{'source': 'raw', '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': 1137, 'n_lines': 50, 'replicate_pairs': 52371} == LOGO (train on 47 non-glioma lines), pooled 3 glioma lines, all train_mean n= 2765 MSE 0.0090 [0.0086, 0.0095] | dMSE 0.0000 [0.0000, 0.0000] win 0.00 | r 0.654 [0.648, 0.660] | dr 0.000 [0.000, 0.000] nn1_baseline n= 2765 MSE 0.0109 [0.0104, 0.0115] | dMSE 0.0019 [0.0018, 0.0020] win 0.03 | r 0.591 [0.584, 0.599] | dr -0.063 [-0.065, -0.061] nn5_baseline n= 2765 MSE 0.0087 [0.0083, 0.0091] | dMSE -0.0003 [-0.0004, -0.0003] win 0.62 | r 0.666 [0.660, 0.673] | dr 0.012 [0.011, 0.014] ridge_baseline_pca10 n= 2765 MSE 0.0086 [0.0082, 0.0091] | dMSE -0.0004 [-0.0004, -0.0003] win 0.98 | r 0.672 [0.666, 0.677] | dr 0.018 [0.017, 0.018] null_random_line n= 2765 MSE 0.0133 [0.0126, 0.0141] | dMSE 0.0043 [0.0040, 0.0046] win 0.00 | r 0.504 [0.497, 0.510] | dr -0.150 [-0.152, -0.148] null_ridge_shuffled n= 2765 MSE 0.0090 [0.0086, 0.0095] | dMSE 0.0000 [-0.0000, 0.0000] win 0.49 | r 0.654 [0.648, 0.660] | dr 0.000 [-0.000, 0.000] duplicate n= 2765 MSE 0.0094 [0.0091, 0.0098] | dMSE 0.0004 [0.0000, 0.0007] win 0.51 | r 0.712 [0.705, 0.719] | dr 0.058 [0.054, 0.063] IC:train_mean n= 1402 MSE 0.0091 [0.0085, 0.0098] | 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= 1402 MSE 0.0087 [0.0081, 0.0093] | dMSE -0.0005 [-0.0006, -0.0004] win 0.71 | r 0.672 [0.662, 0.682] | dr 0.019 [0.018, 0.021] IC:incontext_scaled_mean n= 1402 MSE 0.0091 [0.0085, 0.0098] | dMSE -0.0000 [-0.0000, -0.0000] win 0.51 | r 0.653 [0.643, 0.663] | dr -0.000 [-0.000, 0.000] _noise_floor_mse 0.0047 [0.0045, 0.0049] _oracle_pearson_ceiling 0.8328 [0.8282, 0.8373] A-172 n 1123 mean r 0.727 [0.722, 0.733] ridge dMSE -0.0004 [-0.0005, -0.0004] nn5 dMSE -0.0003 [-0.0005, -0.0002] dup r 0.828 [0.820, 0.836] IC scaled dMSE 0.0000 [-0.0000, 0.0000] H4 n 1114 mean r 0.680 [0.672, 0.687] ridge dMSE -0.0003 [-0.0004, -0.0003] nn5 dMSE -0.0003 [-0.0004, -0.0002] dup r 0.712 [0.703, 0.721] IC scaled dMSE -0.0000 [-0.0001, -0.0000] SW 1088 n 528 mean r 0.444 [0.433, 0.455] ridge dMSE -0.0004 [-0.0004, -0.0003] nn5 dMSE -0.0005 [-0.0006, -0.0004] dup r 0.467 [0.454, 0.479] IC scaled dMSE -0.0000 [-0.0000, 0.0000] glioma sibling mean - 47-line mean: {'m': '0.0116 [0.0111, 0.0122]', 'p': '0.5577 [0.5504, 0.5653]', 'dm': '0.0027 [0.0025, 0.0028]', 'dp': '-0.0961 [-0.0997, -0.0926]'} == LOGO (train on 47 non-glioma lines), pooled 3 glioma lines, effective train_mean n= 960 MSE 0.0101 [0.0091, 0.0113] | dMSE 0.0000 [0.0000, 0.0000] win 0.00 | r 0.721 [0.714, 0.729] | dr 0.000 [0.000, 0.000] nn1_baseline n= 960 MSE 0.0127 [0.0115, 0.0140] | dMSE 0.0026 [0.0024, 0.0028] win 0.05 | r 0.667 [0.658, 0.676] | dr -0.054 [-0.058, -0.051] nn5_baseline n= 960 MSE 0.0093 [0.0084, 0.0104] | dMSE -0.0008 [-0.0010, -0.0006] win 0.72 | r 0.740 [0.732, 0.748] | dr 0.019 [0.016, 0.021] ridge_baseline_pca10 