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Accurate identification of these fine-scale structures is crucial for advancing our understanding of cellular biological processes and the mechanisms underlying disease. However, due to the inherent complexity and dynamic of chromatin interactions, existing methods often fail to adequately characterize and capture multi-dimensional features. To address these limitations, we introduce GraphLooper, a novel framework using hierarchical multi-view graph pooling to enhance training and inference on large-scale data. GraphLooper transforms Hi-C data into a graph-structured representation, integrating multi-dimensional epigenomic features to construct a robust chromatin interaction model. Employing a hierarchical multi-view graph pooling mechanism, it effectively aggregates multi-scale features, enhancing representation learning. Evaluations across diverse cell lines demonstrate that GraphLooper outperforms state-of-the-art methods in prediction accuracy and generalization, particularly in capturing long-range chromatin interactions critical for precise spatial gene regulation.<\/jats:p>","DOI":"10.1093\/bib\/bbag217","type":"journal-article","created":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T12:48:19Z","timestamp":1776430099000},"source":"Crossref","is-referenced-by-count":0,"title":["GraphLooper: predicting chromatin loops based on hierarchical multi-view graph pooling method"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3244-3629","authenticated-orcid":false,"given":"Siguo","family":"Wang","sequence":"first","affiliation":[{"name":"School of Mathematics and Computer Science, Zhejiang Agriculture and Forestry University , No. 666, Wusu Street, Lin'an District, Hangzhou, Zhejiang 311300 ,","place":["China"]},{"name":"Ningbo Institute of Digital Twin, Eastern Institute of Technology , No. 299, Donghai Avenue, Zhenhai District, Ningbo, Zhejiang 315200 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhipeng","family":"Li","sequence":"additional","affiliation":[{"name":"Ningbo Institute of Digital Twin, Eastern Institute of Technology , No. 299, Donghai Avenue, Zhenhai District, Ningbo, Zhejiang 315200 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hailin","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Mathematics and Computer Science, Zhejiang Agriculture and Forestry University , No. 666, Wusu Street, Lin'an District, Hangzhou, Zhejiang 311300 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Cui","sequence":"additional","affiliation":[{"name":"School of Data and Computer Science, Shandong Women's University , No. 2, Daxue Road, Changqing District, Jinan, Shandong 250300 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1965-6988","authenticated-orcid":false,"given":"Zhen-Hao","family":"Guo","sequence":"additional","affiliation":[{"name":"Ningbo Institute of Digital Twin, Eastern Institute of Technology , No. 299, Donghai Avenue, Zhenhai District, Ningbo, Zhejiang 315200 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6796-104X","authenticated-orcid":false,"given":"Qi","family":"Liao","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University , No. 818, Fenghua Road, Jiangbei District, Ningbo, Zhejiang 315211 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zuquan","family":"Hu","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center (2011) for Medical and Health Big Data of Guizhou Province, School of Biology and Engineering (School of Modern Industry for Health and Medicine), Guizhou Medical University , University Town, Guian New District, Guiyang, Guizhou 550025 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenjian","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Data Science, City University of Macau, Avenida Padre Tom\u00e1s Pereira, Taipa, Macau 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinhu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Ningbo Institute of Digital Twin, Eastern Institute of Technology , No. 299, Donghai Avenue, Zhenhai District, Ningbo, Zhejiang 315200 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"De-Shuang","family":"Huang","sequence":"additional","affiliation":[{"name":"Ningbo Institute of Digital Twin, Eastern Institute of 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