Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_fivefold.csv

@@ -0,0 +1,53 @@
+figure,dataset,metric,series,arm_file,value,n_scored,source
+sec09_fivefold,immicro,coverage,zs_raw,zs__raw,0.191838,107,scores/immicro/pooled/summary.json
+sec09_fivefold,immicro,coverage,sconly,pseudo_full__raw,0.0853583,107,scores/immicro/pooled/summary.json
+sec09_fivefold,immicro,coverage,lora,real_lora__raw,0.784299,107,scores/immicro/pooled/summary.json
+sec09_fivefold,immicro,coverage,ref_pseudo,zs__pseudo,0.524424,,scores/immicro/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,coverage,zs_raw,zs__raw,0.0673171,82,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,coverage,sconly,pseudo_full__raw,0.134146,82,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,coverage,lora,real_lora__raw,0.82935,82,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,coverage,ref_pseudo,zs__pseudo,0.48,,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,contrast_r,zs_raw,zs__raw,-0.0118027,82,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,contrast_r,sconly,pseudo_full__raw,0.148538,82,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,contrast_r,lora,real_lora__raw,0.526761,82,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,contrast_r,ref_broadcast,real_lora__raw (raw real bulk),0.315946,,scores/ye2026_sepsis/pooled/summary.json
+sec09_fivefold,ye2026_sepsis,deg,zs_raw,zs__raw,9,82,scores/ye2026_sepsis/pooled_deg/summary.json
+sec09_fivefold,ye2026_sepsis,deg,sconly,pseudo_full__raw,10,82,scores/ye2026_sepsis/pooled_deg/summary.json
+sec09_fivefold,ye2026_sepsis,deg,lora,real_lora__raw,23,82,scores/ye2026_sepsis/pooled_deg/summary.json
+sec09_fivefold,ye2026_sepsis,deg,ref_broadcast,real_lora__raw (raw real bulk),21,,scores/ye2026_sepsis/pooled_deg/summary.json
+sec09_fivefold,imperial_eskd,coverage,zs_raw,zs__raw,0.111958,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,coverage,sconly,pseudo_full__raw,0.0166511,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,coverage,lora,real_lora__raw,0.850013,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,coverage,ref_pseudo,zs__pseudo,0.703688,,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,contrast_r,zs_raw,zs__raw,0.643984,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,contrast_r,sconly,pseudo_full__raw,0.468808,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,contrast_r,lora,real_lora__raw,0.818745,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,contrast_r,ref_broadcast,real_lora__raw (raw real bulk),0.660605,,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,deg,zs_raw,zs__raw,106,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,deg,sconly,pseudo_full__raw,54,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,deg,lora,real_lora__raw,143,157,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,imperial_eskd,deg,ref_broadcast,real_lora__raw (raw real bulk),84,,scores/imperial_eskd/pooled/summary.json
+sec09_fivefold,giroux2022,coverage,zs_raw,zs__raw,0.281111,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,coverage,sconly,pseudo_full__raw,0.414167,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,coverage,lora,real_lora__raw,0.928056,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,coverage,ref_pseudo,zs__pseudo,0.864722,,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,contrast_r,zs_raw,zs__raw,0.416431,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,contrast_r,sconly,pseudo_full__raw,0.433206,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,contrast_r,lora,real_lora__raw,0.50417,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,contrast_r,ref_broadcast,real_lora__raw (raw real bulk),0.638105,,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,deg,zs_raw,zs__raw,20,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,deg,sconly,pseudo_full__raw,13,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,deg,lora,real_lora__raw,25,24,scores/giroux2022/pooled/summary.json
+sec09_fivefold,giroux2022,deg,ref_broadcast,real_lora__raw (raw real bulk),39,,scores/giroux2022/pooled/summary.json