n= 960 MSE 0.0094 [0.0084, 0.0104] | dMSE -0.0007 [-0.0009, -0.0006] win 0.99 | r 0.743 [0.736, 0.750] | dr 0.021 [0.021, 0.022] null_random_line n= 960 MSE 0.0167 [0.0150, 0.0187] | dMSE 0.0066 [0.0059, 0.0074] win 0.00 | r 0.561 [0.552, 0.571] | dr -0.160 [-0.164, -0.156] null_ridge_shuffled n= 960 MSE 0.0101 [0.0091, 0.0113] | dMSE -0.0000 [-0.0000, 0.0000] win 0.54 | r 0.721 [0.714, 0.729] | dr 0.000 [0.000, 0.000] duplicate n= 960 MSE 0.0071 [0.0066, 0.0077] | dMSE -0.0030 [-0.0039, -0.0022] win 0.78 | r 0.820 [0.811, 0.829] | dr 0.099 [0.091, 0.107] IC:train_mean n= 473 MSE 0.0102 [0.0091, 0.0114] | dMSE 0.0000 [0.0000, 0.0000] win 0.00 | r 0.726 [0.717, 0.736] | dr 0.000 [0.000, 0.000] IC:incontext_nn5_response n= 473 MSE 0.0091 [0.0081, 0.0101] | dMSE -0.0011 [-0.0014, -0.0009] win 0.85 | r 0.755 [0.745, 0.764] | dr 0.029 [0.026, 0.031] IC:incontext_scaled_mean n= 473 MSE 0.0102 [0.0090, 0.0114] | dMSE -0.0001 [-0.0001, -0.0000] win 0.59 | r 0.726 [0.717, 0.736] | dr 0.000 [-0.000, 0.000] _noise_floor_mse 0.0036 [0.0033, 0.0038] _oracle_pearson_ceiling 0.9010 [0.8953, 0.9063] A-172 n 526 mean r 0.747 [0.741, 0.754] ridge dMSE -0.0007 [-0.0009, -0.0006] nn5 dMSE -0.0008 [-0.0010, -0.0005] dup r 0.877 [0.870, 0.884] IC scaled dMSE 0.0000 [-0.0000, 0.0000] H4 n 404 mean r 0.695 [0.684, 0.706] ridge dMSE -0.0006 [-0.0007, -0.0006] nn5 dMSE -0.0007 [-0.0009, -0.0004] dup r 0.757 [0.742, 0.772] IC scaled dMSE -0.0001 [-0.0002, -0.0001] SW 1088 n 30 mean r 0.615 [0.568, 0.656] ridge dMSE -0.0018 [-0.0023, -0.0014] nn5 dMSE -0.0023 [-0.0033, -0.0013] dup r 0.662 [0.608, 0.708] IC scaled dMSE 0.0000 [-0.0000, 0.0001] glioma sibling mean - 47-line mean: {'m': '0.0140 [0.0127, 0.0154]', 'p': '0.6281 [0.6189, 0.6375]', 'dm': '0.0040 [0.0036, 0.0044]', 'dp': '-0.0933 [-0.0986, -0.0879]'} == 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 NCI-H661 556 31 0.420 0.627 0.196 0.374 -0.013 0.004 -0.005 0.023 0.425 1 4 1 4 46 SW 1271 887 54 0.438 0.632 0.225 0.447 -0.003 0.038 -0.001 0.024 0.424 2 5 2 9 48 SW 1088 528 30 0.448 0.620 0.232 0.433 -0.020 -0.030 -0.000 0.027 0.467 3 3 3 6 43 AN3 CA 1106 175 0.515 0.563 0.268 0.324 -0.029 -0.008 -0.026 0.014 0.529 4 2 4 2 39 CHP-212 1071 202 0.534 0.543 0.293 0.313 -0.015 0.048 -0.016 0.014 0.548 5 1 5 1 45 C-33 A 1119 551 0.628 0.649 0.381 0.399 -0.093 -0.039 -0.070 0.009 0.720 6 8 6 5 7 COLO 205 1118 429 0.631 0.654 0.417 0.440 -0.065 -0.012 -0.022 0.011 0.748 7 9 8 8 20 SNU-1 1114 339 0.640 0.646 0.420 0.435 -0.047 0.005 -0.019 0.011 0.691 8 7 9 7 29 HepG2/C3A 1122 373 0.645 0.664 0.432 0.454 -0.006 0.093 -0.010 0.012 0.708 9 10 10 10 47 SW48 1119 400 0.655 0.682 0.455 0.485 -0.055 -0.052 0.000 0.015 0.702 10 12 12 12 24 BT-474 1121 631 0.658 0.675 0.442 0.457 -0.029 0.037 -0.022 0.011 0.748 11 11 11 11 38 SHP-77 1121 242 0.665 0.644 0.385 0.341 -0.053 0.041 -0.090 0.008 0.753 12 6 7 3 25 HCT15 1119 377 0.673 0.691 