Inferring LncRNA-disease associations based on graph autoencoder matrix completion. (August 2020)

• Record Type: Journal Article
• Authors: Wu, Ximin; Lan, Wei; Chen, Qingfeng; Dong, Yi; Liu, Jin; Peng, Wei
• Is Part Of: Computational biology and chemistry. Volume 87(2020)
• Publication Date: 2020-08
• Subjects: LncRNA-disease association -- Matrix completion -- Graph convolutional network -- Inner product; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2020.107282
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Accumulating studies have indicated that long non-coding RNAs (lncRNAs) play crucial roles in large amount of biological processes. Predicting lncRNA-disease associations can help biologist to understand the molecular mechanism of human disease and benefit for disease diagnosis, treatment and prevention. Highlights: We introduce a graph autoencoder matrix completion to predict associations between lncRNAs and diseases. The imbalance between positive and negative tackled by the cost-sensitive neural networks. The experimental results show our method outperforms than other state of the art methods in prediction performance. Abstract: Accumulating studies have indicated that long non-coding RNAs (lncRNAs) play crucial roles in large amount of biological processes. Predicting lncRNA-disease associations can help biologist to understand the molecular mechanism of human disease and benefit for disease diagnosis, treatment and prevention. In this paper, we introduce a computational framework based on graph autoencoder matrix completion (GAMCLDA) to identify lncRNA-disease associations. In our method, the graph convolutional network is utilized to encode local graph structure and features of nodes for learning latent factor vectors of lncRNA and disease. Further, the inner product of lncRNA factor vector and disease factor vector is used as decoder to reconstruct the lncRNA-disease association matrix. In addition, the cost-sensitive neural network is utilized to deal with the imbalance between positive and negative samples. The experimental results show GAMLDA outperforms other state-of-the-art methods in prediction performance which is evaluated by AUC value, AUPR value, PPV and F1-score. Moreover, the case study shows our method is the effectively tool for potential lncRNA-disease prediction.