{"id":"https://openalex.org/W3200220209","doi":"https://doi.org/10.1109/tcbb.2021.3113326","title":"DHNLDA: A Novel Deep Hierarchical Network Based Method for Predicting lncRNA-Disease Associations","display_name":"DHNLDA: A Novel Deep Hierarchical Network Based Method for Predicting lncRNA-Disease Associations","publication_year":2021,"publication_date":"2021-09-20","ids":{"openalex":"https://openalex.org/W3200220209","doi":"https://doi.org/10.1109/tcbb.2021.3113326","mag":"3200220209","pmid":"https://pubmed.ncbi.nlm.nih.gov/34543201"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3113326","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3113326","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5083234038","display_name":"Fansen Xie","orcid":"https://orcid.org/0000-0002-2847-9135"},"institutions":[{"id":"https://openalex.org/I61565387","display_name":"Dalian Minzu University","ror":"https://ror.org/02hxfx521","country_code":"CN","type":"education","lineage":["https://openalex.org/I61565387"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fansen Xie","raw_affiliation_strings":["Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0002-2847-9135","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I61565387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114339957","display_name":"Ziqi Yang","orcid":"https://orcid.org/0000-0003-0488-7457"},"institutions":[{"id":"https://openalex.org/I61565387","display_name":"Dalian Minzu University","ror":"https://ror.org/02hxfx521","country_code":"CN","type":"education","lineage":["https://openalex.org/I61565387"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziqi Yang","raw_affiliation_strings":["Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0003-0488-7457","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I61565387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100664739","display_name":"Jinmiao Song","orcid":"https://orcid.org/0000-0003-0847-9813"},"institutions":[{"id":"https://openalex.org/I61565387","display_name":"Dalian Minzu University","ror":"https://ror.org/02hxfx521","country_code":"CN","type":"education","lineage":["https://openalex.org/I61565387"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinmiao Song","raw_affiliation_strings":["SEAC Key Laboratory of Big Data Applied Technology, Dalian Key Lab of Digital Technology for National Culture, Dalian Minzu University, Dalian, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0003-0847-9813","affiliations":[{"raw_affiliation_string":"SEAC Key Laboratory of Big Data Applied Technology, Dalian Key Lab of Digital Technology for National Culture, Dalian Minzu University, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I61565387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101021629","display_name":"Qiguo Dai","orcid":null},"institutions":[{"id":"https://openalex.org/I61565387","display_name":"Dalian Minzu University","ror":"https://ror.org/02hxfx521","country_code":"CN","type":"education","lineage":["https://openalex.org/I61565387"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiguo Dai","raw_affiliation_strings":["Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I61565387"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079789170","display_name":"Xiaodong Duan","orcid":"https://orcid.org/0000-0003-2345-4155"},"institutions":[{"id":"https://openalex.org/I61565387","display_name":"Dalian Minzu University","ror":"https://ror.org/02hxfx521","country_code":"CN","type":"education","lineage":["https://openalex.org/I61565387"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaodong Duan","raw_affiliation_strings":["Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, SEAC Key Laboratory of Big Data Applied Technology, Dalian Minzu University, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I61565387"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I61565387"],"apc_list":null,"apc_paid":null,"fwci":0.2625,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.47934727,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"6","first_page":"3395","last_page":"3403"},"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":0.6443444490432739},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.587018609046936},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5028807520866394},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4771401584148407},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.465167760848999},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4335900545120239},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.43237584829330444},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.41122376918792725},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3901050090789795},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38433724641799927},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.37825947999954224},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18213552236557007},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15430665016174316}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.6443444490432739},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.587018609046936},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5028807520866394},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4771401584148407},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.465167760848999},