{'source': 'de', 'eff_file': None, 'n_genes': 2000, 'min_cells': 50, 'q_eff': 2.0, 'nboot': 2000, 'lambdas': [0.01, 0.1, 1, 10, 100, 1000, 10000.0], 'n_conditions': 1135, 'n_lines': 50, 'replicate_pairs': 6939} == LOGO (train on 47 non-glioma lines), pooled 3 glioma lines, all train_mean n= 3149 MSE 0.3748 [0.3623, 0.3881] | dMSE 0.0000 [0.0000, 0.0000] win 0.00 | r 0.574 [0.567, 0.580] | dr 0.000 [0.000, 0.000] nn1_baseline n= 3149 MSE 0.4277 [0.4141, 0.4423] | dMSE 0.0529 [0.0502, 0.0560] win 0.01 | r 0.469 [0.461, 0.476] | dr -0.105 [-0.108, -0.103] nn5_baseline n= 3149 MSE 0.3819 [0.3697, 0.3949] | dMSE 0.0071 [0.0062, 0.0080] win 0.15 | r 0.555 [0.548, 0.562] | dr -0.019 [-0.020, -0.018] ridge_baseline_pca10 n= 3149 MSE 0.3719 [0.3597, 0.3849] | dMSE -0.0029 [-0.0034, -0.0024] win 0.87 | r 0.581 [0.575, 0.587] | dr 0.007 [0.007, 0.008] null_random_line n= 3149 MSE 0.4959 [0.4801, 0.5132] | dMSE 0.1211 [0.1153, 0.1280] win 0.00 | r 0.409 [0.402, 0.416] | dr -0.165 [-0.167, -0.163] null_ridge_shuffled n= 3149 MSE 0.3748 [0.3623, 0.3881] | dMSE 0.0000 [0.0000, 0.0000] win 0.39 | r 0.574 [0.567, 0.580] | dr -0.000 [-0.000, -0.000] duplicate n= 406 MSE 0.6394 [0.5937, 0.6866] | dMSE 0.3422 [0.3073, 0.3779] win 0.01 | r 0.252 [0.214, 0.288] | dr -0.352 [-0.389, -0.313] IC:train_mean n= 1572 MSE 0.3733 [0.3453, 0.4026] | dMSE 0.0000 [0.0000, 0.0000] win 0.00 | r 0.573 [0.561, 0.585] | dr 0.000 [0.000, 0.000] IC:incontext_nn5_response n= 1572 MSE 0.3760 [0.3477, 0.4053] | dMSE 0.0027 [0.0013, 0.0038] win 0.30 | r 0.568 [0.556, 0.581] | dr -0.005 [-0.006, -0.004] IC:incontext_scaled_mean n= 1572 MSE 0.3731 [0.3450, 0.4024] | dMSE -0.0002 [-0.0004, -0.0001] win 0.58 | r 0.573 [0.561, 0.585] | dr 0.000 [-0.000, 0.000] _noise_floor_mse 0.3231 [0.3087, 0.3374] _oracle_pearson_ceiling 0.6799 [0.6712, 0.6894] A-172 n 1132 mean r 0.730 [0.723, 0.737] ridge dMSE -0.0028 [-0.0034, -0.0023] nn5 dMSE 0.0064 [0.0052, 0.0074] dup r 0.400 [0.334, 0.465] IC scaled dMSE -0.0000 [-0.0003, 0.0003] H4 n 1130 mean r 0.622 [0.614, 0.630] ridge dMSE -0.0031 [-0.0036, -0.0027] nn5 dMSE 0.0081 [0.0064, 0.0099] dup r 0.226 [0.189, 0.262] IC scaled dMSE -0.0004 [-0.0008, -0.0002] SW 1088 n 887 mean r 0.313 [0.302, 0.323] ridge dMSE -0.0026 [-0.0033, -0.0020] nn5 dMSE 0.0069 [0.0054, 0.0084] dup r 0.095 [0.078, 0.114] IC scaled dMSE -0.0002 [-0.0004, -0.0001] glioma sibling mean - 47-line mean: {'m': '0.5563 [0.5380, 0.5755]', 'p': '0.3653 [0.3560, 0.3755]', 'dm': '0.1815 [0.1751, 0.1882]', 'dp': '-0.2083 [-0.2132, -0.2033]'} == LOGO (train on 47 non-glioma lines), pooled 3 glioma lines, effective train_mean n= 2474 MSE 0.1917 [0.1763, 0.2085] | dMSE 0.0000 [0.0000, 0.0000] win 0.00 | r 0.654 [0.647, 0.661] | dr 0.000 [0.000, 0.000] nn1_baseline n= 2474 MSE 0.2464 [0.2288, 0.2661] | dMSE 0.0547 [0.0516, 0.0582] win 0.00 | r 0.536 [0.527, 0.544] | dr -0.119 [-0.121, -0.116] nn5_baseline n= 2474 MSE 0.1985 [0.1834, 0.2152] | dMSE 0.0068 [0.0057, 0.0078] win 0.14 | r 0.633 [0.626, 0.641] | dr -0.021 [-0.023, -0.019] ridge_baseline_pca10 n= 2474 MSE 0.1884 [0.1735, 0.2048] | dMSE -0.0033 [-0.0039, -0.0027] win 0.92 | r 0.662 [0.656, 0.669] | dr 0.008 [0.008, 0.009] null_random_line n= 2474 MSE 0.3170 [0.2962, 0.3418] | dMSE 0.1253 [0.1184, 0.1333] win 0.00 | r 0.467 [0.460, 0.475] | dr -0.187 [-0.189, -0.185] null_ridge_shuffled n= 2474 MSE 0.1917 [0.1764, 0.2085] | dMSE 0.0000 [0.0000, 0.0000] win 0.36 | r 0.654 [0.647, 0.661] | dr -0.000 [-0.000, -0.000] duplicate n= 346 MSE 0.4684 [0.4162, 0.5191] | dMSE 0.2368 [0.2090, 0.2650] win 0.01 | r 0.283 [0.242, 0.323] | dr -0.367 [-0.412, -0.322] IC:train_mean n= 1235 MSE 0.1896 [0.1674, 0.2131] | dMSE 0.0000 [0.0000, 0.0000] win 0.00 | r 0.653 [0.643, 0.663] | dr 0.000 [0.000, 0.000] IC:incontext_nn5_response n= 1235 MSE 0.1920 [0.1692, 0.2159] | dMSE 0.0023 [0.0007, 0.0037] win 0.30 | r 0.648 [0.638, 0.658] | dr -0.005 [-0.007, -0.004] IC:incontext_scaled_mean n= 1235 MSE 0.1893 [0.1671, 0.2127] | dMSE -0.0003 [-0.0005, -0.0001] win 0.57 | r 0.653 [0.643, 0.663] | dr 0.000 [-0.000, 0.000] _noise_floor_mse 0.1236 [0.1149, 0.1329] _oracle_pearson_ceiling 0.7828 [0.7776, 0.7880] A-172 n 1126 mean r 0.732 [0.725, 0.738] ridge dMSE -0.0028 [-0.0034, -0.0023] nn5 dMSE 0.0063 [0.0052, 0.0073] dup r 0.400 [0.334, 0.465] IC scaled dMSE -0.0000 [-0.0003, 0.0003] H4 n 1090 mean r 0.629 [0.621, 0.637] ridge dMSE -0.0032 [-0.0038, -0.0028] nn5 dMSE 0.0077 [0.0059, 0.0094] dup r 0.227 [0.191, 0.262] IC scaled dMSE -0.0005 [-0.0008, -0.0002] SW 1088 n 258 mean r 0.422 [0.404, 0.438] ridge dMSE -0.0053 [-0.0075, -0.0035] nn5 dMSE 0.0050 [0.0009, 0.0088] dup r 0.121 [0.095, 0.155] IC scaled dMSE -0.0005 [-0.0011, -0.0000] glioma sibling mean - 47-line mean: {'m': '0.4094 [0.3921, 0.4298]', 'p': '0.4019 [0.3925, 0.4122]', 'dm': '0.2178 [0.2092, 0.2270]', 'dp': '-0.2522 [-0.2608, -0.2435]'} == LOO all 50 lines skipped NCI-H2122 skipped NCI-H596 line n n_eff r_mean_all r_mean_eff R2_mean_all R2_mean_eff ridge_rel_dMSE nn5_rel_dMSE IC_scaled_rel_dMSE effnorm2 dup_r rank_r_mean_all rank_r_mean_eff rank_R2_mean_all rank_R2_mean_eff rank_ridge_gain SW 1088 887 258 0.314 0.424 0.099 0.195 -0.003 0.006 -0.000 1.123 0.095 1 2 1 2 40 NCI-H661 1011 518 0.349 0.387 0.133 0.163 -0.003 0.039 -0.001 0.622 