Accurate molecular subtypes prediction of cancer patients is significant for personalized cancer diagnosis and treatments. Large amount of multi-omics data and the advancement of data-driven methods are expected to facilitate molecular subtyping of cancer. Most existing machine learning–based methods usually classify samples according to single omics data, fail to integrate multi-omics data to learn comprehensive representations of the samples, and ignore that information transfer and aggregation among samples can better represent them and ultimately help in classification. We propose a novel framework named multi-omics graph convolutional network (M-GCN) for molecular subtyping based on robust graph convolutional networks integrating multi-omics data. We first apply the Hilbert–Schmidt independence criterion least absolute shrinkage and selection operator (HSIC Lasso) to select the molecular subtype-related transcriptomic features and then construct a sample–sample similarity graph with low noise by using these features. Next, we take the selected gene expression, single nucleotide variants (SNV), and copy number variation (CNV) data as input and learn the multi-view representations of samples. On this basis, a robust variant of graph convolutional network (GCN) model is finally developed to obtain samples’ new representations by aggregating their subgraphs. Experimental results of breast and stomach cancer demonstrate that the classification performance of M-GCN is superior to other existing methods. Moreover, the identified subtype-specific biomarkers are highly consistent with current clinical understanding and promising to assist accurate diagnosis and targeted drug development.

Molecular subtyping of cancer is recognized as a critical and challenging step towards individualized therapy. Most existing computational methods solve this problem via multi-classification of gene-expressions of cancer samples. Although these methods, especially deep learning, perform well in data classification, they usually require large amounts of data for model training and have limitations in interpretability. Besides, as cancer is a complex systemic disease, the phenotypic difference between cancer samples can hardly be fully understood by only analyzing single molecules, and differential expression-based molecular subtyping methods are reportedly not conserved. To address the above issues, we present here a new framework for molecular subtyping of cancer through identifying a robust specific co-expression module for each subtype of cancer, generating network features for each sample by perturbing correlation levels of specific edges, and then training a deep neural network for multi-class classification. When applied to breast cancer (BRCA) and stomach adenocarcinoma (STAD) molecular subtyping, it has superior classification performance over existing methods. In addition to improving classification performance, we consider the specific co-expressed modules selected for subtyping to be biologically meaningful, which potentially offers new insight for diagnostic biomarker design, mechanistic studies of cancer, and individualized treatment plan selection.

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