Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_slide_text.json

@@ -0,0 +1,190 @@
+{
+ "section": "09",
+ "slides": [
+  {
+   "title": "Five paired cohorts",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_cohorts.png"
+   ],
+   "keywords": [
+    "403 paired samples, 275 donors",
+    "Only identity-pass pairs; donor-level splits",
+    "Ji bulk: whole blood, not PBMC"
+   ],
+   "footnote": "Usable pair = passed the pairing identity check and >= 200 cells (fold >= 0 in data/<cohort>/folds.csv); dropped 15 identity-fail, 11 borderline and 1 low-cell pairs of 430. ImMicro: no identity flag, all used. Imperial, Giroux, Ji: several pairs per donor. Case vs control = samples in scores/<cohort>/pooled/summary.json. Giroux 'moderate' = GEO 'severe' (paper term). Labels: data/<cohort>/QC_REPORT.md; ImMicro: GEO GSE314922/GSE314416.",
+   "numbers": [
+    {
+     "value": "403 paired samples (sum of usable rows)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_usable_rows)"
+    },
+    {
+     "value": "275 donors (sum of usable donors)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_usable_donors)"
+    },
+    {
+     "value": "dropped 15 identity-fail, 11 borderline, 1 < 200 cells, of 430",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/features.npz (identity_pass, identity_check); samples.csv (n_cells); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/prepare_dataset.py (MIN_CELLS)"
+    },
+    {
+     "value": "ImMicro 107 pairs / 107 donors",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json"
+    },
+    {
+     "value": "Sepsis 82 pairs / 82 donors; sepsis 61 vs control 21",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json"
+    },
+    {
+     "value": "Imperial 157 pairs / 57 donors; COVID+ 113 vs COVID− 34 (+10 recovery, neither)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/pooled/summary.json"
+    },
+    {
+     "value": "Giroux 24 pairs / 9 donors; moderate 11 vs mild 13",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/pooled/summary.json"
+    },
+    {
+     "value": "Ji 33 pairs / 20 donors; ChILI 18 vs ICI control 15",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json"
+    }
+   ]
+  },
+  {
+   "title": "5 donors: LoRA vs scSemiProfiler — cells",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fewpair_cells.png"
+   ],
+   "keywords": [
+    "LoRA-5 > scSemi-5: coverage, precision 5/5; L1 4/5",
+    "Coverage: LoRA-5 0.69–0.96 vs scSemi-5 0.04–0.61",
+    "Composition gain vs zero-shot: ImMicro only"
+   ],
+   "footnote": "Base f01 6k·1x·E16 (EMA, DDIM 50) + LoRA r=16, 3,000 steps. LoRA-5 / scSemi-5 = LoRA / scSemiProfiler trained on the same 5 donors (5–15 pairs); test = all other usable pairs. scSemi-5 scored in a separate call, same test set and reference (sha-checked); 25/25 draws (missing: none). Verdict = better in >= 80% of shared draws (L1: Giroux split 3/5). Depth-matched P/C: same ranking, coverage LoRA-5 0.83–0.97 vs scSemi-5 0.15–0.28. L1 vs zero-shot: per-donor Wilcoxon, ImMicro p 2e-10; others p >= 0.38. scANVI labels; P/C = PCA-50, k=10 balls. Scores: scores/<cohort>/fewshot_n5/.",
+   "numbers": [
+    {
+     "value": "LoRA-5 vs scSemi-5 coverage (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.036 (5/5, lora); Sepsis 0.694 vs 0.080 (5/5, lora); Imperial 0.737 vs 0.059 (5/5, lora); Giroux 0.961 vs 0.607 (5/5, lora); Ji 0.707 vs 0.145 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 precision (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.518 (5/5, lora); Sepsis 0.906 vs 0.728 (5/5, lora); Imperial 0.853 vs 0.330 (5/5, lora); Giroux 1.000 vs 0.992 (5/5, lora); Ji 0.978 vs 0.840 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 comp_l1 (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.233 (5/5, lora); Sepsis 0.466 vs 0.612 (5/5, lora); Imperial 0.503 vs 0.602 (5/5, lora); Giroux 0.256 vs 0.270 (3/5, split); Ji 0.513 vs 0.592 (4/5, lora) -> LoRA verdicts 4/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 coverage_dm (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.284 (5/5, lora); Sepsis 0.834 vs 0.158 (5/5, lora); Imperial 0.863 vs 0.152 (5/5, lora); Giroux 0.974 vs 0.238 (5/5, lora); Ji 0.908 vs 0.150 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 precision_dm (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.829 (5/5, lora); Sepsis 0.914 vs 0.504 (5/5, lora); Imperial 0.881 vs 0.429 (5/5, lora); Giroux 0.995 vs 0.426 (5/5, lora); Ji 0.974 vs 0.564 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "coverage cohort means over all draws: LoRA-5 ImMicro 0.792, Sepsis 0.694, Imperial 0.737, Giroux 0.961, Ji 0.707; scSemi-5 ImMicro 0.036, Sepsis 0.080, Imperial 0.059, Giroux 0.607, Ji 0.145",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 minus zero-shot-cal composition L1, per-donor Wilcoxon (draw-averaged): ImMicro -0.027, n=107, p=2.2e-10; Sepsis +0.018, n=82, p=0.79; Imperial +0.016, n=57, p=0.38; Giroux -0.065, n=8, p=0.38; Ji -0.012, n=20, p=0.7",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/per_donor.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/folds.csv"
+    },
+    {
+     "value": "scSemiProfiler draws used / LoRA draws: ImMicro 5/5, Sepsis 5/5, Imperial 5/5, Giroux 5/5, Ji 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec09_scsemi_status.csv"
+    },
+    {
+     "value": "training pairs per draw: ImMicro 5, Sepsis 5, Imperial 12–15, Giroux 12–14, Ji 7–9; test pairs: ImMicro 102, Sepsis 77, Imperial 142–145, Giroux 10–12, Ji 24–26",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_train_rows, n_test_rows)"
+    },
+    {
+     "value": "LoRA r = 16; 3000 fixed steps; base runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt; sampling: test donors only, 1,500 cells each, seed 20260927, DDIM 50, EMA, Bernoulli read-out",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fewshot_n5/draw0/lora/RUN.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md"
+    },
+    {
+     "value": "P/C definition: precision/coverage/density (PCA-50 + k = 10 balls fitted on the scored donors' observed R1 cells); PCA components in every summary.json = 50",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py"
+    }
+   ]
+  },
+  {
+   "title": "5 donors: LoRA vs scSemiProfiler — disease signal",
+   "layout": "figure_keywords",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fewpair_disease.png"
+   ],
+   "keywords": [
+    "Top-50 DEG: LoRA-5 higher 3/4; Ji ~0",
+    "logFC r: scSemi-5 wins Giroux; Sepsis split",
+    "Giroux: real-bulk broadcast beats all arms"
+   ],
+   "footnote": "Same draws and verdict rule as the previous slide; DEG tie = half the draws equal or mean gap < 1 gene. logFC r = mean over T/B/Mono/NK of case-vs-control log2FC r (generated vs observed); top-50 DEG = Welch+BH overlap summed over 5 types (max 250; Giroux 51–109, Ji 75–250 per draw). Giroux test = 2 vs 2 subjects per draw. Broadcast = the input real bulk's own logFC. Scores: scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/.",
+   "numbers": [
+    {
+     "value": "Top-50 DEG LoRA-5 vs scSemi-5 (shared-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 5.2 (5/5, 0 tied, lora); Imperial 113.6 vs 46.8 (5/5, 0 tied, lora); Giroux 11.6 vs 1.2 (5/5, 0 tied, lora); Ji 0.2 vs 0.0 (1/5, 4 tied, tie)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv"
+    },
+    {
+     "value": "logFC r LoRA-5 vs scSemi-5 (shared-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs 0.402 (3/5, split); Imperial 0.749 vs 0.562 (5/5, lora); Giroux 0.331 vs 0.398 (0/5, scsemi); Ji 0.333 vs 0.153 (5/5, lora)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv"
+    },
+    {
+     "value": "Giroux broadcast logFC r 0.539 vs best arm 0.398; broadcast DEG 25.4 vs best arm 11.6 (means over all draws)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5/draw<j>{,_scsemi5}/summary.json"
+    },
+    {
+     "value": "DEG maximum per draw: Sepsis 250, Imperial 250, Giroux 51–109, Ji 75–250",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (deg_top50_max)"
+    },
+    {
+     "value": "Giroux test subjects per draw: 2 vs 2 (moderate vs mild); test pairs 10–12",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json (train_donors); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv (group)"
+    }
+   ]
+  },
+  {
+   "title": "All pairs, 5-fold",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fivefold.png"
+   ],
+   "keywords": [
+    "LoRA tops coverage 5/5, logFC r 4/4",
+    "Ji whole blood: baselines 0.11, LoRA 0.86",
+    "Giroux: broadcast r 0.64 > LoRA 0.50"
+   ],
+   "footnote": "Donor-level 5-fold CV; each pair scored once, by the fold model that never trained on its donor (one pooled call per cohort). LoRA r=16 on all training donors' real bulk, early stop on inner-val donors; sc-only = full fine-tune on training donors' sc pseudobulk, calibrated input. Base f01 6k·1x·E16. Top-50 DEG: LoRA best 4/4. Sepsis DEG from pooled_deg. Scores: scores/<cohort>/pooled/summary.json.",
+   "numbers": [
+    {
+     "value": "LoRA best of 3 arms: coverage 5/5, logFC r 4/4, top-50 DEG 4/4",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json)"
+    },
+    {
+     "value": "Ji coverage: zero-shot cal 0.106, sc-only 0.113, LoRA 0.857",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json"
+    },
+    {
+     "value": "Giroux logFC r: broadcast 0.638 vs LoRA 0.504; DEG broadcast 39 vs LoRA 25",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/pooled/summary.json"
+    },
+    {
+     "value": "LoRA logFC r vs broadcast: Sepsis 0.527 vs 0.316, Imperial 0.819 vs 0.661, Giroux 0.504 vs 0.638, Ji 0.479 vs 0.240",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json)"
+    },
+    {
+     "value": "Pooled n (pairs / donors): ImMicro 107/107, Sepsis 82/82, Imperial 157/57, Giroux 24/9, Ji 33/20",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (n_donors); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json"
+    },
+    {
+     "value": "early stopping: About 10 % of each fold's training donors are inner-validation, used only for early stopping",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md"
+    }
+   ]
+  }
+ ],
+ "scripts": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/tools/sec09_paired_validation.py"
+ ],
+ "generated_from": "tools/sec09_paired_validation.py (rerun to refresh; do not edit by hand)",
+ "scsemi_draws_used": "25/25"
+}

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec10_quoted_numbers.csv

@@ -0,0 +1,57 @@
+item,value,source
+"Sepsis controls, paired QC pass",21,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv
+"Sepsis controls, bulk-only (36 adult HC + 17 adult ICU + 1 ped ICU)",54,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json excluded.bulk_samples_without_sc ch_group
