{"id":"https://openalex.org/W4200273574","doi":"https://doi.org/10.1186/s12859-021-04517-6","title":"Class similarity network for coding and long non-coding RNA classification","display_name":"Class similarity network for coding and long non-coding RNA classification","publication_year":2021,"publication_date":"2021-12-01","ids":{"openalex":"https://openalex.org/W4200273574","doi":"https://doi.org/10.1186/s12859-021-04517-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/34930120"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04517-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04517-6","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-021-04517-6.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s12859-021-04517-6.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100433685","display_name":"Yu Zhang","orcid":"https://orcid.org/0000-0003-0982-7584"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I21196054","display_name":"Wellcome/MRC Cambridge Stem Cell Institute","ror":"https://ror.org/05nz0zp31","country_code":"GB","type":"facility","lineage":["https://openalex.org/I21196054","https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I87048295","https://openalex.org/I90344618"]}],"countries":["GB","SG"],"is_corresponding":false,"raw_author_name":"Yu Zhang","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore","Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK","institution_ids":["https://openalex.org/I21196054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066627747","display_name":"Yahui Long","orcid":"https://orcid.org/0000-0002-2765-3007"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yahui Long","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027208445","display_name":"Chee Keong Kwoh","orcid":"https://orcid.org/0000-0002-8547-6387"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Chee Keong Kwoh","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore. asckkwoh@ntu.edu.sg","School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-8547-6387","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore. asckkwoh@ntu.edu.sg","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5027208445"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.35,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.52167262,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"22","issue":"1","first_page":"609","last_page":"609"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9535999894142151,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9535999894142151,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.012500000186264515,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.003000000026077032,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6953313946723938},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6532338261604309},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5819908976554871},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5740181803703308},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.47044816613197327},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4356693923473358},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.42169463634490967},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35843026638031006},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3332597017288208},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1607593595981598},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08097270131111145}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6953313946723938},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6532338261604309},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5819908976554871},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5740181803703308},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.47044816613197327},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4356693923473358},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.42169463634490967},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35843026638031006},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3332597017288208},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1607593595981598},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08097270131111145},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04517-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04517-6","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-021-04517-6.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34930120","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34930120","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:8cf0959309a944ddba8b9805df2dbbf3","is_oa":true,"landing_page_url":"https://doaj.org/article/8cf0959309a944ddba8b9805df2dbbf3","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-14 (2021)","raw_type":"article"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/160163","is_oa":true,"landing_page_url":"https://hdl.handle.net/10356/160163","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8691036","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8691036","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04517-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04517-6","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-021-04517-6.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"},{"id":"https://openalex.org/F4320324110","display_name":"Singapore University of Technology and Design","ror":"https://ror.org/05j6fvn87"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4200273574.pdf","grobid_xml":"https://content.openalex.org/works/W4200273574.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1980069210","https://openalex.org/W2048194168","https://openalex.org/W2075320162","https://openalex.org/W2080052447","https://openalex.org/W2101290298","https://openalex.org/W2153268494","https://openalex.org/W2173732482","https://openalex.org/W2245239316","https://openalex.org/W2415774299","https://openalex.org/W2610159395","https://openalex.org/W2786594824","https://openalex.org/W2805813857","https://openalex.org/W2807607992","https://openalex.org/W2886900083","https://openalex.org/W2897297745","https://openalex.org/W2899322113","https://openalex.org/W2911561283","https://openalex.org/W2914698725","https://openalex.org/W2942942195","https://openalex.org/W2950707602","https://openalex.org/W2951413354","https://openalex.org/W2972172091","https://openalex.org/W2982468037","https://openalex.org/W2991346114","https://openalex.org/W2999743161","https://openalex.org/W3013495013","https://openalex.org/W3039462905","https://openalex.org/W3080427797","https://openalex.org/W3090653878"],"related_works":["https://openalex.org/W3093612317","https://openalex.org/W4287776258","https://openalex.org/W3027997911","https://openalex.org/W2175746458","https://openalex.org/W2732542196","https://openalex.org/W2767651786","https://openalex.org/W2760085659","https://openalex.org/W2883200793","https://openalex.org/W2738221750","https://openalex.org/W3012978760"],"abstract_inverted_index":{"BACKGROUND:":[0],"Long":[1],"non-coding":[2],"RNAs":[3],"(lncRNAs)":[4],"play":[5],"significant":[6],"roles":[7],"in":[8,76,91,142,187],"varieties":[9],"of":[10,16,159],"physiological":[11],"and":[12,79,105,112,134,173,190,207,213],"pathological":[13],"processes.The":[14],"premise":[15],"the":[17,23,43,46,61,99,109,113,123,131,136,149,153,157,165],"lncRNA":[18,80,191],"functional":[19],"study":[20],"is":[21,194],"that":[22],"lncRNAs":[24],"are":[25],"identified":[26],"correctly.":[27],"Recently,":[28],"deep":[29],"learning":[30],"method":[31,170],"like":[32],"convolutional":[33],"neural":[34],"network":[35,71],"(CNN)":[36],"has":[37],"been":[38],"successfully":[39],"applied":[40],"to":[41,126,129,139,164,196],"identify":[42],"lncRNAs.":[44],"However,":[45],"traditional":[47],"CNN":[48],"considers":[49,85],"little":[50],"relationships":[51,87,101],"among":[52,88],"samples":[53,90,104,106],"via":[54],"an":[55],"indirect":[56],"way.":[57,94],"RESULTS:":[58],"Inspired":[59],"by":[60,203],"Siamese":[62],"Neural":[63],"Network":[64,75,84,121,163,186],"(SNN),":[65],"here":[66],"we":[67],"propose":[68],"a":[69,92,143],"novel":[70],"named":[72],"Class":[73,82,119,161,184],"Similarity":[74,83,120,162,185],"coding":[77,188],"RNA":[78,189],"classification.":[81],"more":[86],"input":[89,103],"direct":[93],"It":[95],"focuses":[96],"on":[97,148,177,199],"exploring":[98],"potential":[100],"between":[102],"from":[107],"both":[108],"same":[110,154],"class":[111,128,141],"different":[114,201],"classes.":[115],"To":[116],"achieve":[117],"this,":[118],"trains":[122],"parameters":[124],"specific":[125],"each":[127,140],"obtain":[130],"high-level":[132],"features":[133],"represents":[135],"general":[137],"similarity":[138],"node.":[144],"The":[145],"comparison":[146],"results":[147],"validation":[150],"dataset":[151],"under":[152],"conditions":[155],"illustrate":[156],"superiority":[158],"our":[160,169],"baseline":[166],"CNN.":[167],"Besides,":[168],"performs":[171],"effectively":[172,198],"achieves":[174],"state-of-the-art":[175],"performances":[176],"two":[178,200],"test":[179],"datasets.":[180],"CONCLUSIONS:":[181],"We":[182],"construct":[183],"classification,":[192],"which":[193],"shown":[195],"work":[197],"datasets":[202],"achieving":[204],"accuracy,":[205],"precision,":[206],"F1-score":[208],"as":[209],"98.43%,":[210],"0.9247,":[211],"0.9374,":[212],"97.54%,":[214],"0.9990,":[215],"0.9860,":[216],"respectively.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}