/covid_endpoints.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical 7 COVID / 5 HC samples. Saved effect ratios and donor ranks; no new fits. Reference calibration is not uniformly best.",
+      "footnote_full": "Four predefined endpoints are all retained. Reference calibration improves some plasmablast/composition endpoints but loses HLA-DR donor ranking and overshoots the ISG effect. All generated arms fail the original preregistered gene-wide beyond-broadcast criterion; the alternate pipeline definition is not substituted.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/effects_final/endpoints_paired12.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_endpoints.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/global_r/global_logfc_r_two_definitions.csv",
+      "sources": "plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/effects_final/endpoints_paired12.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_endpoints.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/global_r/global_logfc_r_two_definitions.csv",
+      "notes": "Four predefined endpoints are all retained. Reference calibration improves some plasmablast/composition endpoints but loses HLA-DR donor ranking and overshoots the ISG effect. All generated arms fail the original preregistered gene-wide beyond-broadcast criterion; the alternate pipeline definition is not substituted.\nSources: plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/effects_final/endpoints_paired12.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/covid_endpoints.csv; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/RESULTS.md; plans/utility_studies_final6k_20260925/refcal_scoring/arunachalam/global_r/global_logfc_r_two_definitions.csv",
+      "after_original": 43,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_rare_misses_1",
+      "title": "Rare-state misses: rules 1\u20138",
+      "section_label": "Fig. 5 detail",
+      "figures": [
+        "figures/expanded_master_20261013/disease/rare_misses_1.png"
+      ],
+      "keywords": [],
+      "footnote": "Saved zero-aware diagnostic; all 15 predefined rules are shown across two slides. NA means not evaluable, not zero error.",
+      "footnote_full": "Historical five-donor training can include multiple paired visits in Imperial, Giroux and Ji. It is not the strict five-sample protocol. Existing predictions and frozen marker/label rules are reused. Each percentage is the saved mean across support draws of missed observed-positive donor fraction. Actual donor IDs, zero draws and common depth/cell budget are retained by the existing analysis. Mandatory IGLL5 is absent for the Ji plasmablast marker rule, which stays unavailable.\nSources: plans/paper_figures_strictpairs_20261012/source_data/rare_all_states_aggregate.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/rare_misses_1.csv; plans/paper_figures_strictpairs_20261012/reports/rare_provenance.json; plans/paper_figures_strictpairs_20261012/reports/rare_readiness.md",
+      "sources": "plans/paper_figures_strictpairs_20261012/source_data/rare_all_states_aggregate.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/rare_misses_1.csv; plans/paper_figures_strictpairs_20261012/reports/rare_provenance.json; plans/paper_figures_strictpairs_20261012/reports/rare_readiness.md",
+      "notes": "Historical five-donor training can include multiple paired visits in Imperial, Giroux and Ji. It is not the strict five-sample protocol. Existing predictions and frozen marker/label rules are reused. Each percentage is the saved mean across support draws of missed observed-positive donor fraction. Actual donor IDs, zero draws and common depth/cell budget are retained by the existing analysis. Mandatory IGLL5 is absent for the Ji plasmablast marker rule, which stays unavailable.\nSources: plans/paper_figures_strictpairs_20261012/source_data/rare_all_states_aggregate.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/rare_misses_1.csv; plans/paper_figures_strictpairs_20261012/reports/rare_provenance.json; plans/paper_figures_strictpairs_20261012/reports/rare_readiness.md",
+      "after_original": 50,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_rare_misses_2",
+      "title": "Rare-state misses: rules 9\u201315",
+      "section_label": "Fig. 5 detail",
+      "figures": [
+        "figures/expanded_master_20261013/disease/rare_misses_2.png"
+      ],
+      "keywords": [],
+      "footnote": "Saved zero-aware diagnostic; all 15 predefined rules are shown across two slides. NA means not evaluable, not zero error.",
