SNARE-CNN: A 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data

Nguyen Quoc Khanh Le, Van Nui Nguyen

研究成果: 雜誌貢獻文章同行評審

35 引文 斯高帕斯(Scopus)

摘要

Deep learning has been increasingly and widely used to solve numerous problems in various fields with state-of-the-art performance. It can also be applied in bioinformatics to reduce the requirement for feature extraction and reach high performance. This study attempts to use deep learning to predict SNARE proteins, which is one of the most vital molecular functions in life science. A functional loss of SNARE proteins has been implicated in a variety of human diseases (e.g., neurodegenerative, mental illness, cancer, and so on). Therefore, creating a precise model to identify their functions is a crucial problem for understanding these diseases, and designing the drug targets. Our SNARE-CNN model which uses two-dimensional convolutional neural networks and position-specific scoring matrix profiles could identify SNARE proteins with achieved sensitivity of 76.6%, specificity of 93.5%, accuracy of 89.7%, and MCC of 0.7 in cross- validation dataset. We also evaluate the performance of our model via an independent dataset and the result shows that we are able to solve the overfitting problem. Compared with other state-of-the-art methods, this approach achieved significant improvement in all of the metrics. Throughout the proposed study, we provide an effective model for identifying SNARE proteins and a basis for further research that can apply deep learning in bioinformatics, especially in protein function prediction. SNARE-CNN are freely available at https://github.com/khanhlee/snare-cnn.
原文英語
文章編號e177
期刊PeerJ Computer Science
2019
發行號5
DOIs
出版狀態已發佈 - 1月 1 2019
對外發佈

ASJC Scopus subject areas

  • 電腦科學(全部)

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