+"ChILI before ICI (BC), bulk-only",11,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json excluded.bulk_samples_without_sc Sample_title
+"ChILI before ICI (BC), paired",0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json pairs_by_outcome_timepoint
+"ChILI before ICI (BC), unpaired sc libraries (patients absent from bulk)",4,/home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv
+"ChILI before ICI (BC), bulk-only sex-flagged",1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv sex_discordant_with_geo
+"Arunachalam paired, composition-eligible",0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv composition_eligible
+Arunachalam zero-shot bulk-only samples generated (per input arm),22,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json tags *_bulkonly_a/b bulks
+Arunachalam prereg: populations where any zero-shot arm beats broadcast,0/5,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Giroux QC-pass pairs (not shown),24,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/pairs.csv
+Giroux author bulk columns without sc (not shown),17,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/MANIFEST.json excluded.bulk_count_columns_without_pair (no_sc_library_for_this_subject_day)
+Giroux pooled LoRA vs broadcast: severe-mild r / top-50 DEG sum,0.50 vs 0.64 / 25 vs 39,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/pooled/summary.json
+LoRA rank,16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md
+Ye 2026 sepsis: bulk_total,207,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: seg_train,82,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: seg_nocomp,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: seg_excl,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: bulk_only,122,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: donors_paired_usable,82,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: donors_bulk_only,122,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: donors_excl_only,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: donors_bulk_total,207,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: sex_flag_bulk_only,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Ye 2026 sepsis: LoRA 5-fold comp L1 / LOO null,0.36 / 0.53,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
+Imperial ESKD COVID: bulk_total,336,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: seg_train,157,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: seg_nocomp,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: seg_excl,15,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: bulk_only,164,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: donors_paired_usable,57,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: donors_bulk_only,45,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: donors_excl_only,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: donors_bulk_total,105,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: sex_flag_bulk_only,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Imperial ESKD COVID: LoRA 5-fold comp L1 / LOO null,0.36 / 0.52,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
+Ji 2025 ChILI: bulk_total,128,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: seg_train,33,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: seg_nocomp,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: seg_excl,7,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: bulk_only,88,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: donors_paired_usable,20,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: donors_bulk_only,38,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: donors_excl_only,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: donors_bulk_total,61,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: sex_flag_bulk_only,10,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Ji 2025 ChILI: LoRA 5-fold comp L1 / LOO null,0.51 / 0.51,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
+Arunachalam 2020 COVID: bulk_total,34,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: seg_train,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: seg_nocomp,12,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: seg_excl,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: bulk_only,22,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: donors_paired_usable,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: donors_bulk_only,20,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: donors_excl_only,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: donors_bulk_total,32,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv
+Arunachalam 2020 COVID: sex_flag_bulk_only,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/slides_spec.before_25draws.json

@@ -0,0 +1,304 @@
+{
+  "deck": {
+    "output_pptx": "PBISC-Diffusion_paper_summary_20260930.pptx",
+    "paths": "figure paths are relative to the deck folder",
+    "note": "footnote = on-slide text (max 2 lines, may be a shortened copy); footnote_full = section author's full text, put in speaker notes when it differs. Section 9 text comes from data/sec09_slide_text.json; refresh with tools/sync_sec09_text.py after rerunning tools/sec09_paired_validation.py.",
+    "moved": "The ImMicro external-reference slide (section 4 spec) is placed at the end of section 5, after refcal is introduced, as its author asked."
+  },
+  "slides": [
+    {
+      "kind": "title",
+      "title": "PBISC-Diffusion: bulk-to-single-cell generation",
+      "subtitle": "Paper summary · 2026-09-30"
+    },
+    {
+      "kind": "agenda",
+      "title": "Outline",
+      "items": [
+        "Model overview: diffusion from bulk to cells",
+        "Backbone: SDD, scDiffusion, bulk conditioning",
+        "Architecture ablation: width, context, gene panel",
+        "SLE benchmark vs scSemiProfiler",
+        "Real bulk ≠ pseudobulk",
+        "Fine-tuning on paired bulk–sc data",
+        "LoRA: compute and ablations (K diversification)",
+        "How many bulk–sc pairs are needed",
+        "Paired-cohort validation vs scSemiProfiler",
+        "Next: cohorts with a paired subset (planned)"
+      ]
+    },
+
+    {
+      "kind": "content", "section": "1", "section_label": "1 Model overview",
+      "title": "PBISC-Diffusion: bulk in, cells out",
+      "layout": "full",
+      "figures": ["figures/sec01_slide_a.png"],
+      "keywords": ["Train pair: K-cell pseudobulk → each member cell"],
+      "footnote": "Top: redraw of manuscript Fig. 1b. Bottom: training corpus of the final model (f01 6k 1x); 33.1M cells in the donor-level 80/10/10 train split. K grid = 8,192 recipes/epoch, plus 3,658 top-up recipes over 16 epochs (K 1-4,000), so every train cell is a target once.",
+      "footnote_full": "Top: deck redraw of manuscript Fig. 1b (larger labels; cells differ by x_T and the Bernoulli support draw, Methods 'Support read-out'). Bottom: corpus of final run f01_6k_1x_seed20260627 (index fingerprint matches). Cells per dataset = base + overlay rows (Model 7 e2_full_source/e2_full_index manifests); 33.1M cells in the donor-level 80/10/10 train split. Registered K grid = 8,192 recipes/epoch. Plus 3,658 top-up recipes over 16 epochs (196-283 per epoch, K 1-4,000), so every train cell is a target once (ALLCELL_DATA_CONTRACT.json coverage_after_topup).",
+      "sources": "tools/sec01_overview.py; data/sec01_model_numbers.csv, data/sec01_corpus_datasets.csv, data/sec01_recipe_k.csv"
+    },
+    {
+      "kind": "content", "section": "1", "section_label": "1 Model overview",
+      "title": "Denoiser: joint value + support diffusion",
+      "layout": "diagram",
+      "figures": ["figures/sec01_fig1a_denoiser.png"],
+      "keywords": ["6,000 genes · 54.2M params · Bernoulli support draw"],
+      "footnote": "Redraw of manuscript Fig. 1a. Purple dashed = soft self-conditioning; gold dashed = context to all blocks. Final model f01 6k 1x, epoch 16, EMA; 7 blocks 1024-1024-512-256-512-1024-1024. Sampling: 50 DDIM steps, η = 0; keep gene if u < σ(logit). 16 epochs = one pass over the 131,072-recipe pool.",
+      "footnote_full": "Deck redraw of manuscript Fig. 1a (larger labels, legend dropped). Purple dashed = soft self-conditioning feedback; gold dashed = context to all blocks. Final model f01_6k_1x_seed20260627, checkpoint_epoch_016, EMA; 7 blocks 1024-1024-512-256-512-1024-1024 (effective_config.json, RUN_STATUS.json). Sampling: 50 DDIM steps, η = 0, drawn support read-out, keep gene if u < σ(logit) (methods.tex l.58, l.99). 16 epochs = 16 disjoint 8,192-recipe slots = one pass over the 131,072-recipe pool (manuscript: part 16).",
+      "sources": "tools/sec01_overview.py; data/sec01_model_numbers.csv, data/sec01_fig1_label_pt.csv"
+    },
+
+    {
+      "kind": "content", "section": "2", "section_label": "2 Backbone",
+      "title": "Backbone: SDD → PBISC-Diffusion",
+      "layout": "diagram",
+      "figures": ["figures/sec02_backbone_compare.png"],
+      "keywords": ["Kept from SDD: value + bit, skip-MLP", "Changed: bulk condition, masked loss, Bernoulli read-out"],
+      "footnote": "Luo et al., Bioinformatics 2024; Ostheimer et al., arXiv 2502.02448 (code 1d5423c). PBISC: final model f01 6k 1x, part 16. σ = sigmoid; Bernoulli is the final read-out; the logit > 0 cut is also reported.",
+      "sources": "tools/sec02_backbone.py; data/sec02_backbone_compare.csv, data/sec02_slide_text.csv, data/refs/"
+    },
+    {
+      "kind": "content", "section": "2", "section_label": "2 Backbone",
+      "title": "Bulk conditioning",
+      "layout": "diagram",
+      "figures": ["figures/sec02_bulk_conditioning.png"],
+      "keywords": ["Same bulk condition for every generated cell", "Final: no cell types, proportions, sum constraint", "18,006 → 512 context into every block"],
+      "footnote": "Final model f01 6k 1x, part 16. Bar heights schematic.",
+      "sources": "tools/sec02_backbone.py; data/sec02_bulk_conditioning.csv, data/sec02_slide_text.csv"
+    },
+
+    {
+      "kind": "content", "section": "3", "section_label": "3 Architecture ablation",
+      "title": "Width & context ablation: loss saturation",
+      "layout": "full",
+      "figures": ["figures/sec03_width_loss.png"],
+      "keywords": ["Trunk x4: val loss −31% (0.197 → 0.136)", "ctx x4, prop hint: loss = 1x", "1x flat E8; trunk x4 still falling"],
+      "footnote": "Old 6k panel (1% floor); one validation set. 16x: memory-floor stop after part 2.",
+      "say": "All arms share the 6k panel (1% floor), corpus, seed and schedule; validation = 192 recipes x 64 cells. ctx x4, both x4 and 16x were read from server_2 snapshots.",
+      "sources": "tools/sec03_width_loss.py; data/sec03_width_loss.csv, data/sec03_width_saturation.csv, data/sec03_width_loss_headline.csv"
+    },
+    {
