Geometry-Augmented Molecular Representation Learning for Property Prediction

• Published in: IEEE/ACM transactions on computational biology and bioinformatics 2024-09, Vol.21 (5), p.1518-1528
• Main Authors: Zhang, Yanan, Bai, Xiangzhi
• Format: Article
• Language: English
• Subjects: Chemicals; Computer architecture; Encoding; Geometry; graph neural network molecular representation learning; molecular geometry information; Representation learning; Self-attention mechanism; Three-dimensional displays; Transformers
• ISSN: 1545-5963; 1557-9964; 1557-9964
• DOI: 10.1109/TCBB.2024.3402337

Accurate molecular representation plays a crucial role in expediting the process of drug discovery. Graph neural networks (GNNs) have demonstrated robust capabilities in molecular representation learning, adept at capturing structural and spatial information in molecular graphs. For molecular representation learning, most previous GNN methods are specialized in dealing with 2D or 3D molecular data formats. By further fusing the geometric attributes and structural features of molecules, we can elevate the performance of molecular representation. To realize this, we present a novel geometry-augmented molecular representation learning model, designed to effectively encode both the 2D structural and 3D spatial information inherent in molecular graphs. By incorporating structural and spatial information as attention biases in the graph Transformer framework, our model offers a comprehensive architecture that introduces molecular structural details at both atom and bond levels. We further propose a geometry information fusion module to encode the geometry information within 3D molecular graphs. The experimental results show the efficacy of our model, demonstrating its ability to achieve competitive performance when compared to state-of-the-art (SOTA) models in various property prediction tasks.