Image-Like Graph Representations for Improved Molecular Property Prediction

Abstract

Research into deep learning models for molecular property prediction has primarily focused on the development of better Graph Neural Network (GNN) architectures. Though new GNN variants continue to improve performance, their modifications share a common theme of alleviating problems intrinsic to their fundamental graph-to-graph nature. In this work, we examine these limitations and propose a new molecular representation that bypasses the need for GNNs entirely, dubbed CubeMol. Our fixed-dimensional stochastic representation, when paired with a transformer model, exceeds the performance of state-of-the-art GNN models and provides a path for scalability.