Efficient multi-omics clustering with bipartite graph subspace learning for cancer subtype prediction

Abstract

<p>Due to the complex nature and highly heterogeneous of cancer, as well as different pathogenesis and clinical features among different cancer subtypes, it was crucial to identify cancer subtypes in cancer diagnosis, prognosis, and treatment. The rapid developments of high-throughput technologies have dramatically improved the efficiency of collecting data from various types of omics. Also, integrating multi-omics data related to cancer occurrence and progression can lead to a better understanding of cancer pathogenesis, subtype prediction, and personalized treatment options. Therefore, we proposed an efficient multi-omics bipartite graph subspace learning anchor-based clustering (MBSLC) method to identify cancer subtypes. In contrast, the bipartite graph intended to learn cluster-friendly representations. Experiments showed that the proposed MBSLC method can capture the latent spaces of multi-omics data effectively and showed superiority over other state-of-the-art methods for cancer subtype analysis. Moreover, the survival and clinical analyses further demonstrated the effectiveness of MBSLC. The code and datasets of this paper can be found in <ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://github.com/Julius666/MBSLC">https://github.com/Julius666/MBSLC</ext-link>.</p>