Few-shot Molecular Property Prediction via Hierarchically Structured Learning on Relation Graphs

Abstract

This paper studies few-shot molecular property prediction, which is a fundamental problem in cheminformatics and drug discovery. More recently, graph neural network based model has gradually become the theme of molecular property prediction. However, there is a natural deficiency for existing methods, that is, the scarcity of molecules with desired properties, which makes it hard to build an effective predictive model. In this paper, we propose a novel framework called Hierarchically Structured Learning on Relation Graphs (HSL-RG) for molecular property prediction, which explores the structural semantics of a molecule from both global-level and local-level granularities. Technically, we first leverage graph kernels to construct relation graphs to globally communicate molecular structural knowledge from neighboring molecules and then design self-supervised learning signals of structure optimization to locally learn transformation-invariant representations from molecules themselves. Moreover, we propose a task-adaptive meta-learning algorithm to provide meta knowledge customization for different tasks in few-shot scenarios. Experiments on multiple real-life benchmark datasets show that HSL-RG is superior to existing state-of-the-art approaches.