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To address this issue, it is essential to systematically uncover associations among multilevel elements consisting of disease phenotypes, tissues, cell types and molecules, which could pose a challenge because of their heterogeneity and incompleteness. To address this challenge, we describe a new methodological framework, called Graph Local InfoMax (GLIM), based on a human multilevel network (HMLN) that we established by introducing multiple tissues and cell types on top of molecular networks. GLIM can systematically mine the potential relationships between multilevel elements by embedding the features of the HMLN through contrastive learning. Our simulation results demonstrated that GLIM consistently outperforms other state-of-the-art algorithms in disease gene prediction. Moreover, GLIM was also successfully used to infer cell markers and rewire intercellular and molecular interactions in the context of specific tissues or diseases. As a typical case, the tissue-cell-molecule network underlying gastritis and gastric cancer was first uncovered by GLIM, providing systematic insights into the mechanism underlying the occurrence and development of gastric cancer. Overall, our constructed methodological framework has the potential to systematically uncover complex disease mechanisms and mine high-quality relationships among phenotypical, tissue, cellular and molecular elements.<\/jats:p>","DOI":"10.1093\/bib\/bbac170","type":"journal-article","created":{"date-parts":[[2022,4,19]],"date-time":"2022-04-19T11:19:31Z","timestamp":1650367171000},"source":"Crossref","is-referenced-by-count":16,"title":["Decoding multilevel relationships with the human tissue-cell-molecule network"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5300-6495","authenticated-orcid":false,"given":"Siyu","family":"Hou","sequence":"first","affiliation":[{"name":"Institute for TCM-X, MOE Key Laboratory of Bioinformatics , Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, 100084 Beijing , 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