{"id":"https://openalex.org/W4214543690","doi":"https://doi.org/10.1109/access.2022.3154820","title":"Attention Retrieval Model for Entity Relation Extraction From Biological Literature","display_name":"Attention Retrieval Model for Entity Relation Extraction From Biological Literature","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4214543690","doi":"https://doi.org/10.1109/access.2022.3154820"},"language":"en","primary_location":{"id":"doi:10.1109/access.2022.3154820","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3154820","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09721887.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09721887.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103082575","display_name":"Prashant Srivastava","orcid":"https://orcid.org/0000-0002-0383-8330"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Prashant Srivastava","raw_affiliation_strings":["Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0383-8330","affiliations":[{"raw_affiliation_string":"Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046944026","display_name":"Saptarshi Bej","orcid":"https://orcid.org/0000-0003-1835-6139"},"institutions":[{"id":"https://openalex.org/I4210144923","display_name":"Leibniz-Institute for Food Systems Biology at the Technical University of Munich","ror":"https://ror.org/04sy7nb49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210144923"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Saptarshi Bej","raw_affiliation_strings":["Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany","Leibniz-Institute for Food Systems Biology, Technical University of Munich, Freising, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]},{"raw_affiliation_string":"Leibniz-Institute for Food Systems Biology, Technical University of Munich, Freising, Germany","institution_ids":["https://openalex.org/I4210144923"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084842163","display_name":"Kristian Schultz","orcid":"https://orcid.org/0000-0002-4308-6006"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kristian Schultz","raw_affiliation_strings":["Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055405987","display_name":"Kristina Yordanova","orcid":"https://orcid.org/0000-0002-6428-1062"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kristina Yordanova","raw_affiliation_strings":["Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany"],"raw_orcid":"https://orcid.org/0000-0002-6428-1062","affiliations":[{"raw_affiliation_string":"Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022724143","display_name":"Olaf Wolkenhauer","orcid":"https://orcid.org/0000-0001-6105-2937"},"institutions":[{"id":"https://openalex.org/I4210144923","display_name":"Leibniz-Institute for Food Systems Biology at the Technical University of Munich","ror":"https://ror.org/04sy7nb49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210144923"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Olaf Wolkenhauer","raw_affiliation_strings":["Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany","Leibniz-Institute for Food Systems Biology, Technical University of Munich, Freising, Germany"],"raw_orcid":"https://orcid.org/0000-0001-6105-2937","affiliations":[{"raw_affiliation_string":"Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]},{"raw_affiliation_string":"Leibniz-Institute for Food Systems Biology, Technical University of Munich, Freising, Germany","institution_ids":["https://openalex.org/I4210144923"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1890,"currency":"EUR","value_usd":2038},"fwci":0.0866,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.40369623,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"10","issue":null,"first_page":"22429","last_page":"22440"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9988999962806702,"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":0.9988999962806702,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9955999851226807,"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":0.8453407883644104},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5712478756904602},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5679040551185608},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5334365963935852},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5257999300956726},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5222290754318237},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.5021450519561768},{"id":"https://openalex.org/keywords/question-answering","display_name":"Question answering","score":0.4937308728694916},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.4672088027000427},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.42177438735961914},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.19499504566192627},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.1333356499671936}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8453407883644104},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5712478756904602},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5679040551185608},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5334365963935852},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5257999300956726},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5222290754318237},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.5021450519561768},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.4937308728694916},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.4672088027000427},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.42177438735961914},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.19499504566192627},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.1333356499671936},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/access.2022.3154820","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3154820","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09721887.