+      "kind": "content", "section": "3", "section_label": "3 Architecture ablation",
+      "title": "Width & context ablation: benchmark",
+      "layout": "full",
+      "figures": ["figures/sec03_width_bench.png"],
+      "keywords": ["trunk x4: loss −31%, no DEG gain", "Prop hint: oracle = predicted, L1 worse", "1x kept: ties ctx x4, 54M vs 102M"],
+      "footnote": "SLE, 42 donors, 2,980 genes; old 6k panel. ctx x4: better L1 (0.161 vs 0.197).",
+      "say": "Bars = mean of parts 14-16 with the cut p > 0.5; diamonds = Bernoulli read-out (4 width arms only). Prop hint = 9 L1 cell-type proportions; older panel, not the final model.",
+      "sources": "tools/sec03_width_bench.py; data/sec03_width_bench.csv, data/sec03_width_bench_summary.csv, data/sec03_width_bench_headline.csv"
+    },
+    {
+      "kind": "content", "section": "3", "section_label": "3 Architecture ablation",
+      "title": "Gene context: 2k / 3k / 6k / 15k",
+      "layout": "full",
+      "figures": ["figures/sec03_panel.png"],
+      "keywords": ["6k ≈ 3k: 3k inside 6k seed range", "2k best L1; 15k worst r, L1", "6k kept: first panel with CLEC9A (cDC1)"],
+      "footnote": "SLE, 42 donors, 1,006 benchmark genes in every panel; 6k base seed = best of 5.",
+      "say": "Runs f01_{2k,3k,6k,p15k}_1x, part 16, Bernoulli, EMA, DDIM 50. Different gene axis from the previous slide, so the two slides cannot be compared. Loss curves are divided by each panel's own part-16 value.",
+      "sources": "tools/sec03_panel.py; data/sec03_panel_bench.csv, data/sec03_panel_seeds.csv, data/sec03_panel_loss.csv, data/sec03_panel_headline.csv"
+    },
+
+    {
+      "kind": "content", "section": "4", "section_label": "4 SLE benchmark",
+      "title": "SLE benchmark: PBISC vs scSemiProfiler",
+      "layout": "full",
+      "figures": ["figures/sec04_sle_benchmark.png"],
+      "keywords": ["42 held-out donors, sc-pseudobulk input", "Beats scSemiProfiler on all three metrics", "Ties PBISC-VAE; below bulk-copy baseline"],
+      "footnote": "GSE135779, 42 held-out donors (30 SLE / 12 HC). PBISC f01 6k E16, 5 seeds (mean ± SD); baselines 1 draw. scSemiProfiler also gets real sc of 14 in-cohort donors (1,500 cells each). Dashed: input bulk logFC copied to every type (backup).",
+      "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_benchmark.csv, data/sec04_sle_numbers.csv"
+    },
+    {
+      "kind": "content", "section": "4", "section_label": "4 SLE benchmark",
+      "title": "SLE benchmark: per cell type",
+      "layout": "full",
+      "figures": ["figures/sec04_sle_per_celltype.png"],
+      "keywords": ["Beats scSemiProfiler in T, B, Mono, NK", "Loses in rare DC and Other", "DC: ~15 generated cells per donor"],
+      "footnote": "Same 42 donors, 1,006 genes. PBISC 5 seeds (mean ± SD), baselines 1 draw. Tick %: share of 251,179 real cells. Other top-50 is out of 12 truth genes. Bulk copy: r 0.68, top-50 113 (backup).",
+      "say": "PBISC's DC top list in the base seed has only 13 genes, because few DC cells are generated.",
+      "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_per_celltype.csv, data/sec04_sle_numbers.csv"
+    },
+
+    {
+      "kind": "content", "section": "5", "section_label": "5 Real bulk vs pseudobulk",
+      "title": "Real bulk ≠ pseudobulk (model input)",
+      "layout": "figure_keywords",
+      "figures": ["figures/sec05_condition_space.png"],
+      "keywords": ["Real bulk: 2.46 D from own pseudobulk", "95% of squared offset is one shift", "Shift removed (diagnostic): own donor 7.5% → 75.7%"],
+      "footnote": "ImMicro, 107 healthy donors. Model inputs (log1p CPM, 5,508 genes), not learned ctx. D = median donor-to-donor distance; PCA-30 values are lower bounds (full space 3.19 D, 0.91 shared). Shift removal is a diagnostic that uses paired pseudobulks. Pseudobulk PC1 is sc pool batch (pool R² 0.96 on PC1).",
+      "say": "The two pseudobulk clusters on PC1 are sc pools DB1-3 vs DB4-7, so the pairing lines cross mainly because of sc batch. Shift removal subtracts the mean offset of the other 106 donors; a bulk-only deployment would not have them.",
+      "sources": "tools/sec05_condition_space.py; data/sec05_condition_space_numbers.csv, data/sec05_condition_space_coords.csv"
+    },
+    {
+      "kind": "content", "section": "5", "section_label": "5 Real bulk vs pseudobulk",
+      "title": "Consequence: cells off-manifold",
+      "layout": "two_figures",
+      "figures": ["figures/sec05_cells_umap.png", "figures/sec05_cells_metrics.png"],
+      "keywords": ["Monocytes: raw 30.6% vs real 16.7%", "Same noise: 19% T → monocyte", "Precision/coverage: raw 0.36/0.08, pseudobulk 0.92/0.51"],
+      "footnote": "refcal = cohort-mean bulk anchored to a healthy-PBMC reference (AIFI or AIDA); no paired sc. ImMicro, 107 donors; final model; each cell starts from the same noise under every input. Composition L1: raw 0.455, pseudobulk 0.166, cohort-mean null 0.161. UMAP fitted on real cells; overstates overlap.",
+      "footnote_full": "ImMicro, 107 donors. Final model f01 6k 1× E16 (DDIM 50, EMA); each cell starts from the same noise under every input. Precision/coverage come from one scoring call. Composition L1: raw 0.455, pseudobulk 0.166, cohort-mean null 0.161. The UMAP is fitted on real cells and overstates overlap. refcal definition: plans/utility_studies_final6k_20260925/refcal/RESULTS.md ('Reference-anchored calibration ... anchoring a cohort's mean bulk to the AIFI healthy-PBMC reference'); AIDA reference: refcal_refs/RESULTS.md.",
+      "say": "TPM fixes cell shape (precision 0.87) but not monocytes (34.3%). refcal fixes monocytes (about 17.5%); coverage depends on the reference (AIFI 0.08, AIDA 0.37).",
+      "sources": "tools/sec05_cells_offmanifold.py; data/sec05_cells_metrics.csv, data/sec05_cells_umap_coords.csv"
+    },
+    {
+      "kind": "content", "section": "5", "section_label": "5 Real bulk vs pseudobulk",
+      "title": "Consequence: disease direction flips",
+      "layout": "figure_keywords",
+      "figures": ["figures/sec05_behcet_direction.png"],
+      "keywords": ["CD16 gap: raw −3.97 vs observed +4.94", "C1Q flip vanishes at common depth", "AIFI refcal restores sign, 5/5 seeds"],
+      "footnote": "Behçet, final model. Bulk GSE198533 (BD 9, HC 10), 5,000 cells per sample; observed = sc GSE198616 (BD 4, HC 4, different people; descriptive p). At common depth, raw CD16 is −3.59 (seed 0) and raw C1Q is −0.08 ± 0.09 pp. AIDA refcal does not restore the sign.",
+      "say": "Limitations: AIDA refcal does not restore the sign (C1Q -0.25, CD16 +0.37). Best reference differs by cohort (AIDA for ImMicro, AIFI for Behcet). The sc pseudobulk ceiling uses the 8 sc donors, not the 19 bulk donors. Monocytes stay about 2x observed even under refcal.",
+      "sources": "tools/sec05_behcet_direction.py; data/sec05_behcet_direction.csv"
+    },
+    {
+      "kind": "content", "section": "5", "section_label": "5 Real bulk vs pseudobulk",
+      "title": "Real bulk + refcal vs scSemiProfiler (ImMicro)",
+      "layout": "full",
+      "figures": ["figures/sec04_immicro_external.png"],
+      "keywords": ["Real bulk + refcal; no target sc", "Lower L1, IFN error; rank not better", "No-bulk replay: lower T error, rank ~0"],
+      "footnote": "ImMicro baseline, 107 donors, 1 generation seed, 5,500 genes; CI = paired donor bootstrap. Refcal is fit on the mean of all 107 bulks (transductive). PBISC pretraining includes part of AIFI and is not counted in generation time.",
+      "say": "Section 4 author's slide ('External reference setting'), moved here after refcal is introduced. scSemiProfiler IFN variance ratio 0.036 (Mono) and 0.027 (T), vs PBISC 0.830 and 1.538.",
+      "sources": "tools/sec04_immicro.py; data/sec04_immicro_external.csv, data/sec04_immicro_numbers.csv"
+    },
+
+    {
+      "kind": "content", "section": "6", "section_label": "6 Paired fine-tuning",
+      "title": "Fine-tuning with paired bulk + sc",
+      "layout": "diagram",
+      "figures": ["figures/sec06_ft_method.png"],
+      "keywords": ["LoRA 2–14 min vs pretraining 15.9 h"],
+      "footnote": "Receipts: immicro/fold0/real_lora and ye2026_sepsis/fewshot_n5/draw0/lora RUN.json. Base: f01_6k_1x E16. Times: 40 local LoRA runs.",
+      "sources": "tools/sec06_finetune_method.py; data/sec06_ft_method.csv"
+    },
+
+    {
+      "kind": "content", "section": "7", "section_label": "7 LoRA ablations",
+      "title": "Full vs LoRA vs cond.-encoder-only",
+      "layout": "full",
+      "figures": ["figures/sec07_ft_modes.png"],
+      "keywords": ["LoRA ≈ full FT accuracy (n.s.)", "42× fewer trainable params (1.3 M)", "Cond.-encoder-only: no gain over zero-shot cal"],
+      "footnote": "Base f01_6k_1x E16. Full vs LoRA: paired Wilcoxon, donor L1, p 0.25 / 0.71. Open = fold-0 pilot; compare same marker only. Per-step time: runs early-stop differently.",
+      "sources": "tools/sec07_ft_modes.py; data/sec07_ft_modes_accuracy.csv, data/sec07_ft_modes_compute.csv, data/sec07_ft_modes_wilcoxon.csv"
+    },
+    {
+      "kind": "content", "section": "7", "section_label": "7 LoRA ablations",
+      "title": "K diversification: no gain",
+      "layout": "figure_keywords",
+      "figures": ["figures/sec07_k_aug.png"],
+      "keywords": ["No gain; keep single K 1000", "Multi-K slightly worse on ImMicro (p\u00a00.04)", "Inner-val loss Δ ≤ 1.2e-4"],
+      "footnote": "LoRA r16 on f01_6k_1x E16, 5-fold pooled. p: paired Wilcoxon, donor L1 vs plain LoRA, uncorrected. Recipes arm: K 1000 real bulk + ½-batch pretraining pseudobulk, no multi-K.",
+      "sources": "tools/sec07_k_aug.py; data/sec07_k_aug.csv, data/sec07_k_aug_wilcoxon.csv, data/sec07_k_aug_inner_val_delta.csv"
+    },
+
+    {
+      "kind": "content", "section": "8", "section_label": "8 Pairs needed",
+      "title": "Pairs needed: composition, coverage, training steps",
+      "layout": "full",
+      "figures": ["figures/sec08_pairs_realism.png"],
+      "keywords": ["Coverage, 5+7 pairs: ImMicro 0.84, sepsis 0.77"],
+      "footnote": "Final f01 6k·1× E16 + LoRA; donor 5-fold CV, pooled scoring (ImMicro 107, sepsis 82 donors). N+7 = N training + 7 (sepsis 7–8) inner-val pairs for early stopping. cal = zero-shot + calibration, α fit on all 85–86 / 65–66 fold pairs; with α from the same 5 pairs, coverage 0.54 vs LoRA 0.79 (ImMicro), 0.43 vs 0.69 (sepsis).",
+      "footnote_full": "Final f01 6k·1× epoch-16 + LoRA; donor 5-fold CV, pooled scANVI scoring (ImMicro 107, sepsis 82 donors). N+7 = N training + 7 (sepsis 7–8) inner-val pairs for early stopping. cal = zero-shot + calibration, α fit on all 85–86 / 65–66 fold pairs; with α from the same 5 pairs (Sec. 9 call), coverage 0.54 vs LoRA 0.79 (ImMicro), 0.43 vs 0.69 (sepsis). Sec. 9 5-pair runs: fixed 3k steps, no inner-val. 20k cap reached by ImMicro folds 1/5 (10), 4/5 (20), 5/5 (40, all): val loss still falling, but last 2k steps <0.4% of total drop.",
