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However, while current analytical methods can leverage the additive benefits, they fall short to explore the synergistic insights of joint profiling, thereby diminishing the advantage of joint profiling. Here, we introduce CellMATE, a Multi-head Adversarial Training-based Early-integration approach specifically developed for multimodal joint profiling. CellMATE can capture both additive and synergistic benefits inherent in joint profiling through auto-learning of multimodal distributions and simultaneously represents all features into a unified latent space. Through extensive evaluation across diverse joint profiling scenarios, CellMATE demonstrated its superiority in ensuring utility of cross-modal properties, uncovering cellular heterogeneity and plasticity, and delineating differentiation trajectories. CellMATE uniquely unlocks the full potential of joint profiling to elucidate the dynamic nature of cells during critical processes as differentiation, development, and diseases.<\/jats:p>","DOI":"10.1093\/bib\/bbae582","type":"journal-article","created":{"date-parts":[[2024,11,11]],"date-time":"2024-11-11T05:14:19Z","timestamp":1731302059000},"source":"Crossref","is-referenced-by-count":1,"title":["Unlocking cross-modal interplay of single-cell joint profiling with CellMATE"],"prefix":"10.1093","volume":"25","author":[{"given":"Qi","family":"Wang","sequence":"first","affiliation":[{"name":"Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"National Clinical Research Center for Kidney Disease , Jinling Hospital, , No. 305 Zhongshan East Road, Xuanwu District, Nanjing, Jiangsu 210002 ,","place":["China"]},{"name":"Medical School of Nanjing University , Jinling Hospital, , No. 305 Zhongshan East Road, Xuanwu District, Nanjing, Jiangsu 210002 ,","place":["China"]},{"name":"State Key Laboratory of Pharmaceutical Biotechnology , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"Nanjing University , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]}]},{"given":"Bolei","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of computer science, Nanjing university of posts and telecommunications, No. 9 Wenyuan Road, Qixia District , Nanjing, Jiangsu 210023 ,","place":["China"]}]},{"given":"Yue","family":"Guo","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory of Molecular Medicine , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"Nanjing University , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]}]},{"given":"Luyu","family":"Gong","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory of Molecular Medicine , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"Nanjing University , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]}]},{"given":"Erguang","family":"Li","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory of Molecular Medicine , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"Nanjing University , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"State Key Laboratory of Pharmaceutical Biotechnology , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"Nanjing University , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9655-1162","authenticated-orcid":false,"given":"Jingping","family":"Yang","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory of Molecular Medicine , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"Nanjing University , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"National Clinical Research Center for Kidney Disease , Jinling Hospital, , No. 305 Zhongshan East Road, Xuanwu District, Nanjing, Jiangsu 210002 ,","place":["China"]},{"name":"Medical School of Nanjing University , Jinling Hospital, , No. 305 Zhongshan East Road, Xuanwu District, Nanjing, Jiangsu 210002 ,","place":["China"]},{"name":"State Key Laboratory of Pharmaceutical Biotechnology , Medical School, , No. 22 Hankou Road, Gulou District, Nanjing, Jiangsu 210093 ,","place":["China"]},{"name":"Nanjing 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