Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T142225Z-rare-states-scratch-vs-pretrained/diffusion/dataset/server_1/model8/plans/rare_states_screen_20261004/out/scratch_vs_lora_20261005/confound_depth.csv

@@ -0,0 +1,111 @@
+setting,parent,n_ref_genes,arm,arm_class,n_cells,lib_q10,lib_q25,lib_median,lib_q75,lib_q90,marker_share_median,lib_ratio_vs_obs,marker_sum_ratio_vs_obs,marker_median_ratio_vs_obs,screen_thin,marker_depth_vs_screen_reference
+fold0,ALL,43,OBSERVED (native),observed,131629,724,1350,2022,3041,4517.2,0.0116129,1,1,1,null,null
+fold0,ALL,43,zs__raw,pretrained zero-shot,25500,339,536,1017,1690,2339,0.0237741,0.502967,0.778539,0.533556,0.503,1.54779
+fold0,ALL,43,lora_n5__raw,pretrained LoRA (5 pairs),25500,1019.9,1637,2526,3899,5636,0.00805097,1.24926,0.924132,0.764055,1,0.924132
+fold0,ALL,43,scratch_n5__raw,scratch (5 pairs),25500,807,1387.75,2050,2998,4074.1,0.0098471,1.01385,1.07654,0.839007,1,1.07654
+fold0,ALL,43,real_lora__raw,pretrained LoRA (58 pairs),25500,668,1187,1815,2652,3684,0.00837989,0.897626,0.744557,0.527869,0.898,0.829128
+fold0,ALL,43,real_full__raw,pretrained full FT (58 pairs),25500,546,1062,1736.5,2578,3563,0.00976682,0.858803,0.782964,0.562731,0.859,0.911483
+fold0,ALL,43,scratch_full__raw,"scratch (58 pairs, 100k cap)",25500,611,1203,1800,2569,3384,0.0102481,0.890208,0.836506,0.639088,0.89,0.939895
+fold0,ALL,43,lora_recipe__raw,pretrained LoRA + recipes (58 pairs),25500,599,1146,1805,2618,3578,0.00891233,0.892681,0.676367,0.500399,0.893,0.75741
+fold0,ALL,43,scratch_recipe__raw,scratch + recipes (58 pairs),25500,640.9,1182,1743,2481,3257,0.0100069,0.862018,0.796281,0.614512,0.862,0.92376
+fold0,Monocyte,39,OBSERVED (native),observed,31471,594,1496,2832,4199,5623,0.012835,1,1,1,null,null
+fold0,Monocyte,39,zs__raw,pretrained zero-shot,9506,422,688.25,1179,1829,2497.5,0.0202869,0.416314,0.604946,0.370154,0.416,1.4542
+fold0,Monocyte,39,lora_n5__raw,pretrained LoRA (5 pairs),7183,1154,1984,3254,5018.5,7121.4,0.0072314,1.14901,0.598165,0.563794,1,0.598165
+fold0,Monocyte,39,scratch_n5__raw,scratch (5 pairs),6241,770,1450,2529,3885,5322,0.00913242,0.893008,0.579954,0.562962,0.893,0.649444
+fold0,Monocyte,39,real_lora__raw,pretrained LoRA (58 pairs),3891,708,1218,2171,3490,4915,0.00820934,0.766596,0.470909,0.310993,0.767,0.613962
+fold0,Monocyte,39,real_full__raw,pretrained full FT (58 pairs),4120,607,1080.5,2067,3376.75,4789.2,0.00898876,0.729873,0.492398,0.377758,0.73,0.674518
+fold0,Monocyte,39,scratch_full__raw,"scratch (58 pairs, 100k cap)",4036,561,1305.5,2378,3503,4639.5,0.00917763,0.839689,0.546604,0.453449,0.84,0.650719
+fold0,Monocyte,39,lora_recipe__raw,pretrained LoRA + recipes (58 pairs),3965,662,1134,2064,3296,4610.2,0.00838123,0.728814,0.463118,0.344503,0.729,0.635278