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4335900545120239},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.43237584829330444},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.41122376918792725},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3901050090789795},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38433724641799927},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.37825947999954224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18213552236557007},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15430665016174316},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D013274","descriptor_name":"Stomach Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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:10.1109/tcbb.2021.3113326","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3113326","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34543201","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34543201","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.800000011920929}],"awards":[{"id":"https://openalex.org/G4562443281","display_name":null,"funder_award_id":"61701073","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W611910056","https://openalex.org/W1972943051","https://openalex.org/W1988195734","https://openalex.org/W2002185065","https://openalex.org/W2023940858","https://openalex.org/W2088321564","https://openalex.org/W2113868616","https://openalex.org/W2117977572","https://openalex.org/W2128983843","https://openalex.org/W2153635508","https://openalex.org/W2154851992","https://openalex.org/W2158135353","https://openalex.org/W2295598076","https://openalex.org/W2302255633","https://openalex.org/W2333254191","https://openalex.org/W2531500048","https://openalex.org/W2743353724","https://openalex.org/W2752601635","https://openalex.org/W2754595644","https://openalex.org/W2757497299","https://openalex.org/W2772618228","https://openalex.org/W2787946513","https://openalex.org/W2801501532","https://openalex.org/W2802616725","https://openalex.org/W2930902918","https://openalex.org/W2942942195","https://openalex.org/W2960796721","https://openalex.org/W2962756421","https://openalex.org/W2962949934","https://openalex.org/W2963457766","https://openalex.org/W2970249540","https://openalex.org/W2971132843","https://openalex.org/W2990265059","https://openalex.org/W2993557395","https://openalex.org/W3013787003","https://openalex.org/W3018422715","https://openalex.org/W3027405047","https://openalex.org/W3027711990","https://openalex.org/W3036573187","https://openalex.org/W3046766399","https://openalex.org/W3104097132","https://openalex.org/W3113289897","https://openalex.org/W3216601538","https://openalex.org/W4239510810","https://openalex.org/W6656416788","https://openalex.org/W6779660028"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2159052453","https://openalex.org/W2566616303","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W4297051394","https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4392946183","https://openalex.org/W3088732000"],"abstract_inverted_index":{"Recent":[0],"studies":[1,178],"have":[2,187],"found":[3],"that":[4,165],"lncRNA":[5,43],"(long":[6],"non-coding":[7],"RNA)":[8,12],"in":[9,17,25],"ncRNA":[10],"(non-coding":[11],"is":[13,34,143],"not":[14],"only":[15],"involved":[16],"many":[18,26],"biological":[19,75,85],"processes,":[20],"but":[21],"also":[22],"abnormally":[23],"expressed":[24],"complex":[27],"diseases.":[28],"Identification":[29],"of":[30,35,42,55,93,132,140,155,161,168,179,192],"lncRNA-disease":[31,70,156,198],"associations":[32],"accurately":[33],"great":[36,190],"significance":[37],"for":[38],"understanding":[39],"the":[40,84,88,91,113,116,123,129,138,146,152,166,174,189,196],"function":[41],"and":[44,60,78,90,96,108,115,128,184],"disease":[45],"mechanism.":[46],"In":[47],"this":[48],"paper,":[49],"a":[50],"deep":[51],"learning":[52],"framework":[53],"consisting":[54],"stacked":[56,61,147],"autoencoder(SAE),":[57],"multi-scale":[58,117],"ResNet":[59,118],"ensemble":[62,148],"module,":[63],"named":[64],"DHNLDA,":[65],"was":[66],"constructed":[67],"to":[68,121,150,194],"predict":[69],"associations,":[71],"which":[72],"integrates":[73],"multiple":[74],"data":[76,86],"sources":[77],"constructing":[79],"feature":[80,101,109,142],"matrices.":[81],"Among":[82],"them,":[83],"including":[87],"similarity":[89],"interaction":[92],"lncRNAs,":[94],"diseases":[95],"miRNAs":[97],"are":[98,103,119,135],"integrated.":[99],"The":[100,158],"matrices":[102],"obtained":[104],"by":[105],"node2vec":[106],"embedding":[107],"extraction":[110],"respectively.":[111],"Then,":[112],"SAE":[114],"used":[120],"learn":[122],"complementary":[124],"information":[125],"between":[126],"nodes,":[127],"high-level":[130,141],"features":[131],"node":[133],"attributes":[134],"obtained.":[136],"Finally,":[137],"fusion":[139],"input":[144],"into":[145],"module":[149],"obtain":[151],"prediction":[153],"results":[154,160],"associations.":[157,199],"experimental":[159],"five-fold":[162],"cross-validation":[163],"show":[164],"AUC":[167],"DHNLDA":[169,193],"reaches":[170],"0.975":[171],"better":[172],"than":[173],"existing":[175],"methods.":[176],"Case":[177],"stomach":[180],"cancer,":[181],"breast":[182],"cancer":[183,186],"lung":[185],"shown":[188],"ability":[191],"discover":[195],"potential":[197]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
