Flexible Dual-Branched Message-Passing Neural Network for a Molecular Property Prediction
Jeonghee Jo, Bumju Kwak, Byunghan Lee, Sungroh Yoon
Abstract
A molecule is a complex of heterogeneous components, and the spatial arrangements of these components determine the whole molecular properties and characteristics. With the advent of deep learning in computational chemistry, several studies have focused on how to predict molecular properties based on molecular configurations. MA message-passing neural network provides an effective framework for capturing molecular geometric features with the perspective of a molecule as a graph. However, most of these studies assumed that all heterogeneous molecular features, such as atomic charge, bond length, or other geometric features, always contribute equivalently to the target prediction, regardless of the task type. In this study, we propose a dual-branched neural network for molecular property prediction based on both the message-passing framework and standard multilayer perceptron neural networks. Our model learns heterogeneous molecular features with different scales, which are trained flexibly according to each prediction target. In addition, we introduce a discrete branch to learn single-atom features without local aggregation, apart from message-passing steps. We verify that this novel structure can improve the model performance. The proposed model outperforms other recent models with sparser representations. Our experimental results indicate that, in the chemical property prediction tasks, the diverse chemical nature of targets should be carefully considered for both model performance and generalizability. Finally, we provide the intuitive analysis between the experimental results and the chemical meaning of the target.