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  1. paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_quoted_numbers.csv +51 -0
  2. paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_scsemi_status.csv +26 -0
  3. paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec10_bulk_only_groups.csv +17 -0
  4. paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec10_cohort_counts.csv +5 -0
paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_quoted_numbers.csv ADDED
@@ -0,0 +1,51 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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,"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",/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
16
+ b,quoted on slide,"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",/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
17
+ 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
18
+ 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)"
19
+ 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
20
+ 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
21
+ 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"
22
+ 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, scsemi); 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"
23
+ 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"
24
+ 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)
25
+ 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)
26
+ 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)
27
+ d,quoted on slide,"Ji coverage: zero-shot cal 0.106, sc-only 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
28
+ 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
29
+ 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)
30
+ 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
31
+ 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
32
+ b,"immicro aggregate.json LoRA-5 vs zero-shot L1 Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.027, 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/aggregate.json
33
+ b,"ye2026_sepsis aggregate.json LoRA-5 vs zero-shot L1 Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","+0.020, 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/aggregate.json
34
+ b,"imperial_eskd aggregate.json LoRA-5 vs zero-shot L1 Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.003, 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/aggregate.json
35
+ b,"giroux2022 aggregate.json LoRA-5 vs zero-shot L1 Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.029, 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/aggregate.json
36
+ b,"ji2025_chili aggregate.json LoRA-5 vs zero-shot L1 Wilcoxon over donor-draw rows (pseudo-replicated; not quoted, replaced by the per-donor test)","-0.002, 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/aggregate.json
37
+ d,immicro pooled zs_cal coverage / r / DEG,0.527 / nan / nan,scores/immicro/pooled/summary.json
38
+ d,immicro pooled sconly_cal coverage / r / DEG,0.623 / nan / nan,scores/immicro/pooled/summary.json
39
+ d,immicro pooled lora coverage / r / DEG,0.784 / nan / nan,scores/immicro/pooled/summary.json
40
+ d,ye2026_sepsis pooled zs_cal coverage / r / DEG,0.431 / 0.123 / 11,scores/ye2026_sepsis/pooled/summary.json
41
+ d,ye2026_sepsis pooled sconly_cal coverage / r / DEG,0.726 / 0.296 / 15,scores/ye2026_sepsis/pooled/summary.json
42
+ d,ye2026_sepsis pooled lora coverage / r / DEG,0.829 / 0.527 / 23,scores/ye2026_sepsis/pooled/summary.json
43
+ d,imperial_eskd pooled zs_cal coverage / r / DEG,0.639 / 0.679 / 111,scores/imperial_eskd/pooled/summary.json
44
+ d,imperial_eskd pooled sconly_cal coverage / r / DEG,0.555 / 0.808 / 129,scores/imperial_eskd/pooled/summary.json
45
+ d,imperial_eskd pooled lora coverage / r / DEG,0.850 / 0.819 / 143,scores/imperial_eskd/pooled/summary.json
46
+ d,giroux2022 pooled zs_cal coverage / r / DEG,0.906 / 0.305 / 12,scores/giroux2022/pooled/summary.json
47
+ d,giroux2022 pooled sconly_cal coverage / r / DEG,0.908 / 0.374 / 7,scores/giroux2022/pooled/summary.json