+sec09_fivefold,ji2025_chili,coverage,zs_raw,zs__raw,0.0553535,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,coverage,sconly,pseudo_full__raw,0.0939394,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,coverage,lora,real_lora__raw,0.85697,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,coverage,ref_pseudo,zs__pseudo,0.685051,,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,contrast_r,zs_raw,zs__raw,0.0835223,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,contrast_r,sconly,pseudo_full__raw,0.153139,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,contrast_r,lora,real_lora__raw,0.479288,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,contrast_r,ref_broadcast,real_lora__raw (raw real bulk),0.239875,,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,deg,zs_raw,zs__raw,0,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,deg,sconly,pseudo_full__raw,0,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,deg,lora,real_lora__raw,15,33,scores/ji2025_chili/pooled/summary.json
+sec09_fivefold,ji2025_chili,deg,ref_broadcast,real_lora__raw (raw real bulk),4,,scores/ji2025_chili/pooled/summary.json

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_quoted_numbers.csv

@@ -0,0 +1,61 @@
+slide,item,value,source
+a,quoted on slide,403 paired samples (sum of usable rows),/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)
+a,quoted on slide,275 donors (sum of usable 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 (n_usable_donors)
+a,quoted on slide,"dropped 15 identity-fail, 11 borderline, 1 < 200 cells, of 430","/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)"
+a,quoted on slide,ImMicro 107 pairs / 107 donors,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json
+a,quoted on slide,Sepsis 82 pairs / 82 donors; sepsis 61 vs control 21,/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
+a,quoted on slide,"Imperial 157 pairs / 57 donors; COVID+ 113 vs COVID− 34 (+10 recovery, neither)",/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
+a,quoted on slide,Giroux 24 pairs / 9 donors; moderate 11 vs mild 13,/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
+a,quoted on slide,Ji 33 pairs / 20 donors; ChILI 18 vs ICI control 15,/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
+b,quoted on slide,"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",/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
+b,quoted on slide,"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",/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
+b,quoted on slide,"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",/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
+b,quoted on slide,"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",/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
+b,quoted on slide,"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",/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
+b,quoted on slide,"LoRA-5 vs zero-shot (real bulk) coverage (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.190 (5/5, lora); Sepsis 0.694 vs 0.076 (5/5, lora); Imperial 0.737 vs 0.114 (5/5, lora); Giroux 0.961 vs 0.472 (5/5, lora); Ji 0.707 vs 0.066 (5/5, lora) -> LoRA verdicts 5/5","/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 (arms lora5, zs_raw)"
+b,quoted on slide,"LoRA-5 vs zero-shot (real bulk) precision (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.677 (5/5, lora); Sepsis 0.906 vs 0.625 (5/5, lora); Imperial 0.853 vs 0.500 (5/5, lora); Giroux 1.000 vs 0.980 (5/5, lora); Ji 0.978 vs 0.799 (5/5, lora) -> LoRA verdicts 5/5","/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 (arms lora5, zs_raw)"
+b,quoted on slide,"LoRA-5 vs zero-shot (real bulk) comp_l1 (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.445 (5/5, lora); Sepsis 0.466 vs 0.510 (5/5, lora); Imperial 0.503 vs 0.806 (5/5, lora); Giroux 0.256 vs 0.351 (5/5, lora); Ji 0.513 vs 0.721 (5/5, lora) -> LoRA verdicts 5/5","/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 (arms lora5, zs_raw)"
+b,quoted on slide,"LoRA-5 vs zero-shot (real bulk) coverage_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.213 (5/5, lora); Sepsis 0.834 vs 0.073 (5/5, lora); Imperial 0.863 vs 0.151 (5/5, lora); Giroux 0.974 vs 0.549 (5/5, lora); Ji 0.908 vs 0.199 (5/5, lora) -> LoRA verdicts 5/5","/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 (arms lora5, zs_raw)"