+fold0,Monocyte,39,scratch_recipe__raw,scratch + recipes (58 pairs),3598,582,1286.75,2338.5,3442.75,4688.3,0.0087538,0.825742,0.518384,0.442133,0.826,0.627583
+fold0,T cell,23,OBSERVED (native),observed,61162,999,1479,2060,2771,3761.9,0.00310238,1,1,1,null,null
+fold0,T cell,23,zs__raw,pretrained zero-shot,8631,321,478,949,1668,2314,0.00808081,0.46068,1.07714,0.817815,0.461,2.33652
+fold0,T cell,23,lora_n5__raw,pretrained LoRA (5 pairs),12396,1120.5,1696.75,2503,3657,5068,0.00296648,1.21505,1.41002,1.11002,1,1.41002
+fold0,T cell,23,scratch_n5__raw,scratch (5 pairs),13611,982,1534,2144,2922,3705,0.00363636,1.04078,1.56339,1.29762,1,1.56339
+fold0,T cell,23,real_lora__raw,pretrained LoRA (58 pairs),14147,723,1285.5,1924,2686,3504.4,0.00296384,0.933981,0.822737,0.757304,0.934,0.880875
+fold0,T cell,23,real_full__raw,pretrained full FT (58 pairs),13435,583,1144,1817,2603.5,3367,0.00351975,0.882039,0.86814,0.752517,0.882,0.984286
+fold0,T cell,23,scratch_full__raw,"scratch (58 pairs, 100k cap)",13443,718.2,1358.5,1963,2613,3204,0.00305064,0.952913,1.02384,0.915782,0.953,1.07433
+fold0,T cell,23,lora_recipe__raw,pretrained LoRA + recipes (58 pairs),13851,633,1219.5,1901,2661,3465,0.00298686,0.922816,0.819597,0.729624,0.923,0.887971
+fold0,T cell,23,scratch_recipe__raw,scratch + recipes (58 pairs),13815,731,1336.5,1910,2524.5,3096,0.00317259,0.927184,0.961037,0.864292,0.927,1.03672
+fold0,B cell,25,OBSERVED (native),observed,21022,1045,1359,1800,2621,3956,0.0165151,1,1,1,null,null
+fold0,B cell,25,zs__raw,pretrained zero-shot,4425,403,679,1226,1787,2298.8,0.0356768,0.681111,0.966645,0.37486,0.681,1.41945
+fold0,B cell,25,lora_n5__raw,pretrained LoRA (5 pairs),3997,1294,1709,2330,3283,4748.6,0.0166254,1.29444,1.18405,0.883706,1,1.18405
+fold0,B cell,25,scratch_n5__raw,scratch (5 pairs),2910,995,1394.25,1934,2735.5,3772.2,0.0199557,1.07444,1.20573,1.00214,1,1.20573
+fold0,B cell,25,real_lora__raw,pretrained LoRA (58 pairs),4903,959.2,1315.5,1779,2410.5,3495.6,0.0164997,0.988333,1.16816,0.74537,0.988,1.18234
+fold0,B cell,25,real_full__raw,pretrained full FT (58 pairs),5233,908.2,1308,1788,2435,3376,0.0168507,0.993333,1.23461,0.776494,0.993,1.24331
+fold0,B cell,25,scratch_full__raw,"scratch (58 pairs, 100k cap)",5053,795.2,1207,1624,2119,2865,0.0194291,0.902222,0.883286,0.66425,0.902,0.979253
+fold0,B cell,25,lora_recipe__raw,pretrained LoRA + recipes (58 pairs),5157,988,1367,1840,2463,3373.4,0.0160895,1.02222,0.919897,0.687327,1,0.919897
+fold0,B cell,25,scratch_recipe__raw,scratch + recipes (58 pairs),5051,865,1207.5,1584,2065.5,2731,0.0192901,0.88,0.791429,0.602222,0.88,0.899352
+fold0,NK cell,27,OBSERVED (native),observed,10457,776.2,1153,1510,1938,2823.4,0.0683453,1,1,1,null,null
+fold0,NK cell,27,zs__raw,pretrained zero-shot,1983,296,405,595,914,1259.6,0.0800821,0.39404,0.567986,0.519616,null,null
