title: DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
abstract: Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of function. A powerful predictive model for the function of non-coding DNA can have enormous benefit for both basic science and translational research because over 98% of the human genome is non-coding and 93% of disease-associated variants lie in these regions. To address this need, we propose DanQ, a novel hybrid convolutional and bi-directional long short-term memory recurrent neural network framework for predicting non-coding function de novo from sequence. In the DanQ model, the convolution layer captures regulatory motifs, while the recurrent layer captures long-term dependencies between the motifs in order to learn a regulatory 'grammar' to improve predictions. DanQ improves considerably upon other models across several metrics. For some regulatory markers, DanQ can achieve over a 50% relative improvement in the area under the precision-recall curve metric compared to related models. We have made the source code available at the github repository http://github.com/uci-cbcl/DanQ.
authors.affiliation: Department of Computer Science University of California, Irvine, CA 92697, USA Center for Complex Biological Systems University of California, Irvine, CA 92697, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Quang
authors.affiliation: Department of Computer Science University of California, Irvine, CA 92697, USA Center for Complex Biological Systems University of California, Irvine, CA 92697, USA xhx@uci.edu.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Xie
mesh_terms: D004247:DNA; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D006801:Humans; D016571:Neural Networks, Computer; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012372:ROC Curve; D017422:Sequence Analysis, DNA; D012984:Software; D064878:Web Browser
chemical_list: D004247:DNA