{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T06:59:26Z","timestamp":1784185166001,"version":"3.55.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,11]],"date-time":"2024-11-11T00:00:00Z","timestamp":1731283200000},"content-version":"vor","delay-in-days":49,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Jilin Provincial Key Laboratory of Big Data Intelligent Cognition","award":["20210504003GH"],"award-info":[{"award-number":["20210504003GH"]}]},{"name":"Development Project of Jilin Province of China","award":["20240101364JC"],"award-info":[{"award-number":["20240101364JC"]}]},{"name":"Development Project of Jilin Province of China","award":["20230201065GX"],"award-info":[{"award-number":["20230201065GX"]}]},{"name":"Development Project of Jilin Province of China","award":["20220508125RC"],"award-info":[{"award-number":["20220508125RC"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62072212"],"award-info":[{"award-number":["62072212"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Identifying potential cancer biomarkers is a key task in biomedical research, providing a promising avenue for the diagnosis and treatment of human tumors and cancers. In recent years, several machine learning\u2013based RNA\u2013disease association prediction techniques have emerged. However, they primarily focus on modeling relationships of a single type, overlooking the importance of gaining insights into molecular behaviors from a complete regulatory network perspective and discovering biomarkers of unknown types. Furthermore, effectively handling local and global topological structural information of nodes in biological molecular regulatory graphs remains a challenge to improving biomarker prediction performance. To address these limitations, we propose a multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning (MML-MGNN) for predicting unknown types of cancer biomarkers. MML-MGNN leverages multisimilarity modality hypergraph contrastive learning to delve into local associations in the regulatory network, learning diverse insights into the topological structures of multiple types of similarities, and then globally modeling the multisimilarity modalities through a multichannel graph autoencoder. By combining representations obtained from local-level associations and global-level regulatory graphs, MML-MGNN can acquire molecular feature descriptors benefiting from multitype association properties and the complete regulatory network. Experimental results on predicting three different types of cancer biomarkers demonstrate the outstanding performance of MML-MGNN. Furthermore, a case study on gastric cancer underscores the outstanding ability of MML-MGNN to gain deeper insights into molecular mechanisms in regulatory networks and prominent potential in cancer biomarker prediction.<\/jats:p>","DOI":"10.1093\/bib\/bbae575","type":"journal-article","created":{"date-parts":[[2024,11,11]],"date-time":"2024-11-11T05:10:27Z","timestamp":1731301827000},"source":"Crossref","is-referenced-by-count":14,"title":["A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0554-2936","authenticated-orcid":false,"given":"Xin-Fei","family":"Wang","sequence":"first","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]},{"name":"Jilin University , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lan","family":"Huang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]},{"name":"Jilin University , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4751-0708","authenticated-orcid":false,"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]},{"name":"Jilin University , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7162-7826","authenticated-orcid":false,"given":"Ren-Chu","family":"Guan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]},{"name":"Jilin University , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1266-2696","authenticated-orcid":false,"given":"Zhu-Hong","family":"You","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Youyi West Road, Xi'an,710072 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Sheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]},{"name":"Jilin University , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu-Ping","family":"Xie","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]},{"name":"Jilin University , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi-Xing","family":"Yang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]},{"name":"Jilin University , College of Computer Science and Technology, , No. 2699, Qianjin Street, Changchun 130012 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,11]]},"reference":[{"key":"2024111105101347000_ref1","first-page":"265","article-title":"Breast and ovarian cancer incidence in BRCA1-mutation carriers. 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