DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution

Hi-C is commonly used to study three-dimensional genome organization. However, due to the high sequencing cost and technical constraints, the resolution of most Hi-C datasets is coarse, resulting in a loss of information and biological interpretability. Here we develop DeepHiC, a generative adversarial network, to predict high-resolution Hi-C contact maps from low-coverage sequencing data. We demonstrated that DeepHiC is capable of reproducing high-resolution Hi-C data from as few as 1% downsampled reads. Empowered by adversarial training, our method can restore fine-grained details similar to those in high-resolution Hi-C matrices, boosting accuracy in chromatin loops identification and TADs detection, and outperforms the state-of-the-art methods in accuracy of prediction. Finally, application of DeepHiC to Hi-C data on mouse embryonic development can facilitate chromatin loop detection with higher accuracy. We develop a web-based tool (DeepHiC, http://sysomics.com/deephic) that allows researchers to enhance their own Hi-C data with just a few clicks.\n\nAuthor summaryWe developed a novel method, DeepHiC, for enhancing Hi-C data resolution from low-coverage sequencing data using generative adversarial network. DeepHiC is capable of reproducing highresolution (10-kb) Hi-C data with high quality even using 1/100 downsampled reads. Our method outperforms the previous methods in Hi-C data resolution enhancement, boosting accuracy in chromatin loops identification and TADs detection. Application of DeepHiC on mouse embryonic development data shows that enhancements afforded by DeepHiC facilitates the chromatin loops identification of these data achieving higher accuracy. We also developed a user-friendly web server (http://sysomics.com/deephic) that allows researchers to enhance their own low-resolution Hi-C data (40kb-1 Mb) with just few clicks.