Improving QSAR Modeling for Predictive Toxicology using Publicly Aggregated Semantic Graph Data and Graph Neural Networks

Abstract

Quantitative Structure-Activity Relationship (QSAR) modeling is the most common computational technique for predicting chemical toxicity, but a lack of methodological innovations in QSAR have led to underwhelming performance. We show that contemporary QSAR modeling for predictive toxicology can be substantially improved by incorporating semantic graph data aggregated from open-access public databases, and analyzing those data in the context of graph neural networks (GNNs). Furthermore, we introspect the GNNs to demonstrate how they can lead to more interpretable applications of QSAR, and use ablation analysis to explore the contribution of different data elements to the final models’ performance.