Deep representation learning for temporal inference in cancer omics: a systematic literature review

Deep learning methods, including deep representation learning (DRL) approaches such as variational autoencoders (VAEs), have been widely applied to cancer omics data to address the high dimensionality of these datasets. Despite remarkable advances, cancer is a complex and dynamic disease, making it challenging to study, and the temporal resolution of cancer progression captured by omics-based studies remains limited. In this systematic literature review, we explore the use of DRL, particularly the VAE, in cancer omics studies for modeling time-related processes, such as tumor progression and evolutionary dynamics. Our work reveals that these methods most commonly support subtyping, diagnosis, and prognosis in this context, but rarely emphasize temporal information. We observed that the scarcity of longitudinal omics data currently limits deeper temporal analyses that could enhance these applications. We propose that applying the VAE as a generative model to study cancer in time, particularly focusing on cancer staging, could lead to meaningful advancements in our understanding of the disease.