+b,quoted on slide,"LoRA-5 vs zero-shot (real bulk) precision_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.671 (5/5, lora); Sepsis 0.914 vs 0.595 (5/5, lora); Imperial 0.881 vs 0.561 (5/5, lora); Giroux 0.995 vs 0.996 (2/5, split); Ji 0.974 vs 0.480 (5/5, lora) -> LoRA verdicts 4/5","/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 (arms lora5, zs_raw)"
+b,quoted on slide,"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; zero-shot ImMicro 0.190, Sepsis 0.076, Imperial 0.114, Giroux 0.472, Ji 0.066",/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
+b,quoted on slide,"LoRA-5 minus zero-shot (real bulk) composition L1, per-donor Wilcoxon (draw-averaged): ImMicro -0.270, n=107, p=2.2e-18; Sepsis -0.044, n=82, p=0.15; Imperial -0.348, n=57, p=1.6e-08; Giroux -0.107, n=8, p=0.039; Ji -0.232, n=20, p=0.017 -> gain in 4/5",/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
+b,quoted on slide,"scSemiProfiler draws used / LoRA draws: ImMicro 5/5, Sepsis 5/5, Imperial 5/5, Giroux 5/5, Ji 5/5",/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
+b,quoted on slide,"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","/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)"
+b,quoted on slide,"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",/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
+b,quoted on slide,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,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py
+c,quoted on slide,"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)","/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"
+c,quoted on slide,"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, other); Ji 0.333 vs 0.153 (5/5, lora)","/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"
+c,quoted on slide,"Top-50 DEG LoRA-5 vs zero-shot (real bulk) (same-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 10.0 (4/5, 0 tied, lora); Imperial 113.6 vs 105.6 (5/5, 0 tied, lora); Giroux 11.6 vs 4.4 (4/5, 0 tied, lora); Ji 0.2 vs 0.0 (1/5, 4 tied, tie)","/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 (arms lora5, zs_raw)"
+c,quoted on slide,"logFC r LoRA-5 vs zero-shot (real bulk) (same-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs -0.024 (5/5, lora); Imperial 0.749 vs 0.638 (5/5, lora); Giroux 0.331 vs 0.297 (3/5, split); Ji 0.333 vs 0.087 (5/5, lora)","/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/<cohort>/fewshot_n5/draw<j>/contrast.csv (arms lora5, zs_raw)"
+c,quoted on slide,Giroux broadcast logFC r 0.539 vs best arm 0.398; broadcast DEG 25.4 vs best arm 11.6 (means over all draws),"/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"
+c,quoted on slide,"DEG maximum per draw: Sepsis 250, Imperial 250, Giroux 51–109, Ji 75–250",/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)
+c,quoted on slide,Giroux test subjects per draw: 2 vs 2 (moderate vs mild); test pairs 10–12,/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)
+d,quoted on slide,"LoRA best of 3 arms: coverage 5/5, logFC r 4/4, top-50 DEG 4/4",/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)
+d,quoted on slide,"Ji coverage: zero-shot 0.055, sc-only 0.094, LoRA 0.857",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json
+d,quoted on slide,Giroux logFC r: broadcast 0.638 vs LoRA 0.504; DEG broadcast 39 vs LoRA 25,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/pooled/summary.json
+d,quoted on slide,"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",/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)
+d,quoted on slide,"coverage LoRA / zero-shot / sc-only: ImMicro 0.784 / 0.192 / 0.085, Sepsis 0.829 / 0.067 / 0.134, Imperial 0.850 / 0.112 / 0.017, Giroux 0.928 / 0.281 / 0.414, Ji 0.857 / 0.055 / 0.094",/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)
+d,quoted on slide,"logFC r LoRA / zero-shot / sc-only: Sepsis 0.527 / -0.012 / 0.149, Imperial 0.819 / 0.644 / 0.469, Giroux 0.504 / 0.416 / 0.433, Ji 0.479 / 0.084 / 0.153",/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)
+d,quoted on slide,"top-50 DEG LoRA / zero-shot / sc-only: Sepsis 23 / 9 / 10, Imperial 143 / 106 / 54, Giroux 25 / 20 / 13, Ji 15 / 0 / 0",/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)