+      "footnote_full": "Historical five-donor training can include multiple paired visits in Imperial, Giroux and Ji. It is not the strict five-sample protocol. Existing predictions and frozen marker/label rules are reused. Each percentage is the saved mean across support draws of missed observed-positive donor fraction. Actual donor IDs, zero draws and common depth/cell budget are retained by the existing analysis. Mandatory IGLL5 is absent for the Ji plasmablast marker rule, which stays unavailable.\nSources: plans/paper_figures_strictpairs_20261012/source_data/rare_all_states_aggregate.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/rare_misses_2.csv; plans/paper_figures_strictpairs_20261012/reports/rare_provenance.json; plans/paper_figures_strictpairs_20261012/reports/rare_readiness.md",
+      "sources": "plans/paper_figures_strictpairs_20261012/source_data/rare_all_states_aggregate.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/rare_misses_2.csv; plans/paper_figures_strictpairs_20261012/reports/rare_provenance.json; plans/paper_figures_strictpairs_20261012/reports/rare_readiness.md",
+      "notes": "Historical five-donor training can include multiple paired visits in Imperial, Giroux and Ji. It is not the strict five-sample protocol. Existing predictions and frozen marker/label rules are reused. Each percentage is the saved mean across support draws of missed observed-positive donor fraction. Actual donor IDs, zero draws and common depth/cell budget are retained by the existing analysis. Mandatory IGLL5 is absent for the Ji plasmablast marker rule, which stays unavailable.\nSources: plans/paper_figures_strictpairs_20261012/source_data/rare_all_states_aggregate.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/rare_misses_2.csv; plans/paper_figures_strictpairs_20261012/reports/rare_provenance.json; plans/paper_figures_strictpairs_20261012/reports/rare_readiness.md",
+      "after_original": 50,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_sepsis_rare_support",
+      "title": "Sepsis rare states across paired-data budgets",
+      "section_label": "Fig. 5 detail",
+      "figures": [
+        "figures/expanded_master_20261013/disease/sepsis_rare_support.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical cross-fitted learning curve: n training pairs plus validation, not strict total n. All 15 rules; arm-specific depth matching.",
+      "footnote_full": "Existing pooled predictions for 82 donors and 1500 generated cells per sample. Each donor was held out from its fold model. Raw and pseudobulk are zero-shot controls; numbered/full columns are historical LoRA budgets. Observed cells were thinned separately to each arm's depth, so compare gen/obs within an arm. No new generation or rare-state scoring; the full 15-rule family, including controls, is preserved.\nSources: plans/rare_states_screen_20261004/out/sepsis_summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/sepsis_rare_support.csv; plans/rare_states_screen_20261004/README.md; plans/rare_states_screen_20261004/tools/states.json",
+      "sources": "plans/rare_states_screen_20261004/out/sepsis_summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/sepsis_rare_support.csv; plans/rare_states_screen_20261004/README.md; plans/rare_states_screen_20261004/tools/states.json",
+      "notes": "Existing pooled predictions for 82 donors and 1500 generated cells per sample. Each donor was held out from its fold model. Raw and pseudobulk are zero-shot controls; numbered/full columns are historical LoRA budgets. Observed cells were thinned separately to each arm's depth, so compare gen/obs within an arm. No new generation or rare-state scoring; the full 15-rule family, including controls, is preserved.\nSources: plans/rare_states_screen_20261004/out/sepsis_summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/sepsis_rare_support.csv; plans/rare_states_screen_20261004/README.md; plans/rare_states_screen_20261004/tools/states.json",
+      "after_original": 51,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_sepsis_rare_direction",
+      "title": "Sepsis rare-state direction across support budgets",
+      "section_label": "Fig. 5 detail",
+      "figures": [
+        "figures/expanded_master_20261013/disease/sepsis_rare_direction.png"
+      ],
+      "keywords": [],
+      "footnote": "Saved sign-agreement counts across all 15 rules, including controls. Historical n + validation; directions are not effect-size accuracy.",
