Inferring human miRNA–disease associations via multiple kernel fusion on GCNII

Increasing evidence shows that the occurrence of human complex diseases is closely related to the mutation and abnormal expression of microRNAs(miRNAs). MiRNAs have complex and fine regulatory mechanisms, which makes it a promising target for drug discovery and disease diagnosis. Therefore, predicting the potential miRNA-disease associations has practical significance. In this paper, we proposed an miRNA–disease association predicting method based on multiple kernel fusion on Graph Convolutional Network via Initial residual and Identity mapping (GCNII), called MKFGCNII. Firstly, we built a heterogeneous network of miRNAs and diseases to extract multi-layer features via GCNII. Secondly, multiple kernel fusion method was applied to weight fusion of embeddings at each layer. Finally, Dual Laplacian Regularized Least Squares was used to predict new miRNA–disease associations by the combined kernel in miRNA and disease spaces. Compared with the other methods, MKFGCNII obtained the highest AUC value of 0.9631. Code is available at https://github.com/cuntjx/bioInfo.