{"id":"https://openalex.org/W4220690199","doi":"https://doi.org/10.1093/bib/bbac089","title":"Fully connected autoencoder and convolutional neural network with attention-based method for inferring disease-related lncRNAs","display_name":"Fully connected autoencoder and convolutional neural network with attention-based method for inferring disease-related lncRNAs","publication_year":2022,"publication_date":"2022-03-25","ids":{"openalex":"https://openalex.org/W4220690199","doi":"https://doi.org/10.1093/bib/bbac089","pmid":"https://pubmed.ncbi.nlm.nih.gov/35362511"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac089","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac089","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028616130","display_name":"Ping Xuan","orcid":"https://orcid.org/0000-0001-5328-691X"},"institutions":[{"id":"https://openalex.org/I1300757298","display_name":"Heilongjiang University of Science and Technology","ror":"https://ror.org/030xwyx96","country_code":"CN","type":"education","lineage":["https://openalex.org/I1300757298"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ping Xuan","raw_affiliation_strings":["School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China","institution_ids":["https://openalex.org/I1300757298"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046792153","display_name":"Zhe Gong","orcid":null},"institutions":[{"id":"https://openalex.org/I1300757298","display_name":"Heilongjiang University of Science and Technology","ror":"https://ror.org/030xwyx96","country_code":"CN","type":"education","lineage":["https://openalex.org/I1300757298"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Gong","raw_affiliation_strings":["School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Heilongjiang University, Harbin 150080, China","institution_ids":["https://openalex.org/I1300757298"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004971220","display_name":"Hui Cui","orcid":"https://orcid.org/0000-0001-8224-4698"},"institutions":[{"id":"https://openalex.org/I196829312","display_name":"La Trobe University","ror":"https://ror.org/01rxfrp27","country_code":"AU","type":"education","lineage":["https://openalex.org/I196829312"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Hui Cui","raw_affiliation_strings":["Department of Computer Science and Information Technology, La Trobe University, Melbourne 3083, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technology, La Trobe University, Melbourne 3083, Australia","institution_ids":["https://openalex.org/I196829312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064177369","display_name":"Bochong Li","orcid":"https://orcid.org/0000-0003-1573-5379"},"institutions":[{"id":"https://openalex.org/I159385669","display_name":"Chiba University","ror":"https://ror.org/01hjzeq58","country_code":"JP","type":"education","lineage":["https://openalex.org/I159385669"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Bochong Li","raw_affiliation_strings":["Center for Frontier Medical Engineering, Chiba University, Chiba 2638522, Japan"],"affiliations":[{"raw_affiliation_string":"Center for Frontier Medical Engineering, Chiba University, Chiba 2638522, Japan","institution_ids":["https://openalex.org/I159385669"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004963500","display_name":"Tiangang Zhang","orcid":"https://orcid.org/0000-0002-7528-3581"},"institutions":[{"id":"https://openalex.org/I55022517","display_name":"Heilongjiang University","ror":"https://ror.org/04zyhq975","country_code":"CN","type":"education","lineage":["https://openalex.org/I55022517"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tiangang Zhang","raw_affiliation_strings":["School of Mathematical Science, Heilongjiang University, Harbin 150080, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematical Science, Heilongjiang University, Harbin 150080, China","institution_ids":["https://openalex.org/I55022517"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5004963500"],"corresponding_institution_ids":["https://openalex.org/I55022517"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.0646,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.88358402,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"23","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"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":1.0,"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/autoencoder","display_name":"Autoencoder","score":0.823692798614502},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7179886102676392},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6146456599235535},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.6135628819465637},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5168638825416565},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5160529017448425},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.49366268515586853},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.42594751715660095},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.391406387090683},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3374764323234558},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.3203830122947693},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17734456062316895},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.17041927576065063},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.11519196629524231},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.09960964322090149},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08055108785629272},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.061202555894851685}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.823692798614502},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7179886102676392},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6146456599235535},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6135628819465637},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5168638825416565},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5160529017448425},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