{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T07:19:24Z","timestamp":1773127164288,"version":"3.50.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,12,23]],"date-time":"2020-12-23T00:00:00Z","timestamp":1608681600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61872418"],"award-info":[{"award-number":["61872418"]}],"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":["61972175"],"award-info":[{"award-number":["61972175"]}],"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":["71774154"],"award-info":[{"award-number":["71774154"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007847","name":"Natural Science Foundation of Jilin Province","doi-asserted-by":"publisher","award":["20180101331JC"],"award-info":[{"award-number":["20180101331JC"]}],"id":[{"id":"10.13039\/100007847","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007847","name":"Natural Science Foundation of Jilin Province","doi-asserted-by":"publisher","award":["20180101050JC"],"award-info":[{"award-number":["20180101050JC"]}],"id":[{"id":"10.13039\/100007847","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Non-coding RNAs (ncRNAs) play crucial roles in multiple biological processes. However, only a few ncRNAs\u2019 functions have been well studied. Given the significance of ncRNAs classification for understanding ncRNAs\u2019 functions, more and more computational methods have been introduced to improve the classification automatically and accurately. In this paper, based on a convolutional neural network and a deep forest algorithm, multi-grained cascade forest (GcForest), we propose a novel deep fusion learning framework, GcForest fusion method (GCFM), to classify alignments of ncRNA sequences for accurate clustering of ncRNAs. GCFM integrates a multi-view structure feature representation including sequence-structure alignment encoding, structure image representation and shape alignment encoding of structural subunits, enabling us to capture the potential specificity between ncRNAs. For the classification of pairwise alignment of two ncRNA sequences, the F-value of GCFM improves 6% than an existing alignment-based method. Furthermore, the clustering of ncRNA families is carried out based on the classification matrix generated from GCFM. Results suggest better performance (with 20% accuracy improved) than existing ncRNA clustering methods (RNAclust, Ensembleclust and CNNclust). Additionally, we apply GCFM to construct a phylogenetic tree of ncRNA and predict the probability of interactions between RNAs. Most ncRNAs are located correctly in the phylogenetic tree, and the prediction accuracy of RNA interaction is 90.63%. A web server (http:\/\/bmbl.sdstate.edu\/gcfm\/) is developed to maximize its availability, and the source code and related data are available at the same URL.<\/jats:p>","DOI":"10.1093\/bib\/bbaa354","type":"journal-article","created":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T12:19:21Z","timestamp":1606997961000},"source":"Crossref","is-referenced-by-count":11,"title":["Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations"],"prefix":"10.1093","volume":"22","author":[{"given":"Ying","family":"Li","sequence":"first","affiliation":[{"name":"College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China"}]},{"given":"Qi","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Jilin University, Changchun, China"}]},{"given":"Zhaoqian","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Mathematics, Shandong University, and now she is a visiting scholar at Ohio State University"}]},{"given":"Cankun","family":"Wang","sequence":"additional","affiliation":[{"name":"Ohio State University"}]},{"given":"Siyu","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Faculty of Engineering, University of Bristol"}]},{"given":"Qin","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Ohio State University"}]},{"given":"Wei","family":"Du","sequence":"additional","affiliation":[{"name":"College of Computer Science and Technology, Jilin University, Changchun, China"}]}],"member":"286","published-online":{"date-parts":[[2020,12,23]]},"reference":[{"issue":"1","key":"2021072117052190600_ref1","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.cell.2014.03.008","article-title":"The 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