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  1. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_fivefold.csv +120 -0
  2. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_quoted_numbers.csv +99 -0
  3. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_same_pairs.csv +5 -0
  4. paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_same_pairs_budget.csv +5 -0
paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_fivefold.csv ADDED
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+ sec09_fivefold,ji2025_chili,limma_deg,sconly_cal,pseudo_full__cal,0,33,scores/ji2025_chili/pooled/summary.json
118
+ sec09_fivefold,ji2025_chili,limma_deg,scsemi_all,scsemi__raw,0,33,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/scsemi_cv_20261002/pooled/summary.json
119
+ sec09_fivefold,ji2025_chili,limma_deg,lora,real_lora__raw,16,33,scores/ji2025_chili/pooled/summary.json
120
+ sec09_fivefold,ji2025_chili,limma_deg,ref_broadcast,real_lora__raw (raw real bulk),15,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/ji2025_chili/pooled
paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_quoted_numbers.csv ADDED
@@ -0,0 +1,99 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ slide,item,value,source
2
+ 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)
3
+ 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)
4
+ 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)"
5
+ 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
6
+ 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
7
+ 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
8
+ 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
9
+ 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
10
+ 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
11
+ 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
12
+ 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
13
+ 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
14
+ 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
15
+ b,quoted on slide,"LoRA-5 vs zero-shot + calibration coverage (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.792 vs 0.535 (5/5, lora); Sepsis 0.694 vs 0.428 (5/5, lora); Imperial 0.737 vs 0.634 (5/5, lora); Giroux 0.961 vs 0.944 (5/5, lora); Ji 0.707 vs 0.114 (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_cal)"
16
+ b,quoted on slide,"LoRA-5 vs zero-shot + calibration precision (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.952 vs 0.904 (5/5, lora); Sepsis 0.906 vs 0.899 (3/5, split); Imperial 0.853 vs 0.845 (3/5, split); Giroux 1.000 vs 0.996 (4/5, lora); Ji 0.978 vs 0.782 (5/5, lora) -> LoRA verdicts 3/5","/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_cal)"
17
+ b,quoted on slide,"LoRA-5 vs zero-shot + calibration comp_l1 (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.176 vs 0.203 (5/5, lora); Sepsis 0.466 vs 0.446 (2/5, split); Imperial 0.503 vs 0.506 (2/5, split); Giroux 0.256 vs 0.288 (2/5, split); Ji 0.513 vs 0.514 (3/5, split) -> LoRA verdicts 1/5","/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_cal)"
18
+ b,quoted on slide,"LoRA-5 vs zero-shot + calibration coverage_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.966 vs 0.780 (5/5, lora); Sepsis 0.834 vs 0.658 (5/5, lora); Imperial 0.863 vs 0.681 (5/5, lora); Giroux 0.974 vs 0.937 (5/5, lora); Ji 0.908 vs 0.357 (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_cal)"
19
+ b,quoted on slide,"LoRA-5 vs zero-shot + calibration precision_dm (same-draw means; LoRA-better draws/n; verdict): ImMicro 0.975 vs 0.940 (5/5, lora); Sepsis 0.914 vs 0.909 (3/5, split); Imperial 0.881 vs 0.868 (3/5, split); Giroux 0.995 vs 0.989 (5/5, lora); Ji 0.974 vs 0.658 (5/5, lora) -> LoRA verdicts 3/5","/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_cal)"
20
+ 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)"
21
+ 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)"
22
+ 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)"
23
+ 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)"
24
+ 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)"
25
+ 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 + calibration ImMicro 0.535, Sepsis 0.428, Imperial 0.634, Giroux 0.944, Ji 0.114; 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
26
+ b,quoted on slide,"LoRA-5 minus zero-shot + calibration 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 -> gain in 1/5",/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
27
+ 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
28
+ 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
29
+ 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)"
30
+ 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
31