+      "say": "Keywords say +7; 2 of 5 sepsis folds use 8 inner-val pairs.",
+      "sources": "tools/sec08_pairs_needed.py; data/sec08_pairs_realism.csv, data/sec08_selected_steps.csv, data/sec08_slide_numbers.csv"
+    },
+    {
+      "kind": "content", "section": "8", "section_label": "8 Pairs needed",
+      "title": "Pairs needed: donor and disease signal",
+      "layout": "figure_keywords",
+      "figures": ["figures/sec08_pairs_signal.png"],
+      "keywords": ["logFC r above broadcast from 10+7 pairs", "DEG matches broadcast at 40+7 pairs", "NK r 0.70 at 40+7 (cal 0.50)"],
+      "footnote": "Sepsis 61 case vs 21 control. logFC r = mean over T/B/Mono/NK (mean CP10K); DEG = Welch top-50 overlap summed over T/B/Mono/NK/DC. ≤10 pairs: NK r and DEG below cal; T r below cal until 40 pairs, Mono until all. DEG gain is Mono/DC.",
+      "footnote_full": "Same runs and pooled scoring as previous slide; sepsis 61 case vs 21 control. N+7 = N training + 7 (sepsis 7–8) inner-val pairs. logFC r = mean over T/B/Mono/NK (mean CP10K); DEG = Welch top-50 overlap summed over T/B/Mono/NK/DC. ≤10 pairs: NK r (0.20/0.40) and DEG (5/8) below cal (0.50, 11); T r below cal until 40 pairs, Mono until all. DEG gain is Mono/DC; T overlap 5 (cal) → 0–1 from 20 pairs, NK 0 at every n (broadcast T 3, NK 2).",
+      "sources": "tools/sec08_pairs_needed.py; data/sec08_pairs_signal.csv, data/sec08_slide_numbers.csv"
+    },
+
+    {
+      "kind": "content", "section": "9", "section_label": "9 Paired validation",
+      "sec09_index": 0,
+      "title": "Five paired cohorts",
+      "layout": "full",
+      "figures": ["figures/sec09_cohorts.png"],
+      "keywords": ["403 paired samples, 275 donors", "Only identity-pass pairs; donor-level splits", "Ji bulk: whole blood, not PBMC"],
+      "footnote": "Usable pair = passed the pairing identity check and >= 200 cells; dropped 15 identity-fail, 11 borderline and 1 low-cell pairs of 430. ImMicro: no identity flag, all used. Imperial, Giroux, Ji: several pairs per donor. Giroux 'moderate' = GEO 'severe' (paper term).",
+      "footnote_full": "Usable pair = passed the pairing identity check and >= 200 cells (fold >= 0 in data/<cohort>/folds.csv); dropped 15 identity-fail, 11 borderline and 1 low-cell pairs of 430. ImMicro: no identity flag, all used. Imperial, Giroux, Ji: several pairs per donor. Case vs control = samples in scores/<cohort>/pooled/summary.json. Giroux 'moderate' = GEO 'severe' (paper term). Labels: data/<cohort>/QC_REPORT.md; ImMicro: GEO GSE314922/GSE314416.",
+      "sources": "tools/sec09_paired_validation.py; data/sec09_cohorts.csv, data/sec09_quoted_numbers.csv, data/sec09_slide_text.json"
+    },
+    {
+      "kind": "content", "section": "9", "section_label": "9 Paired validation",
+      "sec09_index": 1,
+      "title": "5 donors: LoRA vs scSemiProfiler — cells",
+      "layout": "full",
+      "figures": ["figures/sec09_fewpair_cells.png"],
+      "keywords": ["LoRA-5 > scSemi-5: coverage, precision 5/5; L1 4/5", "Coverage: LoRA-5 0.69–0.96 vs scSemi-5 0.04–0.61", "Composition gain vs zero-shot: ImMicro only"],
+      "footnote": "LoRA-5 / scSemi-5 = LoRA r=16 (3,000 steps) / scSemiProfiler trained on the same 5 donors (5–15 pairs); test = all other usable pairs. scSemi-5: 23/25 draws. Verdict = better in >= 80% of shared draws. L1 vs zero-shot: per-donor Wilcoxon, ImMicro p 2e-10; others p >= 0.38.",
+      "footnote_full": "Base f01 6k·1x·E16 (EMA, DDIM 50) + LoRA r=16, 3,000 steps. LoRA-5 / scSemi-5 = LoRA / scSemiProfiler trained on the same 5 donors (5–15 pairs); test = all other usable pairs. scSemi-5 scored in a separate call, same test set and reference (sha-checked); 23/25 draws (missing: ImMicro draw4, Sepsis draw4). Verdict = better in >= 80% of shared draws (L1: Giroux split 3/5). Depth-matched P/C: same ranking, coverage LoRA-5 0.83–0.97 vs scSemi-5 0.15–0.29. L1 vs zero-shot: per-donor Wilcoxon, ImMicro p 2e-10; others p >= 0.38. scANVI labels; P/C = PCA-50, k=10 balls. Scores: scores/<cohort>/fewshot_n5/.",
+      "say": "scSemi-5 is missing draw4 for ImMicro and Sepsis. When those arrive, rerun tools/sec09_paired_validation.py, then tools/sync_sec09_text.py, then generate_deck.py.",
+      "sources": "tools/sec09_paired_validation.py; data/sec09_fewpair_cells.csv, data/sec09_scsemi_status.csv, data/sec09_slide_text.json"
+    },
+    {
+      "kind": "content", "section": "9", "section_label": "9 Paired validation",
+      "sec09_index": 2,
+      "title": "5 donors: LoRA vs scSemiProfiler — disease signal",
+      "layout": "figure_keywords",
+      "figures": ["figures/sec09_fewpair_disease.png"],
+      "keywords": ["Top-50 DEG: LoRA-5 higher 3/4; Ji ~0", "logFC r: scSemi-5 wins Giroux; Sepsis split", "Giroux: real-bulk broadcast beats all arms"],
+      "footnote": "Same draws and verdict rule as the previous slide; DEG tie = half the draws equal or mean gap < 1 gene. logFC r = mean over T/B/Mono/NK; top-50 DEG = Welch+BH overlap summed over 5 types. Giroux test = 2 vs 2 subjects per draw. Broadcast = the input real bulk's own logFC.",
+      "footnote_full": "Same draws and verdict rule as the previous slide; DEG tie = half the draws equal or mean gap < 1 gene. logFC r = mean over T/B/Mono/NK of case-vs-control log2FC r (generated vs observed); top-50 DEG = Welch+BH overlap summed over 5 types (max 250; Giroux 51–109, Ji 75–250 per draw). Giroux test = 2 vs 2 subjects per draw. Broadcast = the input real bulk's own logFC. Scores: scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/.",
+      "sources": "tools/sec09_paired_validation.py; data/sec09_fewpair_disease.csv, data/sec09_slide_text.json"
+    },
+    {
+      "kind": "content", "section": "9", "section_label": "9 Paired validation",
+      "sec09_index": 3,
+      "title": "All pairs, 5-fold",
+      "layout": "full",
+      "figures": ["figures/sec09_fivefold.png"],
+      "keywords": ["LoRA tops coverage 5/5, logFC r 4/4", "Ji whole blood: baselines 0.11, LoRA 0.86", "Giroux: broadcast r 0.64 > LoRA 0.50"],
+      "footnote": "Donor-level 5-fold CV; each pair scored once, by the fold model that never trained on its donor. LoRA r=16 on training donors' real bulk, early stop on inner-val donors; sc-only = full fine-tune on training donors' sc pseudobulk, calibrated input. Top-50 DEG: LoRA best 4/4.",
+      "footnote_full": "Donor-level 5-fold CV; each pair scored once, by the fold model that never trained on its donor (one pooled call per cohort). LoRA r=16 on all training donors' real bulk, early stop on inner-val donors; sc-only = full fine-tune on training donors' sc pseudobulk, calibrated input. Base f01 6k·1x·E16. Top-50 DEG: LoRA best 4/4. Sepsis DEG from pooled_deg. Scores: scores/<cohort>/pooled/summary.json.",
+      "sources": "tools/sec09_paired_validation.py; data/sec09_fivefold.csv, data/sec09_slide_text.json"
+    },
+
+    {
+      "kind": "content", "section": "10", "section_label": "10 Paired-subset cohorts",
+      "title": "Next: cohorts with a paired subset (planned)",
+      "layout": "figure_keywords",
+      "figures": ["figures/sec10_paired_subset_cohorts.png"],
+      "keywords": ["Train LoRA on pairs, generate bulk-only", "Sepsis controls: 21 paired + 54 bulk-only", "ChILI pre-ICI: 11 bulk, 4 unpaired sc"],
+      "footnote": "Counts from pairing manifests. QC = identity check (Imperial also >=200 cells); sex-flag = bulk sex differs from metadata or is ambiguous. Not shown: Asan (no donor map), Giroux (24 pairs, 17 bulk-only; broadcast beats LoRA). Model: f01 6k 1x E16 + LoRA r16.",
+      "say": "Planned: no LoRA cells exist yet for any bulk-only sample. Ji bulk is PAXgene whole blood. Only 7 of the Arunachalam pairs are strict same-visit pairs. Asan is omitted because it has no donor map.",
+      "sources": "tools/sec10_paired_subset_cohorts.py; data/sec10_cohort_counts.csv, data/sec10_bulk_only_groups.csv, data/sec10_quoted_numbers.csv"
+    },
+
+    {
+      "kind": "divider",
+      "title": "Backup"
+    },
+    {
+      "kind": "content", "section": "4", "section_label": "Backup · 4 SLE benchmark", "backup": true,
+      "title": "Bulk broadcast baseline",
+      "layout": "full",
+      "figures": ["figures/sec04_sle_broadcast.png"],
+      "keywords": ["Bulk logFC copied: r 0.68 vs 0.37", "Type-specific part: partial r 0.21", "PBISC-VAE same; scSemiProfiler 0.17"],
+      "footnote": "SLE held-out, 42 donors, 1,006 genes; PBISC 5 seeds. Partial r: truth and method logFC residualised on bulk logFC. Broadcast has no residual, so it is not scored. Split-half and BayesPrism checks: sle_broadcast/RESULTS.md.",
+      "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_broadcast.csv, data/sec04_sle_numbers.csv"
+    },
+    {
+      "kind": "content", "section": "5", "section_label": "Backup · 5 Real bulk vs pseudobulk", "backup": true,
+      "title": "Same shift in three paired cohorts",
+      "layout": "full",
+      "figures": ["figures/sec05_shift_cohorts.png"],
+      "keywords": ["Shared shift in all 3 cohorts"],
+      "footnote": "Model inputs only, no generation. PCA is fitted on each cohort's sc pseudobulks (Arunachalam: 11 PCs, n = 12). D uses same-condition pairs only for Randolph and Arunachalam. Shift removal is a leave-one-out diagnostic.",
+      "sources": "tools/sec05_shift_cohorts.py; data/sec05_shift_cohorts.csv"
+    },
+    {
+      "kind": "content", "section": "6", "section_label": "Backup · 6 Paired fine-tuning", "backup": true,
+      "title": "Evaluation design",
+      "layout": "full",
+      "figures": ["figures/sec06_eval_design.png"],
+      "keywords": ["Donor-level splits; test donors never trained", "5-fold: other folds · few: 5 donors", "Giroux few-pair trains 12–14 of 24 pairs"],
+      "footnote": "Counts: data/<cohort>/folds.csv and fewshot_n5/DRAWS.json; QC-failed pairs (fold −1) excluded. Bars: Ye 2026 sepsis.",
+      "sources": "tools/sec06_finetune_method.py; data/sec06_eval_design.csv, data/sec06_eval_design_sepsis_roles.csv"
+    }
+  ]
+}

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/slides_spec.before_short_footnotes.json

@@ -0,0 +1,622 @@
+{
+ "deck": {
+  "output_pptx": "PBISC-Diffusion_paper_summary_20260930.pptx",
+  "paths": "figure paths are relative to the deck folder",
+  "note": "footnote = on-slide text (max 2 lines, may be a shortened copy); footnote_full = section author's full text, put in speaker notes when it differs. Section 9 text comes from data/sec09_slide_text.json; refresh with tools/sync_sec09_text.py after rerunning tools/sec09_paired_validation.py.",
+  "moved": "The ImMicro external-reference slide (section 4 spec) is placed at the end of section 5, after refcal is introduced, as its author asked."
