Table 2 Evaluations of 5 × 10-fold cross-validation of random forest, ChemProp, DeepDelta, LGBMsub, and Delta LGBMsub
From: DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning
Dataset | Pearson’s r | Mean absolute error | Root mean squared error | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
RF | ChemProp | DeepDelta | LGBMsub | Delta LGBMsub | RF | ChemProp | DeepDelta | LGBMsub | Delta LGBMsub | RF | ChemProp | DeepDelta | LGBMsub | Delta LGBMsub | |
Fraction Unbound, Brain | 0.535 ± 0.008 | 0.483 ± 0.023 | 0.701 ± 0.013 | 0.47 ± 0.041 | 0.53 ± 0.015 | 0.713 ± 0.008 | 0.740 ± 0.01 | 0.642 ± 0.014 | 1.003 ± 0.008 | 0.726 ± 0.011 | 0.928 ± 0.01 | 0.965 ± 0.019 | 0.830 ± 0.023 | 1.311 ± 0.014 | 0.939 ± 0.014 |
Renal Clearance | 0.461 ± 0.01 | 0.478 ± 0.013 | 0.465 ± 0.023 | 0.283 ± 0.016 | 0.443 ± 0.007 | 0.256 ± 0.002 | 0.262 ± 0.004 | 0.269 ± 0.006 | 0.307 ± 0.003 | 0.265 ± 0.002 | 0.337 ± 0.002 | 0.339 ± 0.005 | 0.350 ± 0.008 | 0.396 ± 0.004 | 0.344 ± 0.002 |
Free Solvation | 0.843 ± 0.005 | 0.967 ± 0.0 | 0.971 ± 0.001 | 0.589 ± 0.007 | 0.898 ± 0.003 | 1.874 ± 0.028 | 0.937 ± 0.006 | 0.806 ± 0.003 | 4.23 ± 0.058 | 1.656 ± 0.027 | 2.914 ± 0.045 | 1.372 ± 0.009 | 1.290 ± 0.023 | 5.472 ± 0.064 | 2.415 ± 0.037 |
Microsomal Clearance | 0.444 ± 0.002 | 0.451 ± 0.011 | 0.468 ± 0.007 | 0.273 ± 0.011 | 0.42 ± 0.01 | 0.434 ± 0.002 | 0.436 ± 0.003 | 0.444 ± 0.002 | 0.509 ± 0.004 | 0.443 ± 0.002 | 0.544 ± 0.001 | 0.546 ± 0.005 | 0.557 ± 0.002 | 0.638 ± 0.005 | 0.556 ± 0.003 |
Hemolytic Toxicity | 0.821 ± 0.002 | 0.778 ± 0.003 | 0.842 ± 0.002 | 0.706 ± 0.007 | 0.816 ± 0.003 | 0.506 ± 0.002 | 0.566 ± 0.006 | 0.487 ± 0.004 | 0.897 ± 0.008 | 0.516 ± 0.004 | 0.663 ± 0.005 | 0.729 ± 0.007 | 0.635 ± 0.006 | 1.127 ± 0.01 | 0.672 ± 0.005 |
Hepatic Clearance | 0.438 ± 0.004 | 0.431 ± 0.005 | 0.392 ± 0.007 | 0.28 ± 0.013 | 0.424 ± 0.013 | 0.45 ± 0.002 | 0.455 ± 0.002 | 0.494 ± 0.003 | 0.529 ± 0.006 | 0.46 ± 0.005 | 0.564 ± 0.002 | 0.570 ± 0.002 | 0.622 ± 0.004 | 0.663 ± 0.008 | 0.575 ± 0.005 |
Caco2 | 0.829 ± 0.006 | 0.851 ± 0.005 | 0.853 ± 0.005 | 0.565 ± 0.013 | 0.829 ± 0.004 | 0.472 ± 0.006 | 0.451 ± 0.006 | 0.444 ± 0.006 | 0.82 ± 0.012 | 0.473 ± 0.005 | 0.614 ± 0.01 | 0.575 ± 0.007 | 0.572 ± 0.008 | 1.036 ± 0.014 | 0.61 ± 0.007 |
Aqueous Solubility | 0.837 ± 0.003 | 0.951 ± 0.001 | 0.957 ± 0.001 | 0.596 ± 0.006 | 0.852 ± 0.003 | 1.237 ± 0.003 | 0.687 ± 0.005 | 0.644 ± 0.006 | 2.184 ± 0.029 | 1.197 ± 0.004 | 1.623 ± 0.011 | 0.915 ± 0.008 | 0.859 ± 0.012 | 2.783 ± 0.038 | 1.562 ± 0.011 |
Volume of Distribution at Steady State | 0.728 ± 0.003 | 0.697 ± 0.003 | 0.746 ± 0.005 | 0.578 ± 0.006 | 0.719 ± 0.003 | 0.483 ± 0.003 | 0.505 ± 0.004 | 0.470 ± 0.004 | 0.772 ± 0.006 | 0.493 ± 0.003 | 0.632 ± 0.003 | 0.670 ± 0.004 | 0.618 ± 0.006 | 0.969 ± 0.008 | 0.64 ± 0.003 |
Half-life | 0.529 ± 0.006 | 0.508 ± 0.008 | 0.534 ± 0.004 | 0.330 ± 0.007 | 0.514 ± 0.003 | 0.586 ± 0.003 | 0.600 ± 0.003 | 0.597 ± 0.003 | 0.662 ± 0.003 | 0.594 ± 0.005 | 0.762 ± 0.003 | 0.784 ± 0.004 | 0.778 ± 0.004 | 0.849 ± 0.003 | 0.771 ± 0.002 |