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The functions of mRNAs have been shown to be closely linked with their localizations. As such, understanding of the subcellular localizations of mRNAs can help elucidate gene regulatory networks. Despite several computational methods that have been developed to predict mRNA localizations within cells, there is still much room for improvement in predictive performance, especially for the multiple-location prediction. In this study, we proposed a novel multi-label multi-class predictor, termed Clarion, for mRNA subcellular localization prediction. Clarion was developed based on a manually curated benchmark dataset and leveraged the weighted series method for multi-label transformation. Extensive benchmarking tests demonstrated Clarion achieved competitive predictive performance and the weighted series method plays a crucial role in securing superior performance of Clarion. In addition, the independent test results indicate that Clarion outperformed the state-of-the-art methods and can secure accuracy of 81.47, 91.29, 79.77, 92.10, 89.15, 83.74, 80.74, 79.23 and 84.74% for chromatin, cytoplasm, cytosol, exosome, membrane, nucleolus, nucleoplasm, nucleus and ribosome, respectively. The webserver and local stand-alone tool of Clarion is freely available at http:\/\/monash.bioweb.cloud.edu.au\/Clarion\/.<\/jats:p>","DOI":"10.1093\/bib\/bbac467","type":"journal-article","created":{"date-parts":[[2022,11,7]],"date-time":"2022-11-07T10:01:19Z","timestamp":1667815279000},"source":"Crossref","is-referenced-by-count":33,"title":["Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations"],"prefix":"10.1093","volume":"23","author":[{"given":"Yue","family":"Bi","sequence":"first","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800 , Australia"},{"name":"Monash Data Futures Institute, Monash University , Melbourne, Victoria 3800 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuyi","family":"Li","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800 , Australia"},{"name":"College of Information Engineering, Northwest A&F University , Yangling, 712100 , China"},{"name":"Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , 792 Elizabeth Street, Melbourne, Victoria 3000 , Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xudong","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Northwest A&F University , Yangling, 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhikang","family":"Wang","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800 , 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Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianhua","family":"Yao","sequence":"additional","affiliation":[{"name":"Tencent AI Lab , Shenzhen , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4682-2881","authenticated-orcid":false,"given":"Cangzhi","family":"Jia","sequence":"additional","affiliation":[{"name":"School of Science, Dalian Maritime University , Dalian 116026 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8031-9086","authenticated-orcid":false,"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800 , Australia"},{"name":"Monash Data Futures Institute, Monash University , Melbourne, Victoria 3800 , 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