+ },
+ "slides": [
+  {
+   "kind": "title",
+   "title": "PBISC-Diffusion: bulk-to-single-cell generation",
+   "subtitle": "Paper summary · 2026-09-30"
+  },
+  {
+   "kind": "agenda",
+   "title": "Outline",
+   "items": [
+    "Model overview: diffusion from bulk to cells",
+    "Backbone: SDD, scDiffusion, bulk conditioning",
+    "Architecture ablation: width, context, gene panel",
+    "SLE benchmark vs scSemiProfiler",
+    "Real bulk ≠ pseudobulk",
+    "Fine-tuning on paired bulk–sc data",
+    "LoRA: compute and ablations (K diversification)",
+    "How many bulk–sc pairs are needed",
+    "Paired-cohort validation vs scSemiProfiler",
+    "Next: cohorts with a paired subset (planned)"
+   ]
+  },
+  {
+   "kind": "content",
+   "section": "1",
+   "section_label": "1 Model overview",
+   "title": "PBISC-Diffusion: bulk in, cells out",
+   "layout": "full",
+   "figures": [
+    "figures/sec01_slide_a.png"
+   ],
+   "keywords": [
+    "Train pair: K-cell pseudobulk → each member cell"
+   ],
+   "footnote": "Top: redraw of manuscript Fig. 1b. Bottom: training corpus of the final model (f01 6k 1x); 33.1M cells in the donor-level 80/10/10 train split. K grid = 8,192 recipes/epoch, plus 3,658 top-up recipes over 16 epochs (K 1-4,000), so every train cell is a target once.",
+   "footnote_full": "Top: deck redraw of manuscript Fig. 1b (larger labels; cells differ by x_T and the Bernoulli support draw, Methods 'Support read-out'). Bottom: corpus of final run f01_6k_1x_seed20260627 (index fingerprint matches). Cells per dataset = base + overlay rows (Model 7 e2_full_source/e2_full_index manifests); 33.1M cells in the donor-level 80/10/10 train split. Registered K grid = 8,192 recipes/epoch. Plus 3,658 top-up recipes over 16 epochs (196-283 per epoch, K 1-4,000), so every train cell is a target once (ALLCELL_DATA_CONTRACT.json coverage_after_topup).",
+   "sources": "tools/sec01_overview.py; data/sec01_model_numbers.csv, data/sec01_corpus_datasets.csv, data/sec01_recipe_k.csv"
+  },
+  {
+   "kind": "content",
+   "section": "1",
+   "section_label": "1 Model overview",
+   "title": "Denoiser: joint value + support diffusion",
+   "layout": "diagram",
+   "figures": [
+    "figures/sec01_fig1a_denoiser.png"
+   ],
+   "keywords": [
+    "6,000 genes · 54.2M params · Bernoulli support draw"
+   ],
+   "footnote": "Redraw of manuscript Fig. 1a. Purple dashed = soft self-conditioning; gold dashed = context to all blocks. Final model f01 6k 1x, epoch 16, EMA; 7 blocks 1024-1024-512-256-512-1024-1024. Sampling: 50 DDIM steps, η = 0; keep gene if u < σ(logit). 16 epochs = one pass over the 131,072-recipe pool.",
+   "footnote_full": "Deck redraw of manuscript Fig. 1a (larger labels, legend dropped). Purple dashed = soft self-conditioning feedback; gold dashed = context to all blocks. Final model f01_6k_1x_seed20260627, checkpoint_epoch_016, EMA; 7 blocks 1024-1024-512-256-512-1024-1024 (effective_config.json, RUN_STATUS.json). Sampling: 50 DDIM steps, η = 0, drawn support read-out, keep gene if u < σ(logit) (methods.tex l.58, l.99). 16 epochs = 16 disjoint 8,192-recipe slots = one pass over the 131,072-recipe pool (manuscript: part 16).",
+   "sources": "tools/sec01_overview.py; data/sec01_model_numbers.csv, data/sec01_fig1_label_pt.csv"
+  },
+  {
+   "kind": "content",
+   "section": "2",
+   "section_label": "2 Backbone",
+   "title": "Backbone: SDD → PBISC-Diffusion",
+   "layout": "diagram",
+   "figures": [
+    "figures/sec02_backbone_compare.png"
+   ],
+   "keywords": [
+    "Kept from SDD: value + bit, skip-MLP",
+    "Changed: bulk condition, masked loss, Bernoulli read-out"
+   ],
+   "footnote": "Luo et al., Bioinformatics 2024; Ostheimer et al., arXiv 2502.02448 (code 1d5423c). PBISC: final model f01 6k 1x, part 16. σ = sigmoid; Bernoulli is the final read-out; the logit > 0 cut is also reported.",
+   "sources": "tools/sec02_backbone.py; data/sec02_backbone_compare.csv, data/sec02_slide_text.csv, data/refs/"
+  },
+  {
+   "kind": "content",
+   "section": "2",
+   "section_label": "2 Backbone",
+   "title": "Bulk conditioning",
+   "layout": "diagram",
+   "figures": [
+    "figures/sec02_bulk_conditioning.png"
+   ],
+   "keywords": [
+    "Same bulk condition for every generated cell",
+    "Final: no cell types, proportions, sum constraint",
+    "18,006 → 512 context into every block"
+   ],
+   "footnote": "Final model f01 6k 1x, part 16. Bar heights schematic.",
+   "sources": "tools/sec02_backbone.py; data/sec02_bulk_conditioning.csv, data/sec02_slide_text.csv"
+  },
+  {
+   "kind": "content",
+   "section": "3",
+   "section_label": "3 Architecture ablation",
+   "title": "Width & context ablation: loss saturation",
+   "layout": "full",
+   "figures": [
+    "figures/sec03_width_loss.png"
+   ],
+   "keywords": [
+    "Trunk x4: val loss −31% (0.197 → 0.136)",
+    "ctx x4, prop hint: loss = 1x",
+    "1x flat E8; trunk x4 still falling"
+   ],
+   "footnote": "Old 6k panel (1% floor); one validation set. 16x: memory-floor stop after part 2.",
+   "say": "All arms share the 6k panel (1% floor), corpus, seed and schedule; validation = 192 recipes x 64 cells. ctx x4, both x4 and 16x were read from server_2 snapshots.",
+   "sources": "tools/sec03_width_loss.py; data/sec03_width_loss.csv, data/sec03_width_saturation.csv, data/sec03_width_loss_headline.csv"
+  },
+  {
+   "kind": "content",
+   "section": "3",
+   "section_label": "3 Architecture ablation",
+   "title": "Width & context ablation: benchmark",
+   "layout": "full",
+   "figures": [
+    "figures/sec03_width_bench.png"
+   ],
+   "keywords": [
+    "trunk x4: loss −31%, no DEG gain",
+    "Prop hint: oracle = predicted, L1 worse",
+    "1x kept: ties ctx x4, 54M vs 102M"
+   ],
+   "footnote": "SLE, 42 donors, 2,980 genes; old 6k panel. ctx x4: better L1 (0.161 vs 0.197).",
+   "say": "Bars = mean of parts 14-16 with the cut p > 0.5; diamonds = Bernoulli read-out (4 width arms only). Prop hint = 9 L1 cell-type proportions; older panel, not the final model.",
+   "sources": "tools/sec03_width_bench.py; data/sec03_width_bench.csv, data/sec03_width_bench_summary.csv, data/sec03_width_bench_headline.csv"
+  },
+  {
+   "kind": "content",
+   "section": "3",
+   "section_label": "3 Architecture ablation",
+   "title": "Gene context: 2k / 3k / 6k / 15k",
+   "layout": "full",
+   "figures": [
+    "figures/sec03_panel.png"
+   ],
+   "keywords": [
+    "6k ≈ 3k: 3k inside 6k seed range",
+    "2k best L1; 15k worst r, L1",
+    "6k kept: first panel with CLEC9A (cDC1)"
+   ],
+   "footnote": "SLE, 42 donors, 1,006 benchmark genes in every panel; 6k base seed = best of 5.",
+   "say": "Runs f01_{2k,3k,6k,p15k}_1x, part 16, Bernoulli, EMA, DDIM 50. Different gene axis from the previous slide, so the two slides cannot be compared. Loss curves are divided by each panel's own part-16 value.",
+   "sources": "tools/sec03_panel.py; data/sec03_panel_bench.csv, data/sec03_panel_seeds.csv, data/sec03_panel_loss.csv, data/sec03_panel_headline.csv"
+  },
+  {
+   "kind": "content",
+   "section": "4",
+   "section_label": "4 SLE benchmark",
+   "title": "SLE benchmark: PBISC vs scSemiProfiler",
+   "layout": "full",
+   "figures": [
+    "figures/sec04_sle_benchmark.png"
+   ],
+   "keywords": [
+    "42 held-out donors, sc-pseudobulk input",
+    "Beats scSemiProfiler on all three metrics",
+    "Ties PBISC-VAE; below bulk-copy baseline"
+   ],
+   "footnote": "GSE135779, 42 held-out donors (30 SLE / 12 HC). PBISC f01 6k E16, 5 seeds (mean ± SD); baselines 1 draw. scSemiProfiler also gets real sc of 14 in-cohort donors (1,500 cells each). Dashed: input bulk logFC copied to every type (backup).",
+   "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_benchmark.csv, data/sec04_sle_numbers.csv"
+  },
+  {
+   "kind": "content",
+   "section": "4",
+   "section_label": "4 SLE benchmark",
+   "title": "SLE benchmark: per cell type",
+   "layout": "full",
+   "figures": [
+    "figures/sec04_sle_per_celltype.png"
+   ],
+   "keywords": [
+    "Beats scSemiProfiler in T, B, Mono, NK",
+    "Loses in rare DC and Other",
+    "DC: ~15 generated cells per donor"
+   ],
+   "footnote": "Same 42 donors, 1,006 genes. PBISC 5 seeds (mean ± SD), baselines 1 draw. Tick %: share of 251,179 real cells. Other top-50 is out of 12 truth genes. Bulk copy: r 0.68, top-50 113 (backup).",
+   "say": "PBISC's DC top list in the base seed has only 13 genes, because few DC cells are generated.",
+   "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_per_celltype.csv, data/sec04_sle_numbers.csv"
+  },
+  {
+   "kind": "content",
+   "section": "5",
