| BINDINGDB Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| gat ecfp 2.6672 ± 0.4774 1.9156 ± 0.1894 | |
| gat selfies 1.8164 ± 0.2667 1.3696 ± 0.1159 | |
| gat smiles 1.7932 ± 0.2338 1.3722 ± 0.1176 | |
| gcn ecfp 2.1744 ± 0.3132 1.5856 ± 0.1452 | |
| gcn selfies 1.7671 ± 0.2332 1.3612 ± 0.1056 | |
| gcn smiles 1.8313 ± 0.2654 1.3773 ± 0.1171 | |
| gin ecfp 2.0116 ± 0.3040 1.4942 ± 0.1247 | |
| gin selfies 1.7480 ± 0.2425 1.3502 ± 0.1123 | |
| gin smiles 1.7566 ± 0.2513 1.3585 ± 0.1048 | |
| gp+tanimoto ecfp 1.6921 ± 0.2544 1.2645 ± 0.1051 | |
| gp+tanimoto selfies 1.8034 ± 0.2504 1.3793 ± 0.1135 | |
| gp+tanimoto smiles 1.6945 ± 0.2640 1.2650 ± 0.1057 | |
| sage ecfp 2.1945 ± 0.3115 1.6303 ± 0.1384 | |
| sage selfies 1.9251 ± 0.3445 1.4001 ± 0.1262 | |
| sage smiles 1.8614 ± 0.3434 1.3816 ± 0.1282 | |
| BOILINGPOINT Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| gat ecfp 73.1437 ± 6.6197 53.9304 ± 4.6799 | |
| gat selfies 60.0938 ± 4.9932 44.2603 ± 3.9387 | |
| gat smiles 60.0681 ± 4.7094 45.0223 ± 3.8590 | |
| gcn ecfp 63.2157 ± 5.0890 48.2488 ± 3.9244 | |
| gcn selfies 66.5821 ± 5.0110 50.7737 ± 4.1893 | |
| gcn smiles 68.6942 ± 5.0914 52.5543 ± 4.2683 | |
| gin ecfp 59.5471 ± 5.0798 44.7224 ± 3.9753 | |
| gin selfies 72.0029 ± 5.4545 54.6066 ± 4.6104 | |
| gin smiles 70.0021 ± 4.9849 55.1386 ± 4.2748 | |
| gp ecfp 51.6225 ± 4.9579 37.8647 ± 3.4987 | |
| gp selfies 79.3254 ± 5.8622 63.3404 ± 4.5846 | |
| gp smiles 51.5120 ± 5.3235 37.8171 ± 3.5411 | |
| sage ecfp 64.4034 ± 5.4008 47.8241 ± 4.1397 | |
| sage selfies 59.2558 ± 4.7487 44.8262 ± 3.8195 | |
| sage smiles 62.0991 ± 4.6785 46.6419 ± 4.0569 | |
| ESOL Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| gat ecfp 1.2483 ± 0.1534 0.9410 ± 0.1059 | |
| gat selfies 1.5646 ± 0.1858 1.1441 ± 0.1370 | |
| gat smiles 1.5192 ± 0.1740 1.1516 ± 0.1287 | |
| gcn ecfp 1.1634 ± 0.1252 0.8822 ± 0.0988 | |
| gcn selfies 1.6861 ± 0.1825 1.3087 ± 0.1381 | |
| gcn smiles 1.7133 ± 0.1825 1.3146 ± 0.1394 | |
| gin ecfp 1.1526 ± 0.1277 0.8507 ± 0.1042 | |
| gin selfies 1.6538 ± 0.1885 1.2690 ± 0.1427 | |
| gin smiles 1.6409 ± 0.1715 1.2461 ± 0.1419 | |
| gp+tanimoto ecfp 1.0513 ± 0.1187 0.7792 ± 0.0866 | |
| gp+tanimoto selfies 2.1744 ± 0.1980 1.7338 ± 0.1715 | |
