GeoT: A Geometry-Aware Transformer for Reliable Molecular Property Prediction and Chemically Interpretable Representation Learning

Abstract

In recent years, molecular representation learning has emerged as a key area of focus in various chemical tasks. However, many existing models fail to fully consider the geometric information on molecular structures, resulting in less intuitive representations. Moreover, the widely used message passing mechanism is limited to providing the interpretation of experimental results from a chemical perspective. To address these challenges, we introduce a novel transformer-based framework for molecular representation learning, named the geometry-aware transformer (GeoT). The GeoT learns molecular graph structures through attention-based mechanisms specifically designed to offer reliable interpretability as well as molecular property prediction. Consequently, the GeoT can generate attention maps of the interatomic relationships associated with training objectives. In addition, the GeoT demonstrates performance comparable to that of MPNN-based models while achieving reduced computational complexity. Our comprehensive experiments, including an empirical simulation, reveal that the GeoT effectively learns chemical insights into molecular structures, bridging the gap between artificial intelligence and molecular sciences.