+d,quoted on slide,"Pooled n (pairs / donors): ImMicro 107/107, Sepsis 82/82, Imperial 157/57, Giroux 24/9, Ji 33/20",/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
+d,quoted on slide,"early stopping: About 10 % of each fold's training donors are inner-validation, used only for early stopping",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/README.md
+b,"immicro LoRA-5 minus zero-shot (real bulk) L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.270, n=510, p 3e-80","/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fewshot_n5/draw<j>/per_donor.csv (comp_l1, arms lora5 / zs_raw); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv (sample -> donor)"
+b,"ye2026_sepsis LoRA-5 minus zero-shot (real bulk) L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.044, n=385, p 0.0031","/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fewshot_n5/draw<j>/per_donor.csv (comp_l1, arms lora5 / zs_raw); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/folds.csv (sample -> donor)"
+b,"imperial_eskd LoRA-5 minus zero-shot (real bulk) L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.303, n=715, p 3.8e-60","/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/fewshot_n5/draw<j>/per_donor.csv (comp_l1, arms lora5 / zs_raw); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/folds.csv (sample -> donor)"
+b,"giroux2022 LoRA-5 minus zero-shot (real bulk) L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.093, n=54, p 7.6e-05","/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5/draw<j>/per_donor.csv (comp_l1, arms lora5 / zs_raw); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv (sample -> donor)"
+b,"ji2025_chili LoRA-5 minus zero-shot (real bulk) L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.210, n=126, p 1.9e-07","/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/fewshot_n5/draw<j>/per_donor.csv (comp_l1, arms lora5 / zs_raw); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/folds.csv (sample -> donor)"
+d,immicro pooled zs_raw (zs__raw) coverage / precision / L1 / r / DEG,0.192 / 0.680 / 0.455 / nan / nan,scores/immicro/pooled/summary.json
+d,immicro pooled sconly (pseudo_full__raw) coverage / precision / L1 / r / DEG,0.085 / 0.429 / 0.444 / nan / nan,scores/immicro/pooled/summary.json
+d,immicro pooled lora (real_lora__raw) coverage / precision / L1 / r / DEG,0.784 / 0.924 / 0.162 / nan / nan,scores/immicro/pooled/summary.json
+d,ye2026_sepsis pooled zs_raw (zs__raw) coverage / precision / L1 / r / DEG,0.067 / 0.614 / 0.511 / -0.012 / 9,scores/ye2026_sepsis/pooled/summary.json; DEG: scores/ye2026_sepsis/pooled_deg/summary.json
+d,ye2026_sepsis pooled sconly (pseudo_full__raw) coverage / precision / L1 / r / DEG,0.134 / 0.606 / 0.472 / 0.149 / 10,scores/ye2026_sepsis/pooled/summary.json; DEG: scores/ye2026_sepsis/pooled_deg/summary.json
+d,ye2026_sepsis pooled lora (real_lora__raw) coverage / precision / L1 / r / DEG,0.829 / 0.926 / 0.362 / 0.527 / 23,scores/ye2026_sepsis/pooled/summary.json; DEG: scores/ye2026_sepsis/pooled_deg/summary.json
+d,imperial_eskd pooled zs_raw (zs__raw) coverage / precision / L1 / r / DEG,0.112 / 0.489 / 0.808 / 0.644 / 106,scores/imperial_eskd/pooled/summary.json
+d,imperial_eskd pooled sconly (pseudo_full__raw) coverage / precision / L1 / r / DEG,0.017 / 0.217 / 0.813 / 0.469 / 54,scores/imperial_eskd/pooled/summary.json
+d,imperial_eskd pooled lora (real_lora__raw) coverage / precision / L1 / r / DEG,0.850 / 0.847 / 0.376 / 0.819 / 143,scores/imperial_eskd/pooled/summary.json
+d,giroux2022 pooled zs_raw (zs__raw) coverage / precision / L1 / r / DEG,0.281 / 0.909 / 0.325 / 0.416 / 20,scores/giroux2022/pooled/summary.json
+d,giroux2022 pooled sconly (pseudo_full__raw) coverage / precision / L1 / r / DEG,0.414 / 0.981 / 0.269 / 0.433 / 13,scores/giroux2022/pooled/summary.json
+d,giroux2022 pooled lora (real_lora__raw) coverage / precision / L1 / r / DEG,0.928 / 0.998 / 0.258 / 0.504 / 25,scores/giroux2022/pooled/summary.json
+d,ji2025_chili pooled zs_raw (zs__raw) coverage / precision / L1 / r / DEG,0.055 / 0.717 / 0.738 / 0.084 / 0,scores/ji2025_chili/pooled/summary.json