| gp+tanimoto smiles 1.0503 ± 0.1235 0.7798 ± 0.1002 | |
| sage ecfp 1.1407 ± 0.1321 0.8713 ± 0.0983 | |
| sage selfies 1.6127 ± 0.1710 1.2302 ± 0.1312 | |
| sage smiles 1.5419 ± 0.1694 1.1597 ± 0.1326 | |
| FREESOLV Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| gat ecfp 2.5469 ± 0.5988 1.7310 ± 0.3236 | |
| gat selfies 3.7543 ± 0.7218 2.8503 ± 0.3962 | |
| gat smiles 3.5968 ± 0.7350 2.6242 ± 0.4419 | |
| gcn ecfp 2.5038 ± 0.6450 1.6743 ± 0.3326 | |
| gcn selfies 3.8168 ± 0.8156 2.7834 ± 0.4549 | |
| gcn smiles 3.8458 ± 0.8551 2.8537 ± 0.4530 | |
| gin ecfp 2.3410 ± 0.5840 1.5615 ± 0.3094 | |
| gin selfies 3.7603 ± 0.8412 2.7327 ± 0.4461 | |
| gin smiles 3.7822 ± 0.8187 2.7178 ± 0.4620 | |
| gp+tanimoto ecfp 2.0696 ± 0.6732 1.3354 ± 0.2849 | |
| gp+tanimoto selfies 4.1141 ± 0.8004 3.0900 ± 0.4399 | |
| gp+tanimoto smiles 2.0787 ± 0.7082 1.3375 ± 0.2831 | |
| sage ecfp 2.5430 ± 0.6463 1.7124 ± 0.3320 | |
| sage selfies 3.8307 ± 0.8413 2.7317 ± 0.4656 | |
| sage smiles 3.7483 ± 0.8613 2.6734 ± 0.4676 | |
| IC50 Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| gat ecfp 1.1000 ± 0.0907 0.8420 ± 0.0685 | |
| gat selfies 0.7474 ± 0.0619 0.6026 ± 0.0412 | |
| gat smiles 0.7569 ± 0.0620 0.6190 ± 0.0446 | |
| gcn ecfp 1.0079 ± 0.0862 0.7721 ± 0.0615 | |
| gcn selfies 0.7475 ± 0.0764 0.5828 ± 0.0459 | |
| gcn smiles 0.7451 ± 0.0747 0.5863 ± 0.0470 | |
| gin ecfp 0.9375 ± 0.0819 0.7075 ± 0.0634 | |
| gin selfies 0.7501 ± 0.0693 0.5891 ± 0.0450 | |
| gin smiles 0.7487 ± 0.0718 0.5905 ± 0.0436 | |
| gp+tanimoto ecfp 0.7660 ± 0.0707 0.5961 ± 0.0485 | |
| gp+tanimoto selfies 0.7833 ± 0.0769 0.6129 ± 0.0476 | |
| gp+tanimoto smiles 0.7647 ± 0.0698 0.5965 ± 0.0480 | |
| sage ecfp 1.0252 ± 0.0872 0.7877 ± 0.0658 | |
| sage selfies 0.7415 ± 0.0736 0.5863 ± 0.0426 | |
| sage smiles 0.7418 ± 0.0683 0.5868 ± 0.0440 | |
| LIPOPHIL Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| gat ecfp 0.9952 ± 0.0666 0.7434 ± 0.0423 | |
| gat selfies 1.1282 ± 0.0480 0.9185 ± 0.0418 | |
| gat smiles 1.1348 ± 0.0519 0.9200 ± 0.0441 | |
| gcn ecfp 0.8879 ± 0.0524 0.6652 ± 0.0397 | |
| gcn selfies 1.1611 ± 0.0534 0.9350 ± 0.0464 | |
| gcn smiles 1.1608 ± 0.0494 0.9434 ± 0.0482 | |
| gin ecfp 0.8650 ± 0.0551 0.6453 ± 0.0374 | |
