Enhancing Cancer Driver Genes Prediction via Multi-view Hypergraph and Dynamic Reward-Penalty Model

Cancer driver genes can grant cancer cells the ability to proliferate continuously and resist apoptosis, thereby promoting tumor evolution toward malignancy. Identifying cancer driver genes not only helps to reveal the molecular pathological network of cancer, but also provides important targets for the development of precise targeted drugs. Although the existing methods can partially compensate for the limitations of single-omics data to a certain extent, they are still inadequate in mining deep relationships among diverse omics features and gene synergy, thus impacting the accuracy of driver gene identification. In this paper, a cancer driver gene identification method integrating the multi-view hypergraph with the dynamic reward-penalty model is proposed and termed MHDP. Firstly, the functional module and spatial co-localization hypergraphs are constructed independently in functional and spatial dimensions, respectively, to capture the synergistic information among genes, as well as the functional and spatial information of genes. Secondly, the Bhattacharyya distance is employed to evaluate gene expression differences between normal and tumor samples. Then, miRNA importance scores are calculated based on the number of miRNA connections for each gene within the mRNA-miRNA bipartite graph. Finally, through analysis of correlations among different features, we propose a Dynamic Reward-Penalty model that adaptively adjusts weights of omics features to achieve efficient multi-omics integration. Experimental evaluation using breast, lung adenocarcinoma, and prostate cancer datasets demonstrates that MHDP markedly outperforms 8 state-of-the-art methods, including HWC, DriverRWH, and WMDS.netP, exhibiting significant improvements in accuracy, functional consistency, and partial area under the ROC curve (PAUC). MHDP source code can be obtained from https://github.com/DriverGene/MHDP.git.