+d,ji2025_chili pooled sconly (pseudo_full__raw) coverage / precision / L1 / r / DEG,0.094 / 0.718 / 0.596 / 0.153 / 0,scores/ji2025_chili/pooled/summary.json
+d,ji2025_chili pooled lora (real_lora__raw) coverage / precision / L1 / r / DEG,0.857 / 0.971 / 0.504 / 0.479 / 15,scores/ji2025_chili/pooled/summary.json

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_slide_text.json

@@ -0,0 +1,234 @@
+{
+ "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.",
+   "footnote_short": "Usable pair = passed identity check and ≥ 200 cells: 403 of 430 pairs; donor-level splits.",
+   "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",
+    "LoRA-5 coverage 0.69–0.96; scSemi-5 0.04–0.61",
+    "Lower L1 than zero-shot: all but Sepsis"
+   ],
+   "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. Zero-shot = base model without fine-tuning, fed each test pair's real bulk as measured (same call as LoRA-5). scSemi-5 scored in a separate call, same test set and reference (sha-checked); 25/25 draws. Verdict = better in >= 80% of shared draws. LoRA-5 lower L1 than scSemi-5 in 4/5 (Giroux split 3/5). LoRA-5 > zero-shot: coverage 5/5, precision 5/5, depth-matched 5/5 and 4/5 cohorts. Depth-matched P/C vs scSemi-5: same ranking, coverage LoRA-5 0.83–0.97 vs scSemi-5 0.15–0.28. L1 LoRA-5 minus zero-shot, per-donor Wilcoxon (gain = p < 0.05): ImMicro -0.27 (p 2e-18), Sepsis -0.04 (p 0.15), Imperial -0.35 (p 2e-08), Giroux -0.11 (p 0.04), Ji -0.23 (p 0.02). scANVI labels; P/C = PCA-50, k=10 balls. Scores: scores/<cohort>/fewshot_n5/.",
+   "footnote_short": "5 draws per cohort; test = all other usable pairs. Zero-shot = base model on real bulk. scANVI labels.",
+   "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": "LoRA-5 vs zero-shot (real bulk) coverage (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.190 (5/5, lora); Sepsis 0.694 vs 0.076 (5/5, lora); Imperial 0.737 vs 0.114 (5/5, lora); Giroux 0.961 vs 0.472 (5/5, lora); Ji 0.707 vs 0.066 (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 (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) precision (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.677 (5/5, lora); Sepsis 0.906 vs 0.625 (5/5, lora); Imperial 0.853 vs 0.500 (5/5, lora); Giroux 1.000 vs 0.980 (5/5, lora); Ji 0.978 vs 0.799 (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 (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) comp_l1 (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.445 (5/5, lora); Sepsis 0.466 vs 0.510 (5/5, lora); Imperial 0.503 vs 0.806 (5/5, lora); Giroux 0.256 vs 0.351 (5/5, lora); Ji 0.513 vs 0.721 (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 (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) coverage_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.213 (5/5, lora); Sepsis 0.834 vs 0.073 (5/5, lora); Imperial 0.863 vs 0.151 (5/5, lora); Giroux 0.974 vs 0.549 (5/5, lora); Ji 0.908 vs 0.199 (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 (arms lora5, zs_raw)"
+    },
+    {
+     "value": "LoRA-5 vs zero-shot (real bulk) precision_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.671 (5/5, lora); Sepsis 0.914 vs 0.595 (5/5, lora); Imperial 0.881 vs 0.561 (5/5, lora); Giroux 0.995 vs 0.996 (2/5, split); Ji 0.974 vs 0.480 (5/5, 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 (arms lora5, zs_raw)"
+    },
+    {
+     "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; zero-shot ImMicro 0.190, Sepsis 0.076, Imperial 0.114, Giroux 0.472, Ji 0.066",
+     "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 (real bulk) composition L1, per-donor Wilcoxon (draw-averaged): ImMicro -0.270, n=107, p=2.2e-18; Sepsis -0.044, n=82, p=0.15; Imperial -0.348, n=57, p=1.6e-08; Giroux -0.107, n=8, p=0.039; Ji -0.232, n=20, p=0.017 -> gain in 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>/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 > scSemi-5 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. LoRA-5 vs zero-shot (real bulk), LoRA-better draws: logFC r Sepsis lora 5/5, Imperial lora 5/5, Giroux split 3/5, Ji lora 5/5; DEG Sepsis lora 4/5, Imperial lora 5/5, Giroux lora 4/5, Ji tie 1/5. Broadcast = the input real bulk's own logFC. Scores: scores/<cohort>/fewshot_n5/draw<j>{,_scsemi5}/.",