| gin selfies 1.1683 ± 0.0516 0.9407 ± 0.0470 | |
| gin smiles 1.1698 ± 0.0581 0.9380 ± 0.0485 | |
| gp+tanimoto ecfp 0.7498 ± 0.0454 0.5594 ± 0.0341 | |
| gp+tanimoto selfies 1.1848 ± 0.0545 0.9536 ± 0.0448 | |
| gp+tanimoto smiles 0.7494 ± 0.0456 0.5600 ± 0.0316 | |
| sage ecfp 0.9368 ± 0.0571 0.7010 ± 0.0418 | |
| sage selfies 1.1439 ± 0.0534 0.9102 ± 0.0435 | |
| sage smiles 1.1332 ± 0.0455 0.9405 ± 0.0445 | |
| POLYATOMIC Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| polyatomic unknown 1.5655 ± 0.1263 1.2717 ± 0.0984 | |
| polyatomic unknown 1.0860 ± 0.1354 0.8171 ± 0.0812 | |
| polyatomic unknown 1.5153 ± 0.3395 1.0409 ± 0.2181 | |
| polyatomic unknown 0.6975 ± 0.0551 0.5724 ± 0.0436 | |
| polyatomic unknown 0.7913 ± 0.0575 0.5953 ± 0.0382 | |
| polyatomic unknown 0.7043 ± 0.1095 0.5150 ± 0.0722 | |
| polyatomic unknown 48.1815 ± 5.4987 33.3759 ± 3.7307 | |
| POLYATOMICBASIC Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| polyatomicbasic unknown 1.5608 ± 0.1286 1.2846 ± 0.0970 | |
| polyatomicbasic unknown 1.6139 ± 0.3575 1.1024 ± 0.2127 | |
| polyatomicbasic unknown 0.8041 ± 0.0534 0.6136 ± 0.0394 | |
| polyatomicbasic unknown 48.0145 ± 5.1040 34.3959 ± 3.6937 | |
| polyatomicbasic unknown 1.2799 ± 0.1198 0.9838 ± 0.0891 | |
| polyatomicbasic unknown 0.7214 ± 0.0589 0.5949 ± 0.0452 | |
| polyatomicbasic unknown 0.6955 ± 0.1043 0.5174 ± 0.0707 | |
| QM9 Benchmark Summary: | |
| Model Encoding RMSE ± MAE ± | |
| ----------------------------------------------------------------- | |
| gat ecfp 3.4215 ± 0.2718 2.6676 ± 0.2061 | |
| gat selfies 2.0540 ± 0.1546 1.6340 ± 0.1216 | |
| gat smiles 2.0858 ± 0.1508 1.6694 ± 0.1175 | |
| gcn ecfp 3.0271 ± 0.2273 2.3643 ± 0.1876 | |
| gcn selfies 2.8783 ± 0.1980 2.3116 ± 0.1699 | |
| gcn smiles 2.8837 ± 0.2133 2.3072 ± 0.1694 | |
| gin ecfp 2.8340 ± 0.2436 2.1962 ± 0.1761 | |
| gin selfies 2.8427 ± 0.2038 2.2164 ± 0.1699 | |
| gin smiles 3.2328 ± 0.2544 2.5469 ± 0.1975 | |
| gp+tanimoto ecfp 2.2497 ± 0.2188 1.6977 ± 0.1431 | |
| gp+tanimoto selfies 3.9735 ± 0.3086 3.1156 ± 0.2450 | |
| gp+tanimoto smiles 2.2494 ± 0.2074 1.7009 ± 0.1444 | |
| sage ecfp 3.2668 ± 0.2386 2.6014 ± 0.1890 | |
| sage selfies 2.1091 ± 0.1556 1.6486 ± 0.1295 | |
| sage smiles 2.0653 ± 0.1655 1.6209 ± 0.1244 | |