Dual-Modality Representation Learning for Molecular Property Prediction

Abstract

Molecular property prediction has attracted substantial attention recently. Accurate prediction of drug properties relies heavily on effective molecular representations. The structures of chemical compounds are commonly represented as graphs or SMILES sequences. Recent advances in learning drug properties commonly employ Graph Neural Networks (GNNs) based on the graph representation. For the SMILES representation, Transformer-based architectures have been adopted by treating each SMILES string as a sequence of tokens. Because each representation has its own advantages and disadvantages, combining both representations in learning drug properties is a promising direction. We propose a method named Dual-Modality Cross-Attention (DMCA) that can effectively combine the strengths of two representations by employing the cross-attention mechanism. DMCA was evaluated across eight datasets including both classification and regression tasks. Results show that our method achieves the best overall performance, highlighting its effectiveness in leveraging the complementary information from both graph and SMILES modalities.