{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,30]],"date-time":"2025-08-30T16:25:03Z","timestamp":1756571103646,"version":"3.41.2"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,4,4]],"date-time":"2024-04-04T00:00:00Z","timestamp":1712188800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62372205","61932008"],"award-info":[{"award-number":["62372205","61932008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The crisis of antibiotic resistance, which causes antibiotics used to treat bacterial infections to become less effective, has emerged as one of the foremost challenges to public health. Identifying the properties of antibiotic resistance genes (ARGs) is an essential way to mitigate this issue. Although numerous methods have been proposed for this task, most of these approaches concentrate solely on predicting antibiotic class, disregarding other important properties of ARGs. In addition, existing methods for simultaneously predicting multiple properties of ARGs fail to account for the causal relationships among these properties, limiting the predictive performance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we propose a causality-guided framework for annotating properties of ARGs, in which causal inference is utilized for representation learning. More specifically, the hidden biological patterns determining the properties of ARGs are described by a Gaussian Mixture Model, and procedure of causal representation learning is used to derive the hidden features. In addition, a causal graph among different properties is constructed to capture the causal relationships among properties of ARGs, which is integrated into the task of annotating properties of ARGs. The experimental results on a real-world dataset demonstrate the effectiveness of the proposed framework on the task of annotating properties of ARGs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The data and source codes are available in GitHub at https:\/\/github.com\/David-WZhao\/CausalARG.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae180","type":"journal-article","created":{"date-parts":[[2024,4,4]],"date-time":"2024-04-04T01:13:26Z","timestamp":1712193206000},"source":"Crossref","is-referenced-by-count":1,"title":["Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8552-6084","authenticated-orcid":false,"given":"Weizhong","family":"Zhao","sequence":"first","affiliation":[{"name":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China"},{"name":"School of Computer, Central China Normal University , Wuhan, Hubei 430079, P.R. China"},{"name":"National Language Resources Monitoring & Research Center for Network Media, Central China Normal University , Wuhan, Hubei 430079, P.R. China"}]},{"given":"Junze","family":"Wu","sequence":"additional","affiliation":[{"name":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8848-9300","authenticated-orcid":false,"given":"Xingpeng","family":"Jiang","sequence":"additional","affiliation":[{"name":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China"}]},{"given":"Tingting","family":"He","sequence":"additional","affiliation":[{"name":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China"}]},{"given":"Xiaohua","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Computing & Informatics, Drexel University , Philadelphia, PA 19104, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,4,3]]},"reference":[{"key":"2024041900012484900_btae180-B1","first-page":"D517","article-title":"Card 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024041900012484900_btae180-B2","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1080\/10643389.2019.1692611","article-title":"Understanding human health risks caused by antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) in water environments: current knowledge and questions to be answered","volume":"50","author":"Amarasiri","year":"2020","journal-title":"Crit Rev Environ Sci 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