0.467 0.488 -0.048 -0.026 -0.010 0.011 0.732 13 13 13 13 27 H4 1114 404 0.683 0.699 0.501 0.519 -0.047 -0.019 -0.007 0.015 0.712 14 15 15 16 28 C32 1122 604 0.687 0.698 0.485 0.491 -0.028 0.056 -0.007 0.011 0.802 15 14 14 14 40 hTERT-HPNE 1121 516 0.695 0.712 0.509 0.526 -0.080 -0.045 -0.003 0.011 0.767 16 16 16 17 10 SK-MEL-2 1119 672 0.707 0.722 0.528 0.542 -0.023 0.094 -0.001 0.011 0.774 17 17 18 19 41 RKO 1119 530 0.709 0.729 0.528 0.542 -0.036 -0.027 -0.004 0.011 0.814 18 19 19 20 35 AsPC-1 1123 741 0.716 0.725 0.509 0.515 -0.046 -0.040 -0.011 0.010 0.826 19 18 17 15 30 A-427 1116 515 0.721 0.746 0.545 0.567 -0.069 0.005 -0.003 0.010 0.777 20 25 21 24 16 RPMI-7951 1121 530 0.721 0.740 0.555 0.575 -0.069 0.040 -0.001 0.011 0.757 21 24 23 25 17 KATO III 1122 767 0.727 0.738 0.556 0.565 -0.100 -0.112 -0.000 0.011 0.836 22 23 24 23 6 NCI-H1573 1122 861 0.730 0.735 0.529 0.532 -0.034 0.034 0.000 0.012 0.843 23 20 20 18 36 A-172 1123 526 0.730 0.751 0.562 0.577 -0.085 -0.004 0.001 0.012 0.828 24 28 26 26 8 NCI-H23 1120 540 0.734 0.760 0.576 0.597 -0.061 -0.033 -0.001 0.012 0.802 25 29 28 30 21 NCI-H1792 1121 686 0.737 0.750 0.568 0.578 -0.068 -0.083 -0.006 0.013 0.821 26 27 27 27 18 MIA PaCa-2 1122 531 0.737 0.736 0.561 0.564 -0.022 0.026 -0.009 0.014 0.842 27 22 25 22 42 HT-29 1122 701 0.738 0.748 0.579 0.589 -0.083 -0.101 -0.001 0.012 0.837 28 26 29 28 9 Hs 766T 1121 446 0.739 0.735 0.555 0.553 -0.018 0.103 -0.000 0.011 0.793 29 21 22 21 44 NCI-H2030 1123 489 0.749 0.777 0.589 0.612 -0.051 -0.029 -0.008 0.013 0.828 30 34 32 33 26 HS-578T 1122 497 0.749 0.774 0.593 0.613 -0.121 -0.063 -0.012 0.013 0.811 31 33 34 34 2 SW 900 1123 655 0.750 0.765 0.601 0.617 -0.030 0.110 -0.001 0.011 0.781 32 30 35 35 37 SNU-423 1123 534 0.752 0.773 0.592 0.610 -0.071 -0.018 -0.018 0.014 0.802 33 32 33 32 14 LS 180 1122 712 0.753 0.766 0.580 0.592 -0.122 -0.154 -0.004 0.012 0.823 34 31 30 29 1 SW1417 1123 643 0.757 0.779 0.605 0.625 -0.078 -0.004 -0.004 0.010 0.796 35 35 36 38 11 LOX-IMVI 1123 486 0.763 0.782 0.615 0.632 -0.042 0.065 -0.005 0.012 0.844 36 37 40 43 32 HEC-1-A 1123 608 0.764 0.785 0.585 0.604 -0.042 -0.006 -0.001 0.010 0.837 37 40 31 31 33 Panc 03.27 1122 680 0.764 0.784 0.624 0.642 -0.067 -0.044 -0.004 0.012 0.801 38 38 45 46 19 J82 1123 625 0.765 0.781 0.613 0.626 -0.059 0.032 0.000 0.011 0.836 39 36 38 42 22 CFPAC-1 1123 595 0.770 0.786 0.621 0.636 -0.101 -0.084 -0.006 0.011 0.853 40 41 44 45 5 A549 1123 448 0.773 0.796 0.620 0.634 -0.071 -0.111 -0.020 0.013 0.856 41 45 42 44 15 NCI-H2347 1123 625 0.774 0.789 0.615 0.626 -0.074 -0.084 -0.002 0.012 0.867 42 42 39 41 13 LoVo 1123 689 0.776 0.791 0.611 0.620 -0.120 -0.094 -0.001 0.011 0.870 43 44 37 37 3 HOP62 1123 718 0.777 0.784 0.621 0.625 -0.110 -0.072 -0.018 0.013 0.887 44 39 43 40 4 A498 1123 513 0.782 0.791 0.618 0.619 -0.057 -0.012 -0.007 0.012 0.874 45 43 41 36 23 NCI-H460 1123 685 0.800 0.803 0.628 0.625 -0.042 0.011 -0.000 0.011 0.912 46 46 46 39 34 SW480 1123 795 0.811 0.818 0.666 0.671 -0.078 0.021 -0.003 0.009 0.911 47 47 47 47 12 PANC-1 1123 595 0.820 0.832 0.688 0.696 -0.046 0.088 -0.012 0.011 0.905 48 48 48 48 31 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 1123 526 0.730 0.751 0.562 0.577 -0.085 -0.004 0.001 0.012 0.828 24 28 26 26 8 H4 1114 404 0.683 0.699 0.501 0.519 -0.047 -0.019 -0.007 0.015 0.712 14 15 15 16 28 SW 1088 528 30 0.448 0.620 0.232 0.433 -0.020 -0.030 -0.000 0.027 0.467 3 3 3 6 43 similarity: { "A-172": { "top5": [ [ "SW 1088", 0.48159554600715637 ], [ "HS-578T", 0.4052586853504181 ], [ "RPMI-7951", 0.381763219833374 ], [ "H4", 0.368960440158844 ], [ "hTERT-HPNE", 0.3219931721687317 ] ], "rank_of_other_glioma": [ 4, 1 ], "corr_other_glioma": [ 0.368960440158844, 0.48159554600715637 ], "median_corr_nonglioma": -0.10021283477544785 }, "H4": { "top5": [ [ "SW 1088", 0.5575143098831177 ], [ "HS-578T", 0.5018192529678345 ], [ "RPMI-7951", 0.4229643940925598 ], [ "hTERT-HPNE", 0.40830954909324646 ], [ "HOP62", 0.3924192190170288 ] ], "rank_of_other_glioma": [ 6, 1 ], "corr_other_glioma": [ 0.368960440158844, 0.5575143098831177 ], "median_corr_nonglioma": -0.065591961145401 }, "SW 1088": { "top5": [ [ "HS-578T", 0.5802528262138367 ], [ "H4", 0.5575143098831177 ], [ "RPMI-7951", 0.5342063903808594 ], [ "hTERT-HPNE", 0.5052321553230286 ], [ "A-172", 0.48159554600715637 ] ], "rank_of_other_glioma": [ 5, 2 ], "corr_other_glioma": [ 0.48159554600715637, 0.5575143098831177 ], "median_corr_nonglioma": -0.0636770948767662 } } { "A-172": { "top5": [ [ "HS-578T", 0.7415080918653767 ], [ "J82", 0.722157465904654 ], [ "A498", 0.7136338017734751 ], [ "SNU-423", 0.7099164805596341 ], [ "HOP62", 0.7010409154652287 ] ], "corr_other_glioma": { "H4": 0.6720388573936994, "SW 1088": 0.5689912718439408 }, "rank_of_other_glioma": [ 8, 29 ], "median_corr_nonglioma": 0.6010858757310541 }, "H4": { "top5": [ [ "HOP62", 0.714707828930806 ], [ "HS-578T", 0.7029899655803147 ], [ "RPMI-7951", 0.6825298984536745 ], [ "LOX-IMVI", 0.6726176424101243 ], [ "A-172", 0.6720388573936994 ] ], "corr_other_glioma": { "A-172": 0.6720388573936994, "SW 1088": 0.5907139037535608 }, "rank_of_other_glioma": [ 4, 22 ], "median_corr_nonglioma": 0.588147302080815 }, "SW 1088": { "top5": [ [ "HS-578T", 0.5958095951045992 ], [ "H4", 0.5907139037535609 ], [ "RPMI-7951", 0.5765112248169274 ], [ "hTERT-HPNE", 0.5727673985859708 ], [ "SNU-423", 0.5699254941584859 ] ], "corr_other_glioma": { "A-172": 0.5689912718439408, "H4": 0.5907139037535609 }, "rank_of_other_glioma": [ 5, 1 ], "median_corr_nonglioma": 0.48153329261098377 } } CD44 {'A-172': (7.64, 10), 'H4': (7.1, 11), 'SW 1088': (5.52, 15), 'median_all': 1.54} VIM {'A-172': (26.54, 7), 'H4': (11.72, 19), 'SW 1088': (13.25, 16), 'median_all': 5.59} EGFR {'A-172': (4.22, 7), 'H4': (3.55, 10), 'SW 1088': (4.39, 6), 'median_all': 1.38}