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/sec06_eval_design.csv

@@ -0,0 +1,51 @@
+dataset,name,setting,unit,train_rows,inner_val_rows,test_rows,train_donors,inner_val_donors,test_donors,usable_rows,usable_donors,excluded_rows,pairs_per_donor_min,pairs_per_donor_median,pairs_per_donor_max,source
+immicro,ImMicro 2026,5fold,0,78,7,22,78,7,22,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv
+immicro,ImMicro 2026,5fold,1,78,7,22,78,7,22,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv
+immicro,ImMicro 2026,5fold,2,79,7,21,79,7,21,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv
+immicro,ImMicro 2026,5fold,3,79,7,21,79,7,21,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv
+immicro,ImMicro 2026,5fold,4,79,7,21,79,7,21,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/folds.csv
+immicro,ImMicro 2026,fewpair,0,5,0,102,5,0,102,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json
+immicro,ImMicro 2026,fewpair,1,5,0,102,5,0,102,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json
+immicro,ImMicro 2026,fewpair,2,5,0,102,5,0,102,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json
+immicro,ImMicro 2026,fewpair,3,5,0,102,5,0,102,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json
+immicro,ImMicro 2026,fewpair,4,5,0,102,5,0,102,107,107,0,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro/fewshot_n5/DRAWS.json
+ye2026_sepsis,Ye 2026,5fold,0,58,7,17,58,7,17,82,82,3,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/folds.csv
+ye2026_sepsis,Ye 2026,5fold,1,58,7,17,58,7,17,82,82,3,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/folds.csv
+ye2026_sepsis,Ye 2026,5fold,2,58,8,16,58,8,16,82,82,3,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/folds.csv
+ye2026_sepsis,Ye 2026,5fold,3,58,8,16,58,8,16,82,82,3,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/folds.csv
+ye2026_sepsis,Ye 2026,5fold,4,59,7,16,59,7,16,82,82,3,1,1.0,1,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/folds.csv
+ye2026_sepsis,Ye 2026,fewpair,0,5,0,77,5,0,77,82,82,3,1,1.0,1,/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
+ye2026_sepsis,Ye 2026,fewpair,1,5,0,77,5,0,77,82,82,3,1,1.0,1,/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
+ye2026_sepsis,Ye 2026,fewpair,2,5,0,77,5,0,77,82,82,3,1,1.0,1,/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
+ye2026_sepsis,Ye 2026,fewpair,3,5,0,77,5,0,77,82,82,3,1,1.0,1,/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
+ye2026_sepsis,Ye 2026,fewpair,4,5,0,77,5,0,77,82,82,3,1,1.0,1,/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
+imperial_eskd,Imperial ESKD,5fold,0,97,13,47,40,5,12,157,57,15,1,3.0,8,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/folds.csv
+imperial_eskd,Imperial ESKD,5fold,1,121,11,25,40,5,12,157,57,15,1,3.0,8,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/folds.csv
+imperial_eskd,Imperial ESKD,5fold,2,121,7,29,41,5,11,157,57,15,1,3.0,8,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/folds.csv
+imperial_eskd,Imperial ESKD,5fold,3,115,18,24,41,5,11,157,57,15,1,3.0,8,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/folds.csv
+imperial_eskd,Imperial ESKD,5fold,4,111,14,32,41,5,11,157,57,15,1,3.0,8,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/imperial_eskd/folds.csv
+imperial_eskd,Imperial ESKD,fewpair,0,15,0,142,5,0,52,157,57,15,1,3.0,8,/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
+imperial_eskd,Imperial ESKD,fewpair,1,14,0,143,5,0,52,157,57,15,1,3.0,8,/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
+imperial_eskd,Imperial ESKD,fewpair,2,15,0,142,5,0,52,157,57,15,1,3.0,8,/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
+imperial_eskd,Imperial ESKD,fewpair,3,12,0,145,5,0,52,157,57,15,1,3.0,8,/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
+imperial_eskd,Imperial ESKD,fewpair,4,14,0,143,5,0,52,157,57,15,1,3.0,8,/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
+giroux2022,Giroux 2022,5fold,0,18,2,4,6,1,2,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv
