4.7 Article

Association prediction of CircRNAs and diseases using multi-homogeneous graphs and variational graph auto-encoder

期刊

COMPUTERS IN BIOLOGY AND MEDICINE
卷 151, 期 -, 页码 -

出版社

PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.compbiomed.2022.106289

关键词

CircRNA-disease association; Graph neural network; Variational graph auto -encoder; Random forest

资金

  1. Natural Science Foundation of Shan-dong Province of China
  2. [ZR2020QF037]

向作者/读者索取更多资源

This paper proposes a new predictor, VGAERF, which combines VGAE and RF to explore the molecular mechanism of circRNA-disease associations and improve prediction performance, contributing to the diagnosis of circRNA-related diseases.
As a non-coding RNA molecule with closed-loop structure, circular RNA (circRNA) is tissue-specific and cell -specific in expression pattern. It regulates disease development by modulating the expression of disease -related genes. Therefore, exploring the circRNA-disease relationship can reveal the molecular mechanism of disease pathogenesis. Biological experiments for detecting circRNA-disease associations are time-consuming and laborious. Constrained by the sparsity of known circRNA-disease associations, existing algorithms cannot obtain relatively complete structural information to represent features accurately. To this end, this paper proposes a new predictor, VGAERF, combining Variational Graph Auto-Encoder (VGAE) and Random Forest (RF). Firstly, circRNA homogeneous graph structure and disease homogeneous graph structure are constructed by Gaussian interaction profile (GIP) kernel similarity, semantic similarity, and known circRNA-disease associations. VGAEs with the same structure are employed to extract the higher-order features by the encoding and decoding of input graph structures. To further increase the completeness of the network structure information, the deep features acquired from the two VGAEs are summed, and then train the RF with sparse data processing capability to perform the prediction task. On the independent test set, the Area Under ROC Curve (AUC), accuracy, and Area Under PR Curve (AUPR) of the proposed method reach up to 0.9803, 0.9345, and 0.9894, respectively. On the same dataset, the AUC, accuracy, and AUPR of VGAERF are 2.09%, 5.93%, and 1.86% higher than the best -performing method (AEDNN). It is anticipated that VGAERF will provide significant information to decipher the molecular mechanisms of circRNA-disease associations, and promote the diagnosis of circRNA-related diseases.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

暂无数据
暂无数据