Graph Sampling-based Meta-Learning for Molecular Property Prediction

Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be recorded with several different properties simultaneously. To effectively utilize many-to-many correlations of molecules and properties, we propose a Graph Sampling-based Meta-learning (GS-Meta) framework for few-shot molecular property prediction. First, we construct a Molecule-Property relation Graph (MPG): molecule and properties are nodes, while property labels decide edges. Then, to utilize the topological information of MPG, we reformulate an episode in meta-learning as a subgraph of the MPG, containing a target property node, molecule nodes, and auxiliary property nodes. Third, as episodes in the form of sub-graphs are no longer independent of each other, we propose to schedule the subgraph sampling process with a contrastive loss function, which considers the consistency and discrimination of subgraphs. Extensive experiments on 5 commonly-used benchmarks show GS-Meta consistently outperforms state-of-the-art methods by 5.71%-6.93% in ROC-AUC and verify the effectiveness of each proposed module. Our code is available at https://github.com/HICAI-ZJU/GS-Meta.