+giroux2022,Giroux 2022,5fold,1,16,3,5,6,1,2,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv
+giroux2022,Giroux 2022,5fold,2,15,3,6,6,1,2,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv
+giroux2022,Giroux 2022,5fold,3,16,2,6,6,1,2,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv
+giroux2022,Giroux 2022,5fold,4,16,5,3,6,2,1,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/folds.csv
+giroux2022,Giroux 2022,fewpair,0,13,0,11,5,0,4,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json
+giroux2022,Giroux 2022,fewpair,1,14,0,10,5,0,4,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json
+giroux2022,Giroux 2022,fewpair,2,12,0,12,5,0,4,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json
+giroux2022,Giroux 2022,fewpair,3,13,0,11,5,0,4,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json
+giroux2022,Giroux 2022,fewpair,4,14,0,10,5,0,4,24,9,2,2,3.0,3,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/DRAWS.json
+ji2025_chili,Ji 2025,5fold,0,23,3,7,14,2,4,33,20,7,1,2.0,2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/folds.csv
+ji2025_chili,Ji 2025,5fold,1,23,4,6,14,2,4,33,20,7,1,2.0,2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/folds.csv
+ji2025_chili,Ji 2025,5fold,2,24,3,6,14,2,4,33,20,7,1,2.0,2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/folds.csv
+ji2025_chili,Ji 2025,5fold,3,22,3,8,14,2,4,33,20,7,1,2.0,2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/folds.csv
+ji2025_chili,Ji 2025,5fold,4,24,3,6,14,2,4,33,20,7,1,2.0,2,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ji2025_chili/folds.csv
+ji2025_chili,Ji 2025,fewpair,0,8,0,25,5,0,15,33,20,7,1,2.0,2,/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
+ji2025_chili,Ji 2025,fewpair,1,7,0,26,5,0,15,33,20,7,1,2.0,2,/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
+ji2025_chili,Ji 2025,fewpair,2,7,0,26,5,0,15,33,20,7,1,2.0,2,/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
+ji2025_chili,Ji 2025,fewpair,3,8,0,25,5,0,15,33,20,7,1,2.0,2,/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
+ji2025_chili,Ji 2025,fewpair,4,9,0,24,5,0,15,33,20,7,1,2.0,2,/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

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec06_eval_design_sepsis_roles.csv

@@ -0,0 +1,83 @@
+donor_id,group,fold,cv_fold1,cv_fold2,cv_fold3,cv_fold4,cv_fold5,fewpair_draw1,fewpair_draw2,fewpair_draw3,fewpair_draw4,fewpair_draw5
+Abd-PS19,ped_sepsis,0,test,train,inner_val,train,train,test,test,test,test,test
+Abd-PS23,ped_sepsis,0,test,train,train,train,train,test,test,test,test,test
+Abd-S123,adult_sepsis,0,test,train,train,train,train,test,test,test,test,test
+Abd-S39,adult_sepsis,0,test,inner_val,train,train,train,test,test,test,test,test
+Abd-S47,adult_sepsis,0,test,train,train,train,train,test,test,test,test,test
+Abd-S66,adult_sepsis,0,test,train,train,train,train,train,test,test,test,test
+HC01,adult_HC,0,test,inner_val,train,inner_val,train,test,test,test,test,test
+HC07,adult_HC,0,test,train,train,train,train,train,test,test,test,test
+IC23,adult_ICU_ctrl,0,test,train,inner_val,inner_val,train,test,test,test,test,train
+PHC03,ped_HC,0,test,train,train,train,train,test,test,test,test,test
+PIC04,ped_ICU_ctrl,0,test,train,inner_val,train,train,test,test,test,test,test
+Res-PS25,ped_sepsis,0,test,train,train,train,train,test,test,test,test,test
+Res-S139,adult_sepsis,0,test,train,train,train,train,test,test,test,train,test
+Res-S26,adult_sepsis,0,test,train,train,train,train,test,test,test,test,test
+Res-S77,adult_sepsis,0,test,train,train,train,train,train,test,train,test,test
+Skin-S140,adult_sepsis,0,test,train,train,train,train,test,test,test,test,test
+Uri-S147,adult_sepsis,0,test,train,inner_val,train,inner_val,test,train,test,test,test
+Abd-PS07,ped_sepsis,1,train,test,train,train,train,test,test,test,test,test
+Abd-S120,adult_sepsis,1,train,test,train,train,train,test,test,test,test,test
+Abd-S156,adult_sepsis,1,train,test,train,train,inner_val,test,test,test,test,test