48
+ d,giroux2022 pooled lora coverage / r / DEG,0.928 / 0.504 / 25,scores/giroux2022/pooled/summary.json
49
+ d,ji2025_chili pooled zs_cal coverage / r / DEG,0.106 / 0.142 / 0,scores/ji2025_chili/pooled/summary.json
50
+ d,ji2025_chili pooled sconly_cal coverage / r / DEG,0.113 / 0.245 / 0,scores/ji2025_chili/pooled/summary.json
51
+ d,ji2025_chili pooled lora coverage / r / DEG,0.857 / 0.479 / 15,scores/ji2025_chili/pooled/summary.json
paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec09_scsemi_status.csv ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ dataset,draw,dir,status,reason
2
+ immicro,0,scores/immicro/fewshot_n5/draw0_scsemi5,used,
3
+ immicro,1,scores/immicro/fewshot_n5/draw1_scsemi5,used,
4
+ immicro,2,scores/immicro/fewshot_n5/draw2_scsemi5,used,
5
+ immicro,3,scores/immicro/fewshot_n5/draw3_scsemi5,used,
6
+ immicro,4,scores/immicro/fewshot_n5/draw4_scsemi5,used,
7
+ ye2026_sepsis,0,scores/ye2026_sepsis/fewshot_n5/draw0_scsemi5,used,
8
+ ye2026_sepsis,1,scores/ye2026_sepsis/fewshot_n5/draw1_scsemi5,used,
9
+ ye2026_sepsis,2,scores/ye2026_sepsis/fewshot_n5/draw2_scsemi5,used,
10
+ ye2026_sepsis,3,scores/ye2026_sepsis/fewshot_n5/draw3_scsemi5,used,
11
+ ye2026_sepsis,4,scores/ye2026_sepsis/fewshot_n5/draw4_scsemi5,used,
12
+ ji2025_chili,0,scores/ji2025_chili/fewshot_n5/draw0_scsemi5,used,
13
+ ji2025_chili,1,scores/ji2025_chili/fewshot_n5/draw1_scsemi5,used,
14
+ ji2025_chili,2,scores/ji2025_chili/fewshot_n5/draw2_scsemi5,used,
15
+ ji2025_chili,3,scores/ji2025_chili/fewshot_n5/draw3_scsemi5,used,
16
+ ji2025_chili,4,scores/ji2025_chili/fewshot_n5/draw4_scsemi5,used,
17
+ giroux2022,0,scores/giroux2022/fewshot_n5/draw0_scsemi5,used,
18
+ giroux2022,1,scores/giroux2022/fewshot_n5/draw1_scsemi5,used,
19
+ giroux2022,2,scores/giroux2022/fewshot_n5/draw2_scsemi5,used,
20
+ giroux2022,3,scores/giroux2022/fewshot_n5/draw3_scsemi5,used,
21
+ giroux2022,4,scores/giroux2022/fewshot_n5/draw4_scsemi5,used,
22
+ imperial_eskd,0,scores/imperial_eskd/fewshot_n5/draw0_scsemi5,used,
23
+ imperial_eskd,1,scores/imperial_eskd/fewshot_n5/draw1_scsemi5,used,
24
+ imperial_eskd,2,scores/imperial_eskd/fewshot_n5/draw2_scsemi5,used,
25
+ imperial_eskd,3,scores/imperial_eskd/fewshot_n5/draw3_scsemi5,used,
26
+ imperial_eskd,4,scores/imperial_eskd/fewshot_n5/draw4_scsemi5,used,
paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec10_bulk_only_groups.csv ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ cohort,group,paired_usable,bulk_only,source
2
+ Ye 2026 sepsis,control,21,54,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json (excluded.bulk_samples_without_sc); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv
3
+ Ye 2026 sepsis,sepsis,61,68,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json (excluded.bulk_samples_without_sc); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv
4
+ Imperial ESKD COVID,covid_negative,34,19,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json (excluded.bulk_samples_without_sc); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv
5
+ Imperial ESKD COVID,covid_positive,113,143,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json (excluded.bulk_samples_without_sc); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv
6
+ Imperial ESKD COVID,recovery,10,2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json (excluded.bulk_samples_without_sc); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv
7
+ Ji 2025 ChILI,ChILI,18,36,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json (excluded.bulk_samples_without_sc); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv
8
+ Ji 2025 ChILI,control,15,52,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json (excluded.bulk_samples_without_sc); /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv
9
+ Ji 2025 ChILI,detail:chili_BC,0,11,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json
10
+ Ji 2025 ChILI,detail:chili_FU1,8,6,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json
11
+ Ji 2025 ChILI,detail:chili_FU2,0,7,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json