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:cdae36f10ac84227a3192a5c4dbfb28f","is_oa":true,"landing_page_url":"https://doaj.org/article/cdae36f10ac84227a3192a5c4dbfb28f","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":"IEEE Access, Vol 10, Pp 22429-22440 (2022)","raw_type":"article"},{"id":"pmh:oai:mediatum.ub.tum.de:node/1771289","is_oa":true,"landing_page_url":"https://mediatum.ub.tum.de/1771289","pdf_url":null,"source":{"id":"https://openalex.org/S4377196330","display_name":"mediaTUM  (Technical University of Munich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I62916508","host_organization_name":"Technical University of Munich","host_organization_lineage":["https://openalex.org/I62916508"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2022.3154820","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3154820","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09721887.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8299999833106995,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4214543690.pdf","grobid_xml":"https://content.openalex.org/works/W4214543690.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1583412584","https://openalex.org/W2048296798","https://openalex.org/W2107580398","https://openalex.org/W2116702276","https://openalex.org/W2132267839","https://openalex.org/W2133564696","https://openalex.org/W2138275182","https://openalex.org/W2177317049","https://openalex.org/W2403934794","https://openalex.org/W2740460881","https://openalex.org/W2906406865","https://openalex.org/W2913694513","https://openalex.org/W2951615992","https://openalex.org/W2971221499","https://openalex.org/W2972795848","https://openalex.org/W2978461222","https://openalex.org/W3028004046","https://openalex.org/W3081978500","https://openalex.org/W3082216319","https://openalex.org/W3093053585","https://openalex.org/W3127542603","https://openalex.org/W3169066049","https://openalex.org/W3210986045","https://openalex.org/W4287687350","https://openalex.org/W6607318932","https://openalex.org/W6631190155","https://openalex.org/W6638444622","https://openalex.org/W6679434410","https://openalex.org/W6739901393","https://openalex.org/W6781816295"],"related_works":["https://openalex.org/W842810586","https://openalex.org/W4319940250","https://openalex.org/W2352298027","https://openalex.org/W2092919065","https://openalex.org/W3138801416","https://openalex.org/W4236762297","https://openalex.org/W1984061923","https://openalex.org/W2444550338","https://openalex.org/W2169232658","https://openalex.org/W2369351710"],"abstract_inverted_index":{"Natural":[0],"Language":[1],"Processing":[2],"(NLP)":[3],"has":[4],"contributed":[5],"to":[6,86,129,140,162],"extracting":[7],"relationships":[8,152],"among":[9],"biological":[10],"entities,":[11],"such":[12],"as":[13,55],"genes,":[14],"their":[15,131],"mutations,":[16],"proteins,":[17],"diseases,":[18],"processes,":[19],"phenotypes,":[20],"and":[21,26,136],"drugs,":[22],"for":[23,36,51,91,126,146,179],"a":[24,56,94,105,123,127,142],"comprehensive":[25],"concise":[27],"understanding":[28],"of":[29,82],"information":[30],"in":[31,46,64,113,157],"the":[32,73,80,87,102,109,114,158],"literature.":[33],"Self-attention-based":[34],"models":[35,50,84],"Relationship":[37],"Extraction":[38],"(RE)":[39],"have":[40],"played":[41],"an":[42,69,117,173],"increasingly":[43],"important":[44],"role":[45],"NLP.":[47],"However,":[48],"self-attention":[49,119],"RE":[52],"are":[53,154],"framed":[54],"classification":[57,89],"problem,":[58],"which":[59,78],"limits":[60],"its":[61],"practical":[62,144],"usability":[63],"several":[65],"ways.":[66],"We":[67],"present":[68,112],"alternative":[70,174],"framework":[71,125,178],"called":[72],"Attention":[74],"Retrieval":[75],"Model":[76],"(ARM),":[77],"enhances":[79],"applicability":[81],"attention-based":[83],"compared":[85],"regular":[88],"approach,":[90],"RE.":[92,147],"Given":[93],"text":[95],"sequence":[96],"containing":[97],"related":[98],"entities/keywords,":[99],"ARM":[100,121,148,171],"learns":[101],"association":[103],"between":[104],"chosen":[106],"entity/keyword":[107],"with":[108],"other":[110],"entities":[111],"sequence,":[115],"using":[116],"underlying":[118],"mechanism.":[120],"provides":[122,172],"flexible":[124],"modeller":[128],"customise":[130],"model,":[132],"facilitate":[133],"data":[134],"integration,":[135],"integrate":[137],"expert":[138],"knowledge":[139],"provide":[141],"more":[143],"approach":[145],"can":[149,182],"extract":[150],"unseen":[151],"that":[153,181],"not":[155],"annotated":[156],"training":[159],"data,":[160],"analogous":[161],"<italic":[163],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[164],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">zero-shot":[165],"learning</i>":[166],".":[167],"To":[168],"sum":[169],"up,":[170],"self-attention-based":[175],"deep":[176],"learning":[177],"RE,":[180],"capture":[183],"directed":[184],"entity":[185],"relationships.":[186]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