+fold0,NK cell,27,lora_n5__raw,pretrained LoRA (5 pairs),964,764.6,1069,1418.5,1871,2502.4,0.071202,0.939404,0.97626,0.642287,null,null
+fold0,NK cell,27,scratch_n5__raw,scratch (5 pairs),2046,795,1116,1383.5,1693.75,2057.5,0.0969704,0.916225,1.19995,0.904929,null,null
+fold0,NK cell,27,real_lora__raw,pretrained LoRA (58 pairs),1504,661.9,943.5,1248,1609.75,2020.6,0.0624571,0.82649,0.743317,0.520292,null,null
+fold0,NK cell,27,real_full__raw,pretrained full FT (58 pairs),1380,545.7,856.75,1172,1534.25,1944,0.0635716,0.776159,0.719253,0.581221,null,null
+fold0,NK cell,27,scratch_full__raw,"scratch (58 pairs, 100k cap)",2155,510.4,914.5,1211,1498.5,1831,0.0833333,0.801987,0.915429,0.603253,null,null
+fold0,NK cell,27,lora_recipe__raw,pretrained LoRA + recipes (58 pairs),1350,644.9,923,1225.5,1550,1957.1,0.0617255,0.811589,0.711115,0.512398,null,null
+fold0,NK cell,27,scratch_recipe__raw,scratch + recipes (58 pairs),2184,630.3,934,1178,1430,1761.8,0.0801054,0.780132,0.893951,0.700505,null,null
+loco,ALL,46,OBSERVED (native),observed,589478,597,1271,1967,2945,4340,0.0119956,1,1,1,null,null
+loco,ALL,46,zs__raw,pretrained zero-shot,123000,339,525,973,1623,2300,0.0247934,0.494662,0.772794,0.473764,0.495,1.5612
+loco,ALL,46,xcalL_K1000,pretrained zero-shot + cross-cohort calibration,123000,676,1073,1628,2432,3541,0.0175987,0.827656,0.964497,0.438425,0.828,1.16485
+loco,ALL,46,locoL_lora16sat_s26750_K1000,pretrained LoRA r16 (cross-cohort),123000,612,813.75,1135,1605,2213,0.014993,0.577021,0.603201,0.286871,0.577,1.04541
+loco,ALL,46,locoL_lora64sat_s59000_K1000,pretrained LoRA r64 (cross-cohort),123000,555,733,1013,1415,1952,0.0163399,0.514997,0.600577,0.290433,0.515,1.16617
+loco,ALL,46,locoL_fullsat_s20000_K1000,pretrained full FT 20k (cross-cohort),123000,535,731,1070,1593,2259.1,0.0175439,0.543976,0.704334,0.414666,0.544,1.29473
+loco,ALL,46,locoL_fullsat_s108500_K1000,pretrained full FT 108.5k saturated (cross-cohort),123000,549,740,1055,1518,2106,0.0201641,0.53635,0.795484,0.520015,0.536,1.48411
+loco,ALL,46,locoL_scratchsat_s50000_K1000,scratch 50k (cross-cohort),123000,8355,10888,13891,17070,20099.1,0.00161569,7.06202,0.873332,0.430889,1,0.873332
+loco,ALL,46,locoL_scratchsat_s100000_K1000,scratch 100k (cross-cohort),123000,12481,15574,19138,22793,26169,0.00103672,9.72954,0.825002,0.433788,1,0.825002
+loco,ALL,46,locoL_scratchsat_s150000_K1000,scratch 150k (cross-cohort),123000,13751,16901,20524,24263.2,27706.1,0.000940206,10.4342,0.79003,0.445726,1,0.79003
+loco,ALL,46,locoL_scratchsat_s162000_K1000,scratch 162k final (cross-cohort),123000,13834,16956,20606,24319,27742,0.000943502,10.4759,0.817913,0.444744,1,0.817913
