Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw0/score/arms/lora/deg_top50_lists.csv

@@ -0,0 +1,131 @@
+celltype,source,rank,gene_id
+T cell,observed,1,ENSG00000148773
+T cell,observed,2,ENSG00000175063
+T cell,observed,3,ENSG00000089685
+T cell,observed,4,ENSG00000171848
+T cell,observed,5,ENSG00000176890
+T cell,observed,6,ENSG00000166803
+T cell,observed,7,ENSG00000135077
+T cell,observed,8,ENSG00000138670
+T cell,observed,9,ENSG00000004468
+T cell,observed,10,ENSG00000112139
+T cell,observed,11,ENSG00000089692
+T cell,observed,12,ENSG00000088325
+T cell,observed,13,ENSG00000117399
+T cell,observed,14,ENSG00000145850
+T cell,observed,15,ENSG00000115590
+T cell,observed,16,ENSG00000198502
+T cell,observed,17,ENSG00000140284
+T cell,observed,18,ENSG00000109906
+T cell,observed,19,ENSG00000101057
+T cell,observed,20,ENSG00000117228
+T cell,observed,21,ENSG00000228696
+T cell,observed,22,ENSG00000188677
+T cell,observed,23,ENSG00000147459
+T cell,observed,24,ENSG00000005961
+T cell,observed,25,ENSG00000138160
+T cell,observed,26,ENSG00000118513
+T cell,observed,27,ENSG00000145990
+T cell,observed,28,ENSG00000159335
+T cell,observed,29,ENSG00000179344
+T cell,observed,30,ENSG00000117724
+T cell,observed,31,ENSG00000169583
+T cell,observed,32,ENSG00000184113
+T cell,observed,33,ENSG00000137812
+T cell,observed,34,ENSG00000109805
+T cell,observed,35,ENSG00000066279
+T cell,observed,36,ENSG00000129226
+T cell,observed,37,ENSG00000100292
+T cell,observed,38,ENSG00000172215
+T cell,observed,39,ENSG00000120875
+T cell,observed,40,ENSG00000010030
+T cell,observed,41,ENSG00000221869
+T cell,observed,42,ENSG00000145386
+T cell,observed,43,ENSG00000182985
+T cell,observed,44,ENSG00000162722
+T cell,observed,45,ENSG00000115415
+T cell,observed,46,ENSG00000011590
+T cell,observed,47,ENSG00000035664
+T cell,observed,48,ENSG00000188375
+T cell,observed,49,ENSG00000126787
+T cell,observed,50,ENSG00000135114
+T cell,generated,1,ENSG00000156675
+B cell,observed,1,ENSG00000060138
+B cell,observed,2,ENSG00000171467
+B cell,observed,3,ENSG00000188641
+B cell,observed,4,ENSG00000213445
+B cell,observed,5,ENSG00000241343
+B cell,observed,6,ENSG00000127184
+B cell,observed,7,ENSG00000134419
+B cell,observed,8,ENSG00000137818
+B cell,observed,9,ENSG00000142937
+Monocyte,observed,1,ENSG00000156535
+Monocyte,observed,2,ENSG00000156265
+Monocyte,observed,3,ENSG00000137936
+Monocyte,observed,4,ENSG00000121101
+Monocyte,observed,5,ENSG00000106952
+Monocyte,observed,6,ENSG00000058091
+Monocyte,observed,7,ENSG00000196187
+Monocyte,observed,8,ENSG00000241343
+Monocyte,observed,9,ENSG00000183943
+Monocyte,observed,10,ENSG00000164733
+NK cell,observed,1,ENSG00000155846
+NK cell,observed,2,ENSG00000178965
+NK cell,observed,3,ENSG00000128040
+NK cell,observed,4,ENSG00000142185
+NK cell,observed,5,ENSG00000096060
+NK cell,observed,6,ENSG00000169504
+NK cell,observed,7,ENSG00000138639
+NK cell,observed,8,ENSG00000143226
+NK cell,observed,9,ENSG00000189013
+NK cell,observed,10,ENSG00000182010
+NK cell,observed,11,ENSG00000172264
+NK cell,observed,12,ENSG00000276070
+NK cell,observed,13,ENSG00000063438
+NK cell,observed,14,ENSG00000142235
+NK cell,observed,15,ENSG00000259207
+NK cell,observed,16,ENSG00000149571
+NK cell,observed,17,ENSG00000117228
+NK cell,observed,18,ENSG00000115415
+NK cell,observed,19,ENSG00000007545
+NK cell,observed,20,ENSG00000171488
+NK cell,observed,21,ENSG00000143842
+NK cell,observed,22,ENSG00000186187
+NK cell,observed,23,ENSG00000115687
+NK cell,observed,24,ENSG00000135114
+NK cell,observed,25,ENSG00000144554
+NK cell,observed,26,ENSG00000034053
+NK cell,observed,27,ENSG00000151208
+NK cell,observed,28,ENSG00000266714
+NK cell,observed,29,ENSG00000196187
+NK cell,observed,30,ENSG00000130589
+NK cell,observed,31,ENSG00000104228