+      "footnote_full": "Counts summarize existing same_direction booleans; no thresholds or p-values are recomputed. All rule-family members are retained, including weak or failed states and positive/negative controls. A matching sign does not establish that a rare state's abundance or marker co-expression is reproduced.\nSources: plans/rare_states_screen_20261004/out/sepsis_contrasts.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/sepsis_rare_direction.csv; plans/rare_states_screen_20261004/README.md",
+      "sources": "plans/rare_states_screen_20261004/out/sepsis_contrasts.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/sepsis_rare_direction.csv; plans/rare_states_screen_20261004/README.md",
+      "notes": "Counts summarize existing same_direction booleans; no thresholds or p-values are recomputed. All rule-family members are retained, including weak or failed states and positive/negative controls. A matching sign does not establish that a rare state's abundance or marker co-expression is reproduced.\nSources: plans/rare_states_screen_20261004/out/sepsis_contrasts.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/sepsis_rare_direction.csv; plans/rare_states_screen_20261004/README.md",
+      "after_original": 51,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_external_rare_screen",
+      "title": "Rare-state screen in DRESS, Kawasaki and SLE",
+      "section_label": "Rare-state appendix",
+      "figures": [
+        "figures/expanded_master_20261013/disease/external_rare_screen.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical one-seed zero-shot screen conditioned on each sample's own sc pseudobulk. DRESS was in training; real-bulk validation is separate.",
+      "footnote_full": "All 15 predefined states are shown. Samples' own sc pseudobulk conditions remove the real-bulk shift. Observed marker states are thinned to generated depth. DRESS includes cultured/stimulated samples and was seen during training. This is descriptive capability evidence, not an unseen-disease paired validation or Figure 6 reproduction.\nSources: plans/rare_states_screen_20261004/out/summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/external_rare_screen.csv; plans/rare_states_screen_20261004/README.md; plans/rare_states_screen_20261004/tools/states.json",
+      "sources": "plans/rare_states_screen_20261004/out/summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/external_rare_screen.csv; plans/rare_states_screen_20261004/README.md; plans/rare_states_screen_20261004/tools/states.json",
+      "notes": "All 15 predefined states are shown. Samples' own sc pseudobulk conditions remove the real-bulk shift. Observed marker states are thinned to generated depth. DRESS includes cultured/stimulated samples and was seen during training. This is descriptive capability evidence, not an unseen-disease paired validation or Figure 6 reproduction.\nSources: plans/rare_states_screen_20261004/out/summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/external_rare_screen.csv; plans/rare_states_screen_20261004/README.md; plans/rare_states_screen_20261004/tools/states.json",
+      "after_original": 51,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_c1q_cross_disease",
+      "title": "C1Q: single-gene detection versus co-detection",
+      "section_label": "Rare-state appendix",
+      "figures": [
+        "figures/expanded_master_20261013/disease/c1q_cross_disease.png"
+      ],
+      "keywords": [],
+      "footnote": "Existing pseudobulk-conditioned comparison at matched depth. Multi-gene C1Q rates remain compressed, including in-corpus DRESS.",
+      "footnote_full": "One sampling seed. DRESS has seven samples, including four cultured/stimulated samples; Kawasaki has 15 and SLE 56. Corpus inclusion is not randomized and DRESS samples were seen in training. Retain the distinction between any-gene detection and at least two C1Q genes in the same cell; no causal claim about pretraining exposure.\nSources: plans/c1q_crossdisease_20261004/out/summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/c1q_cross_disease.csv; plans/c1q_crossdisease_20261004/README.md",
+      "sources": "plans/c1q_crossdisease_20261004/out/summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/c1q_cross_disease.csv; plans/c1q_crossdisease_20261004/README.md",
+      "notes": "One sampling seed. DRESS has seven samples, including four cultured/stimulated samples; Kawasaki has 15 and SLE 56. Corpus inclusion is not randomized and DRESS samples were seen in training. Retain the distinction between any-gene detection and at least two C1Q genes in the same cell; no causal claim about pretraining exposure.\nSources: plans/c1q_crossdisease_20261004/out/summary.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/c1q_cross_disease.csv; plans/c1q_crossdisease_20261004/README.md",
+      "after_original": 52,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_behcet_k4000",
