A Comprehensive Review of Deep Learning Applications with Multi-Omics Data in Cancer Research

The integration of deep learning (DL) with multi-omics data has significantly advanced our understanding of biological systems, particularly in cancer research. DL enables the analysis of high-dimensional datasets and the discovery of novel disease mechanisms and biomarkers, contributing to improved patient treatment and management. This review provides a detailed overview of recent developments in deep learning models applied to genomics data, with a focus on cancer type classification, driver gene identification, survival analysis, and drug response prediction. We introduce the foundational concepts of machine and deep learning and explain the characteristics of multi-omics data, addressing a broad and interdisciplinary audience. Methods published since 2020 are systematically reviewed, including their model architectures, datasets, and key innovations.