+NK cell,observed,32,ENSG00000072071
+NK cell,observed,33,ENSG00000198420
+NK cell,observed,34,ENSG00000130669
+NK cell,observed,35,ENSG00000145990
+NK cell,observed,36,ENSG00000133195
+NK cell,observed,37,ENSG00000171492
+NK cell,observed,38,ENSG00000138496
+NK cell,observed,39,ENSG00000125834
+NK cell,observed,40,ENSG00000135148
+NK cell,observed,41,ENSG00000105339
+NK cell,observed,42,ENSG00000164080
+NK cell,observed,43,ENSG00000078269
+NK cell,observed,44,ENSG00000162714
+NK cell,observed,45,ENSG00000103222
+NK cell,observed,46,ENSG00000172183
+NK cell,observed,47,ENSG00000198918
+NK cell,observed,48,ENSG00000124343
+NK cell,observed,49,ENSG00000068024
+NK cell,observed,50,ENSG00000104381
+DC,observed,1,ENSG00000179388
+DC,observed,2,ENSG00000184381
+DC,observed,3,ENSG00000121542
+DC,observed,4,ENSG00000109184
+DC,observed,5,ENSG00000142347
+DC,observed,6,ENSG00000122026
+all (input bulk),broadcast,1,ENSG00000152766
+all (input bulk),broadcast,2,ENSG00000189430
+all (input bulk),broadcast,3,ENSG00000163568
+all (input bulk),broadcast,4,ENSG00000126822

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw0/score/contrast.csv

@@ -0,0 +1,14 @@
+arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
+lora,T cell,mean_cp10k,3038,0.5318576611939548,0.21197028589936057,0.5153236409448303,0.1663490712781621,14,11,14,11,44851,18080,,,,,,,,,,,
+lora,T cell,pseudobulk_log1p_cpm,3038,0.158785526937719,0.3111080127833571,0.1393825832908705,0.0861846875303183,14,11,14,11,44851,18080,,,,,,,,,,,
+lora,B cell,mean_cp10k,3233,0.1660831852373693,0.10073938447302222,0.1560653117640351,0.11811354873667035,14,11,14,11,4424,2250,,,,,,,,,,,
+lora,B cell,pseudobulk_log1p_cpm,3233,0.008596932211882024,0.012072638770403557,0.007624332279454709,0.08277549879429334,14,11,14,11,4424,2250,,,,,,,,,,,
+lora,Monocyte,mean_cp10k,3193,0.42074556421338766,0.3732268158395985,0.3707516482513127,0.23056059070075982,14,11,14,11,22847,9804,,,,,,,,,,,
+lora,Monocyte,pseudobulk_log1p_cpm,3193,0.2726016662389149,0.3506580485024196,0.24008565625575978,0.14277137957470457,14,11,14,11,22847,9804,,,,,,,,,,,
+lora,NK cell,mean_cp10k,3059,0.3046411903489653,0.1665379702415652,0.2854017514751144,0.1616943494618234,14,11,14,11,14219,4408,,,,,,,,,,,
+lora,NK cell,pseudobulk_log1p_cpm,3059,0.10290286195880947,0.15048321474174686,0.09220658154685848,0.07999852657848801,14,11,14,11,14219,4408,,,,,,,,,,,
+lora,T cell,welch_top50_deg,5752,,,,,14,11,14,11,44851,18080,True,0,0.0,50,1,1831,1,0,0.0,4,4
+lora,B cell,welch_top50_deg,5752,,,,,14,11,14,11,4424,2250,True,0,0.0,9,0,9,0,0,0.0,4,4
+lora,Monocyte,welch_top50_deg,5752,,,,,14,11,14,11,22847,9804,True,0,0.0,10,0,10,0,0,0.0,4,4
+lora,NK cell,welch_top50_deg,5752,,,,,14,11,14,11,14219,4408,True,0,0.0,50,0,358,0,0,0.0,4,4
+lora,DC,welch_top50_deg,5752,,,,,12,11,14,11,1176,1086,True,0,0.0,6,0,6,0,0,0.0,4,4

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw0/score/per_donor.csv

@@ -0,0 +1,26 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
+lora,N064_TOL,TOL,1500,2498,150,0.4673333333333333,0.6517213771016813,0.07666666666666666,0.044035228182546036,0.252,0.1677341873498799,0.13133333333333333,0.07606084867894315,0.028666666666666667,0.010008006405124099,0.044,0.05044035228182546,0.38165679210034686,0.3779557749494401,0.8566812123625087,13,False,0.9666666666666667,0.9466666666666667,0.9266666666666666,0.96,25.2,16.77341873498799,729.0,662.0
+lora,N064_FU1,FU1,1500,4659,150,0.6266666666666667,0.6396222365314446,0.056666666666666664,0.016527151749302426,0.14866666666666667,0.13865636402661516,0.07866666666666666,0.19167203262502683,0.015333333333333332,0.00472204335694355,0.074,0.008800171710667526,0.251921871646276,0.3574146776605954,0.8548475618612733,9,False,0.9533333333333334,0.6666666666666666,0.9066666666666666,0.9266666666666666,14.866666666666667,13.865636402661515,649.0,925.0
