Molecular Property Prediction Based on a Multichannel Substructure Graph

Abstract

Molecular property prediction is important to drug design. With the development of artificial intelligence, deep learning methods are effective for extracting molecular features. In this paper, we propose a multichannel substructure-graph gated recurrent unit (GRU) architecture, which is a novel GRU-based neural network with attention mechanisms applied to molecular substructures to learn and predict properties. In the architecture, molecular features are extracted at the node level and molecule level for capturing fine-grained and coarse-grained information. In addition, three bidirectional GRUs are adopted to extract the features on three channels to generate the molecular representations. Different attention weights are assigned to the entities in the molecule to evaluate their contributions. Experiments are implemented to compare our model with benchmark models in molecular property prediction for both regression and classification tasks, and the results show that our model has strong robustness and generalizability.

Keywords

• Molecular graph
• molecular property prediction
• substructure-graph