+   "section_label": "5 Real bulk vs pseudobulk",
+   "title": "Real bulk ≠ pseudobulk (model input)",
+   "layout": "figure_keywords",
+   "figures": [
+    "figures/sec05_condition_space.png"
+   ],
+   "keywords": [
+    "Real bulk: 2.46 D from own pseudobulk",
+    "95% of squared offset is one shift",
+    "Shift removed (diagnostic): own donor 7.5% → 75.7%"
+   ],
+   "footnote": "ImMicro, 107 healthy donors. Model inputs (log1p CPM, 5,508 genes), not learned ctx. D = median donor-to-donor distance; PCA-30 values are lower bounds (full space 3.19 D, 0.91 shared). Shift removal is a diagnostic that uses paired pseudobulks. Pseudobulk PC1 is sc pool batch (pool R² 0.96 on PC1).",
+   "say": "The two pseudobulk clusters on PC1 are sc pools DB1-3 vs DB4-7, so the pairing lines cross mainly because of sc batch. Shift removal subtracts the mean offset of the other 106 donors; a bulk-only deployment would not have them.",
+   "sources": "tools/sec05_condition_space.py; data/sec05_condition_space_numbers.csv, data/sec05_condition_space_coords.csv"
+  },
+  {
+   "kind": "content",
+   "section": "5",
+   "section_label": "5 Real bulk vs pseudobulk",
+   "title": "Consequence: cells off-manifold",
+   "layout": "two_figures",
+   "figures": [
+    "figures/sec05_cells_umap.png",
+    "figures/sec05_cells_metrics.png"
+   ],
+   "keywords": [
+    "Monocytes: raw 30.6% vs real 16.7%",
+    "Same noise: 19% T → monocyte",
+    "Precision/coverage: raw 0.36/0.08, pseudobulk 0.92/0.51"
+   ],
+   "footnote": "refcal = cohort-mean bulk anchored to a healthy-PBMC reference (AIFI or AIDA); no paired sc. ImMicro, 107 donors; final model; each cell starts from the same noise under every input. Composition L1: raw 0.455, pseudobulk 0.166, cohort-mean null 0.161. UMAP fitted on real cells; overstates overlap.",
+   "footnote_full": "ImMicro, 107 donors. Final model f01 6k 1× E16 (DDIM 50, EMA); each cell starts from the same noise under every input. Precision/coverage come from one scoring call. Composition L1: raw 0.455, pseudobulk 0.166, cohort-mean null 0.161. The UMAP is fitted on real cells and overstates overlap. refcal definition: plans/utility_studies_final6k_20260925/refcal/RESULTS.md ('Reference-anchored calibration ... anchoring a cohort's mean bulk to the AIFI healthy-PBMC reference'); AIDA reference: refcal_refs/RESULTS.md.",
+   "say": "TPM fixes cell shape (precision 0.87) but not monocytes (34.3%). refcal fixes monocytes (about 17.5%); coverage depends on the reference (AIFI 0.08, AIDA 0.37).",
+   "sources": "tools/sec05_cells_offmanifold.py; data/sec05_cells_metrics.csv, data/sec05_cells_umap_coords.csv"
+  },
+  {
+   "kind": "content",
+   "section": "5",
+   "section_label": "5 Real bulk vs pseudobulk",
+   "title": "Consequence: disease direction flips",
+   "layout": "figure_keywords",
+   "figures": [
+    "figures/sec05_behcet_direction.png"
+   ],
+   "keywords": [
+    "CD16 gap: raw −3.97 vs observed +4.94",
+    "C1Q flip vanishes at common depth",
+    "AIFI refcal restores sign, 5/5 seeds"
+   ],
+   "footnote": "Behçet, final model. Bulk GSE198533 (BD 9, HC 10), 5,000 cells per sample; observed = sc GSE198616 (BD 4, HC 4, different people; descriptive p). At common depth, raw CD16 is −3.59 (seed 0) and raw C1Q is −0.08 ± 0.09 pp. AIDA refcal does not restore the sign.",
+   "say": "Limitations: AIDA refcal does not restore the sign (C1Q -0.25, CD16 +0.37). Best reference differs by cohort (AIDA for ImMicro, AIFI for Behcet). The sc pseudobulk ceiling uses the 8 sc donors, not the 19 bulk donors. Monocytes stay about 2x observed even under refcal.",
+   "sources": "tools/sec05_behcet_direction.py; data/sec05_behcet_direction.csv"
+  },
+  {
+   "kind": "content",
+   "section": "5",
+   "section_label": "5 Real bulk vs pseudobulk",
+   "title": "Real bulk + refcal vs scSemiProfiler (ImMicro)",
+   "layout": "full",
+   "figures": [
+    "figures/sec04_immicro_external.png"
+   ],
+   "keywords": [
+    "Real bulk + refcal; no target sc",
+    "Lower L1, IFN error; rank not better",
+    "No-bulk replay: lower T error, rank ~0"
+   ],
+   "footnote": "ImMicro baseline, 107 donors, 1 generation seed, 5,500 genes; CI = paired donor bootstrap. Refcal is fit on the mean of all 107 bulks (transductive). PBISC pretraining includes part of AIFI and is not counted in generation time.",
+   "say": "Section 4 author's slide ('External reference setting'), moved here after refcal is introduced. scSemiProfiler IFN variance ratio 0.036 (Mono) and 0.027 (T), vs PBISC 0.830 and 1.538.",
+   "sources": "tools/sec04_immicro.py; data/sec04_immicro_external.csv, data/sec04_immicro_numbers.csv"
+  },
+  {
+   "kind": "content",
+   "section": "6",
+   "section_label": "6 Paired fine-tuning",
+   "title": "Fine-tuning with paired bulk + sc",
+   "layout": "diagram",
+   "figures": [
+    "figures/sec06_ft_method.png"
+   ],
+   "keywords": [
+    "LoRA 2–14 min vs pretraining 15.9 h"
+   ],
+   "footnote": "Receipts: immicro/fold0/real_lora and ye2026_sepsis/fewshot_n5/draw0/lora RUN.json. Base: f01_6k_1x E16. Times: 40 local LoRA runs.",
+   "sources": "tools/sec06_finetune_method.py; data/sec06_ft_method.csv"
+  },
+  {
+   "kind": "content",
+   "section": "7",
+   "section_label": "7 LoRA ablations",
+   "title": "Full vs LoRA vs cond.-encoder-only",
+   "layout": "full",
+   "figures": [
+    "figures/sec07_ft_modes.png"
+   ],
+   "keywords": [
+    "LoRA ≈ full FT accuracy (n.s.)",
+    "42× fewer trainable params (1.3 M)",
+    "Cond.-encoder-only: no gain over zero-shot cal"
+   ],
+   "footnote": "Base f01_6k_1x E16. Full vs LoRA: paired Wilcoxon, donor L1, p 0.25 / 0.71. Open = fold-0 pilot; compare same marker only. Per-step time: runs early-stop differently.",
+   "sources": "tools/sec07_ft_modes.py; data/sec07_ft_modes_accuracy.csv, data/sec07_ft_modes_compute.csv, data/sec07_ft_modes_wilcoxon.csv"
+  },
+  {
+   "kind": "content",
+   "section": "7",
+   "section_label": "7 LoRA ablations",
+   "title": "K diversification: no gain",
+   "layout": "figure_keywords",
+   "figures": [
+    "figures/sec07_k_aug.png"
+   ],
+   "keywords": [
+    "No gain; keep single K 1000",
+    "Multi-K slightly worse on ImMicro (p 0.04)",
+    "Inner-val loss Δ ≤ 1.2e-4"
+   ],
+   "footnote": "LoRA r16 on f01_6k_1x E16, 5-fold pooled. p: paired Wilcoxon, donor L1 vs plain LoRA, uncorrected. Recipes arm: K 1000 real bulk + ½-batch pretraining pseudobulk, no multi-K.",
+   "sources": "tools/sec07_k_aug.py; data/sec07_k_aug.csv, data/sec07_k_aug_wilcoxon.csv, data/sec07_k_aug_inner_val_delta.csv"
+  },
+  {
+   "kind": "content",
+   "section": "8",
+   "section_label": "8 Pairs needed",
+   "title": "Pairs needed: composition, coverage, training steps",
+   "layout": "full",
+   "figures": [
+    "figures/sec08_pairs_realism.png"
+   ],
+   "keywords": [
+    "Coverage, 5+7 pairs: ImMicro 0.84, sepsis 0.77"
+   ],
+   "footnote": "Final f01 6k·1× E16 + LoRA; donor 5-fold CV, pooled scoring (ImMicro 107, sepsis 82 donors). N+7 = N training + 7 (sepsis 7–8) inner-val pairs for early stopping. cal = zero-shot + calibration, α fit on all 85–86 / 65–66 fold pairs; with α from the same 5 pairs, coverage 0.54 vs LoRA 0.79 (ImMicro), 0.43 vs 0.69 (sepsis).",
+   "footnote_full": "Final f01 6k·1× epoch-16 + LoRA; donor 5-fold CV, pooled scANVI scoring (ImMicro 107, sepsis 82 donors). N+7 = N training + 7 (sepsis 7–8) inner-val pairs for early stopping. cal = zero-shot + calibration, α fit on all 85–86 / 65–66 fold pairs; with α from the same 5 pairs (Sec. 9 call), coverage 0.54 vs LoRA 0.79 (ImMicro), 0.43 vs 0.69 (sepsis). Sec. 9 5-pair runs: fixed 3k steps, no inner-val. 20k cap reached by ImMicro folds 1/5 (10), 4/5 (20), 5/5 (40, all): val loss still falling, but last 2k steps <0.4% of total drop.",
+   "say": "Keywords say +7; 2 of 5 sepsis folds use 8 inner-val pairs.",
+   "sources": "tools/sec08_pairs_needed.py; data/sec08_pairs_realism.csv, data/sec08_selected_steps.csv, data/sec08_slide_numbers.csv"
+  },
+  {
+   "kind": "content",
+   "section": "8",
+   "section_label": "8 Pairs needed",
+   "title": "Pairs needed: donor and disease signal",
+   "layout": "figure_keywords",
+   "figures": [
+    "figures/sec08_pairs_signal.png"
+   ],
+   "keywords": [
+    "logFC r above broadcast from 10+7 pairs",
+    "DEG matches broadcast at 40+7 pairs",
+    "NK r 0.70 at 40+7 (cal 0.50)"
+   ],
+   "footnote": "Sepsis 61 case vs 21 control. logFC r = mean over T/B/Mono/NK (mean CP10K); DEG = Welch top-50 overlap summed over T/B/Mono/NK/DC. ≤10 pairs: NK r and DEG below cal; T r below cal until 40 pairs, Mono until all. DEG gain is Mono/DC.",
