DeepANF: A deep attentive neural framework with distributed representation for chromatin accessibility prediction

The identification of chromatin accessibility is a significant part of the genomics and genetics. However, high-throughput experimental techniques are costly and impractical for systematic identification of accessibility. Many computational methods were proposed to predict the functional regions of chromatin purely relying on DNA sequences, but they could not take full advantage of sequence information to capture hidden complex motifs among DNA sequences. Recently, deep learning algorithms have been incorporated into the chromatin accessibility predication and achieved the remarkable results. Nevertheless, there still exists a problem in chromatin accessibility prediction as how to effectively represent the complex features merely from DNA sequences. Thus, developing efficient computational methods is becoming increasingly urgent to identify functional regions of the genome. In this paper, combining convolutional and gated recurrent unit neural networks with attention mechanism, we develop a discriminative computational framework DeepANF to adaptively extract hidden pattern features and identify the chromatin accessibility based on distributed representation of DNA sequences. To verify the efficacy of the DeepANF framework, we conduct extensive experiments on five large scale datasets, and experimental results reveal that our framework not only consistently outperforms these published methods for chromatin accessibility prediction tasks, but also extracts more discriminative features from pure DNA sequences than published methods, especially on MCF-7 dataset. (C) 2019 Elsevier B.V. All rights reserved.