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However, current experimental techniques, such as Hi\u2010C, remain costly and labor\u2010intensive, limiting their application in large\u2010scale and disease\u2010related studies. To address this challenge, ChromNet is presented, a multi\u2010task learning framework that integrates epigenetic signals across diverse cell types to enable high\u2010precision prediction of chromatin architecture. By incorporating noise perturbation and auxiliary classification tasks, ChromNet improves the identification of topologically associating domains (TADs) and cell\u2010type\u2010specific chromatin structures, demonstrating superior generalization performance. Notably, ChromNet accurately predicts chromatin interactions in acute myeloid leukemia (AML) samples by leveraging epigenetic signals from both normal and diseased cells, highlighting its potential for studying disease\u2010associated chromatin remodeling. Across multiple key benchmarks, ChromNet consistently outperforms existing models, providing a robust and cost\u2010effective solution for large\u2010scale chromatin conformation studies. This framework enables the exploration of chromatin structural variations across both cell types and disease states, offering new insights into the relationship between 3D genome architecture and gene\u00a0regulation.<\/jats:p>","DOI":"10.1002\/advs.202508110","type":"journal-article","created":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:09:15Z","timestamp":1761894555000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["ChromNet: A Multi\u2010Task Learning Framework for Cross\u2010Cell Type Prediction of 3D Chromatin Interactions Using Epigenetic Signals"],"prefix":"10.1002","volume":"13","author":[{"given":"Bin","family":"Wang","sequence":"first","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha 410083 China"},{"name":"Xiangjiang Laboratory Changsha 410205 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaokai","family":"Wang","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha 410083 China"},{"name":"Department of Mathematics Hong Kong University of Science and Technology Clear Water Bay Hong Kong SAR 999077 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liqing","family":"Ding","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha 410083 China"},{"name":"Xiangjiang Laboratory Changsha 410205 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongdong","family":"Li","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha 410083 China"},{"name":"Xiangjiang Laboratory Changsha 410205 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaohang","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science Old Dominion University Norfolk VA 23529 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1516-0480","authenticated-orcid":false,"given":"Jianxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha 410083 China"},{"name":"Xiangjiang Laboratory Changsha 410205 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,10,30]]},"reference":[{"key":"e_1_2_9_1_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.09.014"},{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.10.061"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1181369"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.04.085"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.11.024"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11082"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11049"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1896"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11232"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.01.010"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.64320"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00362-w"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-018-0060-8"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-020-0602-9"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05365-x"},{"key":"e_1_2_9_16_1","first-page":"837","volume":"132","author":"Luo H.","year":"2018","journal-title":"Blood, J. 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