+   "footnote_short": "Same draws as previous slide. Top-50 DEG = Welch + BH overlap, summed over 5 cell types.",
+   "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, other); 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": "Top-50 DEG LoRA-5 vs zero-shot (real bulk) (same-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 10.0 (4/5, 0 tied, lora); Imperial 113.6 vs 105.6 (5/5, 0 tied, lora); Giroux 11.6 vs 4.4 (4/5, 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>/summary.json (arms lora5, zs_raw)"
+    },
+    {
+     "value": "logFC r LoRA-5 vs zero-shot (real bulk) (same-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs -0.024 (5/5, lora); Imperial 0.749 vs 0.638 (5/5, lora); Giroux 0.331 vs 0.297 (3/5, split); Ji 0.333 vs 0.087 (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>/contrast.csv (arms lora5, zs_raw)"
+    },
+    {
+     "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: LoRA 0.86, others 0.06–0.09",
+    "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. Zero-shot = base model without fine-tuning; sc-only = full fine-tune on training donors' sc pseudobulk; both are fed the test pair's real bulk as measured. Base f01 6k·1x·E16. Top-50 DEG: LoRA best 4/4. Sepsis DEG from pooled_deg. Scores: scores/<cohort>/pooled/summary.json.",
+   "footnote_short": "Donor-level 5-fold CV; each pair scored by a model that never saw its donor. sc-only: tuned on sc pseudobulk.",
+   "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 0.055, sc-only 0.094, 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": "coverage LoRA / zero-shot / sc-only: ImMicro 0.784 / 0.192 / 0.085, Sepsis 0.829 / 0.067 / 0.134, Imperial 0.850 / 0.112 / 0.017, Giroux 0.928 / 0.281 / 0.414, Ji 0.857 / 0.055 / 0.094",
+     "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": "logFC r LoRA / zero-shot / sc-only: Sepsis 0.527 / -0.012 / 0.149, Imperial 0.819 / 0.644 / 0.469, Giroux 0.504 / 0.416 / 0.433, Ji 0.479 / 0.084 / 0.153",
+     "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": "top-50 DEG LoRA / zero-shot / sc-only: Sepsis 23 / 9 / 10, Imperial 143 / 106 / 54, Giroux 25 / 20 / 13, Ji 15 / 0 / 0",
+     "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/20260930T090852Z-summary-deck-final-path-story/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/slides_spec.json

@@ -0,0 +1,616 @@
+{
+  "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."
+  },
+  "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: why zero-shot fails",
+        "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": "Fig. 1b redraw. Final model corpus: 33.1M train cells; K = 1–4,000 cells per pseudobulk.",
+      "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": "Fig. 1a redraw. Final model f01 6k 1x, epoch 16, EMA; 50 DDIM steps.",
+      "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": "SDD: Ostheimer et al., arXiv 2502.02448. scDiffusion: Luo et al., Bioinformatics 2024.",
+      "sources": "tools/sec02_backbone.py; data/sec02_backbone_compare.csv, data/sec02_slide_text.csv, data/refs/",
+      "footnote_full": "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."
+    },
+    {
+      "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. Bar heights schematic.",
+      "sources": "tools/sec02_backbone.py; data/sec02_bulk_conditioning.csv, data/sec02_slide_text.csv",
+      "footnote_full": "Final model f01 6k 1x, part 16. Bar heights schematic."
+    },
+    {
+      "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 r, DEG inside 6k seed range",
+        "2k best L1; 15k worst r, L1",
+        "6k kept: first panel with CLEC9A (cDC1)"
+      ],
+      "footnote": "SLE, 42 donors, 1,006 genes in every panel. 6k: 5 seeds; base seed best of 5 on r and DEG.",
+      "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",
+        "Copying bulk logFC scores higher (backup)"
+      ],
+      "footnote": "GSE135779, 42 held-out donors (30 SLE / 12 HC). PBISC: 5 seeds, mean ± SD; scSemiProfiler: 1 run.",
+      "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_benchmark.csv, data/sec04_sle_numbers.csv",
+      "footnote_full": "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)."
