Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape

H. Dai, R. Umarov, H. Kuwahara, Y. Li, L. Song, X. Gao
Bioinformatics, btx480, (2017)

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape

Keywords

Sequence2Vec, Novel, Embedding, Modeling, Transcription, Factor, Binding, Affinity landscape

Abstract

Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem.

Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these hidden Markov models into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA datasets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods.

Code

https://doi.org/10.1093/bioinformatics/btx480

Sources

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