An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network | |
Wang, L (Wang, Lei)[ 1 ]; You, ZH (You, Zhu-Hong)[ 1 ]; Huang, YA (Huang, Yu-An)[ 2 ]; Huang, DS (Huang, De-Shuang)[ 3 ]; Chan, KCC (Chan, Keith C. C.)[ 2 ] | |
刊名 | BIOINFORMATICS |
2020 | |
卷号 | 36期号:13页码:4038-4046 |
ISSN号 | 1367-4803 |
DOI | 10.1093/bioinformatics/btz825 |
英文摘要 | Motivation: Emerging evidence indicates that circular RNA (circRNA) plays a crucial role in human disease. Using circRNA as biomarker gives rise to a new perspective regarding our diagnosing of diseases and understanding of disease pathogenesis. However, detection of circRNA-disease associations by biological experiments alone is often blind, limited to small scale, high cost and time consuming. Therefore, there is an urgent need for reliable computational methods to rapidly infer the potential circRNA-disease associations on a large scale and to provide the most promising candidates for biological experiments. Results: In this article, we propose an efficient computational method based on multi-source information combined with deep convolutional neural network (CNN) to predict circRNA-disease associations. The method first fuses multi-source information including disease semantic similarity, disease Gaussian interaction profile kernel similarity and circRNA Gaussian interaction profile kernel similarity, and then extracts its hidden deep feature through the CNN and finally sends them to the extreme learning machine classifier for prediction. The 5-fold cross-validation results show that the proposed method achieves 87.21% prediction accuracy with 88.50% sensitivity at the area under the curve of 86.67% on the CIRCR2Disease dataset. In comparison with the state-of-the-art SVM classifier and other feature extraction methods on the same dataset, the proposed model achieves the best results. In addition, we also obtained experimental support for prediction results by searching published literature. As a result, 7 of the top 15 circRNA-disease pairs with the highest scores were confirmed by literature. These results demonstrate that the proposed model is a suitable method for predicting circRNA-disease associations and can provide reliable candidates for biological experiments. |
WOS记录号 | WOS:000550133900012 |
内容类型 | 期刊论文 |
源URL | [http://ir.xjipc.cas.cn/handle/365002/7398] |
专题 | 新疆理化技术研究所_多语种信息技术研究室 |
通讯作者 | You, ZH (You, Zhu-Hong)[ 1 ] |
作者单位 | 1.Tongji Univ, Inst Machine Learning & Syst Biol, Sch Elect & Informat Engn, Shanghai 201804, Peoples R China 2.Hong Kong Polytech Univ, Dept Comp, Hong Kong 999077, Peoples R China 3.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi 830011, Peoples R China |
推荐引用方式 GB/T 7714 | Wang, L ,You, ZH ,Huang, YA ,et al. An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network[J]. BIOINFORMATICS,2020,36(13):4038-4046. |
APA | Wang, L ,You, ZH ,Huang, YA ,Huang, DS ,&Chan, KCC .(2020).An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network.BIOINFORMATICS,36(13),4038-4046. |
MLA | Wang, L ,et al."An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network".BIOINFORMATICS 36.13(2020):4038-4046. |
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