+      "title": "Beh\u00e7et: K=4,000 changes direction more than identity",
+      "section_label": "Beh\u00e7et diagnostic",
+      "figures": [
+        "figures/expanded_master_20261013/disease/behcet_k4000.png"
+      ],
+      "keywords": [],
+      "footnote": "Two existing sampling seeds; 6 BD / 10 HC held-out bulks. K is condition size; each bulk still generates 5,000 cells. Descriptive.",
+      "footnote_full": "The real reference is 4 BD and 4 HC sc donors, mostly unmatched and including training donors. The three BD-only training candidates include two primary identity passes and one uncertain candidate. K4000 strengthens the any-C1Q group direction, but \u22652-gene cells remain far below observed. Same-pair calibration can also recover direction; this plot does not claim LoRA uniquely does so. No p-values are promoted.\nSources: plans/behcet_c1q_lora3_20261004/out/group_table.csv; plans/behcet_c1q_lora3_20261004/out/group_table_k4000.csv; plans/behcet_c1q_lora3_20261004/out/capability.csv; plans/behcet_c1q_lora3_20261004/out/capability_k4000.csv; plans/behcet_c1q_lora3_20261004/README.md; plans/paper_figures_strictpairs_20261012/reports/rare_behcet_provenance.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/behcet_k4000.csv",
+      "sources": "plans/behcet_c1q_lora3_20261004/out/group_table.csv; plans/behcet_c1q_lora3_20261004/out/group_table_k4000.csv; plans/behcet_c1q_lora3_20261004/out/capability.csv; plans/behcet_c1q_lora3_20261004/out/capability_k4000.csv; plans/behcet_c1q_lora3_20261004/README.md; plans/paper_figures_strictpairs_20261012/reports/rare_behcet_provenance.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/behcet_k4000.csv",
+      "notes": "The real reference is 4 BD and 4 HC sc donors, mostly unmatched and including training donors. The three BD-only training candidates include two primary identity passes and one uncertain candidate. K4000 strengthens the any-C1Q group direction, but \u22652-gene cells remain far below observed. Same-pair calibration can also recover direction; this plot does not claim LoRA uniquely does so. No p-values are promoted.\nSources: plans/behcet_c1q_lora3_20261004/out/group_table.csv; plans/behcet_c1q_lora3_20261004/out/group_table_k4000.csv; plans/behcet_c1q_lora3_20261004/out/capability.csv; plans/behcet_c1q_lora3_20261004/out/capability_k4000.csv; plans/behcet_c1q_lora3_20261004/README.md; plans/paper_figures_strictpairs_20261012/reports/rare_behcet_provenance.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/behcet_k4000.csv",
+      "after_original": 52,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_k4000_quality",
+      "title": "K=4,000 recipe: paired reconstruction quality",
+      "section_label": "Recipe sensitivity",
+      "figures": [
+        "figures/expanded_master_20261013/disease/k4000_quality.png"
+      ],
+      "keywords": [],
+      "footnote": "Existing paired benchmark, five support draws per cohort and 1,500 cells/test sample. Bars = means; dots = draws. No new runs.",
+      "footnote_full": "The stored K1000 re-score exactly matched 25 original metrics in every draw. K4000 uses a changed condition recipe and draw-specific seeds; it is not a perfectly isolated one-factor K test. Imperial training uses all visits from five donors. Disease logFC/DEG are the historical sample-level estimators, not the new patient-aware strict metrics. No donor-draw p-values are used here; overlapping test donors are not independent replicates.\nSources: plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/AGGREGATE.md; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/AGGREGATE.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_quality.csv; plans/bulkonly_lora5_k4000_20261006/README.md",
+      "sources": "plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/AGGREGATE.md; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/AGGREGATE.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_quality.csv; plans/bulkonly_lora5_k4000_20261006/README.md",
+      "notes": "The stored K1000 re-score exactly matched 25 original metrics in every draw. K4000 uses a changed condition recipe and draw-specific seeds; it is not a perfectly isolated one-factor K test. Imperial training uses all visits from five donors. Disease logFC/DEG are the historical sample-level estimators, not the new patient-aware strict metrics. No donor-draw p-values are used here; overlapping test donors are not independent replicates.\nSources: plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/AGGREGATE.md; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/AGGREGATE.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_quality.csv; plans/bulkonly_lora5_k4000_20261006/README.md",
