MCDHGN: Heterogeneous network-based cancer driver gene prediction and interpretability analysis.

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Abstract

Accurately predicting the driver genes of cancer is of great significance for carcinogenesis progress research and cancer treatment. In recent years, more and more deep-learning-based methods have been used for predicting cancer driver genes. However, deep learning algorithms often have black box properties and cannot interpret the output results. Here, we propose a novel cancer driver gene mining method based on heterogeneous network metapaths (MCDHGN), which uses meta-path aggregation to enhance the interpretability of predictions.MCDHGN constructs a heterogeneous network by using several types of multi-omics data that are biologically linked to genes. And the differential probabilities of SNV, DNA methylation, and gene expression data between cancerous tissues and normal tissues are extracted as initial features of genes. Nine meta-paths are manually selected, and the representation vectors obtained by aggregating information within and across metapath nodes are used as new features for subsequent classification and prediction tasks. By comparing with eight homogeneous and heterogeneous network models on two pan-cancer datasets, MCDHGN has better performance on AUC and AUPR values. Additionally, MCDHGN provides interpretability of predicted cancer driver genes through the varying weights of biologically meaningful meta-paths.https://github.com/1160300611/MCDHGN.Supplementary data are available at Bioinformatics online.© The Author(s) 2024. Published by Oxford University Press.