Enhancer-LSTMAtt: A Bi-LSTM and Attention-Based Deep Learning Method for Enhancer Recognition

被引:8
|
作者
Huang, Guohua [1 ]
Luo, Wei [1 ]
Zhang, Guiyang [1 ]
Zheng, Peijie [1 ]
Yao, Yuhua [2 ]
Lyu, Jianyi [1 ]
Liu, Yuewu [3 ]
Wei, Dong-Qing [4 ,5 ]
机构
[1] Shaoyang Univ, Sch Elect Engn, Shaoyang 422000, Peoples R China
[2] Hainan Normal Univ, Sch Math & Stat, Haikou 571158, Hainan, Peoples R China
[3] Hunan Agr Univ, Coll Informat & Intelligence, Changsha 410083, Peoples R China
[4] Shanghai Jiao Tong Univ, State Key Lab Microbial Metab, Shanghai 200240, Peoples R China
[5] Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Shanghai 200240, Peoples R China
基金
中国国家自然科学基金;
关键词
enhancer; promoter; deep learning; feed-forward attention; convolution neural network; long-short term memory; residual neural network; CD-HIT; TRANSCRIPTIONAL ENHANCERS; IDENTIFYING ENHANCERS; PREDICTING ENHANCERS; CHROMATIN SIGNATURES; PROTEIN; MODEL; DISCRIMINATION; EVOLUTION; ELEMENTS;
D O I
10.3390/biom12070995
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Enhancers are short DNA segments that play a key role in biological processes, such as accelerating transcription of target genes. Since the enhancer resides anywhere in a genome sequence, it is difficult to precisely identify enhancers. We presented a bi-directional long-short term memory (Bi-LSTM) and attention-based deep learning method (Enhancer-LSTMAtt) for enhancer recognition. Enhancer-LSTMAtt is an end-to-end deep learning model that consists mainly of deep residual neural network, Bi-LSTM, and feed-forward attention. We extensively compared the Enhancer-LSTMAtt with 19 state-of-the-art methods by 5-fold cross validation, 10-fold cross validation and independent test. Enhancer-LSTMAtt achieved competitive performances, especially in the independent test. We realized Enhancer-LSTMAtt into a user-friendly web application. Enhancer-LSTMAtt is applicable not only to recognizing enhancers, but also to distinguishing strong enhancer from weak enhancers. Enhancer-LSTMAtt is believed to become a promising tool for identifying enhancers.
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页数:18
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