Improving cancer driver gene identification using multi-task learning on graph convolutional network

• Published in: Briefings in bioinformatics Vol. 23; no. 1
• Main Authors: Peng, Wei, Tang, Qi, Dai, Wei, Chen, Tielin
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 17.01.2022; Oxford Publishing Limited (England)
• Subjects: Artificial neural networks; Bayes Theorem; Bayesian analysis; Biomarkers; Cancer; Embedding; Genes; Humans; Learning; Mutation; Neoplasms - genetics; Oncogenes; Protein interaction; Protein Interaction Maps; Proteins; multi-task learning; graph convolutional neural network; cancer genes; cancer driver genes
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbab432

Abstract Cancer is thought to be caused by the accumulation of driver genetic mutations. Therefore, identifying cancer driver genes plays a crucial role in understanding the molecular mechanism of cancer and developing precision therapies and biomarkers. In this work, we propose a Multi-Task learning method, called MTGCN, based on the Graph Convolutional Network to identify cancer driver genes. First, we augment gene features by introducing their features on the protein-protein interaction (PPI) network. After that, the multi-task learning framework propagates and aggregates nodes and graph features from input to next layer to learn node embedding features, simultaneously optimizing the node prediction task and the link prediction task. Finally, we use a Bayesian task weight learner to balance the two tasks automatically. The outputs of MTGCN assign each gene a probability of being a cancer driver gene. Our method and the other four existing methods are applied to predict cancer drivers for pan-cancer and some single cancer types. The experimental results show that our model shows outstanding performance compared with the state-of-the-art methods in terms of the area under the Receiver Operating Characteristic (ROC) curves and the area under the precision-recall curves. The MTGCN is freely available via https://github.com/weiba/MTGCN.