A molecular hypergraph convolutional network with functional group information

Junyoung Park, Fangying Chen, Jinkyoo Park

Keywords: Molecule, Functional group, graph, hypergraph, chemistry

Abstract: We propose a Molecular Hypergraph Convolutional Network (MolHGCN) that predicts the molecular properties of a molecule using the atom and functional group information as inputs. Molecules can contain many types of functional groups, which will affect the properties the molecules. For example, the toxicity of a molecule is associated with toxicophores, such as nitroaromatic groups and thiourea. Conventional graph-based methods that consider the pair-wise interactions between nodes are inefficient in expressing the complex relationship between multiple nodes in a graph flexibly, and applying multi-hops may result in oversmoothing and overfitting problems. Hence, we propose MolHGCN to capture the substructural difference between molecules using the atom and functional group information. MolHGCN constructs a hypergraph representation of a molecule using functional group information from the input SMILES strings, extracts hidden representation using a two-stage message passing process (atom and functional group message passing), and predicts the properties of the molecules using the extracted hidden representation. We evaluate the performance of our model using Tox21, ClinTox, SIDER, BBBP, BACE, ESOL, FreeSolv and Lipophilicity datasets. We show that our model is able to outperform other baseline methods for most of the datasets. We particularly show that incorporating functional group information along with atom information results in better separability in the latent space, thus increasing the prediction accuracy of the molecule property prediction.