Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec07_ft_modes_accuracy.csv

@@ -0,0 +1,23 @@
+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 + calibration,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,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__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 + calibration,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,,,,
+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__cal,sc-only FT (+ cal.),82,0.3603070909296258,0.7255284552845529,0.8628455284552845,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,0.2956255561818948,61.0,21.0,/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__cal,zero-shot + calibration,82,0.40065324062398555,0.4308130081300813,0.9034146341463415,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/pooled/summary.json,0.12267970089558217,61.0,21.0,/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__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
+ye2026_sepsis,fold0,zs__cal,zero-shot + calibration,17,0.3875193921429544,0.6262745098039215,0.984313725490196,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/fold0/summary.json,0.25525815962656967,12.0,5.0,/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/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec07_ft_modes_wilcoxon.csv

@@ -0,0 +1,33 @@
+dataset,call,comparison,arm_a,arm_b,metric,mean_diff,frac_donors_a_lower,frac_donors_a_better,wilcoxon_p,n,source
+immicro,pooled,full - LoRA comp_l1,real_full__raw,real_lora__raw,comp_l1,-0.004508279004248297,0.5700934579439252,0.5700934579439252,0.24760598984759485,107,/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,comp_l1,-0.29764586903801876,0.9626168224299065,0.9626168224299065,7.29720615143116e-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,comp_l1,-0.2931375900337705,0.9626168224299065,0.9626168224299065,1.678562631844877e-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,comp_l1,0.051323043599441294,0.09090909090909091,0.09090909090909091,2.6226043701171875e-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 - LoRA coverage,real_condenc__raw,real_lora__raw,coverage,-0.18636363636363634,1.0,0.0,3.986543522315485e-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,comp_l1,-0.28004245611750506,0.9545454545454546,0.9545454545454546,9.5367431640625e-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
+immicro,pooled,full - zero-shot + cal comp_l1,real_full__raw,zs__cal,comp_l1,-0.04128213065335577,0.6728971962616822,0.6728971962616822,3.712086471400376e-07,107,/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 + cal coverage,real_full__raw,zs__cal,coverage,0.16816199376947044,0.04672897196261682,0.9532710280373832,8.486777473582784e-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 + cal comp_l1,real_lora__raw,zs__cal,comp_l1,-0.03677385164910749,0.6915887850467289,0.6915887850467289,1.930319432195753e-07,107,/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 + cal coverage,real_lora__raw,zs__cal,coverage,0.25707165109034275,0.037383177570093455,0.9532710280373832,7.34315021996262e-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,fold0,cond.-encoder-only - zero-shot + cal comp_l1,real_condenc__raw,zs__cal,comp_l1,0.03574507951216376,0.45454545454545453,0.45454545454545453,0.05869007110595703,22,/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 + cal coverage,real_condenc__raw,zs__cal,coverage,0.0030303030303030247,0.45454545454545453,0.45454545454545453,0.6809807400315375,22,/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,LoRA - zero-shot + cal comp_l1,real_lora__raw,zs__cal,comp_l1,-0.015577964087277536,0.5454545454545454,0.5454545454545454,0.2902231216430664,22,/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,LoRA - zero-shot + cal coverage,real_lora__raw,zs__cal,coverage,0.18939393939393936,0.0,0.9545454545454546,5.9569779074563595e-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,pooled,zero-shot + cal - zero-shot comp_l1,zs__cal,zs__raw,comp_l1,-0.256363738384663,0.9158878504672897,0.9158878504672897,9.504068560045531e-17,107,/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,zero-shot + cal - zero-shot coverage,zs__cal,zs__raw,coverage,0.3353894080996885,0.0,1.0,2.72803381740563e-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
+ye2026_sepsis,pooled,full - LoRA comp_l1,real_full__raw,real_lora__raw,comp_l1,0.009828762599665206,0.4878048780487805,0.4878048780487805,0.7132287608306445,82,/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,comp_l1,-0.13917275833217932,0.6951219512195121,0.6951219512195121,0.00034910604889623414,82,/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,comp_l1,-0.14900152093184452,0.6707317073170732,0.6707317073170732,0.0006293040873854114,82,/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,comp_l1,0.007056506251358439,0.4117647058823529,0.4117647058823529,0.51708984375,17,/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 - LoRA coverage,real_condenc__raw,real_lora__raw,coverage,-0.11764705882352941,0.8235294117647058,0.058823529411764705,0.0012063162374293,17,/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,comp_l1,-0.0703743144265139,0.5882352941176471,0.5882352941176471,0.3778228759765625,17,/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
+ye2026_sepsis,pooled,full - zero-shot + cal comp_l1,real_full__raw,zs__cal,comp_l1,-0.028999799640969225,0.524390243902439,0.524390243902439,0.2357081943386491,82,/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 + cal coverage,real_full__raw,zs__cal,coverage,0.36382113821138207,0.0,1.0,3.6598948603870226e-15,82,/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 + cal comp_l1,real_lora__raw,zs__cal,comp_l1,-0.03882856224063442,0.5365853658536586,0.5365853658536586,0.19313667138032242,82,/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 + cal coverage,real_lora__raw,zs__cal,coverage,0.3985365853658537,0.0,1.0,3.6592804410205364e-15,82,/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 - zero-shot + cal comp_l1,real_condenc__raw,zs__cal,comp_l1,-0.007215248306052927,0.4117647058823529,0.4117647058823529,0.926513671875,17,/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 + cal coverage,real_condenc__raw,zs__cal,coverage,0.11450980392156862,0.11764705882352941,0.8823529411764706,0.0007113968360959945,17,/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,LoRA - zero-shot + cal comp_l1,real_lora__raw,zs__cal,comp_l1,-0.014271754557411379,0.4117647058823529,0.4117647058823529,0.963226318359375,17,/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
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paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec08_pairs_realism.csv

@@ -0,0 +1,45 @@
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paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec08_pairs_signal.csv

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