+   "footnote_full": "Same runs and pooled scoring as previous slide; sepsis 61 case vs 21 control. N+7 = N training + 7 (sepsis 7–8) inner-val pairs. logFC r = mean over T/B/Mono/NK (mean CP10K); DEG = Welch top-50 overlap summed over T/B/Mono/NK/DC. ≤10 pairs: NK r (0.20/0.40) and DEG (5/8) below cal (0.50, 11); T r below cal until 40 pairs, Mono until all. DEG gain is Mono/DC; T overlap 5 (cal) → 0–1 from 20 pairs, NK 0 at every n (broadcast T 3, NK 2).",
+   "sources": "tools/sec08_pairs_needed.py; data/sec08_pairs_signal.csv, data/sec08_slide_numbers.csv"
+  },
+  {
+   "kind": "content",
+   "section": "9",
+   "section_label": "9 Paired validation",
+   "sec09_index": 0,
+   "title": "Five paired cohorts",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_cohorts.png"
+   ],
+   "keywords": [
+    "403 paired samples, 275 donors",
+    "Only identity-pass pairs; donor-level splits",
+    "Ji bulk: whole blood, not PBMC"
+   ],
+   "footnote": "Usable pair = passed the pairing identity check and >= 200 cells (fold >= 0 in data/<cohort>/folds.csv); dropped 15 identity-fail, 11 borderline and 1 low-cell pairs of 430. ImMicro: no identity flag, all used. Imperial, Giroux, Ji: several pairs per donor. Case vs control = samples in scores/<cohort>/pooled/summary.json. Giroux 'moderate' = GEO 'severe' (paper term). Labels: data/<cohort>/QC_REPORT.md; ImMicro: GEO GSE314922/GSE314416.",
+   "footnote_full": "Usable pair = passed the pairing identity check and >= 200 cells (fold >= 0 in data/<cohort>/folds.csv); dropped 15 identity-fail, 11 borderline and 1 low-cell pairs of 430. ImMicro: no identity flag, all used. Imperial, Giroux, Ji: several pairs per donor. Case vs control = samples in scores/<cohort>/pooled/summary.json. Giroux 'moderate' = GEO 'severe' (paper term). Labels: data/<cohort>/QC_REPORT.md; ImMicro: GEO GSE314922/GSE314416.",
+   "sources": "tools/sec09_paired_validation.py; data/sec09_cohorts.csv, data/sec09_quoted_numbers.csv, data/sec09_slide_text.json",
+   "numbers": [
+    {
+     "value": "403 paired samples (sum of usable rows)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_usable_rows)"
+    },
+    {
+     "value": "275 donors (sum of usable donors)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_usable_donors)"
+    },
+    {
+     "value": "dropped 15 identity-fail, 11 borderline, 1 < 200 cells, of 430",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/features.npz (identity_pass, identity_check); samples.csv (n_cells); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/prepare_dataset.py (MIN_CELLS)"
+    },
+    {
+     "value": "ImMicro 107 pairs / 107 donors",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json"
+    },
+    {
+     "value": "Sepsis 82 pairs / 82 donors; sepsis 61 vs control 21",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json"
+    },
+    {
+     "value": "Imperial 157 pairs / 57 donors; COVID+ 113 vs COVID− 34 (+10 recovery, neither)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/pooled/summary.json"
+    },
+    {
+     "value": "Giroux 24 pairs / 9 donors; moderate 11 vs mild 13",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/pooled/summary.json"
+    },
+    {
+     "value": "Ji 33 pairs / 20 donors; ChILI 18 vs ICI control 15",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/fewshot_n5/DRAWS.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json"
+    }
+   ]
+  },
+  {
+   "kind": "content",
+   "section": "9",
+   "section_label": "9 Paired validation",
+   "sec09_index": 1,
+   "title": "5 donors: LoRA vs scSemiProfiler — cells",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fewpair_cells.png"
+   ],
+   "keywords": [
+    "LoRA-5 > scSemi-5: coverage, precision 5/5; L1 4/5",
+    "Coverage: LoRA-5 0.69–0.96 vs scSemi-5 0.04–0.61",
+    "Composition gain vs zero-shot: ImMicro only"
+   ],
+   "footnote": "Base f01 6k·1x·E16 (EMA, DDIM 50) + LoRA r=16, 3,000 steps. LoRA-5 / scSemi-5 = LoRA / scSemiProfiler trained on the same 5 donors (5–15 pairs); test = all other usable pairs. scSemi-5 scored in a separate call, same test set and reference (sha-checked); 25/25 draws (missing: none). Verdict = better in >= 80% of shared draws (L1: Giroux split 3/5). Depth-matched P/C: same ranking, coverage LoRA-5 0.83–0.97 vs scSemi-5 0.15–0.28. L1 vs zero-shot: per-donor Wilcoxon, ImMicro p 2e-10; others p >= 0.38. scANVI labels; P/C = PCA-50, k=10 balls. Scores: scores/<cohort>/fewshot_n5/.",
+   "footnote_full": "Base f01 6k·1x·E16 (EMA, DDIM 50) + LoRA r=16, 3,000 steps. LoRA-5 / scSemi-5 = LoRA / scSemiProfiler trained on the same 5 donors (5–15 pairs); test = all other usable pairs. scSemi-5 scored in a separate call, same test set and reference (sha-checked); 23/25 draws (missing: ImMicro draw4, Sepsis draw4). Verdict = better in >= 80% of shared draws (L1: Giroux split 3/5). Depth-matched P/C: same ranking, coverage LoRA-5 0.83–0.97 vs scSemi-5 0.15–0.29. L1 vs zero-shot: per-donor Wilcoxon, ImMicro p 2e-10; others p >= 0.38. scANVI labels; P/C = PCA-50, k=10 balls. Scores: scores/<cohort>/fewshot_n5/.",
+   "say": "scSemi-5 is missing draw4 for ImMicro and Sepsis. When those arrive, rerun tools/sec09_paired_validation.py, then tools/sync_sec09_text.py, then generate_deck.py.",
+   "sources": "tools/sec09_paired_validation.py; data/sec09_fewpair_cells.csv, data/sec09_scsemi_status.csv, data/sec09_slide_text.json",
+   "numbers": [
+    {
+     "value": "LoRA-5 vs scSemi-5 coverage (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.036 (5/5, lora); Sepsis 0.694 vs 0.080 (5/5, lora); Imperial 0.737 vs 0.059 (5/5, lora); Giroux 0.961 vs 0.607 (5/5, lora); Ji 0.707 vs 0.145 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 precision (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.518 (5/5, lora); Sepsis 0.906 vs 0.728 (5/5, lora); Imperial 0.853 vs 0.330 (5/5, lora); Giroux 1.000 vs 0.992 (5/5, lora); Ji 0.978 vs 0.840 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 comp_l1 (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.233 (5/5, lora); Sepsis 0.466 vs 0.612 (5/5, lora); Imperial 0.503 vs 0.602 (5/5, lora); Giroux 0.256 vs 0.270 (3/5, split); Ji 0.513 vs 0.592 (4/5, lora) -> LoRA verdicts 4/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 coverage_dm (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.284 (5/5, lora); Sepsis 0.834 vs 0.158 (5/5, lora); Imperial 0.863 vs 0.152 (5/5, lora); Giroux 0.974 vs 0.238 (5/5, lora); Ji 0.908 vs 0.150 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 vs scSemi-5 precision_dm (shared-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.829 (5/5, lora); Sepsis 0.914 vs 0.504 (5/5, lora); Imperial 0.881 vs 0.429 (5/5, lora); Giroux 0.995 vs 0.426 (5/5, lora); Ji 0.974 vs 0.564 (5/5, lora) -> LoRA verdicts 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "coverage cohort means over all draws: LoRA-5 ImMicro 0.792, Sepsis 0.694, Imperial 0.737, Giroux 0.961, Ji 0.707; scSemi-5 ImMicro 0.036, Sepsis 0.080, Imperial 0.059, Giroux 0.607, Ji 0.145",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json and draw<j>_scsemi5/summary.json"
+    },
+    {
+     "value": "LoRA-5 minus zero-shot-cal composition L1, per-donor Wilcoxon (draw-averaged): ImMicro -0.027, n=107, p=2.2e-10; Sepsis +0.018, n=82, p=0.79; Imperial +0.016, n=57, p=0.38; Giroux -0.065, n=8, p=0.38; Ji -0.012, n=20, p=0.7",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/per_donor.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/folds.csv"
+    },
+    {
+     "value": "scSemiProfiler draws used / LoRA draws: ImMicro 5/5, Sepsis 5/5, Imperial 5/5, Giroux 5/5, Ji 5/5",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec09_scsemi_status.csv"
+    },
+    {
+     "value": "training pairs per draw: ImMicro 5, Sepsis 5, Imperial 12–15, Giroux 12–14, Ji 7–9; test pairs: ImMicro 102, Sepsis 77, Imperial 142–145, Giroux 10–12, Ji 24–26",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json (n_train_rows, n_test_rows)"
+    },
+    {
+     "value": "LoRA r = 16; 3000 fixed steps; base runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt; sampling: test donors only, 1,500 cells each, seed 20260927, DDIM 50, EMA, Bernoulli read-out",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fewshot_n5/draw0/lora/RUN.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md"
+    },
+    {
+     "value": "P/C definition: precision/coverage/density (PCA-50 + k = 10 balls fitted on the scored donors' observed R1 cells); PCA components in every summary.json = 50",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py"
+    }
+   ]
+  },
+  {
+   "kind": "content",
+   "section": "9",
