Fast and Accurate Molecular Property Prediction: Learning Atomic Interactions and Potentials with Neural Networks.

Abstract

The discovery of molecules with specific properties is crucial to developing effective materials and useful drugs. Recently, to accelerate such discoveries with machine learning, deep neural networks (DNNs) have been applied to quantum chemistry calculations based on the density functional theory (DFT). While various DNNs for quantum chemistry have been proposed, these networks require various chemical descriptors as inputs and a large number of learning parameters to model atomic interactions. In this paper, we propose a new DNN-based molecular property prediction that (i) does not depend on descriptors, (ii) is more compact, and (iii) involves additional neural networks to model the interactions between all the atoms in a molecular structure. In the consideration of the molecular structure, we also model the potentials between all the atoms; this allows the neural networks to simultaneously learn the atomic interactions and potentials. We emphasize that these atomic "pair" interactions and potentials are characterized using the global molecular structure, a function of the depth of the neural networks; this leads to the implicit or indirect consideration of atomic "many-body" interactions and potentials within the DNNs. In the evaluation of our model with the benchmark QM9 data set, we achieved fast and accurate prediction performances for various quantum chemical properties. In addition, we analyzed the effects of learning the interactions and potentials on each property. Furthermore, we demonstrated an extrapolation evaluation, i.e., we trained a model with small molecules and tested it with large molecules. We believe that insights into the extrapolation evaluation will be useful for developing more practical applications in DNN-based molecular property predictions.