+lora,N038_BC,BC,1500,2801,150,0.342,0.5608711174580507,0.059333333333333335,0.0046411995715815784,0.3253333333333333,0.16565512317029632,0.19266666666666668,0.2170653338093538,0.04666666666666667,0.034273473759371655,0.034,0.017493752231345947,0.4865395692014757,0.2990892646419849,0.8732847128839789,5,False,0.9933333333333333,0.6866666666666666,0.9866666666666667,0.9333333333333333,32.53333333333333,16.565512317029633,970.0,1317.0
+lora,N038_AC,AC,1500,3976,150,0.31666666666666665,0.6830985915492958,0.078,0.00829979879275654,0.3473333333333333,0.1290241448692153,0.16266666666666665,0.12072434607645875,0.035333333333333335,0.03194164989939638,0.06,0.026911468812877263,0.7328638497652581,0.4382292825861123,0.8762238929015582,2,False,0.9466666666666667,0.94,0.96,0.9733333333333334,34.733333333333334,12.90241448692153,890.0,910.5
+lora,N055_AC,AC,1500,4308,150,0.2846666666666667,0.340297121634169,0.064,0.07799442896935933,0.49066666666666664,0.32474466109563604,0.088,0.2051996285979573,0.028666666666666667,0.0060352831940575676,0.044,0.0457288765088208,0.37710677808727944,0.3381802929616731,0.8787860773206174,6,False,0.9733333333333334,0.8933333333333333,0.98,0.9933333333333333,49.06666666666666,32.47446610956361,1201.5,1139.5
+lora,N136_TOL,TOL,1500,759,150,0.444,0.48616600790513836,0.048,0.10013175230566534,0.29133333333333333,0.19104084321475626,0.06466666666666666,0.0922266139657444,0.029333333333333333,0.0013175230566534915,0.12266666666666666,0.12911725955204217,0.25661660079051385,0.3267042557350408,0.8592274342624536,5,False,0.98,0.56,0.9266666666666666,0.98,29.133333333333333,19.104084321475625,761.5,1837.0
+lora,N136_FU1,FU1,1500,2927,150,0.41733333333333333,0.4246668944311582,0.058666666666666666,0.14724974376494704,0.3373333333333333,0.19337205329689103,0.068,0.09531943969935087,0.028666666666666667,0.0023915271609156134,0.09,0.13700034164673727,0.3404728390843867,0.43670640284299445,0.8643838379903611,9,False,0.9666666666666667,0.8466666666666667,0.9533333333333334,0.9933333333333333,33.733333333333334,19.3372053296891,781.0,1501.0
+lora,N128_BC,BC,1500,3902,150,0.3913333333333333,0.5158892875448488,0.074,0.06817016914402871,0.322,0.29420809841107126,0.11866666666666667,0.07842132239876987,0.038,0.03331624807790876,0.056,0.00999487442337263,0.24911190842303085,0.237517218766578,0.8762151432015457,1,True,0.9733333333333334,0.8533333333333334,0.92,0.9666666666666667,32.2,29.420809841107125,834.5,1088.0
+lora,N128_AC,AC,1500,2713,150,0.384,0.5488389237007003,0.07933333333333334,0.06524143015112421,0.31333333333333335,0.2790269074824917,0.14333333333333334,0.07077036490969407,0.034666666666666665,0.029487652045705862,0.04533333333333334,0.006634721710283818,0.32967784740140066,0.2595394391709072,0.8721649645416198,3,False,0.9733333333333334,0.7666666666666667,0.9733333333333334,0.96,31.333333333333336,27.90269074824917,849.0,1181.0
+lora,N129_BC,BC,1500,3087,150,0.37333333333333335,0.5963718820861678,0.07266666666666667,0.11305474570780694,0.328,0.08357628765792031,0.15,0.18140589569160998,0.037333333333333336,0.013281503077421444,0.03866666666666667,0.012309685779073534,0.5896650469711693,0.3871201592227091,0.8727931767768953,10,False,0.98,0.8533333333333334,0.98,0.9866666666666667,32.800000000000004,8.35762876579203,959.5,1059.0
+lora,N129_AC,AC,1500,2798,150,0.332,0.7076483202287348,0.062,0.04932094353109364,0.34,0.07969978556111508,0.18933333333333333,0.13366690493209435,0.03266666666666666,0.0228734810578985,0.044,0.006790564689063617,0.7512966404574697,0.4740323616378469,0.8669804370700627,12,False,0.98,0.96,0.98,0.9866666666666667,34.0,7.969978556111508,898.0,759.0
