Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/144053
Title: SNARE-CNN : a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data
Authors: Le, Nguyen Quoc Khanh
Nguyen, Van-Nui
Keywords: Humanities::General
Issue Date: 2019
Source: Le, N. Q. K., & Nguyen, V.-N. (2019). SNARE-CNN : a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data. PeerJ Computer Science, 5, e177-. doi:10.7717/peerj-cs.177
Journal: PeerJ Computer Science
Abstract: 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.
URI: https://hdl.handle.net/10356/144053
ISSN: 2376-5992
DOI: 10.7717/peerj-cs.177
Rights: © 2019 The Author(s) (published by PeerJ). This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SoH Journal Articles

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