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/sec05_condition_space_coords.csv

@@ -0,0 +1,108 @@
+donor_id,pool,pseudo_pc1,pseudo_pc2,raw_pc1,raw_pc2
+HS1,DB1,-9.61713,-0.55152,42.6165,2.41872
+HS2,DB2,-7.33282,4.21985,43.17775,6.71158
+HS3,DB3,-10.97921,1.80254,38.64898,4.27987
+HS4,DB4,15.3954,10.69257,46.01859,16.65612
+HS6,DB3,-9.3702,14.88896,37.3268,20.77616
+HS7,DB1,-10.4201,-1.16176,41.43051,3.53735
+HS8,DB1,-10.97906,-1.79828,38.16363,7.46242
+HS9,DB3,-12.36423,2.96736,40.88008,5.29263
+HS10,DB4,12.63252,0.16199,44.72803,8.79803
+HS11,DB6,7.21576,5.60082,41.45447,8.82278
+HS12,DB2,-8.28499,1.98255,42.83486,1.70609
+HS13,DB5,12.04883,4.8106,41.29679,14.18219
+HS14,DB3,-10.87878,5.05657,41.73463,5.19173
+HS15,DB4,14.1581,14.80566,43.51193,21.07933
+HS16,DB4,15.49375,6.33614,46.04723,13.81186
+HS17,DB6,6.02535,-6.15285,43.75982,4.47298
+HS18,DB4,9.94194,-1.43412,41.00132,5.4448
+HS19,DB5,15.30722,1.3385,44.03653,11.56656
+HS20,DB7,2.66251,-17.43886,40.57808,-7.71145
+HS21,DB1,-11.42858,1.05251,39.82156,5.37074
+HS23,DB6,5.48061,5.36723,39.40535,18.08322
+HS24,DB6,3.73778,-0.37894,40.66809,13.63467
+HS25,DB6,8.69203,13.93028,42.22339,20.14667
+HS26,DB2,-10.61027,1.5018,39.02409,1.92053
+HS27,DB2,-11.62205,-3.59542,38.46596,-4.2298
+HS28,DB5,15.80363,-0.36902,43.44492,9.72471
+HS29,DB5,11.54225,3.20336,41.01234,14.1553
+HS30,DB3,-10.37882,12.22067,39.73388,12.61877
+HS31,DB3,-6.02405,10.33367,43.76537,9.48927
+HS32,DB6,2.21714,-6.5624,42.21099,9.60073
+HS34,DB5,11.36265,-0.11421,41.38828,11.95868
+HS35,DB7,8.95221,0.13424,40.88777,7.7549
+HS36,DB5,12.05377,-0.79112,44.59488,8.57436
+HS37,DB6,7.20152,3.8843,42.43193,12.2631
+HS38,DB2,-2.47063,15.82708,42.73763,17.84238
+HS39,DB6,4.38805,-3.78041,39.74989,14.45901
+HS40,DB2,-8.51565,7.33372,38.61259,12.96258
+HS41,DB7,7.24928,-9.00969,42.40406,2.50027
+HS42,DB1,-12.3169,-0.93474,36.03886,7.40787
+HS43,DB5,10.7766,-5.83957,42.71067,2.05951
+HS44,DB5,14.93081,-0.21861,41.61509,6.8324
+HS45,DB7,5.34618,-8.07472,41.50518,9.11468
+HS46,DB1,-13.75506,-2.52479,35.61914,4.30421
+HS47,DB3,-12.59707,-2.55333,38.9408,-2.18683
+HS48,DB5,10.30591,-6.78846,41.48421,-2.38463
+HS49,DB3,-9.9929,4.3712,35.75639,3.02695
+HS50,DB5,11.75336,-3.23001,40.75749,-1.72735
+HS51,DB3,-14.64274,-2.6428,38.87011,-0.93118
+HS52,DB1,-13.85565,-6.89379,39.2513,-0.84658
+HS53,DB7,1.27415,-18.04145,37.35799,-0.76556
+HS54,DB3,-17.07848,-10.80351,35.92947,-11.5539
+HS55,DB1,-12.89292,1.73692,34.68515,5.30361
