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/sec03_panel_bench.csv

@@ -0,0 +1,6 @@
+arm,method,n_genes,params,val_loss_e16,n_seeds,logfc_r,top50,comp_l1,logfc_r_sd,top50_sd,comp_l1_sd,logfc_r_base_seed,top50_base_seed,comp_l1_base_seed,eval_genes,n_donors,part,readout,source
+2k,diffusion_f012k_e16,2000.0,23457184.0,0.09676088026571901,1.0,0.3482764431678152,53.0,0.1312519655714672,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+3k,diffusion_f013k_e16,3000.0,31139184.0,0.10918324212700364,1.0,0.3584411943962801,72.0,0.163812117118193,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+6k,diffusion_f016k_e16,6000.0,54185184.0,0.1369124204543195,5.0,0.37128127582159925,76.2,0.18076362220515757,0.017657234388334934,3.7013511046643495,0.003104479026911492,0.3991172272882592,81.0,0.1811408199822934,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+15k,diffusion_f01p15k_e16,15114.0,124198932.0,0.18702995903269065,1.0,0.3437945151700011,62.0,0.2971466704417127,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.csv
+scSemiProfiler,scSemiProfiler,,,,,0.3179103699610459,56.0,0.2643486790566219,,,,,,,1006,42,16,Bernoulli (drawn),/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/metrics_1006/summary_tidy.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/sec03_width_bench_summary.csv

@@ -0,0 +1,12 @@
+arm,readout,logfc_r,top50,comp_l1,panel_genes,n_donors,source,run_to_run_resolution_r,run_to_run_resolution_deg
+1x,bernoulli,0.28634830577858145,67.66666666666667,0.1965802312187439,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+1x,cut_p>0.5,0.2454306757496367,59.666666666666664,0.19869969115206496,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+4x,bernoulli,0.2587798754002981,59.333333333333336,0.26355193673169414,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+4x,cut_p>0.5,0.2531444292242156,58.666666666666664,0.2638292168410435,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+ctx4x,bernoulli,0.2783976735416536,68.0,0.16122444256041193,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+ctx4x,cut_p>0.5,0.24548355965577903,61.0,0.16135845886185732,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+prop_oracle,cut_p>0.5,0.2658679517393759,61.666666666666664,0.24375773441517443,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+prop_pred,cut_p>0.5,0.26302786049672094,61.333333333333336,0.24473855778352002,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+trunk4x,bernoulli,0.2681776909360299,61.666666666666664,0.18140091685493046,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+trunk4x,cut_p>0.5,0.265002442274151,60.666666666666664,0.18134384231801878,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2
+scSemiProfiler,reference,0.2431693343193305,52.0,0.2489601293057801,2980,42,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/analysis/scsemi_benchmark_diffusion_20260913/metrics_arch_epochs/scanvi_server2/summary_tidy_latest.csv,0.018,7.2

paper-releases/pbisc-diffusion/updates/20260930T090852Z-summary-deck-final-path-story/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec04_sle_benchmark.csv

@@ -0,0 +1,35 @@
+axis_genes,metric,method,value,seed_sd,source
+1006,logfc_r,PBISC 6k 5-seed mean,0.3712812758215992,0.0176572343883349,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,logfc_r,scSemiProfiler,0.3179103699610459,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,logfc_r,broadcast (input bulk),0.6769568951083694,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/tables/summary_mean_r_top50.csv
+1006,logfc_r,diffusion_f016k_e16,0.3991172272882592,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,logfc_r,diffusion_f016ks1_e16,0.3785261205502202,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,logfc_r,diffusion_f016ks2_e16,0.3592398986673997,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,logfc_r,diffusion_f016ks3_e16,0.3619273868311772,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,logfc_r,diffusion_f016ks4_e16,0.35759574577094,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,top50,PBISC 6k 5-seed mean,76.2,3.7013511046643495,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,top50,scSemiProfiler,56.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,top50,broadcast (input bulk),113.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/tables/summary_mean_r_top50.csv
+1006,top50,diffusion_f016k_e16,81.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,top50,diffusion_f016ks1_e16,79.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,top50,diffusion_f016ks2_e16,74.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,top50,diffusion_f016ks3_e16,75.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+1006,top50,diffusion_f016ks4_e16,72.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+2279,logfc_r,PBISC 6k 5-seed mean,0.3327056228632508,0.0160677167611957,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,logfc_r,scSemiProfiler,0.2699204110614752,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,logfc_r,broadcast (input bulk),0.6431665153721157,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/tables/summary_mean_r_top50.csv
+2279,logfc_r,diffusion_f016k_e16,0.3548047163709348,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,logfc_r,diffusion_f016ks1_e16,0.3355121563388878,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,logfc_r,diffusion_f016ks2_e16,0.3139723508970225,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,logfc_r,diffusion_f016ks3_e16,0.3204965329394827,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,logfc_r,diffusion_f016ks4_e16,0.3387423577699264,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,top50,PBISC 6k 5-seed mean,82.2,3.492849839314596,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,top50,scSemiProfiler,56.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,top50,broadcast (input bulk),117.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle_broadcast/tables/summary_mean_r_top50.csv
+2279,top50,diffusion_f016k_e16,84.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,top50,diffusion_f016ks1_e16,87.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,top50,diffusion_f016ks2_e16,80.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,top50,diffusion_f016ks3_e16,82.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+2279,top50,diffusion_f016ks4_e16,78.0,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_2279.csv
+labels only,comp_l1,PBISC 6k 5-seed mean,0.1807636222051575,0.0031044790269114,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv
+labels only,comp_l1,scSemiProfiler,0.2643486790566219,,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/sle/tables_1006.csv