SurProGenes: Survival Risk-Ordered Representation of Cancer Patients and Genes for the Identification of Prognostic Genes

Identifying prognostic genes associated with patient survival is an important goal in cancer genomics, as this information could inform treatment approaches and improve patient outcomes. However, the identification of prognostic genes is complicated by the high dimensionality of genetic data, which makes their identification computationally intensive. Furthermore, most cancer genomics studies lack appropriate low-risk groups against which to compare. To address these issues, we present a framework that identifies candidate prognostic genes by integrating representation learning and statistical analysis approaches. Specifically, we propose a collaborative filtering-derived mechanism to represent patients in order of their survival risk, facilitating their dichotomization. We also propose a mechanism that allows embedded gene vectors to be polarized on the extremities of, or centered on, both reference axes to facilitate recommendations. Restricting our analysis to a few representative genes within each cluster allowed for the efficient identification of prognostic genes. Finally, we demonstrate the potential of this proposed framework for identifying prognostic genes.