Table 9.
Summary of final results for the PharmaBench based on scaffold split.
| Property | Metrices | RF | XGBoost | CMPNN | FPGNN | DHTNN | KANO | MPG | Unimol | Trans-M |
|---|---|---|---|---|---|---|---|---|---|---|
| LogD | R | 0.527 | 0.688 | 0.854 | 0.815 | 0.784 | 0.859 | 0.862 | 0.875 | 0.867 |
| MAE | 0.934 | 0.776 | 0.548 | 0.604 | 0.681 | 0.528 | 0.526 | 0.517 | 0.504 | |
| RMSE | 1.249 | 1.071 | 0.807 | 0.838 | 0.912 | 0.766 | 0.758 | 0.745 | 0.737 | |
| Solubility | R | 0.337 | 0.485 | 0.463 | 0.625 | 0.535 | 0.615 | 0.627 | 0.674 | 0.522 |
| MAE | 0.734 | 0.654 | 0.663 | 0.573 | 0.634 | 0.58 | 0.581 | 0.53 | 0.626 | |
| RMSE | 0.918 | 0.832 | 0.858 | 0.747 | 0.828 | 0.772 | 0.758 | 0.707 | 0.834 | |
| PPB | R | 0.292 | 0.489 | 0.514 | 0.543 | 0.197 | 0.581 | 0.718 | 0.733 | 0.668 |
| MAE | 0.142 | 0.122 | 0.13 | 0.114 | 0.173 | 0.106 | 0.099 | 0.095 | 0.097 | |
| RMSE | 0.204 | 0.186 | 0.236 | 0.179 | 0.235 | 0.185 | 0.17 | 0.179 | 0.172 | |
| CYP 3A4 | R | 0.101 | 0.154 | 0.327 | 0.368 | 0.144 | 0.483 | 0.457 | 0.425 | 0.317 |
| MAE | 10.572 | 10.619 | 8.114 | 9.925 | 10.43 | 8.425 | 8.201 | 8.532 | 8.955 | |
| RMSE | 16.54 | 16.123 | 16.701 | 15.606 | 16.156 | 15.307 | 14.376 | 15.895 | 15.867 | |
| CYP 2C9 | R | 0.05 | 0.061 | 0.203 | 0.32 | −0.118 | 0.147 | 0.307 | 0.318 | 0.229 |
| MAE | 11.911 | 11.201 | 9.684 | 10.028 | 10.58 | 11.64 | 9.504 | 9.524 | 10.194 | |
| RMSE | 18.471 | 17.582 | 18.377 | 16.933 | 17.449 | 17.35 | 17.417 | 17.774 | 18.08 | |
| CYP 2D6 | R | 0.293 | 0.197 | 0.201 | 0.301 | 0.23 | 0.37 | 0.482 | 0.269 | 0.464 |
| MAE | 11.728 | 12.024 | 10.453 | 11.173 | 12.199 | 10.881 | 10.13 | 10.283 | 9.961 | |
| RMSE | 18.041 | 17.819 | 19.156 | 17.611 | 17.89 | 17.622 | 17.527 | 18.071 | 17.677 | |
| HLMC | R | 0.469 | 0.628 | 0.345 | 0.665 | 0.609 | 0.722 | 0.751 | 0.722 | 0.733 |
| MAE | 0.592 | 0.459 | 0.63 | 0.444 | 0.519 | 0.395 | 0.375 | 0.426 | 0.392 | |
| RMSE | 0.813 | 0.647 | 0.921 | 0.604 | 0.729 | 0.554 | 0.541 | 0.613 | 0.567 | |
| RLMC | R | 0.337 | 0.564 | 0.194 | 0.642 | 0.44 | 0.621 | 0.731 | 0.645 | 0.664 |
| MAE | 0.698 | 0.557 | 0.696 | 0.496 | 0.694 | 0.522 | 0.433 | 0.483 | 0.463 | |
| RMSE | 0.958 | 0.819 | 0.939 | 0.716 | 0.915 | 0.762 | 0.685 | 0.651 | 0.677 | |
| MLMC | R | 0.488 | 0.672 | 0.399 | 0.732 | 0.61 | 0.729 | 0.749 | 0.727 | 0.753 |
| MAE | 0.73 | 0.579 | 0.808 | 0.568 | 0.665 | 0.549 | 0.499 | 0.568 | 0.518 | |
| RMSE | 0.987 | 0.844 | 1.13 | 0.774 | 0.926 | 0.767 | 0.723 | 0.824 | 0.744 | |
| BBB | ACC | 0.825 | 0.837 | 0.84 | 0.851 | 0.85 | 0.846 | 0.858 | 0.844 | 0.871 |
| AUC | 0.731 | 0.75 | 0.887 | 0.923 | 0.909 | 0.915 | 0.923 | 0.92 | 0.935 | |
| F1 | 0.885 | 0.892 | 0.809 | 0.887 | 0.895 | 0.888 | 0.833 | 0.819 | 0.846 | |
| AMES | ACC | 0.762 | 0.769 | 0.793 | 0.771 | 0.765 | 0.743 | 0.798 | 0.818 | 0.799 |
| AUC | 0.761 | 0.768 | 0.858 | 0.858 | 0.844 | 0.865 | 0.869 | 0.878 | 0.869 | |
| F1 | 0.776 | 0.783 | 0.793 | 0.786 | 0.767 | 0.78 | 0.798 | 0.818 | 0.799 |