Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan 650500, P. R. China and Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology, Kunming, Yunnan 650500, P. R. China.
Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan 650500, P. R. China.
Brief Bioinform. 2023 Nov 22;25(1). doi: 10.1093/bib/bbad524.
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.
正确预测与疾病相关的 miRNAs 在疾病预防和治疗中起着至关重要的作用。目前用于预测与疾病相关的 miRNAs 的计算方法基于各种 miRNA 特性和疾病特性构建不同的 miRNA 视图和疾病视图,然后整合多视图来预测 miRNAs 和疾病之间的关系。然而,大多数现有方法忽略了视图之间的信息交互以及多个视图中 miRNA 特征(疾病特征)的一致性。本研究提出了一种基于多超图对比学习(MHCLMDA)的计算方法来预测 miRNA-疾病关联。MHCLMDA 首先基于各种 miRNA 相似度和疾病相似度构建多个 miRNA 超图和疾病超图,并对每个超图进行超图卷积以捕获节点之间的高阶相互作用,然后进行超图对比学习以学习不同视图下一致的 miRNA 特征表示和疾病特征表示。然后,变分自编码器用于提取已知 miRNA-疾病关联关系中的 miRNA 和疾病特征。最后,MHCLMDA 融合来自不同视图的 miRNA 和疾病特征来预测 miRNA-疾病关联。模型的参数以端到端的方式进行优化。我们将 MHCLMDA 应用于人类 miRNA-疾病关联的预测。实验结果表明,在接收器操作特征曲线下面积和精度召回曲线下面积方面,我们的方法优于其他几种最先进的方法。