+ 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
32
+ c,quoted on slide,"Giroux sex by contrast arm (subjects, F/M): scored moderate 4F/0M vs mild 0F/5M; all paired 4F/1M vs 0F/5M",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/features.npz (sex_bulk_expr = sex_sc_expr = sex_geo); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv
33
+ c,quoted on slide,"Giroux sex-linked genes excluded from the disease metrics: 196 listed (43 chrY non-PAR + 153 X escape), 65 of 5563 scoring genes",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/BUILD.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json (gene_exclusion)
34
+ 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 0.2 vs 0.0 (1/5, 4 tied, tie); 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 (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
35
+ c,quoted on slide,"Top-50 DEG LoRA-5 vs zero-shot + calibration (shared-draw means; LoRA-better / tied draws; verdict): Sepsis 16.4 vs 9.4 (4/5, 0 tied, lora); Imperial 113.6 vs 103.8 (5/5, 0 tied, lora); Giroux 0.2 vs 0.0 (1/5, 4 tied, tie); 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 (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
36
+ c,quoted on slide,"Top-50 DEG LoRA-5 vs zero-shot (real bulk) (shared-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 0.2 vs 0.0 (1/5, 4 tied, tie); 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 (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
37
+ 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 0.297 vs 0.397 (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 (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
38
+ c,quoted on slide,"logFC r LoRA-5 vs zero-shot + calibration (shared-draw means; LoRA-better draws; verdict): Sepsis 0.350 vs 0.096 (4/5, lora); Imperial 0.749 vs 0.676 (5/5, lora); Giroux 0.297 vs 0.228 (4/5, lora); Ji 0.333 vs 0.140 (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 (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
39
+ c,quoted on slide,"logFC r LoRA-5 vs zero-shot (real bulk) (shared-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 0.297 vs 0.255 (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>{,_scsemi5}/summary.json and contrast.csv (Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/)"
40
+ c,quoted on slide,"Sepsis broadcast logFC r 0.320 vs best arm 0.402; broadcast DEG 20.0 vs best arm 16.4 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)","/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>{,_scsemi5}/summary.json"
41
+ c,quoted on slide,"Imperial broadcast logFC r 0.656 vs best arm 0.749; broadcast DEG 74.8 vs best arm 113.6 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)","/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>{,_scsemi5}/summary.json"
42
+ c,quoted on slide,"Giroux broadcast logFC r 0.492 vs best arm 0.397; broadcast DEG 0.0 vs best arm 0.2 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)","/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw<j>{,_scsemi5}/summary.json"
43
+ c,quoted on slide,"Ji broadcast logFC r 0.234 vs best arm 0.333; broadcast DEG 1.0 vs best arm 0.2 (means over all draws; arms: zero-shot, zero-shot + calibration, scSemi-5, LoRA-5)","/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>{,_scsemi5}/summary.json"
44
+ c,quoted on slide,"DEG maximum per draw: Sepsis 250, Imperial 250, Giroux 1–63, 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; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex)
45
+ 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)
46
+ d,quoted on slide,"LoRA best of 5 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; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)
47
+ d,quoted on slide,"Ji coverage: zero-shot 0.055, zero-shot + calibration 0.106, sc-only (+ calibration) 0.113, 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
48
+ d,quoted on slide,Giroux logFC r: broadcast 0.575 vs LoRA 0.461; DEG broadcast 5 vs LoRA 5,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json
49
+ d,quoted on slide,"LoRA logFC r vs broadcast: Sepsis 0.527 vs 0.316, Imperial 0.819 vs 0.661, Giroux 0.461 vs 0.575, 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; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)
50
+ d,quoted on slide,"coverage LoRA / zero-shot + calibration / zero-shot / sc-only (+ calibration): ImMicro 0.784 / 0.527 / 0.192 / 0.623, Sepsis 0.829 / 0.431 / 0.067 / 0.726, Imperial 0.850 / 0.639 / 0.112 / 0.555, Giroux 0.928 / 0.906 / 0.281 / 0.908, Ji 0.857 / 0.106 / 0.055 / 0.113",/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; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)
51
