SGNN-T: Space graph neural network coupled transformer for molecular property prediction

Abstract

Molecular properties play a crucial role in material discovery, protein interaction and drug development. The appearance of Graph Neural Network (GNN) significantly improved the performance of molecular property prediction. However, nodes in GNN only update the features of neighbor nodes, resulting in insufficient ability to encode global feature information. The self- attention mechanism in transformer can encode the global information except for local information of molecules, while its spatial information is insufficient. Since molecules are three-dimensional spatial structures, spatial geometry information is an important attribute for molecules properties. To consider these factors, a network model of Space Graph Neural Network coupled Transformer (SGNN-T) is proposed in this paper which can combine global and local molecule information with three-dimensional spatial structures for molecular properties prediction. In this model, Graph neural network Geometric Feature Fusion Module (GGFF) and Transformer Spatial Geometric Feature Enhancement Module (TSGFE) are included to enhance the spatial geometry learning ability of the network. The GGFF module constructs a parallel graph neural network by thinking over atoms, bonds and bond angles at the same time which effectively complements the spatial information of the network by leading into bond angles than normal GNN. The TSGFE module introduces the coordinates and centrality degree features coupled with the features by GGFF into transformer to further enhance the geometric expression ability of the module. Through these two parts, SGNN-T model can encode local and global information of molecules at the same time. Property prediction experiments are executed on the QM9, OMDB and MEGNet dataset. The results of MAE show the proposed model has the best performance than the popular models.