Recent Advances in Deep Learning-Based Drug-Target Binding Affinity Prediction

Abstract

Computational approaches to drug discovery involve multiple sub-problems, and among them, drug-target binding affinity prediction plays an important role. Despite recent advances, accurately predicting binding affinity remains an open research area. The major objective of our paper is to perform a comprehensive review and comparative analysis of recent machine learning methods for drug-target binding affinity prediction, with a focus on identifying strengths, limitations, and research gaps. We review representative recent deep learning approaches that use common benchmark datasets and evaluation metrics, covering a range of neural network architectures and representation strategies. In addition, we analyze seven widely used benchmark datasets and commonly adopted evaluation metrics for drug-target binding affinity prediction. Our analysis indicates that although many methods report strong performance on standard benchmarks, their effectiveness is often influenced by dataset bias and limited evaluation settings. Furthermore, most methods exhibit reduced performance in cold-start scenarios, highlighting challenges in generalization. We identify several limitations of current approaches, including dataset imbalance, the lack of standardized evaluation, limited real-world applicability, and challenges in cold-start scenarios. We also discuss future research directions, including better dataset design, more robust evaluation methods, improved handling of cold-start problems, and the integration of multimodal representations.