+    },
+    {
+      "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 Other; DC r ties, fewer DEGs",
+        "DC: ~15 generated cells per donor"
+      ],
+      "footnote": "Same 42 donors, 1,006 genes. PBISC: 5 seeds, mean ± SD; scSemiProfiler: 1 run. Other: top-50 of 12.",
+      "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",
+      "footnote_full": "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)."
+    },
+    {
+      "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 input space (log1p CPM). D = median donor-to-donor distance.",
+      "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",
+      "footnote_full": "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)."
+    },
+    {
+      "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% of T cells become monocytes",
+        "Precision: raw 0.36 vs pseudobulk 0.92"
+      ],
+      "footnote": "ImMicro, 107 donors; same starting noise for every input. Coverage: raw 0.08, sc pseudobulk 0.51.",
+      "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 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.",
+      "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",
+        "sc pseudobulk: right sign in 5/5 seeds"
+      ],
+      "footnote": "Behçet. Bulk GSE198533 (9 BD / 10 HC); sc GSE198616 (4 / 4, different people) gives observed and pseudobulk.",
+      "say": "Raw bulk gives the wrong sign for CD16 and C1Q in 5/5 seeds. At one common monocyte depth the C1Q gap is −0.08 ± 0.09 pp (1/5 seeds positive), so the C1Q flip is a depth effect; the CD16 flip stays at −3.59. sc pseudobulk of the 8 sc donors gives the observed sign in 5/5 seeds (CD16 +5.48, C1Q +1.82). Observed p is descriptive (4 vs 4). No paired data in this cohort, so no fine-tune here.",
+      "sources": "tools/sec05_behcet_direction.py; data/sec05_behcet_direction.csv",
+      "footnote_full": "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."
+    },
+    {
+      "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": "Base: final model f01 6k 1x E16. Times from 40 LoRA runs on this host.",
+      "sources": "tools/sec06_finetune_method.py; data/sec06_ft_method.csv",
+      "footnote_full": "Receipts: immicro/fold0/real_lora and ye2026_sepsis/fewshot_n5/draw0/lora RUN.json. Base: f01_6k_1x E16. Times: 40 local LoRA runs."
+    },
+    {
+      "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: behind LoRA on ImMicro"
+      ],
+      "footnote": "Paired Wilcoxon, donor L1: full vs LoRA p 0.25 / 0.71; cond.-enc. vs LoRA p 3e-5 / 0.52 (fold 0).",
+      "sources": "tools/sec07_ft_modes.py; data/sec07_ft_modes_accuracy.csv, data/sec07_ft_modes_compute.csv, data/sec07_ft_modes_wilcoxon.csv",
+      "footnote_full": "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."
+    },
+    {
+      "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, 5-fold pooled. p = paired Wilcoxon on donor L1, uncorrected.",
+      "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",
+      "footnote_full": "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."
+    },
+    {
+      "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 0.84 / 0.77 with 5+7 pairs",
+        "Zero-shot on real bulk: 0.19 / 0.07",
+        "L1 below zero-shot from 5+7 pairs"
+      ],
+      "footnote": "ImMicro / sepsis, donor 5-fold CV (107 / 82 donors). N+7 = N training + 7 early-stop pairs.",
+      "footnote_full": "0 = zero-shot on real bulk (no pairs). ImMicro L1 axis is broken (zero-shot 0.45). L1 at 5+7 pairs: 0.171 vs 0.455 (ImMicro, p 7e-18), 0.428 vs 0.511 (sepsis, p 0.042). 20k step cap reached by ImMicro folds 1/5 (10), 4/5 (20), 5/5 (40, all); last 2k steps <0.4% of total loss 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 (zero-shot 0.49)"
+      ],
+      "footnote": "Sepsis: 61 case vs 21 control. logFC r = mean over T / B / Mono / NK.",
