Recent Developments in GNNs for Drug Discovery

In this paper, we review recent developments and the role of Graph Neural Networks (GNNs) in computational drug discovery, including molecule generation, molecular property prediction, and drug-drug interaction prediction. By summarizing the most recent developments in this area, we underscore the capabilities of GNNs to comprehend intricate molecular patterns, while exploring both their current and prospective applications. We initiate our discussion by examining various molecular representations, followed by detailed discussions and categorization of existing GNN models based on their input types and downstream application tasks. We also collect a list of commonly used benchmark datasets for a variety of applications. We conclude the paper with brief discussions and summarize common trends in this important research area.

@article{fang2025_2506.01302,
  title={ Recent Developments in GNNs for Drug Discovery },
  author={ Zhengyu Fang and Xiaoge Zhang and Anyin Zhao and Xiao Li and Huiyuan Chen and Jing Li },
  journal={arXiv preprint arXiv:2506.01302},
  year={ 2025 }
}