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Comparative analyses play significant roles in Hi-C data studies, which are designed to make comparisons between Hi-C contact maps, thus evaluating the consistency of replicate Hi-C experiments (i.e. reproducibility measurement) and detecting statistically differential interacting regions with biological significance (i.e. differential chromatin interaction detection). However, due to the complex and hierarchical nature of Hi-C contact maps, it remains challenging to conduct systematic and reliable comparative analyses of Hi-C data. Here, we proposed sslHiC, a contrastive self-supervised representation learning framework, for precisely modeling the multi-level features of chromosome conformation and automatically producing informative feature embeddings for genomic loci and their interactions to facilitate comparative analyses of Hi-C contact maps. Comprehensive computational experiments on both simulated and real datasets demonstrated that our method consistently outperformed the state-of-the-art baseline methods in providing reliable measurements of reproducibility and detecting differential interactions with biological meanings.<\/jats:p>","DOI":"10.1093\/bib\/bbad193","type":"journal-article","created":{"date-parts":[[2023,6,8]],"date-time":"2023-06-08T04:43:12Z","timestamp":1686199392000},"source":"Crossref","is-referenced-by-count":3,"title":["Improving comparative analyses of Hi-C data via contrastive self-supervised learning"],"prefix":"10.1093","volume":"24","author":[{"given":"Han","family":"Li","sequence":"first","affiliation":[{"name":"Institute for Interdisciplinary Information Sciences, Tsinghua University , 100084 Beijing , China"}]},{"given":"Xuan","family":"He","sequence":"additional","affiliation":[{"name":"Machine Learning Department, Silexon AI Technology Co., Ltd. , 210000 Nanjing , China"}]},{"given":"Lawrence","family":"Kurowski","sequence":"additional","affiliation":[{"name":"Institute for Interdisciplinary Information Sciences, Tsinghua University , 100084 Beijing , China"}]},{"given":"Ruotian","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute for Interdisciplinary Information Sciences, Tsinghua University , 100084 Beijing , China"}]},{"given":"Dan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute for Interdisciplinary Information Sciences, Tsinghua University , 100084 Beijing , China"}]},{"given":"Jianyang","family":"Zeng","sequence":"additional","affiliation":[{"name":"Institute for Interdisciplinary Information Sciences, Tsinghua University , 100084 Beijing , China"}]}],"member":"286","published-online":{"date-parts":[[2023,6,7]]},"reference":[{"issue":"7539","key":"2023072020043480500_ref1","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nature14222","article-title":"Chromatin architecture 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