FunQG: Molecular Representation Learning via Quotient Graphs

To accurately predict molecular properties, it is important to learn expressive molecular representations. Graph neural networks (GNNs) have made significant advances in this area, but they often face limitations like neighbors-explosion, under-reaching, oversmoothing, and oversquashing. Additionally, GNNs tend to have high computational costs due to their large number of parameters. These limitations emerge or increase when dealing with larger graphs or deeper GNN models. One potential solution is to simplify the molecular graph into a smaller, richer, and more informative one that is easier to train GNNs. Our proposed molecular graph coarsening framework called FunQG, uses Functional groups as building blocks to determine a molecule’s properties, based on a graph-theoretic concept called Quotient Graph. We show through experiments that the resulting informative graphs are much smaller than the original molecular graphs and are thus more suitable for training GNNs. We apply FunQG to popular molecular property prediction benchmarks and compare the performance of popular baseline GNNs on the resulting data sets to that of state-of-the-art baselines on the original data sets. Our experiments demonstrate that FunQG yields notable results on various data sets while dramatically reducing the number of parameters and computational costs. By utilizing functional groups, we can achieve an interpretable framework that indicates their significant role in determining the properties of molecular quotient graphs. Consequently, FunQG is a straightforward, computationally efficient, and generalizable solution for addressing the molecular representation learning problem.