+      "after_original": 67,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_k4000_disease",
+      "title": "K=4,000 recipe: disease signal does not improve uniformly",
+      "section_label": "Recipe sensitivity",
+      "figures": [
+        "figures/expanded_master_20261013/disease/k4000_disease.png"
+      ],
+      "keywords": [],
+      "footnote": "Existing paired benchmark, five support draws per cohort and 1,500 cells/test sample. Bars = means; dots = draws. No new runs.",
+      "footnote_full": "The stored K1000 re-score exactly matched 25 original metrics in every draw. K4000 uses a changed condition recipe and draw-specific seeds; it is not a perfectly isolated one-factor K test. Imperial training uses all visits from five donors. Disease logFC/DEG are the historical sample-level estimators, not the new patient-aware strict metrics. No donor-draw p-values are used here; overlapping test donors are not independent replicates.\nSources: plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/AGGREGATE.md; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/AGGREGATE.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_disease.csv; plans/bulkonly_lora5_k4000_20261006/README.md",
+      "sources": "plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/AGGREGATE.md; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/AGGREGATE.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_disease.csv; plans/bulkonly_lora5_k4000_20261006/README.md",
+      "notes": "The stored K1000 re-score exactly matched 25 original metrics in every draw. K4000 uses a changed condition recipe and draw-specific seeds; it is not a perfectly isolated one-factor K test. Imperial training uses all visits from five donors. Disease logFC/DEG are the historical sample-level estimators, not the new patient-aware strict metrics. No donor-draw p-values are used here; overlapping test donors are not independent replicates.\nSources: plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/ye2026_sepsis/AGGREGATE.md; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/per_draw.csv; plans/bulkonly_lora5_k4000_20261006/analysis/benchmark/imperial_eskd/AGGREGATE.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_disease.csv; plans/bulkonly_lora5_k4000_20261006/README.md",
+      "after_original": 67,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_k4000_calibration",
+      "title": "K=4,000 recipe: calibration gains are selective",
+      "section_label": "Recipe sensitivity",
+      "figures": [
+        "figures/expanded_master_20261013/disease/k4000_calibration.png"
+      ],
+      "keywords": [],
+      "footnote": "Saved paired-test gates: 50 features \u00d7 5 draws per cohort. Descriptive counts, not 250 independent biological replicates.",
+      "footnote_full": "Level gate: generated/observed ratio 0.5\u20132 and Spearman at least 0.3. Contrast gate: same sign and generated magnitude 0.5\u20132 times observed. Disease contrasts shown are adult sepsis/HC and COVID+/COVID\u2212. Imperial severity gates are omitted here because historical severity grouping required separate correction. The K4000 bulk-only discovery workflow was not completed and is not inferred from calibration.\nSources: plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/ye2026_sepsis/per_feature.csv; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/ye2026_sepsis/SUMMARY.md; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/imperial_eskd/per_feature.csv; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/imperial_eskd/SUMMARY.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_calibration.csv",
+      "sources": "plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/ye2026_sepsis/per_feature.csv; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/ye2026_sepsis/SUMMARY.md; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/imperial_eskd/per_feature.csv; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/imperial_eskd/SUMMARY.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_calibration.csv",
+      "notes": "Level gate: generated/observed ratio 0.5\u20132 and Spearman at least 0.3. Contrast gate: same sign and generated magnitude 0.5\u20132 times observed. Disease contrasts shown are adult sepsis/HC and COVID+/COVID\u2212. Imperial severity gates are omitted here because historical severity grouping required separate correction. The K4000 bulk-only discovery workflow was not completed and is not inferred from calibration.\nSources: plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/ye2026_sepsis/per_feature.csv; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/ye2026_sepsis/SUMMARY.md; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/imperial_eskd/per_feature.csv; plans/bulkonly_lora5_k4000_20261006/analysis/compare_k1000/imperial_eskd/SUMMARY.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/k4000_calibration.csv",
