MTS-Net: An enriched topology-aware architecture for molecular graph representation learning

Abstract

Molecular graph representation learning has been widely applied in various domains such as drug design. It leverages deep learning techniques to transform molecular graphs into numerical vectors. Graph Transformer architecture is commonly used for molecular graph representation learning. Nevertheless, existing methods based on the Graph Transformer fail to fully exploit the topological structural information of the molecular graphs, leading to information loss for molecular representation. To solve this problem, we propose a novel molecular graph representation learning method called MTS-Net (Molecular Topological Structure-Network), which combines both global and local topological structure of a molecule. In global topological representation, the molecule graph is first transformed into a tree structure and then encoded by employing a hash algorithm for tree. In local topological representation, paths between atom pairs are transcoded and incorporated into the calculation of the Transformer attention coefficients. Moreover, MTS-Net has intuitive interpretability for identifying key structures within molecules. Experiments on eight molecular property prediction datasets show that MTS-Net achieves optimal results in three out of five classification tasks, the average accuracy is 0.85, and all three regression tasks.