Recent Advances in Toxicity Prediction: Applications of Deep Graph Learning

The development of new drugs is time-consuming and expensive, and as such, accurately predicting the potential toxicity of a drug candidate is crucial in ensuring its safety and efficacy. Recently, deep graph learning has become prevalent in this field due to its computational power and cost efficiency. Many novel deep graph learning methods aid toxicity prediction and further prompt drug development. This review aims to connect fundamental knowledge with burgeoning deep graph learning methods. We first summarize the essential components of deep graph learning models for toxicity prediction, including molecular descriptors, molecular representations, evaluation metrics, validation methods, and data sets. Furthermore, based on various graph-related representations of molecules, we introduce several representative studies and methods for toxicity prediction from the perspective of GNN architectures and graph pretrained models. Compared to other types of models, deep graph models not only advance in higher accuracy and efficiency but also provide more intuitive insights, which is significant in the development of model interpretation and generalization ability. The graph pretrained models are emerging as they can extract prominent features from large-scale unlabeled molecular graph data and improve the performance of downstream toxicity prediction tasks. We hope this survey can serve as a handbook for individuals interested in exploring deep graph learning for toxicity prediction.