+      "footnote_full": "Zero-shot on real bulk: logFC r −0.01, DEG 9; LoRA with all pairs: 0.53, 23. ≤10 pairs: NK r (0.20/0.40) and DEG (5/8) below zero-shot (0.49, 9); T r at or above zero-shot from 20 pairs, Mono only with all. DEG gain is Mono/DC; T overlap 3 (zero-shot) → 0–1 from 20 pairs; NK 0 at every LoRA 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 identity check and ≥ 200 cells: 403 of 430 pairs; donor-level splits.",
+      "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": [
+        "figures/sec09_fewpair_cells.png"
+      ],
+      "keywords": [
+        "LoRA-5 > scSemi-5: coverage, precision 5/5",
+        "LoRA-5 coverage 0.69–0.96; scSemi-5 0.04–0.61",
+        "Lower L1 than zero-shot: all but Sepsis"
+      ],
+      "footnote": "5 draws per cohort; test = all other usable pairs. Zero-shot = base model on real bulk. scANVI labels.",
+      "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. Zero-shot = base model without fine-tuning, fed each test pair's real bulk as measured (same call as LoRA-5). scSemi-5 scored in a separate call, same test set and reference (sha-checked); 25/25 draws. Verdict = better in >= 80% of shared draws. LoRA-5 lower L1 than scSemi-5 in 4/5 (Giroux split 3/5). LoRA-5 > zero-shot: coverage 5/5, precision 5/5, depth-matched 5/5 and 4/5 cohorts. Depth-matched P/C vs scSemi-5: same ranking, coverage LoRA-5 0.83–0.97 vs scSemi-5 0.15–0.28. L1 LoRA-5 minus zero-shot, per-donor Wilcoxon (gain = p < 0.05): ImMicro -0.27 (p 2e-18), Sepsis -0.04 (p 0.15), Imperial -0.35 (p 2e-08), Giroux -0.11 (p 0.04), Ji -0.23 (p 0.02). scANVI labels; P/C = PCA-50, k=10 balls. Scores: scores/<cohort>/fewshot_n5/.",
+      "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": [
+        "figures/sec09_fewpair_disease.png"
+      ],
+      "keywords": [
+        "Top-50 DEG: LoRA-5 > scSemi-5 3/4; Ji ~0",
+        "logFC r: scSemi-5 wins Giroux; Sepsis split",
+        "Giroux: real-bulk broadcast beats all arms"
+      ],
+      "footnote": "Same draws as previous slide. Top-50 DEG = Welch + BH overlap, summed over 5 cell types.",
+      "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. LoRA-5 vs zero-shot (real bulk), LoRA-better draws: logFC r Sepsis lora 5/5, Imperial lora 5/5, Giroux split 3/5, Ji lora 5/5; DEG Sepsis lora 4/5, Imperial lora 5/5, Giroux lora 4/5, Ji tie 1/5. 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": [
+        "figures/sec09_fivefold.png"
+      ],
+      "keywords": [
+        "LoRA tops coverage 5/5, logFC r 4/4",
+        "Ji whole blood: LoRA 0.86, others 0.06–0.09",
+        "Giroux: broadcast r 0.64 > LoRA 0.50"
+      ],
+      "footnote": "Donor-level 5-fold CV; each pair scored by a model that never saw its donor. sc-only: tuned on sc pseudobulk.",
+      "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. Zero-shot = base model without fine-tuning; sc-only = full fine-tune on training donors' sc pseudobulk; both are fed the test pair's real bulk as measured. 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. 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",
+      "footnote_full": "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."
+    },
+    {
+      "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",
+        "scSemiProfiler: r 0.32, partial r 0.17"
+      ],
+      "footnote": "SLE, 42 donors, 1,006 genes. Partial r: both logFCs residualised on bulk logFC.",
+      "sources": "tools/sec04_sle_benchmark.py; data/sec04_sle_broadcast.csv, data/sec04_sle_numbers.csv",
+      "footnote_full": "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."
+    },
+    {
+      "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 fitted per cohort on sc pseudobulks.",
+      "sources": "tools/sec05_shift_cohorts.py; data/sec05_shift_cohorts.csv",
+      "footnote_full": "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."
+    },
+    {
+      "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": "Bars: Ye 2026 sepsis. QC-failed pairs excluded.",
+      "sources": "tools/sec06_finetune_method.py; data/sec06_eval_design.csv, data/sec06_eval_design_sepsis_roles.csv",
+      "footnote_full": "Counts: data/<cohort>/folds.csv and fewshot_n5/DRAWS.json; QC-failed pairs (fold −1) excluded. Bars: Ye 2026 sepsis."
+    }
+  ]
+}