+HS56,DB1,-14.57228,-0.42126,35.98978,3.78724
+HS57,DB2,-11.18213,4.97142,38.18214,6.05789
+HS58,DB7,7.77845,5.06041,36.32398,16.88357
+HS59,DB4,11.64835,-0.7792,41.95648,10.36339
+HS60,DB6,6.74964,3.48196,41.9987,11.77944
+HS61,DB7,10.33119,11.51676,37.30697,22.9801
+HS62,DB3,-14.65731,-3.26706,35.80539,-0.41094
+HS63,DB5,10.87588,-4.31628,41.06955,2.69693
+HS64,DB2,-12.38471,-2.25117,40.44937,2.45224
+HS65,DB2,-9.05906,0.96481,36.99709,4.27598
+HS66,DB4,11.55624,-2.35028,40.15834,6.29365
+HS67,DB2,-12.3972,-4.6657,38.19453,0.39067
+HS68,DB6,1.80614,-4.34487,40.54277,4.23049
+HS69,DB6,4.11173,1.27672,37.56598,12.15465
+HS70,DB4,7.95104,-4.34134,39.78068,4.05116
+HS71,DB4,10.54326,-0.49902,40.84646,8.03334
+HS72,DB4,9.95417,-8.96847,43.33897,-2.87116
+HS73,DB2,-8.11222,8.84731,35.11734,15.24105
+HS74,DB5,11.52986,-8.25536,38.55578,0.36289
+HS75,DB6,2.94105,-0.40797,38.12354,8.72079
+HS76,DB1,-12.81068,-2.19251,36.87575,6.29967
+HS77,DB2,-8.7892,7.41962,38.22601,18.16989
+HS78,DB1,-13.17368,-4.7,33.85759,-0.10429
+HS79,DB5,13.07571,-0.20232,42.61762,6.93677
+HS80,DB3,-14.25756,-2.27399,40.42829,-2.91029
+HS81,DB7,4.76334,-3.13572,37.43704,5.61214
+HS82,DB2,-10.57962,-2.08804,36.46475,-1.08873
+HS83,DB6,1.28859,-4.9125,40.78895,7.95954
+HS84,DB3,-12.32516,3.05765,35.95028,8.38138
+HS85,DB5,13.03095,4.40748,37.91744,15.3689
+HS86,DB7,7.99188,3.09063,33.71075,14.84558
+HS87,DB5,13.45047,-7.68906,40.99504,3.58056
+HS88,DB3,-10.95816,3.75741,37.8463,5.90143
+HS89,DB2,-9.19562,4.86468,35.85538,6.78121
+HS90,DB7,5.79012,-7.89814,37.23918,1.66951
+HS91,DB6,3.84781,-5.04181,39.63766,4.21298
+HS92,DB7,3.08234,-12.62922,40.76572,-0.83005
+HS93,DB1,-17.5764,-9.81485,36.11118,-4.37711
+HS94,DB3,-14.31141,-0.71367,37.54154,-0.3301
+HS95,DB1,-12.19123,-3.56832,37.3131,2.75439
+HS96,DB7,11.32907,3.4771,40.8869,15.00156
+HS97,DB4,11.06007,-0.62675,44.19793,7.72107
+HS98,DB2,-6.88436,15.98557,38.8847,24.37978
+HS100,DB6,2.85053,-4.22261,41.58589,13.18
+HS101,DB4,11.65589,4.7708,43.27051,9.62944
+HS102,DB7,7.23299,-5.33202,37.40092,9.2313
+HS103,DB6,4.19661,0.61629,41.27944,4.5354
+HS104,DB4,13.03994,6.53954,42.30663,14.81455
+HS105,DB4,11.7882,-3.38875,43.43993,5.53242
+HS106,DB2,-5.85739,16.41393,38.61409,21.47066
+HS107,DB1,-15.99732,-4.0174,35.57543,-1.37934
+HS108,DB7,5.43296,-8.67726,39.65855,11.26749
+HS109,DB5,14.23783,-1.30434,42.85657,8.98567
+HS110,DB1,-11.99246,-1.99841,36.37358,4.49444
+HS111,DB1,-13.19819,-3.10115,36.21955,1.23994