+      "after_original": 67,
+      "palette": "native",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_bulkonly_verification_history",
+      "title": "Historical bulk-only search: no confirmed new finding",
+      "section_label": "Historical exploration",
+      "figures": [
+        "figures/expanded_master_20261013/disease/bulkonly_verification_history.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical exploratory analysis of existing bulk-only generations. Review dispositions are not experimental validation. Figure 6 reproduction still awaits new data.",
+      "footnote_full": "The original K1000 workflow considered 18 Sepsis and 21 Imperial candidate findings. Both reports retain zero confirmed findings under their internal two-verifier grading rule. This is an account of prior exploration, not newly completed biology. Known weaknesses include shared generation noise across draws, calibration transfer, clinical confounding and some invalid verifier p-values. No novel cell population survived verification; the user-prepared Figure 6 reproduction is still pending.\nSources: plans/bulkonly_lora5_20261006/analysis/wf/findings_ye2026_sepsis.json; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_ye2026_sepsis.md; plans/bulkonly_lora5_20261006/analysis/wf/findings_imperial_eskd.json; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_imperial_eskd.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/bulkonly_verification_history.csv; plans/bulkonly_lora5_20261006/README.md",
+      "sources": "plans/bulkonly_lora5_20261006/analysis/wf/findings_ye2026_sepsis.json; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_ye2026_sepsis.md; plans/bulkonly_lora5_20261006/analysis/wf/findings_imperial_eskd.json; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_imperial_eskd.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/bulkonly_verification_history.csv; plans/bulkonly_lora5_20261006/README.md",
+      "notes": "The original K1000 workflow considered 18 Sepsis and 21 Imperial candidate findings. Both reports retain zero confirmed findings under their internal two-verifier grading rule. This is an account of prior exploration, not newly completed biology. Known weaknesses include shared generation noise across draws, calibration transfer, clinical confounding and some invalid verifier p-values. No novel cell population survived verification; the user-prepared Figure 6 reproduction is still pending.\nSources: plans/bulkonly_lora5_20261006/analysis/wf/findings_ye2026_sepsis.json; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_ye2026_sepsis.md; plans/bulkonly_lora5_20261006/analysis/wf/findings_imperial_eskd.json; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_imperial_eskd.md; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/bulkonly_verification_history.csv; plans/bulkonly_lora5_20261006/README.md",
+      "after_original": 55,
+      "palette": "biological",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_bulkonly_imperial_wave_shift",
+      "title": "Bulk-only exploration: calibration populations differ",
+      "section_label": "Historical exploration",
+      "figures": [
+        "figures/expanded_master_20261013/disease/bulkonly_imperial_wave_shift.png"
+      ],
+      "keywords": [],
+      "footnote": "Historical Imperial sample composition. Paired and bulk-only sets differ in wave; repeated samples are not independent donors.",
+      "footnote_full": "Counts are read from the original synthesis table, including the recorded mixed w1|w2 category rather than silently reallocating it. This describes a calibration-transfer limitation and is not a causal wave effect or novel biological discovery. Figure 6 remains awaiting the user's new reproduction dataset.\nSources: plans/bulkonly_lora5_20261006/analysis/wf/synthesis_imperial_eskd/i00_samples_by_set_group_wave.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/bulkonly_imperial_wave_shift.csv; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_imperial_eskd.md",
+      "sources": "plans/bulkonly_lora5_20261006/analysis/wf/synthesis_imperial_eskd/i00_samples_by_set_group_wave.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/bulkonly_imperial_wave_shift.csv; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_imperial_eskd.md",