+lora,N147_TOL,TOL,1500,3210,150,0.548,0.44205607476635517,0.04,0.00809968847352025,0.25733333333333336,0.4193146417445483,0.10733333333333334,0.07102803738317758,0.015333333333333332,0.0065420560747663555,0.032,0.0529595015576324,0.3658816199376947,0.41393483656294416,0.8688829973397111,9,False,0.98,0.7466666666666667,0.9533333333333334,0.9466666666666667,25.733333333333334,41.93146417445483,1099.0,1461.5
+lora,N158_AC,AC,1500,3749,150,0.43266666666666664,0.24619898639637236,0.042,0.026673779674579887,0.338,0.6295012003200854,0.12,0.04934649239797279,0.03333333333333333,0.024806615097359295,0.034,0.0234729261136303,0.5830024006401707,0.8296165589099086,0.8677517412535415,5,False,0.9933333333333333,0.8933333333333333,0.9866666666666667,0.9866666666666667,33.800000000000004,62.95012003200854,1124.0,1047.0
+lora,N159_BC,BC,1500,3779,150,0.7373333333333333,0.6996559936491136,0.030666666666666665,0.018523418893887273,0.066,0.08123842286319131,0.098,0.173590897062715,0.03133333333333333,0.014024874305371792,0.03666666666666667,0.01296639322572109,0.18165863985181252,0.44104315672042127,0.8437719779378781,1,True,0.9466666666666667,0.9266666666666666,0.9133333333333333,0.92,6.6000000000000005,8.123842286319132,854.5,1045.0
+lora,N001_TOL,TOL,1500,5658,150,0.6326666666666667,0.51926475786497,0.078,0.03375751148815836,0.12066666666666667,0.21067515022976316,0.09866666666666667,0.2163308589607635,0.04,0.003711558854718982,0.03,0.016260162601626018,0.41534535171438675,0.1319697438356509,0.8371710607233346,19,False,0.9666666666666667,0.64,0.9533333333333334,0.88,12.066666666666666,21.067515022976316,732.0,787.5
+lora,N001_FU1,FU1,1500,4547,150,0.3506666666666667,0.29601935341983726,0.068,0.06575764240158347,0.3873333333333333,0.48823400043985044,0.11666666666666667,0.13591378931163403,0.034666666666666665,0.0010996261271167802,0.042666666666666665,0.012975588299978007,0.24029557950296898,0.5380476132456627,0.8799636267330817,3,False,0.9666666666666667,0.58,0.96,0.92,38.733333333333334,48.823400043985046,1104.0,1165.0
+lora,N002_TOL,TOL,1500,6318,150,0.48,0.41579613801836024,0.07133333333333333,0.05777144666033555,0.24133333333333334,0.3779677113010446,0.15066666666666667,0.1179170623615068,0.025333333333333333,0.020101297879075657,0.03133333333333333,0.010446343779677113,0.27326875593542255,0.3320124203615185,0.8613882592227811,13,False,0.9733333333333334,0.72,0.9333333333333333,0.92,24.133333333333333,37.79677113010446,800.0,933.5
+lora,N002_FU1,FU1,1500,4975,150,0.668,0.31618090452261305,0.066,0.07276381909547738,0.10866666666666666,0.45587939698492463,0.09333333333333334,0.12261306532663317,0.016,0.02271356783919598,0.048,0.00984924623115578,0.7799396984924624,0.5230450765198029,0.842568937297052,20,False,0.98,0.52,0.9533333333333334,0.74,10.866666666666665,45.58793969849246,711.0,979.0
+lora,N005_BC,BC,1500,6359,150,0.502,0.7200817738638151,0.05266666666666667,0.05016512030193427,0.254,0.11448340934109137,0.098,0.09891492373014625,0.025333333333333333,0.007705614090265765,0.068,0.008649158672747287,0.4379933951879227,0.4953276467168827,0.8709272586431598,4,False,0.9666666666666667,0.8933333333333333,0.9533333333333334,0.9,25.4,11.448340934109137,815.5,782.0
+lora,N005_AC,AC,1500,3433,150,0.7593333333333333,0.8100786484124672,0.048666666666666664,0.015147101660355374,0.05333333333333334,0.07952228371686572,0.096,0.08243518788231867,0.027333333333333334,0.010195164579085349,0.015333333333333332,0.0026216137489076608,0.1538685309253326,0.675321395814187,0.8414096711494841,6,False,0.9733333333333334,0.62,0.9466666666666667,0.88,5.333333333333334,7.952228371686572,666.0,1126.0