0.049 2 1 2 1 38 SW 1271 1080 333 0.362 0.436 0.140 0.206 -0.001 0.012 -0.000 0.771 0.093 3 3 3 3 44 CHP-212 1116 651 0.432 0.477 0.187 0.238 -0.001 0.051 -0.000 0.540 0.098 4 4 4 4 43 AN3 CA 1126 674 0.440 0.485 0.208 0.255 -0.007 0.067 -0.001 0.433 0.150 5 5 5 5 37 SNU-1 1130 1098 0.558 0.563 0.324 0.333 -0.015 0.145 0.000 0.309 0.199 6 6 6 6 23 HepG2/C3A 1132 1093 0.577 0.583 0.345 0.351 -0.003 0.097 -0.002 0.259 0.293 7 7 8 7 39 C-33 A 1131 1076 0.590 0.597 0.368 0.375 -0.018 0.210 -0.005 0.233 0.269 8 9 9 9 21 COLO 205 1130 1090 0.591 0.596 0.375 0.381 -0.022 0.001 -0.000 0.269 0.264 9 8 10 10 17 SW48 1131 1043 0.594 0.609 0.378 0.396 -0.020 0.021 0.000 0.281 0.279 10 10 11 11 20 SHP-77 1132 1084 0.612 0.622 0.344 0.365 0.017 0.391 -0.021 0.209 0.214 11 11 7 8 48 BT-474 1131 1121 0.622 0.624 0.406 0.407 0.000 0.126 -0.006 0.214 0.322 12 12 13 12 45 H4 1130 1090 0.623 0.630 0.402 0.414 -0.014 0.198 -0.003 0.289 0.226 13 13 12 13 25 HCT15 1133 1088 0.636 0.642 0.412 0.421 -0.020 0.035 -0.000 0.240 0.273 14 15 14 14 19 hTERT-HPNE 1133 1103 0.637 0.642 0.434 0.440 -0.025 0.233 -0.000 0.249 0.268 15 14 15 15 16 C32 1132 1129 0.665 0.666 0.462 0.463 0.010 0.340 0.000 0.222 0.332 16 17 16 17 47 AsPC-1 1133 1133 0.665 0.665 0.463 0.463 -0.033 0.022 -0.005 0.194 0.336 17 16 17 16 12 RKO 1130 1129 0.677 0.677 0.481 0.481 -0.009 0.110 -0.002 0.194 0.330 18 18 19 18 33 SK-MEL-2 1130 1124 0.679 0.680 0.481 0.482 0.008 0.288 -0.003 0.190 0.309 19 19 18 19 46 KATO III 1132 1132 0.681 0.681 0.493 0.493 -0.052 0.009 -0.006 0.184 0.366 20 20 21 20 5 RPMI-7951 1131 1119 0.685 0.687 0.492 0.495 -0.013 0.371 0.000 0.213 0.264 21 21 20 21 28 SW 900 1132 1130 0.709 0.710 0.540 0.541 -0.008 0.429 -0.000 0.193 0.301 22 22 26 26 34 Hs 766T 1131 1124 0.713 0.714 0.506 0.508 -0.007 0.366 0.000 0.207 0.254 23 24 23 23 36 A-427 1131 1131 0.714 0.714 0.506 0.506 -0.013 0.434 -0.020 0.158 0.294 24 23 22 22 29 HT-29 1132 1132 0.715 0.715 0.548 0.548 -0.054 0.036 -0.001 0.177 0.342 25 25 29 29 4 NCI-H1573 1132 1132 0.718 0.718 0.544 0.544 -0.022 0.125 0.000 0.192 0.347 26 26 27 27 18 NCI-H23 1130 1127 0.718 0.719 0.546 0.547 -0.017 0.063 -0.000 0.172 0.355 27 27 28 28 22 NCI-H1792 1132 1132 0.720 0.720 0.539 0.539 -0.029 0.093 -0.001 0.205 0.299 28 28 25 25 14 MIA PaCa-2 1132 1132 0.725 0.725 0.539 0.539 -0.007 0.111 -0.001 0.203 0.289 29 29 24 24 35 HS-578T 1132 1132 0.728 0.728 0.569 0.569 -0.032 0.509 -0.000 0.178 0.303 30 30 32 32 13 LS 180 1132 1132 0.729 0.729 0.560 0.560 -0.068 0.008 -0.001 0.178 0.339 31 31 30 30 2 SNU-423 1132 1131 0.730 0.730 0.573 0.573 -0.025 0.478 0.000 0.182 0.343 32 32 34 34 15 A-172 1132 