Artificial intelligence for comprehensive DNA methylation analysis: overview, challenges, and future directions

This paper offers a comprehensive review of the synergy between artificial intelligence and DNA methylation analysis, encompassing machine learning, deep learning, natural language processing, and explainable artificial intelligence. In this study, we also highlighted the underexplored potential of signal processing and large language models-based models in DNA methylation research. Additionally, we discussed the challenges and limitations faced when managing and analyzing large and complex DNA methylation datasets. Furthermore, this article tries to shed light on the continuing evolution of this field and on the possible directions for future research.