Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec05_cells_metrics.csv

@@ -0,0 +1,20 @@
+arm,metric,value,source
+raw,monocyte_pct,30.554517133956388,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+raw,precision,0.3630529595015576,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+raw,coverage,0.083613707165109,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+raw,comp_L1,0.4552049769720906,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+pseudo,monocyte_pct,14.330218068535824,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+pseudo,precision,0.924859813084112,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+pseudo,coverage,0.5068535825545172,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+pseudo,comp_L1,0.1663566375577628,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+real_R2,monocyte_pct,16.735202492211837,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+real_R2,precision,0.9627414330218068,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+real_R2,coverage,0.9997507788161992,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv
+null,comp_L1_LOO_null,0.1606372707722086,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/input_path_compare/immicro_behcet/tables/immicro_table.csv (column comp_L1_obs_LOO_null)
+raw,pseudo_T_cells_labelled_monocyte_under_raw,0.19152234575009966,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_raw_counts.csv
+raw,n_pseudo_T_cells,112885.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_raw_counts.csv
+raw,n_pseudo_T_to_monocyte,21620.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_raw_counts.csv
+raw,n_cells_in_transition_table,160500.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tables/c_label_transition_pseudo_to_raw_counts.csv
+raw,umap_cells_plotted,3000.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/interactive/cells_5arm.json (cells with set == raw); coordinates in data/sec05_cells_umap_coords.csv
+pseudo,umap_cells_plotted,3000.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/interactive/cells_5arm.json (cells with set == pseudo); coordinates in data/sec05_cells_umap_coords.csv
+real_R2,umap_cells_plotted,3000.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/interactive/cells_5arm.json (cells with set == R2); coordinates in data/sec05_cells_umap_coords.csv

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/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__raw,sc-only FT,107,0.4441023783514959,0.0853582554517134,0.42853582554517133,/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__raw,"zero-shot, real bulk",107,0.4548664935416326,0.1918380062305296,0.6804361370716511,/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__raw,sc-only FT,22,0.42584877452001807,0.25727272727272726,0.7245454545454545,/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__raw,"zero-shot, real bulk",22,0.4842245086233197,0.42272727272727273,0.91,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/summary.json,,,,
+ye2026_sepsis,pooled,real_full__raw,full FT,82,0.3716534409830164,0.7946341463414635,0.8664227642276423,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,0.534366534546327,61.0,21.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/contrast.csv
+ye2026_sepsis,pooled,real_lora__raw,LoRA FT (r 16),82,0.3618246783833512,0.829349593495935,0.9256910569105691,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,0.5267612711229187,61.0,21.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/contrast.csv
+ye2026_sepsis,pooled,pseudo_full__raw,sc-only FT,82,0.47154664243500094,0.13414634146341464,0.6059349593495935,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,0.14853801746689405,61.0,21.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/contrast.csv
+ye2026_sepsis,pooled,zs__raw,"zero-shot, real bulk",82,0.5108261993151957,0.06731707317073171,0.6141463414634146,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,-0.011802666469938328,61.0,21.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/contrast.csv
+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
+ye2026_sepsis,fold0,real_lora__raw,LoRA FT (r 16),17,0.3732476375855431,0.8584313725490196,0.9858823529411764,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/summary.json,0.486854343182844,12.0,5.0,/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,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__raw,sc-only FT,17,0.4220525896292665,0.3509803921568627,0.928235294117647,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/summary.json,0.16656370372106602,12.0,5.0,/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,zs__raw,"zero-shot, real bulk",17,0.45067845826341535,0.1807843137254902,0.8788235294117647,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/summary.json,0.0641712727521753,12.0,5.0,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/contrast.csv

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec07_ft_modes_wilcoxon.csv

@@ -0,0 +1,11 @@
+dataset,call,comparison,arm_a,arm_b,mean_diff,frac_donors_a_lower,wilcoxon_p,n,source
+immicro,pooled,full - LoRA comp_l1,real_full__raw,real_lora__raw,-0.004508279004248297,0.5700934579439252,0.24760598984759485,107,/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,pooled,full - zero-shot comp_l1,real_full__raw,zs__raw,-0.29764586903801876,0.9626168224299065,7.29720615143116e-19,107,/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,pooled,LoRA - zero-shot comp_l1,real_lora__raw,zs__raw,-0.2931375900337705,0.9626168224299065,1.678562631844877e-18,107,/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,fold0,cond.-encoder-only - LoRA comp_l1,real_condenc__raw,real_lora__raw,0.051323043599441294,0.09090909090909091,2.6226043701171875e-05,22,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/per_donor.csv
+immicro,fold0,cond.-encoder-only - zero-shot comp_l1,real_condenc__raw,zs__raw,-0.28004245611750506,0.9545454545454546,9.5367431640625e-07,22,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/fold0/per_donor.csv
+ye2026_sepsis,pooled,full - LoRA comp_l1,real_full__raw,real_lora__raw,0.009828762599665206,0.4878048780487805,0.7132287608306445,82,/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,pooled,full - zero-shot comp_l1,real_full__raw,zs__raw,-0.13917275833217932,0.6951219512195121,0.00034910604889623414,82,/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,pooled,LoRA - zero-shot comp_l1,real_lora__raw,zs__raw,-0.14900152093184452,0.6707317073170732,0.0006293040873854114,82,/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,fold0,cond.-encoder-only - LoRA comp_l1,real_condenc__raw,real_lora__raw,0.007056506251358439,0.4117647058823529,0.51708984375,17,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/per_donor.csv
+ye2026_sepsis,fold0,cond.-encoder-only - zero-shot comp_l1,real_condenc__raw,zs__raw,-0.0703743144265139,0.5882352941176471,0.3778228759765625,17,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/per_donor.csv

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/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,y_axis_break
+comp_l1,immicro,zero_shot,0,0.4548664935416326,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,True
+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,True
+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,True
+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,True
+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,True
+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,True
+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,True
+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,True
+coverage,immicro,zero_shot,0,0.1918380062305296,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/immicro/pooled/summary.json,False
+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,False
+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,False
+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,False
+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,False
+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,False
+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,False
+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,
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