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec05_condition_space_numbers.csv

@@ -0,0 +1,27 @@
+quantity,value,source
+D_pca30,26.62304016610284,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+raw_to_own_pseudo_median_D_pca30,2.4577822046559272,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+raw_to_own_pseudo_median_D_full,3.1917286339519078,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+shared_fraction_sq_offset_pca30,0.9523756918945517,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+shared_fraction_sq_offset_full,0.907860216661042,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+pca30_captured_fraction_of_raw_offset_sq,0.44408438056968147,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+top1_plain_pca30,0.07476635514018691,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+top1_shift_removed_pca30,0.7570093457943925,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+top1_plain_full,0.1308411214953271,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+top1_shift_removed_full,0.9813084112149533,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+top1_chance,0.009345794392523364,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+n_donors,107,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+n_genes,5508,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+pc1_evr,0.2472282600505628,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+pc2_evr,0.0943136896367062,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+gen_raw_to_obs_median_D_pca30,1.411802858360104,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+gen_pseudo_to_obs_median_D_pca30,2.3599000435631616,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+pool_R2_pseudobulk_pca30,0.4723937910068941,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/batch_structure_ImMicro.json
+pool_R2_raw_pca30,0.16825020417323755,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/batch_structure_ImMicro.json
+pool_R2_permutation_null_median,0.05394657531470705,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/batch_structure_ImMicro.json
+pool_R2_pseudobulk_PC1,0.9550414531481362,computed here from /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/coords_ImMicro_native.csv (pca PC1) and pools in /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_sample_size_20260914/features.npz
+pool_R2_raw_PC1,0.4324337707568571,computed here from /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/coords_ImMicro_native.csv (pca PC1) and pools in /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_sample_size_20260914/features.npz
+pseudobulk_PC1_mean_block_DB1+DB2+DB3,-11.295141276595746,computed here from /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/coords_ImMicro_native.csv (pca PC1) and pools in /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_sample_size_20260914/features.npz
+pseudobulk_PC1_mean_block_DB4+DB5+DB6+DB7,8.847860166666667,computed here from /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/coords_ImMicro_native.csv (pca PC1) and pools in /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_sample_size_20260914/features.npz
+n_donors_block_DB1+DB2+DB3,47,computed here from /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/coords_ImMicro_native.csv (pca PC1) and pools in /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_sample_size_20260914/features.npz
+n_donors_block_DB4+DB5+DB6+DB7,60,computed here from /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/coords_ImMicro_native.csv (pca PC1) and pools in /home/sj_server_1/gblee/datalake/paired-pbmc-bulk-sc/analyses/offset_sample_size_20260914/features.npz

paper-releases/pbisc-diffusion/updates/20260930T065633Z-summary-deck-scsemi-final/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/data/sec05_shift_cohorts.csv

@@ -0,0 +1,4 @@
+cohort,setting,pca_components,n,dist_to_own_pseudo_D,shared_fraction,top1,top1_shift_removed,chance,source
+ImMicro,native,30,107,2.4577822046559272,0.9523756918945517,0.07476635514018691,0.7570093457943925,0.009345794392523364,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/ImMicro/metrics_ImMicro.json
+Randolph,fixed,30,178,1.1321624463220292,0.7103251913353301,0.10674157303370786,0.5,0.0056179775280898875,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/Randolph/metrics_Randolph.json
+Arunachalam,raw5000_pseudoNative,11,12,1.2028984536822949,0.9161324776364808,0.3333333333333333,0.9166666666666666,0.08333333333333333,/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/sample_level/Arunachalam/metrics_Arunachalam.json