Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec07_k_aug_inner_val_delta.csv

@@ -0,0 +1,11 @@
+dataset,fold,lora_multik__raw,lora_recipe__raw
+immicro,0,-4.506430455616939e-05,-1.0649540594639961e-05
+immicro,1,-4.51185873576454e-05,-5.378254822316353e-06
+immicro,2,-4.8645905085978325e-05,-2.1863196577348587e-05
+immicro,3,-4.207449299949151e-05,5.1587820053100586e-05
+immicro,4,-5.149947745461403e-06,-2.9564435992918137e-05
+ye2026_sepsis,0,1.1129570858817162e-05,-4.653951951434643e-05
+ye2026_sepsis,1,-6.704883916038018e-05,-0.00011885485478810298
+ye2026_sepsis,2,7.650116458535194e-05,6.359070539474487e-05
+ye2026_sepsis,3,8.483882993459702e-05,2.323416993021965e-05
+ye2026_sepsis,4,2.6776322296681587e-05,-6.495309727533316e-05

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec07_k_aug_inner_val_runs.csv

@@ -0,0 +1,31 @@
+dataset,arm,fold,selected_inner_val_loss,selected_step,wall_seconds,n_trainable,run_json
+immicro,real_lora__raw,0,0.10127227380871773,20000,798.5,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/real_lora/RUN.json
+immicro,real_lora__raw,1,0.1027925041105066,19500,764.5,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/real_lora/RUN.json
+immicro,real_lora__raw,2,0.10265317506023816,20000,787.8,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/real_lora/RUN.json
+immicro,real_lora__raw,3,0.10127385812146324,20000,813.4,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/real_lora/RUN.json
+immicro,real_lora__raw,4,0.10056435902203832,20000,830.3,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/real_lora/RUN.json
+immicro,lora_multik__raw,0,0.10122720950416156,20000,844.4,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/lora_multik/RUN.json
+immicro,lora_multik__raw,1,0.10274738552314895,20000,809.3,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/lora_multik/RUN.json
+immicro,lora_multik__raw,2,0.10260452915515218,19750,767.1,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/lora_multik/RUN.json
+immicro,lora_multik__raw,3,0.10123178362846375,20000,800.4,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/lora_multik/RUN.json
+immicro,lora_multik__raw,4,0.10055920907429286,19750,807.0,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_multik/RUN.json
+immicro,lora_recipe__raw,0,0.10126162426812309,20000,918.8,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/lora_recipe/RUN.json
+immicro,lora_recipe__raw,1,0.10278712585568428,19750,900.8,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/lora_recipe/RUN.json
+immicro,lora_recipe__raw,2,0.10263131186366081,20000,893.2,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/lora_recipe/RUN.json
+immicro,lora_recipe__raw,3,0.10132544594151634,20000,854.0,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/lora_recipe/RUN.json
+immicro,lora_recipe__raw,4,0.1005347945860454,20000,902.7,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/lora_recipe/RUN.json
+ye2026_sepsis,real_lora__raw,0,0.11356728204659053,6500,324.3,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/real_lora/RUN.json
+ye2026_sepsis,real_lora__raw,1,0.11173954180308751,3750,228.4,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/real_lora/RUN.json
+ye2026_sepsis,real_lora__raw,2,0.11297935340553522,13000,639.6,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/real_lora/RUN.json
+ye2026_sepsis,real_lora__raw,3,0.10772703029215336,6250,350.8,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/real_lora/RUN.json
+ye2026_sepsis,real_lora__raw,4,0.11102822955165591,6750,357.6,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/real_lora/RUN.json
+ye2026_sepsis,lora_multik__raw,0,0.11357841161744935,3250,222.8,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_multik/RUN.json
+ye2026_sepsis,lora_multik__raw,1,0.11167249296392713,3750,226.7,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_multik/RUN.json
+ye2026_sepsis,lora_multik__raw,2,0.11305585457012057,5500,300.7,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_multik/RUN.json
+ye2026_sepsis,lora_multik__raw,3,0.10781186912208796,6000,316.6,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_multik/RUN.json
+ye2026_sepsis,lora_multik__raw,4,0.11105500587395259,11750,497.6,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_multik/RUN.json
+ye2026_sepsis,lora_recipe__raw,0,0.11352074252707618,3750,270.2,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_recipe/RUN.json
+ye2026_sepsis,lora_recipe__raw,1,0.11162068694829941,5000,333.6,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_recipe/RUN.json
+ye2026_sepsis,lora_recipe__raw,2,0.11304294411092997,10000,527.8,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_recipe/RUN.json
+ye2026_sepsis,lora_recipe__raw,3,0.10775026446208358,5500,336.8,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_recipe/RUN.json
+ye2026_sepsis,lora_recipe__raw,4,0.11096327645438057,16000,814.7,1296224,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_recipe/RUN.json

