Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Yifeng LiWyeth W Wasserman

Abstract

Sparse linear models approximate target variable(s) by a sparse linear combination of input variables. Since they are simple, fast, and able to select features, they are widely used in classification and regression. Essentially they are shallow feed-forward neural networks that have three limitations: (1) incompatibility to model nonlinearity of features, (2) inability to learn high-level features, and (3) unnatural extensions to select features in a multiclass case. Deep neural networks are models structured by multiple hidden layers with nonlinear activation functions. Compared with linear models, they have two distinctive strengths: the capability to (1) model complex systems with nonlinear structures and (2) learn high-level representation of features. Deep learning has been applied in many large and complex systems where deep models significantly outperform shallow ones. However, feature selection at the input level, which is very helpful to understand the nature of a complex system, is still not well studied. In genome research, the cis-regulatory elements in noncoding DNA sequences play a key role in the expression of genes. Since the activity of regulatory elements involves highly interactive factors, a deep tool is str...Continue Reading

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Citations

Dec 25, 2016·Briefings in Bioinformatics·Yifeng LiAlioune Ngom
Mar 15, 2018·BMC Bioinformatics·Diego FioravantiCesare Furlanello
Dec 16, 2017·Nature Reviews. Drug Discovery·Gisbert Schneider
Nov 22, 2016·Molecular Informatics·Alex T MüllerGisbert Schneider
Jun 2, 2018·BMC Bioinformatics·Yifeng LiWyeth W Wasserman
Dec 14, 2018·Nature Reviews. Rheumatology·Afshin JamshidiJohanne Martel-Pelletier
Dec 24, 2019·Briefings in Bioinformatics·Qiang ShiZhidong Xue
Jan 3, 2019·Journal of the American Medical Informatics Association : JAMIA·Xing SongMei Liu
Oct 2, 2020·BMC Bioinformatics·Md Abid Hasan, Stefano Lonardi
Oct 27, 2020·Journal of Pharmacokinetics and Pharmacodynamics·Ruihao HuangHao Zhu
Aug 4, 2021·Aging and Disease·Fedor GalkinAlex Zhavoronkov
Aug 18, 2020·Journal of Chemical Information and Modeling·Lei DengHui Liu

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
feature extraction
ChIP-seq

Software Mentioned

mathop
R
GeneCards
Theano
Theano package
DECRES
LASSO
glmnet
randomForest
DeclareMathSizes

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