+      "notes": "Counts are read from the original synthesis table, including the recorded mixed w1|w2 category rather than silently reallocating it. This describes a calibration-transfer limitation and is not a causal wave effect or novel biological discovery. Figure 6 remains awaiting the user's new reproduction dataset.\nSources: plans/bulkonly_lora5_20261006/analysis/wf/synthesis_imperial_eskd/i00_samples_by_set_group_wave.csv; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/bulkonly_imperial_wave_shift.csv; plans/bulkonly_lora5_20261006/analysis/wf/REPORT_imperial_eskd.md",
+      "after_original": 55,
+      "palette": "biological",
+      "new_experiment": false
+    },
+    {
+      "kind": "content",
+      "layout": "full",
+      "key": "disease_deconv_expression_coverage",
+      "title": "Deconvolution: expression coverage limits the comparison",
+      "section_label": "Deconvolution detail",
+      "figures": [
+        "figures/expanded_master_20261013/disease/deconv_expression_coverage.png"
+      ],
+      "keywords": [],
+      "footnote": "Completed historical CIBERSORTx five-donor runs. Missing disease correlations remain unavailable; deconvolution does not generate individual cells.",
+      "footnote_full": "Historical five-donor training can include multiple paired visits in Imperial, Giroux and Ji. It is not the strict five-sample protocol. Existing predictions and frozen marker/label rules are reused. Coverage is the saved HiRes covered-gene count; some genes outside the four contrast cell types can be covered even when the disease correlation is unavailable. Two Giroux draws and one Ji draw lack that score. The internal summary field named bayesprism is reused by the old scorer for CIBERSORTx; these values are from CIBERSORTx files. Existing Sepsis method adoption does not mean new corrected strict deconvolution statistics are already complete.\nSources: plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw4_cibersortx/summary.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/deconv_expression_coverage.csv; plans/bayesprism_paired_20261006/results/RESULTS_cibersortx.md",
+      "sources": "plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw4_cibersortx/summary.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/deconv_expression_coverage.csv; plans/bayesprism_paired_20261006/results/RESULTS_cibersortx.md",
+      "notes": "Historical five-donor training can include multiple paired visits in Imperial, Giroux and Ji. It is not the strict five-sample protocol. Existing predictions and frozen marker/label rules are reused. Coverage is the saved HiRes covered-gene count; some genes outside the four contrast cell types can be covered even when the disease correlation is unavailable. Two Giroux draws and one Ji draw lack that score. The internal summary field named bayesprism is reused by the old scorer for CIBERSORTx; these values are from CIBERSORTx files. Existing Sepsis method adoption does not mean new corrected strict deconvolution statistics are already complete.\nSources: plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ye2026_sepsis/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/imperial_eskd/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/giroux2022/fewshot_draw4_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw0_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw1_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw2_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw3_cibersortx/summary.json; plans/bayesprism_paired_20261006/results/ji2025_chili/fewshot_draw4_cibersortx/summary.json; presentations/2026-09-30--paper-summary--r00/data/expanded_master_20261013/disease/deconv_expression_coverage.csv; plans/bayesprism_paired_20261006/results/RESULTS_cibersortx.md",
+      "after_original": 46,
+      "palette": "native",
+      "new_experiment": false
+    }
+  ],
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+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/status.json",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/statistics/donor_bootstrap_2000.csv",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/extras/imperial_eskd/strict/manifest.json",
+        "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scores/imperial_eskd/disease/draw0/contrast/imperial_eskd/strict/manifest.json"
+      ]
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+  "figure6": "new reproduction dataset still pending; bulk-only additions are historical exploration",
+  "deduplicated_root_additions": [
+    "corrected rare-state frequencies",
+    "corrected rare comparison",
+    "Behcet any/multi-C1Q rules"
