Towards Interpretable Molecular Graph Representation Learning

Emmanuel Noutahi, Dominique Beani, Julien Horwood, Prudencio Tossou

TL;DR: We propose a new Laplacian-based hierarchical graph pooling layers that not only outperforms existing GNNs on several graph benchmarks but is also more interpretable.

Abstract:

Recent work in graph neural networks (GNNs) has led to improvements in molecular activity and property prediction tasks. Unfortunately, GNNs often fail to capture the relative importance of interactions between molecular substructures, in part due to the absence of efficient intermediate pooling steps. To address these issues, we propose LaPool (Laplacian Pooling), a novel, data-driven, and interpretable hierarchical graph pooling method that takes into account both node features and graph structure to improve molecular understanding.
We benchmark LaPool and show that it not only outperforms recent GNNs on molecular graph understanding and prediction tasks but also remains highly competitive on other graph types. We then demonstrate the improved interpretability achieved with LaPool using both qualitative and quantitative assessments, highlighting its potential applications in drug discovery.

Code: https://anonymous.4open.science/r/941cb9ee-302f-4c81-bbf9-abcff1e98894/

Keywords: molecular graphs, graph pooling, hierarchical, GNN, Laplacian, drug discovery