ESGC-MDA: Identifying miRNA-disease associations using enhanced Simple Graph Convolutional Networks

MiRNAs play an important role in the occurrence and development of human disease. Identifying potential miRNA-disease associations is valuable for disease diagnosis and treatment. Therefore, it is urgent to develop efficient computational methods for predicting potential miRNA-disease associations to reduce the cost and time associated with biological wet experiments. In addition, high-quality feature representation remains a challenge for miRNA-disease association prediction using graph neural network methods. In this paper, we propose a method named ESGC-MDA, which employs an enhanced Simple Graph Convolution Network to identify miRNA-disease associations. We first construct a bipartite attributed graph for miRNAs and diseases by computing multi-source similarity. Then, we enhance the feature representations of miRNA and disease nodes by applying two strategies in the simple convolution network, which include randomly dropping messages during propagation to ensure the model learns more reliable feature representations, and using adaptive weighting to aggregate features from different layers. Finally, we calculate the prediction scores of miRNA-disease pairs by using a fully connected neural network decoder. We conduct 5-fold cross-validation and 10-fold cross-validation on HDMM v2.0 and HMDD v3.2, respectively, and ESGC-MDA achieves better performance than state-of-the-art baseline methods. The case studies for cardiovascular disease, lung cancer and colon cancer also further confirm the effectiveness of ESGC-MDA. The source codes are available at https://github.com/bixuehua/ESGC-MDA.