+  ],
+  "display_work": "saved-table aggregation/formatting and existing figure reuse only"
+}
diff --git a/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/healthy/annotation_agreement.csv b/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/healthy/annotation_agreement.csv
new file mode 100644
index 0000000000000000000000000000000000000000..dade5764d90e20db73d0123429cc58176cc2b1b6
--- /dev/null
+++ b/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/healthy/annotation_agreement.csv
@@ -0,0 +1,9 @@
+author_gate[manual.celltype] \ frozen,T cell,B cell,Monocyte,NK cell,DC,Other,T cell_row_percent,B cell_row_percent,Monocyte_row_percent,NK cell_row_percent,DC_row_percent,Other_row_percent
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+DC,112,13,873,19,7564,21,1.3020227853987445,0.15112764473378285,10.14880260404557,0.22087886538014415,87.93303882817949,0.2441292722622646
+Other,1272,3,243,166,5,23,74.29906542056075,0.17523364485981308,14.19392523364486,9.69626168224299,0.29205607476635514,1.3434579439252337
+author_mixed,1534,819,2289,425,141,105,28.872576698663654,15.41501976284585,43.08300395256917,7.999247129681912,2.6538678712591754,1.9762845849802373
+author_unlabelled,13606,714,3819,2146,253,996,63.183802359060095,3.3156868208414596,17.734745054332684,9.965635738831615,1.174886226432618,4.625243800501532
diff --git a/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/healthy/annotation_agreement.provenance.json b/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/healthy/annotation_agreement.provenance.json
new file mode 100644
index 0000000000000000000000000000000000000000..f99f4703917c26b6d53bd0e680f046a41ca5a9c8
--- /dev/null
+++ b/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/healthy/annotation_agreement.provenance.json
@@ -0,0 +1,26 @@
+{
+  "key": "annotation_agreement",
+  "source_records": [
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/build_manifest.json",
+      "sha256": "90c9f650705cf0beb1e33f41d6cfad12ecb99d183c17090f206f9e8b245ef785",
+      "role": "frozen annotation comparison provenance"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/confusion_author_vs_frozen_baseline.csv",
+      "sha256": "487ec0dd8b6f470987dda04337a7d3485f0229bf8d787507e3745d95ae9ae434",
+      "role": "saved analysis input"
+    },
+    {
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/out/observed_summary.json",
+      "sha256": "c3f113fd18f54113cc011886490b1664b1e40a8f35bc89f5ba007fb49ce4ae50",
+      "role": "saved analysis metadata"
+    }
+  ],
+  "new_training": false,
+  "new_inference": false,
+  "new_embedding": false,
+  "new_statistical_scoring": false,
+  "display_transform_notes": "Saved observed-cell comparison, not generated-cell model performance. Overall 97.17% agreement uses 365,404 author-labelled cells in the supported six-type gate; mixed/unlabelled categories are displayed in the matrix but excluded from that agreement figure. Other has weak correspondence between taxonomies. The frozen annotation's comparison to author labels is not an independent gold-standard validation. Heatmap is a count-row normalization for display; precision/recall are saved summary metrics.",
+  "palette": "preserved"
+}
diff --git a/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/healthy/depth_matched_quality.csv b/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/healthy/depth_matched_quality.csv
new file mode 100644
index 0000000000000000000000000000000000000000..0f89ce7233fc73e4ea6309c7099db6210ba468db
--- /dev/null
+++ b/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/healthy/depth_matched_quality.csv
@@ -0,0 +1,25 @@
+arm,metric,depth,value
+R2,precision,native,0.9627414330218068
+R2,precision,matched,0.954018691588785
+raw,precision,native,0.3630529595015576
+raw,precision,matched,0.420809968847352
+tpm,precision,native,0.8745171339563863
+tpm,precision,matched,0.892398753894081
+refcal,precision,native,0.765607476635514
+refcal,precision,matched,0.778380062305296
+cal,precision,native,0.9192523364485982
+cal,precision,matched,0.9421806853582556
+pseudo,precision,native,0.924859813084112
+pseudo,precision,matched,0.9467289719626168
+R2,coverage,native,0.9997507788161992
+R2,coverage,matched,0.9997507788161992
+raw,coverage,native,0.083613707165109
+raw,coverage,matched,0.1437383177570093
+tpm,coverage,native,0.4595015576323987
+tpm,coverage,matched,0.6109034267912773
+refcal,coverage,native,0.0806853582554517
+refcal,coverage,matched,0.1939563862928349
+cal,coverage,native,0.5200623052959501
+cal,coverage,matched,0.7796884735202492
+pseudo,coverage,native,0.5068535825545172
+pseudo,coverage,matched,0.74797507788162