Curvature-based Transformer for Molecular Property Prediction

25 Jul 2023  ·  Yili Chen, Zhengyu Li, Zheng Wan, Hui Yu, Xian Wei ·

The prediction of molecular properties is one of the most important and challenging tasks in the field of artificial intelligence-based drug design. Among the current mainstream methods, the most commonly used feature representation for training DNN models is based on SMILES and molecular graphs, although these methods are concise and effective, they also limit the ability to capture spatial information. In this work, we propose Curvature-based Transformer to improve the ability of Graph Transformer neural network models to extract structural information on molecular graph data by introducing Discretization of Ricci Curvature. To embed the curvature in the model, we add the curvature information of the graph as positional Encoding to the node features during the attention-score calculation. This method can introduce curvature information from graph data without changing the original network architecture, and it has the potential to be extended to other models. We performed experiments on chemical molecular datasets including PCQM4M-LST, MoleculeNet and compared with models such as Uni-Mol, Graphormer, and the results show that this method can achieve the state-of-the-art results. It is proved that the discretized Ricci curvature also reflects the structural and functional relationship while describing the local geometry of the graph molecular data.

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