Integrating Multi-Source Directed Gene Networks and Multi-Omics Data to Identify Cancer Driver Genes Based on Graph Neural Networks

Precisely identifying cancer drivers helps us to understand the molecular mechanisms of cancer, offering critical targets for early diagnosis. Despite the increasing application of graph neural networks in predicting cancer driver genes, existing approaches do not fully leverage the information from gene networks, and are unable to effectively extract node features from directed graphs. To this end, we propose MDIGNN, a novel deep learning model designed to identify cancer driver genes by integrating directed gene networks with multi-omics data. First, we construct a directed graph through the integration of existing gene networks from diverse databases and multi-omics data. Then, to encode the edge directionality, we develop a graph neural network based on the magnetic Laplacian, which relies on a complex Hermitian matrix for representing the directed graph structure. Next, we apply the channel attention and spatial attention mechanisms to improve the model's feature representation ability. Finally, MDIGNN uses a fully connected layer to compute the cancer driver probability for each gene. In a comparative evaluation, MDIGNN outperforms existing state-of-the-art methods in the field, and it is capable of detecting potential cancer driver genes.