+loco,ALL,46,lora_n5__raw,"own-cohort pretrained LoRA (5 pairs, cross-fitted)",123000,616,1113,1786,2672,3818,0.00820245,0.907982,0.585326,0.464476,0.908,0.644632
+loco,ALL,46,real_lora__raw,"own-cohort pretrained LoRA (~58 pairs, cross-fitted)",123000,716,1248,1882,2739,3822,0.00894296,0.956787,0.713827,0.53749,0.957,0.7459
+loco,Monocyte,43,OBSERVED (native),observed,111269,731,1610,2821,4236,5802,0.0124138,1,1,1,null,null
+loco,Monocyte,43,zs__raw,pretrained zero-shot,45474,438,709,1187,1859,2549,0.0204861,0.420773,0.608207,0.298182,0.421,1.44467
+loco,Monocyte,43,xcalL_K1000,pretrained zero-shot + cross-cohort calibration,32496,762,1271,2255,3592,4980.5,0.0108932,0.799362,0.601779,0.489772,0.799,0.753165
+loco,Monocyte,43,locoL_lora16sat_s26750_K1000,pretrained LoRA r16 (cross-cohort),22524,619,804,1123,1640,2281,0.00976137,0.398086,0.293533,0.145559,0.398,0.737519
+loco,Monocyte,43,locoL_lora64sat_s59000_K1000,pretrained LoRA r64 (cross-cohort),20054,580,756,1061,1549,2154.7,0.00950119,0.376108,0.268678,0.106637,0.376,0.71457
+loco,Monocyte,43,locoL_fullsat_s20000_K1000,pretrained full FT 20k (cross-cohort),24002,519.1,677,954,1437,2087,0.0117647,0.338178,0.299846,0.215933,0.338,0.887118
+loco,Monocyte,43,locoL_fullsat_s108500_K1000,pretrained full FT 108.5k saturated (cross-cohort),19494,570,740,1043,1561,2233,0.0130375,0.369727,0.352598,0.221038,0.37,0.952969
+loco,Monocyte,43,locoL_scratchsat_s50000_K1000,scratch 50k (cross-cohort),22424,7990,10431,13373,16482,19531,0.00108982,4.74052,0.392276,0.203049,1,0.392276
+loco,Monocyte,43,locoL_scratchsat_s100000_K1000,scratch 100k (cross-cohort),22868,12092,15072,18579,22136,25578.3,0.0007204,6.58596,0.344442,0.162495,1,0.344442
+loco,Monocyte,43,locoL_scratchsat_s150000_K1000,scratch 150k (cross-cohort),24718,13380,16476.2,20053.5,23750,27251.6,0.000686646,7.10865,0.349011,0.170025,1,0.349011
+loco,Monocyte,43,locoL_scratchsat_s162000_K1000,scratch 162k final (cross-cohort),20808,13593.7,16711,20300.5,23943,27419.3,0.000658057,7.19621,0.332371,0.158843,1,0.332371
+loco,Monocyte,43,lora_n5__raw,"own-cohort pretrained LoRA (5 pairs, cross-fitted)",21211,736,1300.5,2317,3715,5407,0.00885559,0.82134,0.525583,0.419889,0.821,0.640174
+loco,Monocyte,43,real_lora__raw,"own-cohort pretrained LoRA (~58 pairs, cross-fitted)",22723,740.2,1320,2321,3632,5015.8,0.00843373,0.822758,0.503876,0.388733,0.823,0.612243
+loco,T cell,25,OBSERVED (native),observed,298117,706,1340,1981,2754,3686,0.00356824,1,1,1,null,null
+loco,T cell,25,zs__raw,pretrained zero-shot,43347,316,461,874,1532,2181,0.0125786,0.441191,1.10963,0.872497,0.441,2.51617
+loco,T cell,25,xcalL_K1000,pretrained zero-shot + cross-cohort calibration,57613,699,1073,1543,2142,2915,0.0188034,0.7789,1.72343,0.98696,0.779,2.21237
+loco,T cell,25,locoL_lora16sat_s26750_K1000,pretrained LoRA r16 (cross-cohort),51586,633,843,1190,1716,2341,0.0075,0.600707,0.832779,0.553696,0.601,1.38566
