Machine learning in prediction of intrinsic aqueous solubility of drug-like compounds: Generalization, complexity, or predictive ability?

Abstract

We present a collection of publicly available intrinsic aqueous solubility data of 829 drug-like compounds. Four different machine learning algorithms (random forests [RF], LightGBM, partial least squares, and least absolute shrinkage and selection operator [LASSO]) coupled with multistage permutation importance for feature selection and Bayesian hyperparameter optimization were used for the prediction of solubility based on chemical structural information. Our results show that LASSO yielded the best predictive ability on an external test set with a root mean square error (RMSE) (test) of 0.70 log points, an R2(test) of 0.80, and 105 features. Taking into account the number of descriptors as well, an RF model achieves the best balance between complexity and predictive ability with an RMSE(test) of 0.72 log points, an R2(test) of 0.78, and with only 17 features. On a more aggressive test set (principal component analysis [PCA]-based split), better generalization was observed for the RF model. We propose a ranking score for choosing the best model, as test set performance is only one of the factors in creating an applicable model. The ranking score is a weighted combination of generalization, number of features, and test performance. Out of the two best learners, a consensus model was built exhibiting the best predictive ability and generalization with RMSE(test) of 0.67 log points and a R2(test) of 0.81. © 2021 The Authors. Journal of Chemometrics published by John Wiley & Sons Ltd.