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To this end, researchers have developed various network-based prediction techniques targeting specific molecular associations. However, limitations imposed by reductionism and network representation learning have led existing studies to narrowly focus on high prediction efficiency within single association type, thereby glossing over the discovery of unknown types of associations. Additionally, effectively utilizing network structure to fit the interaction properties of regulatory networks and combining specific case biomarker validations remains an unresolved issue in cancer biomarker prediction methods. To overcome these limitations, we propose a multi-view learning framework, CeRVE, based on directed graph neural networks (DGNN) for predicting unknown type cancer biomarkers. CeRVE effectively extracts and integrates subgraph information through multi-view feature learning. Subsequently, CeRVE utilizes DGNN to simulate the entire regulatory network, propagating node attribute features and extracting various interaction relationships between molecules. Furthermore, CeRVE constructed a comparative analysis matrix of three cancers and adjacent normal tissues through The Cancer Genome Atlas and identified multiple types of potential cancer biomarkers through differential expression analysis of mRNA, microRNA, and long noncoding RNA. Computational testing of multiple types of biomarkers for 72 cancers demonstrates that CeRVE exhibits superior performance in cancer biomarker prediction, providing a powerful tool and insightful approach for AI-assisted disease biomarker discovery.<\/jats:p>","DOI":"10.1093\/bib\/bbae546","type":"journal-article","created":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T12:21:12Z","timestamp":1730118072000},"source":"Crossref","is-referenced-by-count":11,"title":["Multi-view learning framework for predicting unknown types of cancer markers via directed graph neural networks fitting regulatory networks"],"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":[{"role":"author","vocabulary":"crossref"}]},{"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":[{"role":"author","vocabulary":"crossref"}]},{"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":[{"role":"author","vocabulary":"crossref"}]},{"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, Jilin University, No. 2699, Qianjin Street, Changchun, 130012,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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\u2019an, 710072 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