+lora,N022_TOL,TOL,1500,3651,150,0.29133333333333333,0.4864420706655711,0.064,0.03697617091207888,0.45066666666666666,0.045740892906053134,0.11066666666666666,0.4182415776499589,0.035333333333333335,0.0,0.048,0.01259928786633799,1.0053672966310598,0.5320299851087325,0.8408126437315369,24,False,0.9733333333333334,0.3,0.9933333333333333,0.94,45.06666666666666,4.574089290605313,1012.0,1410.0
+lora,N022_FU1,FU1,1500,2463,150,0.586,0.48477466504263095,0.06733333333333333,0.048721071863580996,0.14266666666666666,0.20259845716605765,0.13266666666666665,0.25334957369062117,0.020666666666666667,0.0,0.050666666666666665,0.010556232237109216,0.36122939504669094,0.20224597719005705,0.8511108432194423,14,False,0.98,0.4666666666666667,0.9533333333333334,0.9533333333333334,14.266666666666666,20.259845716605763,677.5,1459.0
+lora,N035_TOL,TOL,1500,1598,150,0.4766666666666667,0.2853566958698373,0.042,0.016896120150187734,0.24533333333333332,0.31101376720901125,0.176,0.3404255319148936,0.030666666666666665,0.01376720901126408,0.029333333333333333,0.03254067584480601,0.46662661660408844,0.5092117579012594,0.8628671939542232,15,False,0.98,0.28,0.9866666666666667,0.94,24.53333333333333,31.101376720901126,1020.5,1855.5
+lora,N043_TOL,TOL,1500,2074,150,0.726,0.3548698167791707,0.044,0.05737704918032787,0.098,0.04580520732883317,0.056,0.4811957569913211,0.02,0.0028929604628736743,0.056,0.05785920925747348,0.8808640308582449,0.728022429812273,0.8290971938219948,25,False,0.98,0.3333333333333333,0.9266666666666666,0.9266666666666666,9.8,4.580520732883317,621.5,1315.5
+lora,N043_FU1,FU1,1500,3437,150,0.48333333333333334,0.1638056444573756,0.056,0.06779167878964212,0.27666666666666667,0.5728833284841431,0.09733333333333333,0.14896712249054408,0.013333333333333334,0.0034914169333721268,0.07333333333333333,0.043060808844922895,0.7192842595286587,0.7356501997739635,0.8561188457120921,14,False,0.9466666666666667,0.4266666666666667,0.9733333333333334,0.9,27.666666666666668,57.28833284841431,735.0,1422.0

paper-releases/pbisc-diffusion/updates/20261015T072909Z-disease-width-readiness/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw0/score/summary.json

@@ -0,0 +1,539 @@
+{
+ "schema": "paired_ft_scores.v1",
+ "dataset": "ji2025_chili",
+ "written_utc": "2026-10-15T07:26:10.449486+00:00",
+ "command": [
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
+  "--dataset",
+  "ji2025_chili",
+  "--out",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw0/score",
+  "--arm",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/disease/draw0/lora.npz",
+  "--condition",
+  "lora=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw0/test_raw.npz",
+  "--donors",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/disease_width_comparison_20261015/ji2025_chili/draw0/test_samples.txt",
+  "--threads",
+  "2",
+  "--case-groups",
+  "TOL,FU1",
+  "--control-groups",
+  "BC,AC"
+ ],
+ "arms": [
+  "lora"
+ ],
+ "donors": [
+  "N064_TOL",
+  "N064_FU1",
+  "N038_BC",
+  "N038_AC",
+  "N055_AC",
+  "N136_TOL",
+  "N136_FU1",
+  "N128_BC",
+  "N128_AC",
+  "N129_BC",
+  "N129_AC",
+  "N147_TOL",
+  "N158_AC",
+  "N159_BC",
+  "N001_TOL",
+  "N001_FU1",
+  "N002_TOL",
+  "N002_FU1",
+  "N005_BC",
+  "N005_AC",
+  "N022_TOL",
+  "N022_FU1",
+  "N035_TOL",
+  "N043_TOL",
+  "N043_FU1"
+ ],
+ "n_donors": 25,
+ "reference": {
+  "cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili",
+  "reference_sha256": "19c30f56db699eb4f5a642927c1cd6e173212b877c29ff20d84e60a5ecccef6d",
+  "features_sha256": "049795e3a2470a223347015c0c965f56ca90c21143aad6f72d12e39f3e95e58b",
+  "n_r1_cells": 3750,
+  "pca": {
+   "n_components": 50,
+   "explained_variance_ratio_sum": 0.2900843918323517,
+   "n_fit_cells": 3750
+  },
+  "r2_control": {
+   "precision": 0.996,
+   "coverage": 1.0,
+   "density": 2.537386666666667,
+   "n_query": 3750,
+   "depth_matched": {
+    "precision": 0.9957333333333334,
+    "coverage": 1.0,
