Cancer subtype identification using deep learning approach

Abstract

In this paper, a framework using deep learning approach is proposed to identify two subtypes of human colorectal carcinoma cancer. The identification process uses information from gene expression and clinical data which is obtained from data integration process. One of deep learning architecture, multimodal Deep Boltzmann Machines (DBM) is used for data integration process. The joint representation gene expression and clinical is later used as Restricted Boltzmann Machines (RBM) input for cancer subtype identification. Kaplan Meier survival analysis is employed to evaluate the identification result. The curves on survival plot obtained from Kaplan Meier analysis are tested using three statistic tests to ensure that there is a significant difference between those curves. According to Log Rank, Generalized Wilcoxon and Tarone-Ware, the two groups of patients with different cancer subtypes identified using the proposed framework are significantly different.