12
+ Ji 2025 ChILI,detail:chili_TOL,10,12,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json
13
+ Ji 2025 ChILI,detail:control_AC,8,24,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json
14
+ Ji 2025 ChILI,detail:control_BC,7,28,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json
15
+ Arunachalam 2020 COVID,CONV,0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv
16
+ Arunachalam 2020 COVID,COVID,0,9,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv
17
+ Arunachalam 2020 COVID,HC,0,12,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv
paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec10_cohort_counts.csv ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ cohort,specimen,bulk_total,paired,seg_train,seg_nocomp,seg_excl,excl_why,bulk_only,donors_bulk_total,donors_paired_usable,donors_bulk_only,donors_excl_only,bulk_only_groups,sex_flag_bulk_only,sex_flag_ids,lora_cv,lora_comp_l1,comp_null,lora_logfc_r,zs_raw_logfc_r,extra,usable_rule,source,lora_cv_source
2
+ Ye 2026 sepsis,PBMC bulk,207,85,82,0,3,"{""fail"": 3, ""below_200_cells_only"": 0}",122,207,82,122,3,"68 sepsis, 54 control",3,HC23;HC30;Res-S34,5-fold,0.36313994927777793,0.531,0.33274770083650723,0.10948502096950485,controls: paired QC pass 21 + bulk-only 54,identity_pass,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/identity_sex_bulk_all.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/AGGREGATE.md
3
+ Imperial ESKD COVID,"PBMC bulk, longitudinal",336,172,157,0,15,"{""borderline"": 6, ""fail"": 8, ""below_200_cells_only"": 1}",164,105,57,45,3,"143 COVID+, 19 COVID−, 2 recovery",1,C137_positive_2,5-fold,0.3599507436645195,0.522,0.5725738486615508,0.4759335147871225,donors excluded-only: C139;C224;C73,identity_pass and not below_200_cells,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/identity_sex_bulk_all.csv; header of /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/datasets/Zenodo_6497251/raw/htseq_counts.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/AGGREGATE.md
4
+ Ji 2025 ChILI,whole-blood bulk,128,40,33,0,7,"{""borderline"": 5, ""fail"": 2, ""below_200_cells_only"": 0}",88,61,20,38,3,"36 ChILI (11 pre-ICI), 52 control",10,N086_chili_BC;N106_control_BC;N141_control_AC;N141_control_BC;N143_control_AC;N143_control_BC;N146_control_AC;N146_control_BC;N87_control_BC;N96_control_AC,5-fold,0.5124495468387019,0.51,0.24335984930719518,0.01640905275700309,"ChILI before ICI (BC): paired 0, bulk-only 11 (1 sex-flagged: N086_chili_BC), unpaired ChILI BC sc libraries 4 (N014_BC;N016_BC;N037_BC;N127_BC); donors excluded-only: N063;N087;N106",identity_pass,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/MANIFEST.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/pairs.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/identity_sex_bulk_all.csv; /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/processing/ji2025_chili_v1_20260928/pairing/sc_gex_libraries_with_bulk_match.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/aggregate.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ji2025_chili/AGGREGATE.md
5
+ Arunachalam 2020 COVID,PBMC bulk; DC-enriched sc,34,12,0,12,0,"{""identity_fail"": 0}",22,32,0,20,0,"9 COVID, 12 healthy, 1 conv.",0,,none,,,,,"paired identity pass 12/12, composition_eligible 0/12 (material PBMC_to_DC_enriched_remixed_PBMC), strict_identity_eligible 7; zero-shot bulk-only generated: arms cal,raw,tpm, 22 bulks each (/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt); prereg decision rule: best arm beats broadcast in 0/5 populations",identity pass (sex_all_four_agree & expr_identity_own_is_best) AND composition_eligible,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/bulk_cohort.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam/metadata/pairs_reconciliation.csv; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/receipts/receipt_checks.json; /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/arunachalam_4arm/global_r/decision_rule.csv,no paired-FT dataset built