An Efficient Approach based on Multi-sources Information to Predict CircRNA-disease Associations Using Deep Convoltional Neural Network.
Bioinformatics. 2019 Dec 03;:
Authors: Wang L, You ZH, Huang YA, Huang DS, Chan KCC
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 paper, we propose an efficient computational method based on multi-source information combined with deep convolutional neural network 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 convolutional neural network, and finally sends them to the extreme learning machine classifier for prediction. The five-fold cross-validation results show that the proposed method achieves 87.21% prediction accuracy with 88.50% sensitivity at the AUC 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. The source code and datasets explored in this work are available at https://github.com/look0012/circRNA-Disease-association.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
PMID: 31793982 [PubMed – as supplied by publisher]