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec07_k_aug_wilcoxon.csv

@@ -0,0 +1,5 @@
+dataset,arm,comparison,mean_diff,wilcoxon_p,n,source
+immicro,lora_multik__raw,lora_multik__raw - real_lora__raw comp_l1,0.006047731707610531,0.0396370882636532,107,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/per_donor.csv
+immicro,lora_recipe__raw,lora_recipe__raw - real_lora__raw comp_l1,-0.000818977230664886,0.7488721123611232,107,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/per_donor.csv
+ye2026_sepsis,lora_multik__raw,lora_multik__raw - real_lora__raw comp_l1,0.0038602668366013036,0.7029119885350186,82,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/per_donor.csv
+ye2026_sepsis,lora_recipe__raw,lora_recipe__raw - real_lora__raw comp_l1,0.00331606980720521,0.7340179659685326,82,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/per_donor.csv

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec08_pairs_realism.csv

@@ -0,0 +1,39 @@
+panel,dataset,series,pairs,value,source
+comp_l1,immicro,zs_cal,cal,0.19850275515696958,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+comp_l1,immicro,lora,5,0.17145118443734877,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+comp_l1,immicro,lora,10,0.18788133961403,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+comp_l1,immicro,lora,20,0.17232428387355106,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+comp_l1,immicro,lora,40,0.17138488720357878,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+comp_l1,immicro,lora,all,0.16172890350786212,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+comp_l1,immicro,ref_pseudo,,0.20433690901119841,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+comp_l1,immicro,ref_null,,0.1606372707722086,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+coverage,immicro,zs_cal,cal,0.527227414330218,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+coverage,immicro,lora,5,0.839190031152648,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+coverage,immicro,lora,10,0.7856697819314642,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+coverage,immicro,lora,20,0.755202492211838,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+coverage,immicro,lora,40,0.7784423676012461,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+coverage,immicro,lora,all,0.7842990654205607,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+coverage,immicro,ref_pseudo,,0.5244236760124611,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+meta,immicro,n_scored_donors,,107,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json
+meta,immicro,n_pairs_all,all,78–79,RUN.json train_rows: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold0/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold1/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold2/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold3/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/immicro/fold4/real_lora/RUN.json
+meta,immicro,n_inner_val,,7,"RUN.json inner_val_rows (all LoRA arms, 5 folds)"
+meta,immicro,n_alpha_fit_pairs,cal,85–86,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/PREPARE.json fold_sizes train+inner_val
+comp_l1,ye2026_sepsis,zs_cal,cal,0.40065324062398555,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+comp_l1,ye2026_sepsis,lora,5,0.4280613786711354,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+comp_l1,ye2026_sepsis,lora,10,0.38966522903618334,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+comp_l1,ye2026_sepsis,lora,20,0.3802570478327888,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+comp_l1,ye2026_sepsis,lora,40,0.3647568921706022,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+comp_l1,ye2026_sepsis,lora,all,0.3618246783833512,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+comp_l1,ye2026_sepsis,ref_pseudo,,0.233165273351523,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+comp_l1,ye2026_sepsis,ref_null,,0.515468004498372,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+coverage,ye2026_sepsis,zs_cal,cal,0.4308130081300813,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+coverage,ye2026_sepsis,lora,5,0.7666666666666667,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+coverage,ye2026_sepsis,lora,10,0.7858536585365854,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+coverage,ye2026_sepsis,lora,20,0.8066666666666666,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+coverage,ye2026_sepsis,lora,40,0.817560975609756,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+coverage,ye2026_sepsis,lora,all,0.829349593495935,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+coverage,ye2026_sepsis,ref_pseudo,,0.48,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+meta,ye2026_sepsis,n_scored_donors,,82,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json
+meta,ye2026_sepsis,n_pairs_all,all,58–59,RUN.json train_rows: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/real_lora/RUN.json;/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/real_lora/RUN.json
+meta,ye2026_sepsis,n_inner_val,,7–8,"RUN.json inner_val_rows (all LoRA arms, 5 folds)"
+meta,ye2026_sepsis,n_alpha_fit_pairs,cal,65–66,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/PREPARE.json fold_sizes train+inner_val