+loco,T cell,25,locoL_lora64sat_s59000_K1000,pretrained LoRA r64 (cross-cohort),47130,565,757,1067,1507,2011.1,0.00889923,0.538617,0.851023,0.561229,0.539,1.57889
+loco,T cell,25,locoL_fullsat_s20000_K1000,pretrained full FT 20k (cross-cohort),49480,561,791,1226,1880,2518,0.00860318,0.618879,0.962913,0.608385,0.619,1.55559
+loco,T cell,25,locoL_fullsat_s108500_K1000,pretrained full FT 108.5k saturated (cross-cohort),47593,559,778,1146,1641,2172,0.0124902,0.578496,1.0727,0.83544,0.578,1.85588
+loco,T cell,25,locoL_scratchsat_s50000_K1000,scratch 50k (cross-cohort),55016,8613.5,11128,14115,17288.2,20300,0.000586811,7.12519,1.10557,0.789079,1,1.10557
+loco,T cell,25,locoL_scratchsat_s100000_K1000,scratch 100k (cross-cohort),53046,12660,15682,19185,22780.5,26124.5,0.000421972,9.6845,1.01714,0.783476,1,1.01714
+loco,T cell,25,locoL_scratchsat_s150000_K1000,scratch 150k (cross-cohort),51762,13939,16992.2,20614,24297.8,27709.9,0.000433029,10.4059,1.04359,0.781836,1,1.04359
+loco,T cell,25,locoL_scratchsat_s162000_K1000,scratch 162k final (cross-cohort),55309,13936.6,16982,20605,24283,27657,0.000437522,10.4013,1.05448,0.777712,1,1.05448
+loco,T cell,25,lora_n5__raw,"own-cohort pretrained LoRA (5 pairs, cross-fitted)",71032,634,1145,1811,2621,3562,0.00277778,0.914185,0.731194,0.64031,0.914,0.799993
+loco,T cell,25,real_lora__raw,"own-cohort pretrained LoRA (~58 pairs, cross-fitted)",67850,818,1349,1973,2732.75,3606,0.0033845,0.995962,0.863298,0.741341,0.996,0.866765
+loco,B cell,29,OBSERVED (native),observed,99729,929,1397,1933,2754,4202,0.0172224,1,1,1,null,null
+loco,B cell,29,zs__raw,pretrained zero-shot,18316,374,596.75,1111,1703.25,2250,0.0366321,0.574754,0.660508,0.245022,0.575,1.14871
+loco,B cell,29,xcalL_K1000,pretrained zero-shot + cross-cohort calibration,17472,967,1385,1907,2495,3130,0.0205672,0.986549,0.686333,0.343946,0.987,0.695372
+loco,B cell,29,locoL_lora16sat_s26750_K1000,pretrained LoRA r16 (cross-cohort),28860,724,949,1248,1622,2078.1,0.016678,0.645629,0.418542,0.351041,0.646,0.647898
+loco,B cell,29,locoL_lora64sat_s59000_K1000,pretrained LoRA r64 (cross-cohort),33758,619,794,1046,1357,1736,0.0172911,0.541128,0.383085,0.283724,0.541,0.708106
+loco,B cell,29,locoL_fullsat_s20000_K1000,pretrained full FT 20k (cross-cohort),30208,635.7,851,1153,1545,2045,0.0193187,0.596482,0.60107,0.525602,0.596,1.00851
+loco,B cell,29,locoL_fullsat_s108500_K1000,pretrained full FT 108.5k saturated (cross-cohort),33880,587,784,1096,1494,1999.1,0.0203046,0.566994,0.610552,0.545571,0.567,1.07681
+loco,B cell,29,locoL_scratchsat_s50000_K1000,scratch 50k (cross-cohort),22935,8781,11331.5,14355,17557,20620.2,0.00187959,7.42628,0.605408,0.340374,1,0.605408