1126 0.731 0.733 0.560 0.561 -0.014 0.527 -0.001 0.172 0.400 33 33 31 31 26 LOX-IMVI 1132 1132 0.734 0.734 0.578 0.578 -0.014 0.394 -0.000 0.185 0.328 34 34 37 37 27 Panc 03.27 1131 1131 0.735 0.735 0.576 0.576 -0.034 0.079 -0.001 0.169 0.315 35 35 36 36 10 NCI-H2030 1133 1133 0.739 0.739 0.578 0.578 -0.010 0.070 -0.005 0.158 0.378 36 36 38 38 32 SW1417 1132 1132 0.741 0.741 0.573 0.573 -0.036 0.103 -0.013 0.147 0.334 37 37 33 33 8 A549 1132 1132 0.742 0.742 0.588 0.588 -0.038 -0.002 0.002 0.180 0.352 38 38 40 40 7 CFPAC-1 1132 1132 0.747 0.747 0.585 0.585 -0.054 0.093 -0.002 0.165 0.341 39 39 39 39 3 NCI-H2347 1132 1132 0.748 0.748 0.576 0.576 -0.034 0.029 -0.019 0.146 0.371 40 40 35 35 11 J82 1132 1132 0.757 0.757 0.594 0.594 -0.002 0.139 -0.006 0.153 0.357 41 41 41 41 42 HEC-1-A 1133 1133 0.764 0.764 0.607 0.607 -0.015 0.228 -0.012 0.145 0.377 42 42 42 42 24 LoVo 1133 1133 0.764 0.764 0.613 0.613 -0.068 0.075 -0.002 0.160 0.395 43 43 43 43 1 HOP62 1133 1133 0.778 0.778 0.633 0.633 -0.047 0.583 -0.003 0.180 0.394 44 44 45 45 6 A498 1132 1132 0.789 0.789 0.624 0.624 -0.002 0.645 -0.006 0.144 0.389 45 45 44 44 41 NCI-H460 1133 1133 0.797 0.797 0.633 0.633 -0.011 0.379 0.000 0.169 0.376 46 46 46 46 31 SW480 1133 1133 0.815 0.815 0.673 0.673 -0.036 0.256 -0.004 0.142 0.408 47 47 47 47 9 PANC-1 1132 1132 0.823 0.823 0.697 0.697 -0.011 0.620 -0.001 0.141 0.406 48 48 48 48 30 line n n_eff r_mean_all r_mean_eff R2_mean_all R2_mean_eff ridge_rel_dMSE nn5_rel_dMSE IC_scaled_rel_dMSE effnorm2 dup_r rank_r_mean_all rank_r_mean_eff rank_R2_mean_all rank_R2_mean_eff rank_ridge_gain A-172 1132 1126 0.731 0.733 0.560 0.561 -0.014 0.527 -0.001 0.172 0.400 33 33 31 31 26 H4 1130 1090 0.623 0.630 0.402 0.414 -0.014 0.198 -0.003 0.289 0.226 13 13 12 13 25 SW 1088 887 258 0.314 0.424 0.099 0.195 -0.003 0.006 -0.000 1.123 0.095 1 2 1 2 40 similarity: { "A-172": { "top5": [ [ "SW 1088", 0.44861599802970886 ], [ "HS-578T", 0.3997451066970825 ], [ "RPMI-7951", 0.3601222038269043 ], [ "H4", 0.35962870717048645 ], [ "SNU-423", 0.3054219186306 ] ], "rank_of_other_glioma": [ 4, 1 ], "corr_other_glioma": [ 0.35962870717048645, 0.44861599802970886 ], "median_corr_nonglioma": -0.10606753826141357 }, "H4": { "top5": [ [ "SW 1088", 0.5771144032478333 ], [ "HS-578T", 0.46319058537483215 ], [ "hTERT-HPNE", 0.42752131819725037 ], [ "RPMI-7951", 0.4104604125022888 ], [ "HOP62", 0.39403805136680603 ] ], "rank_of_other_glioma": [ 6, 1 ], "corr_other_glioma": [ 0.35962870717048645, 0.5771144032478333 ], "median_corr_nonglioma": -0.05289650708436966 }, "SW 1088": { "top5": [ [ "HS-578T", 0.5888479948043823 ], [ "H4", 0.5771144032478333 ], [ "RPMI-7951", 0.5374318361282349 ], [ "hTERT-HPNE", 0.5013275146484375 ], [ "A-172", 0.44861599802970886 ] ], "rank_of_other_glioma": [ 5, 2 ], "corr_other_glioma": [ 0.44861599802970886, 0.5771144032478333 ], "median_corr_nonglioma": -0.06270762532949448 } } { "A-172": { "top5": [ [ "HOP62", 0.6504888185517308 ], [ "PANC-1", 0.6497005244964713 ], [ "A498", 0.6496399089941783 ], [ "HS-578T", 0.633288364490066 ], [ "J82", 0.6266547483569258 ] ], "corr_other_glioma": { "H4": 0.5201884733298928, "SW 1088": 0.2649999949603613 }, "rank_of_other_glioma": [ 33, 46 ], "median_corr_nonglioma": 0.5555204341011911 }, "H4": { "top5": [ [ "HOP62", 0.558877494841963 ], [ "NCI-H460", 0.5459623667707979 ], [ "PANC-1", 0.5387882331284308 ], [ "A498", 0.5309414524960478 ], [ "SW480", 0.523970930110335 ] ], "corr_other_glioma": { "A-172": 0.5201884733298929, "SW 1088": 0.23461545611869736 }, "rank_of_other_glioma": [ 5, 46 ], "median_corr_nonglioma": 0.4717535846481846 }, "SW 1088": { "top5": [ [ "HOP62", 0.2757520731853467 ], [ "HS-578T", 0.2651102528881258 ], [ "A-172", 0.26499999496036136 ], [ "PANC-1", 0.26465900238828916 ], [ "A498", 0.26448204655289576 ] ], "corr_other_glioma": { "A-172": 0.26499999496036136, "H4": 0.23461545611869733 }, "rank_of_other_glioma": [ 2, 23 ], "median_corr_nonglioma": 0.23352516149747163 } } SOX2 {'A-172': (0.01, 30), 'H4': (0.04, 10), 'SW 1088': (0.02, 15), 'median_all': 0.01} OLIG2 {'A-172': (0.02, 2), 'H4': (0.01, 3), 'SW 1088': (0.0, 21), 'median_all': 0.0} OLIG1 {'A-172': (0.0, 36), 'H4': (0.0, 21), 'SW 1088': (0.0, 27), 'median_all': 0.0} GFAP {'A-172': (0.0, 24), 'H4': (0.0, 17), 'SW 1088': (0.0, 16), 'median_all': 0.0} NES {'A-172': (1.07, 3), 'H4': (0.02, 40), 'SW 1088': (0.06, 23), 'median_all': 0.04} CD44 {'A-172': (12.72, 12), 'H4': (13.05, 10), 'SW 1088': (12.27, 13), 'median_all': 4.25} CHI3L1 {'A-172': (0.01, 6), 'H4': (0.0, 43), 'SW 1088': (0.24, 2), 'median_all': 0.0} VIM {'A-172': (33.34, 7), 'H4': (17.55, 19), 'SW 1088': (22.16, 15), 'median_all': 12.18} S100B {'A-172': (0.0, 16), 'H4': (0.0, 8), 'SW 1088': (0.01, 5), 'median_all': 0.0} PTPRZ1 {'A-172': (0.01, 38), 'H4': (0.01, 27), 'SW 1088': (0.02, 13), 'median_all': 0.01} PDGFRA {'A-172': (0.01, 20), 'H4': (0.03, 12), 'SW 1088': (0.02, 14), 'median_all': 0.01} EGFR {'A-172': (7.54, 8), 'H4': (8.74, 7), 'SW 1088': (9.31, 5), 'median_all': 3.7} SOX10 {'A-172': (0.01, 22), 'H4': (0.01, 14), 'SW 1088': (0.02, 7), 'median_all': 0.01} DLL3 {'A-172': (0.01, 42), 'H4': (0.02, 25), 'SW 1088': (0.01, 34), 'median_all': 0.02} ASCL1 {'A-172': (0.01, 24), 'H4': (0.01, 19), 'SW 1088': (0.03, 5), 'median_all': 0.01}