PCA-constrained multi-core matrix fusion network: A novel approach for cancer subtype identification.

Abstract

Cancer subtyping refers to categorizing a particular cancer type into distinct subtypes or subgroups based on a range of molecular characteristics, clinical manifestations, histological features, and other relevant factors. The identification of cancer subtypes can significantly enhance precision in clinical practice and facilitate personalized diagnosis and treatment strategies. Recent advancements in the field have witnessed the emergence of numerous network fusion methods aimed at identifying cancer subtypes. The majority of these fusion algorithms, however, solely rely on the fusion network of a single core matrix for the identification of cancer subtypes and fail to comprehensively capture similarity. To tackle this issue, in this study, we propose a novel cancer subtype recognition method, referred to as PCA-constrained multi-core matrix fusion network (PCA-MM-FN). The PCA-MM-FN algorithm initially employs three distinct methods to obtain three core matrices. Subsequently, the obtained core matrices are projected into a shared subspace using principal component analysis, followed by a weighted network fusion. Lastly, spectral clustering is conducted on the fused network. The results obtained from conducting experiments on the mRNA expression, DNA methylation, and miRNA expression of five TCGA datasets and three multi-omics benchmark datasets demonstrate that the proposed PCA-MM-FN approach exhibits superior accuracy in identifying cancer subtypes compared to the existing methods.