+    "density": 2.4922933333333335
+   }
+  },
+  "observed_l1_loo_null_mean": 0.4407987171459659
+ },
+ "contrast_definition": {
+  "enabled": true,
+  "rule": "explicit --case-groups / --control-groups",
+  "group_source": "features groups",
+  "case_groups": [
+   "TOL",
+   "FU1"
+  ],
+  "control_groups": [
+   "BC",
+   "AC"
+  ],
+  "n_case_donors": 14,
+  "n_control_donors": 11,
+  "n_donors_in_neither": 0,
+  "case": [
+   true,
+   true,
+   false,
+   false,
+   false,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   true,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   true
+  ],
+  "ctrl": [
+   false,
+   false,
+   true,
+   true,
+   true,
+   false,
+   false,
+   true,
+   true,
+   true,
+   true,
+   false,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   true,
+   true,
+   false,
+   false,
+   false,
+   false,
+   false
+  ],
+  "groups": [
+   "TOL",
+   "FU1",
+   "BC",
+   "AC",
+   "AC",
+   "TOL",
+   "FU1",
+   "BC",
+   "AC",
+   "BC",
+   "AC",
+   "TOL",
+   "AC",
+   "BC",
+   "TOL",
+   "FU1",
+   "TOL",
+   "FU1",
+   "BC",
+   "AC",
+   "TOL",
+   "FU1",
+   "TOL",
+   "TOL",
+   "FU1"
+  ]
+ },
+ "deg_definition": {
+  "enabled": true,
+  "score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
+  "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
+  "functions": [
+   "welch_bh_deg",
+   "top_deg_genes",
+   "jaccard"
+  ],
+  "reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
+  "top_n": 50,
+  "fdr": 0.05,
+  "n_genes": 5752,
+  "types": [
+   "T cell",
+   "B cell",
+   "Monocyte",
+   "NK cell",
+   "DC"
+  ],
+  "aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/ji2025_chili/deg_reference.npz",
+  "aggregates_sha256": "4f5eb8c8389ef1308ce3ec44be8be024cedb97de37351d109d9070c818df5a9e",
+  "aggregates_note": null,
+  "types_not_scored_observed": [],
+  "observed": {
+   "T cell": {
+    "n_significant": 1831,
+    "n_tested": 5660,
+    "n_case_donors": 14,
+    "n_control_donors": 11,
+    "n_cells": 44851,
+    "top_list_size": 50
+   },
+   "B cell": {
+    "n_significant": 9,
+    "n_tested": 5271,
+    "n_case_donors": 14,
+    "n_control_donors": 11,
+    "n_cells": 4424,
+    "top_list_size": 9
+   },
+   "Monocyte": {
+    "n_significant": 10,
+    "n_tested": 5668,
+    "n_case_donors": 14,
+    "n_control_donors": 11,
+    "n_cells": 22847,
+    "top_list_size": 10
+   },
+   "NK cell": {
+    "n_significant": 358,
+    "n_tested": 5459,
+    "n_case_donors": 14,
+    "n_control_donors": 11,
+    "n_cells": 14219,
+    "top_list_size": 50
+   },
+   "DC": {
+    "n_significant": 6,
+    "n_tested": 5020,
+    "n_case_donors": 12,
+    "n_control_donors": 11,
+    "n_cells": 1176,
+    "top_list_size": 6
+   }
+  },
+  "broadcast": "welch_bh_deg + top_deg_genes on the arm's condition bulk_counts (scoring genes, case|control donors), one list compared with every type's observed list (sle_broadcast.py broadcast_input_bulk); not part of the published benchmark"
+ },
+ "headline": {
+  "lora": {
+   "comp_l1": 0.4644622125914209,
+   "comp_l1_obs_loo_null": 0.4407987171459659,
+   "precision": 0.9717333333333333,
+   "coverage": 0.6928,
+   "precision_dm": 0.9552,
+   "coverage_dm": 0.9365333333333333,
+   "pb_r_median": 0.8628671939542232,
+   "pb_top1": 0.08,
+   "mono_pct_gen": 26.144000000000002,
+   "mono_pct_obs": 24.326385304685406,
+   "median_umi_gen": 840.0,
+   "median_umi_obs": 1066.0,
+   "contrast_mean_cp10k_r_gen": 0.35583190024841926,
+   "contrast_pseudobulk_log1p_cpm_r_gen": 0.13572174683683136,
+   "contrast_mean_cp10k_r_broadcast": 0.21311861411338662,
+   "contrast_pseudobulk_log1p_cpm_r_broadcast": 0.2060804786994818,
+   "deg_top50_T": 0,
+   "deg_top50_B": 0,
+   "deg_top50_Mono": 0,
+   "deg_top50_NK": 0,