+ d,quoted on slide,"logFC r LoRA / zero-shot + calibration / zero-shot / sc-only (+ calibration): Sepsis 0.527 / 0.123 / -0.012 / 0.296, Imperial 0.819 / 0.679 / 0.644 / 0.808, Giroux 0.461 / 0.269 / 0.334 / 0.344, Ji 0.479 / 0.142 / 0.084 / 0.245",/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; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)
52
+ d,quoted on slide,"top-50 DEG LoRA / zero-shot + calibration / zero-shot / sc-only (+ calibration): Sepsis 23 / 11 / 9 / 15, Imperial 143 / 111 / 106 / 129, Giroux 5 / 0 / 1 / 0, Ji 15 / 0 / 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; Giroux: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/pooled/summary.json)
53
+ d,quoted on slide,"scSemiProfiler, 5-fold CV: coverage / logFC r / top-50 DEG (n/a = no contrast or rescore pending): ImMicro 0.038 / n/a / n/a, Ji 0.167 / 0.273 / 0",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/pooled/summary.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/scsemi_cv_20261002/pooled/summary.json
54
+ 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
55
+ 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
56
+ b,"immicro LoRA-5 minus zero-shot + calibration L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.027, n=510, p 2.9e-24","/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_cal); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv (sample -> donor)"
57
+ 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)"
58
+ b,"ye2026_sepsis LoRA-5 minus zero-shot + calibration L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","+0.020, n=385, p 0.96","/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_cal); /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)"
59
+ 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)"
60
+ b,"imperial_eskd LoRA-5 minus zero-shot + calibration L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.003, n=715, p 0.11","/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_cal); /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)"
61
+ 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)"
62
+ b,"giroux2022 LoRA-5 minus zero-shot + calibration L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.029, n=54, p 0.5","/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_cal); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv (sample -> donor)"
63
+ 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)"
64
+ b,"ji2025_chili LoRA-5 minus zero-shot + calibration L1, Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.002, n=126, p 0.6","/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_cal); /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)"
65
+ 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)"
66
+ c,"giroux2022 few-pair zs_raw: logFC r / DEG mean over draws, all genes -> sex-linked genes excluded",0.297 / 4.4 -> 0.255 / 0.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5 -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5
67
+ c,"giroux2022 few-pair zs_cal: logFC r / DEG mean over draws, all genes -> sex-linked genes excluded",0.242 / 1.8 -> 0.228 / 0.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5 -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5
68
+ c,"giroux2022 few-pair scsemi5: logFC r / DEG mean over draws, all genes -> sex-linked genes excluded",0.398 / 1.2 -> 0.397 / 0.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5 -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5
69
+ c,"giroux2022 few-pair lora: logFC r / DEG mean over draws, all genes -> sex-linked genes excluded",nan / nan -> 0.297 / 0.2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5 -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5
70
+ c,"giroux2022 few-pair broadcast: logFC r / DEG mean over draws, all genes -> sex-linked genes excluded",nan / nan -> 0.492 / 0.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/fewshot_n5 -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5
71
+ 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
72
+ d,immicro pooled zs_cal (zs__cal) coverage / precision / L1 / r / DEG,0.527 / 0.905 / 0.199 / nan / nan,scores/immicro/pooled/summary.json
73
+ d,immicro pooled sconly_cal (pseudo_full__cal) coverage / precision / L1 / r / DEG,0.623 / 0.805 / 0.240 / nan / nan,scores/immicro/pooled/summary.json
74
+ 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
75
+ 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
76
+ d,ye2026_sepsis pooled zs_cal (zs__cal) coverage / precision / L1 / r / DEG,0.431 / 0.903 / 0.401 / 0.123 / 11,scores/ye2026_sepsis/pooled/summary.json; DEG: scores/ye2026_sepsis/pooled_deg/summary.json
77
+ d,ye2026_sepsis pooled sconly_cal (pseudo_full__cal) coverage / precision / L1 / r / DEG,0.726 / 0.863 / 0.360 / 0.296 / 15,scores/ye2026_sepsis/pooled/summary.json; DEG: scores/ye2026_sepsis/pooled_deg/summary.json