+HC05,adult_HC,1,train,test,train,train,train,test,test,test,test,test
+HC13,adult_HC,1,train,test,train,train,inner_val,test,test,test,test,test
+IC16,adult_ICU_ctrl,1,train,test,train,train,train,test,test,test,test,test
+PHC01,ped_HC,1,train,test,train,inner_val,train,test,test,test,test,test
+PIC05,ped_ICU_ctrl,1,train,test,train,train,train,test,test,test,test,test
+Res-PS12,ped_sepsis,1,train,test,train,train,train,test,test,test,test,test
+Res-PS22,ped_sepsis,1,train,test,train,train,train,test,test,test,test,train
+Res-S10,adult_sepsis,1,inner_val,test,train,train,train,test,test,test,test,test
+Res-S184,adult_sepsis,1,train,test,train,train,train,test,test,test,test,test
+Res-S19,adult_sepsis,1,train,test,inner_val,train,train,test,test,test,test,test
+Skin-S142,adult_sepsis,1,train,test,train,train,train,test,test,test,train,train
+Skin-S46,adult_sepsis,1,train,test,train,train,train,test,test,test,test,train
+Skin-S52,adult_sepsis,1,train,test,train,inner_val,inner_val,test,test,test,test,test
+Uri-S157,adult_sepsis,1,train,test,inner_val,train,train,test,test,test,test,test
+Abd-PS04,ped_sepsis,2,train,train,test,train,train,test,test,test,test,test
+Abd-PS05,ped_sepsis,2,train,train,test,train,train,test,test,test,test,test
+Abd-S57,adult_sepsis,2,train,inner_val,test,train,train,test,test,test,train,test
+Abd-S79,adult_sepsis,2,train,train,test,train,train,test,test,test,test,test
+HC09,adult_HC,2,train,train,test,train,train,test,test,test,test,test
+IC10,adult_ICU_ctrl,2,train,train,test,train,train,test,test,test,test,test
+IC19,adult_ICU_ctrl,2,inner_val,train,test,train,train,test,test,test,test,test
+PHC05,ped_HC,2,train,train,test,train,train,test,test,test,train,test
+Res-PS26,ped_sepsis,2,inner_val,train,test,train,train,test,test,test,test,test
+Res-S146,adult_sepsis,2,train,train,test,train,train,test,test,test,test,test
+Res-S150,adult_sepsis,2,train,train,test,inner_val,train,train,test,test,test,test
+Res-S174,adult_sepsis,2,train,train,test,train,inner_val,test,test,test,train,test
+Res-S177,adult_sepsis,2,train,train,test,train,train,test,test,train,test,test
+Res-S40,adult_sepsis,2,train,train,test,inner_val,train,test,test,test,test,test
+Skin-S152,adult_sepsis,2,train,train,test,train,train,test,test,test,test,test
+Skin-S74,adult_sepsis,2,train,train,test,train,train,train,test,train,test,test
+Abd-S102,adult_sepsis,3,train,inner_val,train,test,train,test,test,test,test,train
+Abd-S103,adult_sepsis,3,train,train,train,test,train,test,test,test,test,test
+Abd-S51,adult_sepsis,3,train,train,train,test,train,test,test,test,test,test
+Abd-S83,adult_sepsis,3,train,train,train,test,train,test,test,test,test,test
+HC12,adult_HC,3,train,train,inner_val,test,train,test,train,test,test,test
+IC22,adult_ICU_ctrl,3,train,inner_val,train,test,inner_val,test,test,test,test,test
+PIC01,ped_ICU_ctrl,3,train,train,train,test,train,test,test,train,test,test
+Res-PS02,ped_sepsis,3,train,train,train,test,train,test,test,test,test,test
+Res-PS16,ped_sepsis,3,train,train,train,test,inner_val,test,test,test,test,test
+Res-PS21,ped_sepsis,3,train,inner_val,train,test,train,test,test,test,test,test
+Res-S125,adult_sepsis,3,train,train,train,test,train,test,test,test,test,test
+Res-S136,adult_sepsis,3,inner_val,train,train,test,train,test,test,train,test,test
+Res-S149,adult_sepsis,3,train,train,train,test,train,test,test,test,test,test
+Skin-S38,adult_sepsis,3,train,train,train,test,train,test,test,test,test,test
+Uri-S134,adult_sepsis,3,train,train,train,test,train,test,train,test,test,test
+Uri-S20,adult_sepsis,3,train,train,train,test,train,test,test,test,test,test
+Abd-PS20,ped_sepsis,4,train,train,train,inner_val,test,test,test,test,test,test
+Abd-PS27,ped_sepsis,4,train,train,train,train,test,test,test,test,test,test
+Abd-S42,adult_sepsis,4,train,train,train,train,test,test,test,test,test,test
+Abd-S54,adult_sepsis,4,train,train,train,train,test,test,test,test,test,test
+Abd-S98,adult_sepsis,4,train,train,inner_val,train,test,test,test,test,test,test
