Learning Topology-Specific Experts for Molecular Property Prediction
This work addresses a bottleneck in molecular property prediction for cheminformatics applications, offering an incremental improvement over existing methods.
The paper tackles the problem of limited prediction performance when using a single graph neural network for diverse molecular structures by proposing TopExpert, which uses topology-specific experts for different molecular groups, resulting in boosted performance and better generalization for new molecules with unseen scaffolds.
Recently, graph neural networks (GNNs) have been successfully applied to predicting molecular properties, which is one of the most classical cheminformatics tasks with various applications. Despite their effectiveness, we empirically observe that training a single GNN model for diverse molecules with distinct structural patterns limits its prediction performance. In this paper, motivated by this observation, we propose TopExpert to leverage topology-specific prediction models (referred to as experts), each of which is responsible for each molecular group sharing similar topological semantics. That is, each expert learns topology-specific discriminative features while being trained with its corresponding topological group. To tackle the key challenge of grouping molecules by their topological patterns, we introduce a clustering-based gating module that assigns an input molecule into one of the clusters and further optimizes the gating module with two different types of self-supervision: topological semantics induced by GNNs and molecular scaffolds, respectively. Extensive experiments demonstrate that TopExpert has boosted the performance for molecular property prediction and also achieved better generalization for new molecules with unseen scaffolds than baselines. The code is available at https://github.com/kimsu55/ToxExpert.