Capsule Network Based Modeling of Multi-omics Data for Discovery of Breast Cancer-Related Genes

Breast cancer is one of the most common cancers all over the world, which bring about more than 450,000 deaths each year. Although this malignancy has been extensively studied by a large number of researchers, its prognosis is still poor. Since therapeutic advance can be obtained based on gene signatures, there is an urgent need to discover genes related to breast cancer that may help uncover the mechanisms in cancer progression. We propose a deep learning method for the discovery of breast cancer-related genes by using Capsule Network based Modeling of Multi-omics Data (CapsNetMMD). In CapsNetMMD, we make use of known breast cancer-related genes to transform the issue of gene identification into the issue of supervised classification. The features of genes are generated through comprehensive integration of multi-omics data, e.g., mRNA expression, z scores for mRNA expression, DNA methylation, and two forms of DNA copy-number alterations (CNAs). By modeling features based on the capsule network, we identify breast cancer-related genes with a significantly better performance than other existing machine learning methods. The predicted genes with prognostic values play potential important roles in breast cancer and may serve as candidates for biologists and medical scientists in the future studies of biomarkers.