+HC16,adult_HC,4,inner_val,train,train,train,test,test,test,test,test,test
+IC15,adult_ICU_ctrl,4,train,train,train,train,test,test,test,test,test,test
+PHC02,ped_HC,4,train,train,train,train,test,test,test,test,test,test
+PIC02,ped_ICU_ctrl,4,train,train,train,train,test,test,test,test,test,test
+Res-PS03,ped_sepsis,4,train,train,train,train,test,test,test,test,test,test
+Res-S127,adult_sepsis,4,inner_val,train,train,inner_val,test,test,test,test,test,test
+Res-S164,adult_sepsis,4,train,train,train,train,test,test,train,test,test,test
+Res-S166,adult_sepsis,4,train,train,train,train,test,test,train,test,test,test
+Res-S87,adult_sepsis,4,train,train,train,train,test,test,test,test,test,test
+Skin-S43,adult_sepsis,4,inner_val,train,train,train,test,test,test,test,test,test
+Uri-S93,adult_sepsis,4,train,inner_val,train,train,test,test,test,test,test,test

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec06_ft_method.csv

@@ -0,0 +1,38 @@
+key,value,display,source
+lora_n_trainable,1296224,1.30 M,/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
+base_n_params,54185184,54.2 M,/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
+lora_trainable_pct,2.3922111254618974,2.4 %,/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
+lora_rank,16,16,/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
+lora_alpha,16.0,16,/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
+lora_n_linear_layers,22,22,/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
+lora_adapters_condition_encoder,2,2,/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
+lora_adapters_time_encoder,2,2,/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
+lora_adapters_context_mixer,1,1,/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
+lora_adapters_down_blocks,8,8,/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
+lora_adapters_up_blocks,6,6,/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
+lora_adapters_output_and_2_heads,3,3,/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
+lr,0.0005,5e-4,/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
+batch_size,256,256,/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
+batch_sampling,"a folds.csv row (one bulk-sc sample pair) drawn uniformly, then one of its cells uniformly: pair-balanced, not donor-balanced when a donor has several samples",pair-balanced,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_sdd.py (draw_batch)
+ema_decay,0.999,0.999,/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
+eval_every_steps,250,250,/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
+patience_evals,8,8,/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
+patience_steps,2000,"2,000",/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
+max_steps_cap,20000,"20,000",/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
+fewpair_fixed_steps,3000,"3,000",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fewshot_n5/draw0/lora/RUN.json
+fewpair_inner_val_rows,0,0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fewshot_n5/draw0/lora/RUN.json
+merge_reload_forward_max_abs_diff,0.0,0,/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
+lora_wall_minutes_min,1.7233333333333334,2,"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/*/fewshot_n5/draw*/lora/RUN.json + runs/*/fold*/real_lora/RUN.json (wall_seconds, n=40; Imperial runs are on server_2, not included)"
+lora_wall_minutes_max,13.838333333333333,14,"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/*/fewshot_n5/draw*/lora/RUN.json + runs/*/fold*/real_lora/RUN.json (wall_seconds, n=40)"
+pretrain_global_steps,764249,"764,249",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/RUN_STATUS.json
+pretrain_wall_hours,15.94193306286858,15.9 h,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/RUN_STATUS.json
+pretrain_epochs,16,E16,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/RUN_STATUS.json
+n_genes,6000,"6,000",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/RUN_STATUS.json
