Accurate, reliable and interpretable solubility prediction of druglike molecules with attention pooling and Bayesian learning

In drug discovery, aqueous solubility is an important pharmacokinetic property which affects absorption and assay availability of drug. Thus, in silico prediction of solubility has been studied for its utility in virtual screening and lead optimization. Recently, machine learning (ML) methods using experimental data has been popular because physics-based methods like quantum mechanics and molecular dynamics are not suitable for high-throughput tasks due to its computational costs. However, ML method can exhibit over-fitting problem in a data-deficient condition, and this is the case for most chemical property datasets. In addition, ML methods are regarded as a black box function in that it is difficult to interpret contribution of hidden features to outputs, hindering analysis and modification of structure-activity relationship. To deal with mentioned issues, we developed Bayesian graph neural networks (GNNs) with the self-attention readout layer. Unlike most GNNs using self-attention in node updates, self-attention applied at readout layer enabled a model to improve prediction performance as well as to identify atom-wise importance, which can help lead optimization as exemplified for three FDA-approved drugs. Also, Bayesian inference enables us to separate more or less accurate results according to uncertainty in solubility prediction task We expect that our accurate, reliable and interpretable model can be used for more careful decision-making and various applications in the development of drugs.