.49366268515586853},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.42594751715660095},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.391406387090683},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3374764323234558},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3203830122947693},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17734456062316895},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.17041927576065063},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.11519196629524231},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.09960964322090149},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08055108785629272},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.061202555894851685},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","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},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac089","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac089","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35362511","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35362511","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G3334349523","display_name":null,"funder_award_id":"2019M650069","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G6259686466","display_name":null,"funder_award_id":"62172143","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7463416688","display_name":null,"funder_award_id":"LH2019F049","funder_id":"https://openalex.org/F4320323085","funder_display_name":"Natural Science Foundation of Heilongjiang Province"},{"id":"https://openalex.org/G7689861867","display_name":null,"funder_award_id":"2020M670939","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G8504959210","display_name":null,"funder_award_id":"61972135","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320323085","display_name":"Natural Science Foundation of Heilongjiang Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W611910056","https://openalex.org/W1990895545","https://openalex.org/W1999008082","https://openalex.org/W2002185065","https://openalex.org/W2014162182","https://openalex.org/W2029348196","https://openalex.org/W2062083667","https://openalex.org/W2067765119","https://openalex.org/W2070777085","https://openalex.org/W2117977572","https://openalex.org/W2128983843","https://openalex.org/W2130388134","https://openalex.org/W2150695488","https://openalex.org/W2152970345","https://openalex.org/W2161607603","https://openalex.org/W2198153867","https://openalex.org/W2259538443","https://openalex.org/W2408796111","https://openalex.org/W2437043110","https://openalex.org/W2462108616","https://openalex.org/W2473876819","https://openalex.org/W2509738156","https://openalex.org/W2512308096","https://openalex.org/W2531500048","https://openalex.org/W2571957366","https://openalex.org/W2611747160","https://openalex.org/W2757497299","https://openalex.org/W2765950793","https://openalex.org/W2772618228","https://openalex.org/W2801501532","https://openalex.org/W2802616725","https://openalex.org/W2894348124","https://openalex.org/W2895679848","https://openalex.org/W2912626494","https://openalex.org/W2942942195","https://openalex.org/W2967598666","https://openalex.org/W2972582951","https://openalex.org/W3027711990","https://openalex.org/W3099929518","https://openalex.org/W4246271082"],"related_works":["https://openalex.org/W2159052453","https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W4365790226","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W3167935049","https://openalex.org/W3029198973"],"abstract_inverted_index":{"Since":[0],"abnormal":[1],"expression":[2],"of":[3,17,28,36,64,98,126,172],"long":[4],"noncoding":[5],"RNAs":[6],"(lncRNAs)":[7],"is":[8,20,206],"often":[9],"closely":[10],"related":[11,38],"to":[12,39,52,107,121,151,167,208],"various":[13],"human":[14],"diseases,":[15],"identification":[16],"disease-associated":[18],"lncRNAs":[19,40],"helpful":[21],"for":[22,43,87],"exploring":[23],"the":[24,55,59,123,133,138,142,148,169,210],"complex":[25],"pathogenesis.":[26],"Most":[27],"recent":[29],"methods":[30],"concentrate":[31],"on":[32,77,161,197],"exploiting":[33],"multiple":[34,178],"kinds":[35],"data":[37],"and":[41,67,81,101,111,129,146,156,174,200],"diseases":[42],"predicting":[44],"candidate":[45],"disease-related":[46,90,212],"lncRNAs.":[47,213],"These":[48],"methods,":[49],"however,":[50],"failed":[51],"deeply":[53],"integrate":[54,108],"topology":[56],"information":[57],"from":[58,177],"meta-paths":[60],"that":[61,96,204],"are":[62],"composed":[63],"lncRNA,":[65,99,127],"disease":[66,100,128,175],"microRNA":[68],"(miRNA)":[69],"nodes.":[70],"We":[71,136],"proposed":[72],"a":[73],"new":[74],"method":[75],"based":[76,160],"fully":[78],"connected":[79,116],"autoencoders":[80],"convolutional":[82,162],"neural":[83,163],"networks,":[84],"called":[85],"ACLDA,":[86],"inferring":[88],"potential":[89,211],"lncRNA":[91,173],"candidates.":[92],"A":[93,158],"heterogeneous":[94,134],"graph":[95],"consists":[97],"miRNA":[102,130],"nodes":[103,131,176],"were":[104],"firstly":[105],"constructed":[106,166],"similarities,":[109],"associations":[110],"interactions":[112],"among":[113],"them.":[114],"Fully":[115],"autoencoder-based":[117],"module":[118,159],"was":[119,165],"established":[120],"extract":[122],"low-dimensional":[124],"features":[125,155],"in":[132],"graph.":[135],"designed":[137],"attention":[139],"mechanisms":[140],"at":[141,147],"node":[143],"feature":[144],"level":[145,150],"meta-path":[149,179],"learn":[152],"more":[153],"informative":[154],"meta-paths.":[157],"networks":[164],"encode":[168],"local":[170],"topologies":[171],"perspectives.":[180],"The":[181],"comprehensive":[182],"experimental":[183],"results":[184],"demonstrated":[185,203],"ACLDA":[186,205],"achieves":[187],"superior":[188],"performance":[189],"than":[190],"several":[191],"state-of-the-art":[192],"prediction":[193],"methods.":[194],"Case":[195],"studies":[196],"breast,":[198],"lung":[199],"colon":[201],"cancers":[202],"able":[207],"discover":[209]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}