{"id":"https://openalex.org/W4372337004","doi":"https://doi.org/10.1109/jbhi.2023.3273333","title":"A Self-Supervised Framework for Learning Biological Entities Representation by Fusing Class Information","display_name":"A Self-Supervised Framework for Learning Biological Entities Representation by Fusing Class Information","publication_year":2023,"publication_date":"2023-05-05","ids":{"openalex":"https://openalex.org/W4372337004","doi":"https://doi.org/10.1109/jbhi.2023.3273333","pmid":"https://pubmed.ncbi.nlm.nih.gov/37145951"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2023.3273333","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3273333","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","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/A5100341006","display_name":"Nan Li","orcid":"https://orcid.org/0000-0001-6484-0998"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Nan Li","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051597671","display_name":"Zhihao Yang","orcid":"https://orcid.org/0000-0001-6186-2024"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihao Yang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100370452","display_name":"Jian Wang","orcid":"https://orcid.org/0000-0002-4656-7446"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023931221","display_name":"Hongfei Lin","orcid":"https://orcid.org/0000-0003-0872-7688"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Lin","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100341006"],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":null,"apc_paid":null,"fwci":0.4777,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.66592109,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"27","issue":"8","first_page":"4178","last_page":"4188"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9986000061035156,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9980000257492065,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.826552152633667},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6855544447898865},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6338368654251099},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5573185682296753},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5479032397270203},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.49822497367858887},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4903702735900879},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4849150776863098},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4727678596973419},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.4655865728855133},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.43496984243392944},{"id":"https://openalex.org/keywords/knowledge-representation-and-reasoning","display_name":"Knowledge representation and reasoning","score":0.413570374250412},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.41237831115722656},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2756462097167969}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.826552152633667},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6855544447898865},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6338368654251099},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5573185682296753},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5479032397270203},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.49822497367858887},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4903702735900879},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4849150776863098},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4727678596973419},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.4655865728855133},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.43496984243392944},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.413570374250412},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.41237831115722656},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2756462097167969},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2023.3273333","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3273333","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:37145951","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37145951","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G442173326","display_name":null,"funder_award_id":"62276043","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7162057143","display_name":null,"funder_award_id":"DUT22ZD205","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W378747138","https://openalex.org/W1522301498","https://openalex.org/W1533230146","https://openalex.org/W1614298861","https://openalex.org/W1974896839","https://openalex.org/W2127426251","https://openalex.org/W2127795553","https://openalex.org/W2132290594","https://openalex.org/W2136410628","https://openalex.org/W2146495783","https://openalex.org/W2152850487","https://openalex.org/W2158191506","https://openalex.org/W2166574880","https://openalex.org/W2184957013","https://openalex.org/W2187089797","https://openalex.org/W2562531153","https://openalex.org/W2624297474","https://openalex.org/W2779933443","https://openalex.org/W2786757148","https://openalex.org/W2799259690","https://openalex.org/W2896457183","https://openalex.org/W2900569176","https://openalex.org/W2908034108","https://openalex.org/W2949434543","https://openalex.org/W2950595506","https://openalex.org/W2951841354","https://openalex.org/W2962969117","https://openalex.org/W2964074409","https://openalex.org/W2965778154","https://openalex.org/W2984788498","https://openalex.org/W3041736495","https://openalex.org/W3094557315","https://openalex.org/W3099442761","https://openalex.org/W3111174583","https://openalex.org/W3112306601","https://openalex.org/W3131901903","https://openalex.org/W3136655674","https://openalex.org/W3184618566","https://openalex.org/W4205773061","https://openalex.org/W4213041764","https://openalex.org/W4221157572","https://openalex.org/W4288384170","https://openalex.org/W6612948155","https://openalex.org/W6631190155","https://openalex.org/W6631964550","https://openalex.org/W6636510571","https://openalex.org/W6678830454","https://openalex.org/W6678846912","https://openalex.org/W6685380521","https://openalex.org/W6739425016","https://openalex.org/W6755207826","https://openalex.org/W6758075616","https://openalex.org/W6787324736","https://openalex.org/W6810128082"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2883748392","https://openalex.org/W3080107865","https://openalex.org/W3203147499","https://openalex.org/W3208204411","https://openalex.org/W4394929514","https://openalex.org/W2018870022","https://openalex.org/W3001243934","https://openalex.org/W3129488702","https://openalex.org/W2966218129"],"abstract_inverted_index":{"Ontologies":[0],"are":[1],"widely":[2],"utilized":[3],"in":[4,45,103],"the":[5,23,40,46,61,80,108,113,118,129,134,141,155,176],"biological":[6],"domain":[7],"for":[8],"data":[9],"annotation,":[10],"integration,":[11],"and":[12,66,136,158],"analysis.":[13],"Some":[14],"representation":[15,24],"learning":[16],"methods":[17],"have":[18],"been":[19],"proposed":[20],"to":[21,27,120,143,153],"learn":[22],"of":[25,37,43,76],"entities":[26,44],"assist":[28],"intelligent":[29],"applications,":[30],"such":[31],"as":[32],"knowledge":[33,62,96],"discovery.":[34],"However,":[35],"most":[36],"them":[38],"neglect":[39],"class":[41,81],"information":[42],"ontology.":[47],"In":[48,69,107,128,147],"this":[49,70],"article,":[50],"we":[51,72,111,132,149],"propose":[52],"a":[53,86],"unified":[54],"framework,":[55],"named":[56],"ERCI,":[57],"which":[58],"jointly":[59],"optimizes":[60],"graph":[63,97],"embedding":[64,98],"model":[65],"self-supervised":[67],"learning.":[68],"way,":[71,110,131],"can":[73,90],"generate":[74],"embeddings":[75,115,138],"bio-entities":[77],"by":[78,117,140],"fusing":[79],"information.":[82],"Moreover,":[83],"ERCI":[84,102,119,142,160,167],"is":[85],"pluggable":[87],"framework":[88],"that":[89,166],"be":[91],"easily":[92],"incorporated":[93],"with":[94,175],"any":[95],"model.":[99],"We":[100],"validate":[101],"two":[104,125],"different":[105,126],"ways.":[106],"first":[109],"utilize":[112],"protein":[114],"learned":[116],"predict":[121,144],"protein-protein":[122],"interactions":[123],"on":[124,161,171],"datasets.":[127],"second":[130],"leverage":[133],"gene":[135],"disease":[137],"generated":[139],"gene-disease":[145],"associations.":[146],"addition,":[148],"create":[150],"three":[151],"datasets":[152],"simulate":[154],"long-tail":[156],"scenario":[157],"evaluate":[159],"these.":[162],"Experimental":[163],"results":[164],"show":[165],"has":[168],"superior":[169],"performance":[170],"all":[172],"metrics":[173],"compared":[174],"state-of-the-art":[177],"methods.":[178]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
