{"id":"https://openalex.org/W4313526672","doi":"https://doi.org/10.1109/bibm55620.2022.9995458","title":"Extraction of Gene Regulatory Relation Using BioBERT","display_name":"Extraction of Gene Regulatory Relation Using BioBERT","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313526672","doi":"https://doi.org/10.1109/bibm55620.2022.9995458"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9995458","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995458","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5085188994","display_name":"Clement Essien","orcid":"https://orcid.org/0000-0003-1876-8889"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Clement Essien","raw_affiliation_strings":["University of Missouri,Department of Electrical Engineering and Computer Science,Columbia,MO,USA","Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri,Department of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087149818","display_name":"Fei He","orcid":"https://orcid.org/0000-0002-3284-9506"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei He","raw_affiliation_strings":["Northeast Normal University,School of Information Science and Technology,Changchun,China","School of Information Science and Technology, Northeast Normal University, Changchun, China"],"affiliations":[{"raw_affiliation_string":"Northeast Normal University,School of Information Science and Technology,Changchun,China","institution_ids":["https://openalex.org/I184983240"]},{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University, Changchun, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009891360","display_name":"Mark Hannink","orcid":"https://orcid.org/0000-0002-7319-6572"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Hannink","raw_affiliation_strings":["University of Missouri,Department of Biochemistry Bond Life Sciences Center,Columbia,MO,USA","Department of Biochemistry Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri,Department of Biochemistry Bond Life Sciences Center,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Biochemistry Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060329217","display_name":"Mihail Popescu","orcid":"https://orcid.org/0000-0002-6145-8096"},"institutions":[{"id":"https://openalex.org/I2800649613","display_name":"University of Missouri Health System","ror":"https://ror.org/03yp8z857","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800649613"]},{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mihail Popescu","raw_affiliation_strings":["University of Missouri,Department of Health Management and Informatics,Columbia,MO,USA","Department of Health Management and Informatics, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri,Department of Health Management and Informatics,Columbia,MO,USA","institution_ids":["https://openalex.org/I2800649613"]},{"raw_affiliation_string":"Department of Health Management and Informatics, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I2800649613","https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["University of Missouri,Department of Electrical Engineering and Computer Science Bond Life Sciences Center,Columbia,MO,USA","Department of Electrical Engineering and Computer Science Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri,Department of Electrical Engineering and Computer Science Bond Life Sciences Center,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5085188994"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.44382911,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"3351","last_page":"3355"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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/T10028","display_name":"Topic Modeling","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.7708295583724976},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6369335651397705},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.5666408538818359},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5071618556976318},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.48375630378723145},{"id":"https://openalex.org/keywords/association-rule-learning","display_name":"Association rule learning","score":0.4509626030921936},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.42344850301742554},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4062807559967041},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40548643469810486},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3754495084285736},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.343711256980896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19096055626869202},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17866560816764832},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12350884079933167}],"concepts":[{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.7708295583724976},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6369335651397705},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.5666408538818359},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5071618556976318},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.48375630378723145},{"id":"https://openalex.org/C193524817","wikidata":"https://www.wikidata.org/wiki/Q386780","display_name":"Association rule learning","level":2,"score":0.4509626030921936},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.42344850301742554},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4062807559967041},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40548643469810486},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3754495084285736},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.343711256980896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19096055626869202},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17866560816764832},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12350884079933167},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm55620.2022.9995458","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995458","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1724588178","https://openalex.org/W1907024343","https://openalex.org/W1988791574","https://openalex.org/W2006258148","https://openalex.org/W2065963191","https://openalex.org/W2097960255","https://openalex.org/W2103316358","https://openalex.org/W2127008962","https://openalex.org/W2133771440","https://openalex.org/W2135006190","https://openalex.org/W2141869602","https://openalex.org/W2145394518","https://openalex.org/W2520156704","https://openalex.org/W2612791346","https://openalex.org/W2740759433","https://openalex.org/W2890531203","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2920198243","https://openalex.org/W2971221499","https://openalex.org/W3017538732","https://openalex.org/W3096568637","https://openalex.org/W3178755335","https://openalex.org/W3191615546","https://openalex.org/W4205730624","https://openalex.org/W6623497120","https://openalex.org/W6639821265","https://openalex.org/W6737487289","https://openalex.org/W6755207826","https://openalex.org/W7002254874"],"related_works":["https://openalex.org/W2976808399","https://openalex.org/W2609844752","https://openalex.org/W2981341912","https://openalex.org/W4285246823","https://openalex.org/W2045408812","https://openalex.org/W4226278302","https://openalex.org/W4385734297","https://openalex.org/W4221160509","https://openalex.org/W2547211086","https://openalex.org/W2888033806"],"abstract_inverted_index":{"Relation":[0],"Extraction":[1],"(RE)":[2],"is":[3],"a":[4,53,65],"critical":[5],"task":[6],"typically":[7,43],"carried":[8],"out":[9],"after":[10],"Named":[11],"Entity":[12],"recognition":[13],"for":[14,57,70],"identifying":[15,71],"gene-gene":[16,41],"association":[17],"from":[18,36,75,81],"scientific":[19],"publication.":[20],"Current":[21],"state-of":[22],"the-art":[23],"tools":[24],"have":[25],"limited":[26],"capacity":[27],"as":[28],"most":[29],"of":[30,55,88],"them":[31],"only":[32],"extract":[33],"entity":[34],"relations":[35,42,74],"abstract":[37],"texts.":[38],"The":[39],"retrieved":[40],"do":[44],"not":[45],"cover":[46],"gene":[47,72],"regulatory":[48,73],"relations.":[49],"There":[50],"still":[51],"exists":[52],"lot":[54],"room":[56],"improvement.":[58],"In":[59],"this":[60],"work,":[61],"we":[62],"propose":[63],"GeREx,":[64],"transformer":[66],"based":[67],"RE":[68],"tool":[69],"full":[76],"texts":[77],"by":[78],"incorporating":[79],"labeling":[80],"pathway":[82],"figures.":[83],"GeREx":[84],"achieved":[85],"an":[86,93],"F1-Score":[87],"83.45%":[89],"when":[90],"evaluated":[91],"on":[92],"independent":[94],"test":[95],"dataset.":[96]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