+   "deg_top50_DC": 0,
+   "deg_top50_sum": 0,
+   "deg_top50_max": 125,
+   "deg_top50_sum_4type": 0,
+   "deg_top50_sum_broadcast": 0,
+   "seconds": 8.5
+  }
+ },
+ "per_arm": {
+  "lora": {
+   "arm": "lora",
+   "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/ji2025_chili/disease/draw0/lora.npz",
+   "npz_sha256": "fba94878b514efea1019e36ad51e83fb58a81305e8b692137775563d44548b09",
+   "receipt_verified": true,
+   "generation": {
+    "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/ji2025_chili/disease/draw0/lora/checkpoint_ft.pt",
+    "checkpoint_sha256": "53488bb1133c0b5969d6094112798d7666e055f1dea3f630c8db1064d892a08b",
+    "input_condition_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw0/test_raw.npz",
+    "input_condition_sha256": "ca5da7eba08208ca5e2ebf107830ad72db4a1e739698e0412fff48edf8d2b2b9",
+    "seed": 20260928,
+    "steps": 50,
+    "support_readout": "bernoulli",
+    "weights": "ema"
+   },
+   "condition_for_broadcast": {
+    "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/ji2025_chili/disease/draw0/test_raw.npz",
+    "sha256": "ca5da7eba08208ca5e2ebf107830ad72db4a1e739698e0412fff48edf8d2b2b9"
+   },
+   "poisson": {
+    "seed": 20260916,
+    "rule": "whole NPZ, rows in NPZ order",
+    "nnz_whole_npz": 7942182,
+    "median_library_whole_npz_panel": 841.0,
+    "n_rows_whole_npz": 37500
+   },
+   "annotation": {
+    "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
+    "zero_padded_model_genes": 1,
+    "label_counts": {
+     "T cell": 18080,
+     "Monocyte": 9804,
+     "NK cell": 4408,
+     "B cell": 2250,
+     "Other": 1872,
+     "DC": 1086
+    },
+    "mean_l2_max_prob": 0.8835420201611519,
+    "predict_seconds": 4.0
+   },
+   "n_donors": 25,
+   "n_generated_cells": 37500,
+   "composition": {
+    "l1_mean": 0.4644622125914209,
+    "l1_median": 0.38165679210034686,
+    "l1_obs_loo_null_mean": 0.4407987171459659,
+    "l1_generated_loo_mean_vs_observed_mean": 0.4340201577570284,
+    "composition_top1": 0.0,
+    "mean_fraction_generated": {
+     "T cell": 0.482133,
+     "B cell": 0.06,
+     "Monocyte": 0.26144,
+     "NK cell": 0.117547,
+     "DC": 0.02896,
+     "Other": 0.04992
+    },
+    "mean_fraction_observed": {
+     "T cell": 0.495831,
+     "B cell": 0.050844,
+     "Monocyte": 0.243264,
+     "NK cell": 0.166912,
+     "DC": 0.012828,
+     "Other": 0.030322
+    }
+   },
+   "pseudobulk": {
+    "n_genes": 5752,
+    "r_median": 0.8628671939542232,
+    "r_mean": 0.8602172280764876,
+    "top1": 0.08,
+    "n_top1": 2,
+    "own_rank_median": 9.0,
+    "chance_top1": 0.04
+   },
+   "precision_coverage": {
+    "precision": 0.9717333333333333,
+    "coverage": 0.6928,
+    "density": 1.09072,
+    "n_query": 3750,
+    "n_reference": 3750
+   },
+   "precision_coverage_depth_matched": {
+    "precision": 0.9552,
+    "coverage": 0.9365333333333333,
+    "density": 1.1414933333333335,
+    "detected_median_before": {
+     "R1": 363.0,
+     "Q": 203.0
+    },
+    "detected_median_after": {
+     "R1": 203.0,
+     "Q": 203.0
+    }
+   },
+   "monocyte_pct": {
+    "generated_mean_over_donors": 26.144000000000002,
+    "observed_mean_over_donors": 24.326385304685406,
+    "generated_pooled_cells": 26.144000000000002
+   },
+   "median_umi_per_cell_scoring_genes": {
+    "generated_pooled": 840.0,
+    "observed_pooled": 1066.0,
+    "generated_mean_of_donor_medians": 859.8200073242188,
+    "observed_mean_of_donor_medians": 1166.7
+   },
+   "contrast": {
+    "mean_cp10k": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.5318576611939548,
+       "r_broadcast": 0.21197028589936057,
+       "partial_r_generated_given_broadcast": 0.5153236409448303,
+       "r_generated_vs_broadcast": 0.1663490712781621,