+pretrain_recipe_k_min,250,250,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec01_recipe_k.csv
+pretrain_recipe_k_max,4000,"4,000",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/presentations/2026-09-30--paper-summary--r00/data/sec01_recipe_k.csv; = max_k in /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/ALLCELL_DATA_CONTRACT.json
+pretrain_topup_recipes_below_grid,3658,"3,658 of 134,730 train recipes are coverage top-ups (actual K without duplicate padding, including K below original 250 minimum)",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/ALLCELL_DATA_CONTRACT.json
+condition_fixed_depth_K,1000,"1,000",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/<cohort>/PREPARE.json (recipe_k; fixed-depth policy of plans/realbulk_generation_20260922/build_realbulk_conditions.py)
+cells_generated_per_bulk_sample,1500,"1,500",/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/draw0/lora__raw.npz
+ddim_steps,50,50,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/draw0/lora__raw.log
+sampler_weights,ema,EMA,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/draw0/lora__raw.log
+support_readout,bernoulli,Bernoulli,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/draw0/lora__raw.npz

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec07_ft_modes_accuracy.csv

@@ -0,0 +1,19 @@
+dataset,call,arm,label,n_donors,comp_l1,coverage,precision,source_summary,logfc_r,n_case,n_control,source_contrast
+immicro,pooled,real_full__raw,full FT,107,0.1572206245036138,0.6953894080996885,0.8895327102803738,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,
+immicro,pooled,real_lora__raw,LoRA FT (r 16),107,0.16172890350786212,0.7842990654205607,0.9241121495327103,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,
+immicro,pooled,pseudo_full__cal,sc-only FT + cal,107,0.24025342946776804,0.6233021806853583,0.8047352024922119,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,
+immicro,pooled,zs__cal,zero-shot + paired cal,107,0.19850275515696958,0.527227414330218,0.9050467289719626,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,,,,
+immicro,fold0,real_full__raw,full FT,22,0.14700077323808897,0.8412121212121212,0.9869696969696969,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/summary.json,,,,
+immicro,fold0,real_lora__raw,LoRA FT (r 16),22,0.15285900890637347,0.9148484848484848,0.9915151515151515,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/summary.json,,,,
+immicro,fold0,real_condenc__raw,cond.-encoder-only FT,22,0.20418205250581475,0.7284848484848485,0.9793939393939394,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/summary.json,,,,
+immicro,fold0,pseudo_full__cal,sc-only FT + cal,22,0.23075401547639995,0.8157575757575758,0.953939393939394,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/summary.json,,,,
+immicro,fold0,zs__cal,zero-shot + paired cal,22,0.168436972993651,0.7254545454545455,0.9848484848484849,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/summary.json,,,,
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+ye2026_sepsis,fold0,real_full__raw,full FT,17,0.38818745233300567,0.8713725490196078,0.9784313725490196,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/summary.json,0.4893218773218223,12.0,5.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/contrast.csv
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+ye2026_sepsis,fold0,real_condenc__raw,cond.-encoder-only FT,17,0.38030414383690153,0.7407843137254903,0.9831372549019608,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/summary.json,0.2612324561498079,12.0,5.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/contrast.csv
+ye2026_sepsis,fold0,pseudo_full__cal,sc-only FT + cal,17,0.3962620259933191,0.8498039215686275,0.9792156862745098,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/summary.json,0.4648923976062872,12.0,5.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/contrast.csv
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