+loco,B cell,29,locoL_scratchsat_s100000_K1000,scratch 100k (cross-cohort),24584,13427.6,16552.2,20102,23843,27263.1,0.00115774,10.3994,0.621966,0.39888,1,0.621966
+loco,B cell,29,locoL_scratchsat_s150000_K1000,scratch 150k (cross-cohort),26415,14532,17723.5,21365,25267,28777,0.00100754,11.0528,0.54707,0.427726,1,0.54707
+loco,B cell,29,locoL_scratchsat_s162000_K1000,scratch 162k final (cross-cohort),26655,14605.4,17789,21460,25286,28734,0.00101858,11.1019,0.612743,0.446074,1,0.612743
+loco,B cell,29,lora_n5__raw,"own-cohort pretrained LoRA (5 pairs, cross-fitted)",21371,872,1255,1769,2429.5,3313,0.0172117,0.915158,0.567906,0.268764,0.915,0.620663
+loco,B cell,29,real_lora__raw,"own-cohort pretrained LoRA (~58 pairs, cross-fitted)",19896,996,1352,1805,2436,3404,0.0164878,0.933782,0.71392,0.466964,0.934,0.764369
+loco,NK cell,29,OBSERVED (native),observed,47832,588,1069,1445,1862,2653,0.0656046,1,1,1,null,null
+loco,NK cell,29,zs__raw,pretrained zero-shot,11566,313,421,622,955.75,1332,0.0823071,0.43045,0.667443,0.608777,null,null
+loco,NK cell,29,xcalL_K1000,pretrained zero-shot + cross-cohort calibration,11794,571,825,1113,1444,1789,0.0849915,0.770242,1.01657,0.456863,null,null
+loco,NK cell,29,locoL_lora16sat_s26750_K1000,pretrained LoRA r16 (cross-cohort),14781,542,670,851,1076,1329,0.0704225,0.588927,0.646272,0.35547,null,null
+loco,NK cell,29,locoL_lora64sat_s59000_K1000,pretrained LoRA r64 (cross-cohort),15756,489,611,785,995,1229,0.070576,0.543253,0.591719,0.294146,null,null
+loco,NK cell,29,locoL_fullsat_s20000_K1000,pretrained full FT 20k (cross-cohort),14602,459,589,784,1041,1324.9,0.0825335,0.542561,0.703005,0.371292,null,null
+loco,NK cell,29,locoL_fullsat_s108500_K1000,pretrained full FT 108.5k saturated (cross-cohort),16738,485,619,816,1058,1311,0.0850978,0.564706,0.729293,0.458783,null,null
+loco,NK cell,29,locoL_scratchsat_s50000_K1000,scratch 50k (cross-cohort),19232,8088.1,10532.8,13438,16530.8,19402.9,0.00658704,9.29965,0.930316,0.548625,null,null
+loco,NK cell,29,locoL_scratchsat_s100000_K1000,scratch 100k (cross-cohort),17631,12232,15248.5,18713,22248.5,25462,0.00446964,12.9502,0.883314,0.528711,null,null
+loco,NK cell,29,locoL_scratchsat_s150000_K1000,scratch 150k (cross-cohort),16217,13428,16472,19902,23484,26720.4,0.00441413,13.773,0.910918,0.532516,null,null
+loco,NK cell,29,locoL_scratchsat_s162000_K1000,scratch 162k final (cross-cohort),16709,13552,16543,20029,23564,26842,0.00440234,13.8609,0.909429,0.569005,null,null
+loco,NK cell,29,lora_n5__raw,"own-cohort pretrained LoRA (5 pairs, cross-fitted)",5168,504.7,792,1139.5,1536.25,1980.3,0.0581402,0.788581,0.735364,0.542924,null,null
+loco,NK cell,29,real_lora__raw,"own-cohort pretrained LoRA (~58 pairs, cross-fitted)",7728,700,994,1293,1657,2097,0.0658013,0.89481,0.895564,0.620919,null,null