+       "n_genes": 3038
+      },
+      "B cell": {
+       "r_generated": 0.1660831852373693,
+       "r_broadcast": 0.10073938447302222,
+       "partial_r_generated_given_broadcast": 0.1560653117640351,
+       "r_generated_vs_broadcast": 0.11811354873667035,
+       "n_genes": 3233
+      },
+      "Monocyte": {
+       "r_generated": 0.42074556421338766,
+       "r_broadcast": 0.3732268158395985,
+       "partial_r_generated_given_broadcast": 0.3707516482513127,
+       "r_generated_vs_broadcast": 0.23056059070075982,
+       "n_genes": 3193
+      },
+      "NK cell": {
+       "r_generated": 0.3046411903489653,
+       "r_broadcast": 0.1665379702415652,
+       "partial_r_generated_given_broadcast": 0.2854017514751144,
+       "r_generated_vs_broadcast": 0.1616943494618234,
+       "n_genes": 3059
+      }
+     },
+     "mean_r_generated": 0.35583190024841926,
+     "mean_r_broadcast": 0.21311861411338662,
+     "mean_partial_r": 0.3318855881088231
+    },
+    "pseudobulk_log1p_cpm": {
+     "per_type": {
+      "T cell": {
+       "r_generated": 0.158785526937719,
+       "r_broadcast": 0.3111080127833571,
+       "partial_r_generated_given_broadcast": 0.1393825832908705,
+       "r_generated_vs_broadcast": 0.0861846875303183,
+       "n_genes": 3038
+      },
+      "B cell": {
+       "r_generated": 0.008596932211882024,
+       "r_broadcast": 0.012072638770403557,
+       "partial_r_generated_given_broadcast": 0.007624332279454709,
+       "r_generated_vs_broadcast": 0.08277549879429334,
+       "n_genes": 3233
+      },
+      "Monocyte": {
+       "r_generated": 0.2726016662389149,
+       "r_broadcast": 0.3506580485024196,
+       "partial_r_generated_given_broadcast": 0.24008565625575978,
+       "r_generated_vs_broadcast": 0.14277137957470457,
+       "n_genes": 3193
+      },
+      "NK cell": {
+       "r_generated": 0.10290286195880947,
+       "r_broadcast": 0.15048321474174686,
+       "partial_r_generated_given_broadcast": 0.09220658154685848,
+       "r_generated_vs_broadcast": 0.07999852657848801,
+       "n_genes": 3059
+      }
+     },
+     "mean_r_generated": 0.13572174683683136,
+     "mean_r_broadcast": 0.2060804786994818,
+     "mean_partial_r": 0.11982478834323587
+    }
+   },
+   "deg_top50": {
+    "types_scored": [
+     "T cell",
+     "B cell",
+     "Monocyte",
+     "NK cell",
+     "DC"
+    ],
+    "types_not_scored": {},
+    "per_type": {
+     "T cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 1,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 44851,
+      "n_cells_gen": 18080
+     },
+     "B cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 9,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 4424,
+      "n_cells_gen": 2250
+     },
+     "Monocyte": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 10,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 22847,
+      "n_cells_gen": 9804
+     },
+     "NK cell": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 50,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 14219,
+      "n_cells_gen": 4408
+     },
+     "DC": {
+      "deg_scored": true,
+      "top50_overlap": 0,
+      "top50_jaccard": 0.0,
+      "obs_top_list_size": 6,
+      "gen_top_list_size": 0,
+      "top50_overlap_broadcast": 0,
+      "top50_jaccard_broadcast": 0.0,
+      "n_cells_obs": 1176,
+      "n_cells_gen": 1086
+     }
+    },
+    "sum": 0,
+    "sum_4type": 0,
+    "max": 125,
+    "mean": 0.0,
+    "sum_broadcast": 0,
+    "sum_broadcast_4type": 0,
+    "broadcast_n_significant": 4,
+    "seconds": 0.06
+   },
+   "seconds": 8.5
+  }
+ },
+ "code_sha256": {
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
+  "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
+ },
+ "seconds": 10.4
+}