+   "section_label": "9 Paired validation",
+   "sec09_index": 2,
+   "title": "5 donors: LoRA vs scSemiProfiler — disease signal",
+   "layout": "figure_keywords",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fewpair_disease.png"
+   ],
+   "keywords": [
+    "Top-50 DEG: LoRA-5 higher 3/4; Ji ~0",
+    "logFC r: scSemi-5 wins Giroux; Sepsis split",
+    "Giroux: real-bulk broadcast beats all arms"
+   ],
+   "footnote": "Same draws and verdict rule as the previous slide; DEG tie = half the draws equal or mean gap < 1 gene. logFC r = mean over T/B/Mono/NK of case-vs-control log2FC r (generated vs observed); top-50 DEG = Welch+BH overlap summed over 5 types (max 250; Giroux 51–109, Ji 75–250 per draw). Giroux test = 2 vs 2 subjects per draw. Broadcast = the input real bulk's own logFC. Scores: scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/.",
+   "footnote_full": "Same draws and verdict rule as the previous slide; DEG tie = half the draws equal or mean gap < 1 gene. logFC r = mean over T/B/Mono/NK of case-vs-control log2FC r (generated vs observed); top-50 DEG = Welch+BH overlap summed over 5 types (max 250; Giroux 51–109, Ji 75–250 per draw). Giroux test = 2 vs 2 subjects per draw. Broadcast = the input real bulk's own logFC. Scores: scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/.",
+   "sources": "tools/sec09_paired_validation.py; data/sec09_fewpair_disease.csv, data/sec09_slide_text.json",
+   "numbers": [
+    {
+     "value": "Top-50 DEG LoRA-5 vs scSemi-5 (shared-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 5.2 (5/5, 0 tied, lora); Imperial 113.6 vs 46.8 (5/5, 0 tied, lora); Giroux 11.6 vs 1.2 (5/5, 0 tied, lora); Ji 0.2 vs 0.0 (1/5, 4 tied, tie)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv"
+    },
+    {
+     "value": "logFC r LoRA-5 vs scSemi-5 (shared-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs 0.402 (3/5, split); Imperial 0.749 vs 0.562 (5/5, lora); Giroux 0.331 vs 0.398 (0/5, scsemi); Ji 0.333 vs 0.153 (5/5, lora)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/summary.json and contrast.csv"
+    },
+    {
+     "value": "Giroux broadcast logFC r 0.539 vs best arm 0.398; broadcast DEG 25.4 vs best arm 11.6 (means over all draws)",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5/draw<j>{,_scsemi5}/summary.json"
+    },
+    {
+     "value": "DEG maximum per draw: Sepsis 250, Imperial 250, Giroux 51–109, Ji 75–250",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/summary.json (deg_top50_max)"
+    },
+    {
+     "value": "Giroux test subjects per draw: 2 vs 2 (moderate vs mild); test pairs 10–12",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json (train_donors); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv (group)"
+    }
+   ]
+  },
+  {
+   "kind": "content",
+   "section": "9",
+   "section_label": "9 Paired validation",
+   "sec09_index": 3,
+   "title": "All pairs, 5-fold",
+   "layout": "full",
+   "figures": [
+    "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/figures/sec09_fivefold.png"
+   ],
+   "keywords": [
+    "LoRA tops coverage 5/5, logFC r 4/4",
+    "Ji whole blood: baselines 0.11, LoRA 0.86",
+    "Giroux: broadcast r 0.64 > LoRA 0.50"
+   ],
+   "footnote": "Donor-level 5-fold CV; each pair scored once, by the fold model that never trained on its donor (one pooled call per cohort). LoRA r=16 on all training donors' real bulk, early stop on inner-val donors; sc-only = full fine-tune on training donors' sc pseudobulk, calibrated input. Base f01 6k·1x·E16. Top-50 DEG: LoRA best 4/4. Sepsis DEG from pooled_deg. Scores: scores/<cohort>/pooled/summary.json.",
+   "footnote_full": "Donor-level 5-fold CV; each pair scored once, by the fold model that never trained on its donor (one pooled call per cohort). LoRA r=16 on all training donors' real bulk, early stop on inner-val donors; sc-only = full fine-tune on training donors' sc pseudobulk, calibrated input. Base f01 6k·1x·E16. Top-50 DEG: LoRA best 4/4. Sepsis DEG from pooled_deg. Scores: scores/<cohort>/pooled/summary.json.",
+   "sources": "tools/sec09_paired_validation.py; data/sec09_fivefold.csv, data/sec09_slide_text.json",
+   "numbers": [
+    {
+     "value": "LoRA best of 3 arms: coverage 5/5, logFC r 4/4, top-50 DEG 4/4",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json)"
+    },
+    {
+     "value": "Ji coverage: zero-shot cal 0.106, sc-only 0.113, LoRA 0.857",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json"
+    },
+    {
+     "value": "Giroux logFC r: broadcast 0.638 vs LoRA 0.504; DEG broadcast 39 vs LoRA 25",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/pooled/summary.json"
+    },
+    {
+     "value": "LoRA logFC r vs broadcast: Sepsis 0.527 vs 0.316, Imperial 0.819 vs 0.661, Giroux 0.504 vs 0.638, Ji 0.479 vs 0.240",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (Sepsis DEG: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled_deg/summary.json)"
+    },
+    {
+     "value": "Pooled n (pairs / donors): ImMicro 107/107, Sepsis 82/82, Imperial 157/57, Giroux 24/9, Ji 33/20",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/pooled/summary.json (n_donors); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/fewshot_n5/DRAWS.json"
+    },
+    {
+     "value": "early stopping: About 10 % of each fold's training donors are inner-validation, used only for early stopping",
+     "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md"
+    }
+   ]
+  },
+  {
+   "kind": "content",
+   "section": "10",
+   "section_label": "10 Paired-subset cohorts",
+   "title": "Next: cohorts with a paired subset (planned)",
+   "layout": "figure_keywords",
+   "figures": [
+    "figures/sec10_paired_subset_cohorts.png"
+   ],
+   "keywords": [
+    "Train LoRA on pairs, generate bulk-only",
+    "Sepsis controls: 21 paired + 54 bulk-only",
+    "ChILI pre-ICI: 11 bulk, 4 unpaired sc"
+   ],
+   "footnote": "Counts from pairing manifests. QC = identity check (Imperial also >=200 cells); sex-flag = bulk sex differs from metadata or is ambiguous. Not shown: Asan (no donor map), Giroux (24 pairs, 17 bulk-only; broadcast beats LoRA). Model: f01 6k 1x E16 + LoRA r16.",
+   "say": "Planned: no LoRA cells exist yet for any bulk-only sample. Ji bulk is PAXgene whole blood. Only 7 of the Arunachalam pairs are strict same-visit pairs. Asan is omitted because it has no donor map.",
+   "sources": "tools/sec10_paired_subset_cohorts.py; data/sec10_cohort_counts.csv, data/sec10_bulk_only_groups.csv, data/sec10_quoted_numbers.csv"
+  },
+  {
+   "kind": "divider",
+   "title": "Backup"
+  },
+  {
+   "kind": "content",
+   "section": "4",
+   "section_label": "Backup · 4 SLE benchmark",
+   "backup": true,
+   "title": "Bulk broadcast baseline",
+   "layout": "full",
+   "figures": [
+    "figures/sec04_sle_broadcast.png"
+   ],
+   "keywords": [
+    "Bulk logFC copied: r 0.68 vs 0.37",
+    "Type-specific part: partial r 0.21",
+    "PBISC-VAE same; scSemiProfiler 0.17"
+   ],
+   "footnote": "SLE held-out, 42 donors, 1,006 genes; PBISC 5 seeds. Partial r: truth and method logFC residualised on bulk logFC. Broadcast has no residual, so it is not scored. Split-half and BayesPrism checks: sle_broadcast/RESULTS.md.",
+   "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_broadcast.csv, data/sec04_sle_numbers.csv"
+  },
+  {
+   "kind": "content",
+   "section": "5",
+   "section_label": "Backup · 5 Real bulk vs pseudobulk",
+   "backup": true,
+   "title": "Same shift in three paired cohorts",
+   "layout": "full",
+   "figures": [
+    "figures/sec05_shift_cohorts.png"
+   ],
+   "keywords": [
+    "Shared shift in all 3 cohorts"
+   ],
+   "footnote": "Model inputs only, no generation. PCA is fitted on each cohort's sc pseudobulks (Arunachalam: 11 PCs, n = 12). D uses same-condition pairs only for Randolph and Arunachalam. Shift removal is a leave-one-out diagnostic.",
+   "sources": "tools/sec05_shift_cohorts.py; data/sec05_shift_cohorts.csv"
+  },
+  {
+   "kind": "content",
+   "section": "6",
+   "section_label": "Backup · 6 Paired fine-tuning",
+   "backup": true,
+   "title": "Evaluation design",
+   "layout": "full",
+   "figures": [
+    "figures/sec06_eval_design.png"
+   ],
+   "keywords": [
+    "Donor-level splits; test donors never trained",
+    "5-fold: other folds · few: 5 donors",
+    "Giroux few-pair trains 12–14 of 24 pairs"
+   ],
+   "footnote": "Counts: data/<cohort>/folds.csv and fewshot_n5/DRAWS.json; QC-failed pairs (fold −1) excluded. Bars: Ye 2026 sepsis.",
+   "sources": "tools/sec06_finetune_method.py; data/sec06_eval_design.csv, data/sec06_eval_design_sepsis_roles.csv"
+  }
+ ]
+}