MHCLMDA: multihypergraph contrastive learning for miRNA–disease association prediction

Abstract The correct prediction of disease-associated miRNAs plays an essential role in disease prevention and treatment. Current computational methods to predict disease-associated miRNAs construct different miRNA views and disease views based on various miRNA properties and disease properties and then integrate the multiviews to predict the relationship between miRNAs and diseases. However, most existing methods ignore the information interaction among the views and the consistency of miRNA features (disease features) across multiple views. This study proposes a computational method based on multiple hypergraph contrastive learning (MHCLMDA) to predict miRNA–disease associations. MHCLMDA first constructs multiple miRNA hypergraphs and disease hypergraphs based on various miRNA similarities and disease similarities and performs hypergraph convolution on each hypergraph to capture higher order interactions between nodes, followed by hypergraph contrastive learning to learn the consistent miRNA feature representation and disease feature representation under different views. Then, a variational auto-encoder is employed to extract the miRNA and disease features in known miRNA–disease association relationships. Finally, MHCLMDA fuses the miRNA and disease features from different views to predict miRNA–disease associations. The parameters of the model are optimized in an end-to-end way. We applied MHCLMDA to the prediction of human miRNA–disease association. The experimental results show that our method performs better than several other state-of-the-art methods in terms of the area under the receiver operating characteristic curve and the area under the precision-recall curve.