78
+ 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
79
+ 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
80
+ d,imperial_eskd pooled zs_cal (zs__cal) coverage / precision / L1 / r / DEG,0.639 / 0.842 / 0.494 / 0.679 / 111,scores/imperial_eskd/pooled/summary.json
81
+ d,imperial_eskd pooled sconly_cal (pseudo_full__cal) coverage / precision / L1 / r / DEG,0.555 / 0.691 / 0.461 / 0.808 / 129,scores/imperial_eskd/pooled/summary.json
82
+ 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
83
+ d,giroux2022 pooled zs_raw (zs__raw) coverage / precision / L1 / r / DEG,0.281 / 0.909 / 0.325 / 0.334 / 1,scores_nosex/giroux2022/pooled/summary.json
84
+ d,"giroux2022 pooled zs_raw (zs__raw) logFC r / broadcast r / DEG / DEG broadcast, all genes -> sex-linked genes excluded",0.416 / 0.638 / 20 / 39 -> 0.334 / 0.575 / 1 / 5,scores/giroux2022/pooled/summary.json -> scores_nosex/giroux2022/pooled/summary.json
85
+ d,giroux2022 pooled zs_cal (zs__cal) coverage / precision / L1 / r / DEG,0.906 / 0.995 / 0.266 / 0.269 / 0,scores_nosex/giroux2022/pooled/summary.json
86
+ d,"giroux2022 pooled zs_cal (zs__cal) logFC r / broadcast r / DEG / DEG broadcast, all genes -> sex-linked genes excluded",0.305 / 0.626 / 12 / 38 -> 0.269 / 0.564 / 0 / 2,scores/giroux2022/pooled/summary.json -> scores_nosex/giroux2022/pooled/summary.json
87
+ d,giroux2022 pooled sconly_cal (pseudo_full__cal) coverage / precision / L1 / r / DEG,0.908 / 0.991 / 0.453 / 0.344 / 0,scores_nosex/giroux2022/pooled/summary.json
88
+ d,"giroux2022 pooled sconly_cal (pseudo_full__cal) logFC r / broadcast r / DEG / DEG broadcast, all genes -> sex-linked genes excluded",0.374 / 0.626 / 7 / 38 -> 0.344 / 0.564 / 0 / 2,scores/giroux2022/pooled/summary.json -> scores_nosex/giroux2022/pooled/summary.json
89
+ d,giroux2022 pooled lora (real_lora__raw) coverage / precision / L1 / r / DEG,0.928 / 0.998 / 0.258 / 0.461 / 5,scores_nosex/giroux2022/pooled/summary.json
90
+ d,"giroux2022 pooled lora (real_lora__raw) logFC r / broadcast r / DEG / DEG broadcast, all genes -> sex-linked genes excluded",0.504 / 0.638 / 25 / 39 -> 0.461 / 0.575 / 5 / 5,scores/giroux2022/pooled/summary.json -> scores_nosex/giroux2022/pooled/summary.json
91
+ 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
92
+ d,ji2025_chili pooled zs_cal (zs__cal) coverage / precision / L1 / r / DEG,0.106 / 0.740 / 0.501 / 0.142 / 0,scores/ji2025_chili/pooled/summary.json
93
+ d,ji2025_chili pooled sconly_cal (pseudo_full__cal) coverage / precision / L1 / r / DEG,0.113 / 0.694 / 0.609 / 0.245 / 0,scores/ji2025_chili/pooled/summary.json
94
+ 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
95
+ d,immicro scSemiProfiler 5-fold (scsemi__raw) lookup,used,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/pooled/summary.json
96
+ d,ye2026_sepsis scSemiProfiler 5-fold (scsemi__raw) lookup,missing,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_cv_20261002
97
+ d,imperial_eskd scSemiProfiler 5-fold (scsemi__raw) lookup,missing,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002
98
+ d,giroux2022 scSemiProfiler 5-fold (scsemi__raw) lookup,missing,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002
99
+ d,ji2025_chili scSemiProfiler 5-fold (scsemi__raw) lookup,used,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/scsemi_cv_20261002/pooled/summary.json
paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_same_pairs.csv ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ dataset,arm,comp_l1,coverage,precision,logfc_r,deg,hours,hours_min,hours_max,n_scored,source
2
+ immicro,lora,0.161729,0.784299,0.924112,,,0.244972,0.235972,0.253139,107,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
3
+ immicro,scsemi,0.217009,0.0384424,0.505421,,,4.74636,4.62666,4.86946,107,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/scsemi_cv_20261002/pooled/summary.json
4
+ ji2025_chili,lora,0.504499,0.85697,0.970909,0.479288,15,0.0739444,0.06875,0.0806389,33,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/pooled/summary.json
5
+ ji2025_chili,scsemi,0.575389,0.166869,0.85798,0.273089,0,1.47934,1.34933,1.57017,33,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/scsemi_cv_20261002/pooled/summary.json
paper-releases/pbisc-diffusion/updates/20261005T133325Z-deck-scratch-samepairs-tracking/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_same_pairs_budget.csv ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ dataset,n,scsemi_l1,lora_l1,scsemi_cov,lora_cov
2
+ immicro,5,0.218449,0.171451,0.0381931,0.83919
3
+ immicro,10,0.226932,0.187881,0.0380062,0.78567
4
+ immicro,20,0.223249,0.172324,0.0371963,0.755202
5
+ immicro,40,0.221315,0.171385,0.0384424,0.778442