{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T18:14:38Z","timestamp":1778868878916,"version":"3.51.4"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T00:00:00Z","timestamp":1648857600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62136004"],"award-info":[{"award-number":["62136004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61876082"],"award-info":[{"award-number":["61876082"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61732006"],"award-info":[{"award-number":["61732006"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFC2001600"],"award-info":[{"award-number":["2018YFC2001600"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFC2001602"],"award-info":[{"award-number":["2018YFC2001602"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2021M691508"],"award-info":[{"award-number":["2021M691508"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CAAI-Huawei MindSpore Open Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacterium smegmatis porin A nanopore trap. Although it can achieve desirable classification results, compared with deep learning (DL) methods, this classic machine learning requires domain knowledge to manually extract features, which is sophisticated, labor-intensive and time-consuming. Meanwhile, the generated original RNA structural events are not strictly equal in length, which is incompatible with the input requirements of DL models. To alleviate this issue, we propose a sequence-to-sequence (S2S) module that transforms the unequal length sequence (UELS) to the equal length sequence. Furthermore, to automatically extract features from the RNA structural events, we propose a sequence-to-sequence neural network based on DL. In addition, we add an attention mechanism to capture vital information for classification, such as dwell time and blockage amplitude. Through quantitative and qualitative analysis, the experimental results have achieved about a 2% performance increase (accuracy) compared to the previous method. The proposed method can also be applied to other nanopore platforms, such as the famous Oxford nanopore. It is worth noting that the proposed method is not only aimed at pursuing state-of-the-art performance but also provides an overall idea to process nanopore data with UELS.<\/jats:p>","DOI":"10.1093\/bib\/bbac098","type":"journal-article","created":{"date-parts":[[2022,3,18]],"date-time":"2022-03-18T20:10:10Z","timestamp":1647634210000},"source":"Crossref","is-referenced-by-count":8,"title":["S2Snet: deep learning for low molecular weight RNA identification with nanopore"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3985-3900","authenticated-orcid":false,"given":"Xiaoyu","family":"Guan","sequence":"first","affiliation":[{"name":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuqin","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China"},{"name":"Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Shao","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongnian","family":"Li","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuo","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China"},{"name":"Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daoqiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,4,2]]},"reference":[{"key":"2022051813461185200_ref1","doi-asserted-by":"crossref","first-page":"2326","DOI":"10.1002\/(SICI)1521-3773(19990816)38:16<2326::AID-ANIE2326>3.0.CO;2-3","article-title":"Tertiary motifs in RNA structure and folding","volume":"38","author":"Batey","year":"1999","journal-title":"Angew Chem Int Ed Engl"},{"key":"2022051813461185200_ref2","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/nrg3681","article-title":"Insights into RNA structure and function from genome-wide studies","volume":"15","author":"Mortimer","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2022051813461185200_ref3","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1126\/science.288.5473.2048","article-title":"A single-molecule study of RNA catalysis and 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