{"id":"https://openalex.org/W7126032960","doi":"https://doi.org/10.1109/bibm66473.2025.11356539","title":"Bio-R <sup>3</sup> : Entity Aware and Domain Adaptive Enhanced Framework for Biomedical Document Level Relation Extraction","display_name":"Bio-R <sup>3</sup> : Entity Aware and Domain Adaptive Enhanced Framework for Biomedical Document Level Relation Extraction","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126032960","doi":"https://doi.org/10.1109/bibm66473.2025.11356539"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356539","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356539","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5017835678","display_name":"Di Zhao","orcid":"https://orcid.org/0000-0002-0876-5126"},"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":"Di Zhao","raw_affiliation_strings":["School of Computer Science and Engineering, Dalian Minzu University,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Dalian Minzu University,Dalian,China","institution_ids":["https://openalex.org/I61565387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001402526","display_name":"Xin Luna Dong","orcid":"https://orcid.org/0009-0000-8667-322X"},"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":"Xin Dong","raw_affiliation_strings":["School of Computer Science and Engineering, Dalian Minzu University,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Dalian Minzu University,Dalian,China","institution_ids":["https://openalex.org/I61565387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123247524","display_name":"Jiana Meng","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":"Jiana Meng","raw_affiliation_strings":["School of Computer Science and Engineering, Dalian Minzu University,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Dalian Minzu University,Dalian,China","institution_ids":["https://openalex.org/I61565387"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124158791","display_name":"Hongfei Lin","orcid":null},"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":["School of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School 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":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"3315","last_page":"3320"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5424000024795532,"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":0.5424000024795532,"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":0.3971000015735626,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.009999999776482582,"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":0.8495000004768372},{"id":"https://openalex.org/keywords/rewriting","display_name":"Rewriting","score":0.8163999915122986},{"id":"https://openalex.org/keywords/domain-adaptation","display_name":"Domain adaptation","score":0.7171000242233276},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.70169997215271},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.6283000111579895},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.6247000098228455},{"id":"https://openalex.org/keywords/adaptation","display_name":"Adaptation (eye)","score":0.6033999919891357}],"concepts":[{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.8495000004768372},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8282999992370605},{"id":"https://openalex.org/C154690210","wikidata":"https://www.wikidata.org/wiki/Q1668499","display_name":"Rewriting","level":2,"score":0.8163999915122986},{"id":"https://openalex.org/C2776434776","wikidata":"https://www.wikidata.org/wiki/Q19246213","display_name":"Domain adaptation","level":3,"score":0.7171000242233276},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.70169997215271},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6283000111579895},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.6247000098228455},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.6033999919891357},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49950000643730164},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.4083999991416931},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4032999873161316},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.36309999227523804},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.34860000014305115},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.3084999918937683},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.298799991607666},{"id":"https://openalex.org/C22367795","wikidata":"https://www.wikidata.org/wiki/Q7625208","display_name":"Structured prediction","level":2,"score":0.28760001063346863},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.28299999237060547},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.27300000190734863},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.2565999925136566}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356539","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356539","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.4361862242221832}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W2341742436","https://openalex.org/W2346452181","https://openalex.org/W2604372572","https://openalex.org/W2794309877","https://openalex.org/W2801290881","https://openalex.org/W2920198243","https://openalex.org/W2952179106","https://openalex.org/W2963021258","https://openalex.org/W2963400328","https://openalex.org/W4309811444","https://openalex.org/W4321015976","https://openalex.org/W4385564995","https://openalex.org/W4385571271","https://openalex.org/W4391721420","https://openalex.org/W4397010262","https://openalex.org/W4401044013","https://openalex.org/W4408464128","https://openalex.org/W4409307063","https://openalex.org/W4411112923"],"related_works":[],"abstract_inverted_index":{"Biomedical":[0],"document-level":[1,50],"relation":[2,51,97],"extraction":[3,52,138],"plays":[4],"a":[5,45,67],"crucial":[6],"role":[7],"in":[8,136],"mining":[9],"structured":[10],"knowledge":[11,30],"from":[12],"biomedical":[13,93,140],"texts.":[14],"However,":[15],"existing":[16,131],"large":[17],"language":[18],"model-based":[19],"methods":[20],"struggle":[21],"with":[22,91],"information":[23],"redundancy,":[24],"noise":[25],"interference,":[26],"and":[27,57,99,103,120],"insufficient":[28],"domain-specific":[29],"when":[31],"processing":[32],"complex":[33],"documents.":[34],"To":[35],"address":[36],"these":[37],"challenges,":[38],"we":[39],"propose":[40],"Bio-":[41,125],"<tex":[42,62,126],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[43,63,127],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$\\mathbf{R}^{\\mathbf{3}}$</tex>,":[44],"novel":[46],"framework":[47],"that":[48,124],"enhances":[49,113],"through":[53],"entity":[54,80],"aware":[55,72],"rewriting":[56,73],"domain-adaptive":[58],"reasoning.":[59],"Our":[60],"Bio-R":[61],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">${":[64],"}^{3}$</tex>":[65],"follows":[66],"\u201cRewrite-Retrieval-Reason\u201d":[68],"pipeline:":[69],"(1)":[70],"Entity":[71],"refocuses":[74],"the":[75,89,118,137],"document":[76,90,141],"content":[77],"on":[78,117],"target":[79],"pairs,":[81],"reducing":[82],"irrelevant":[83],"context;":[84],"(2)":[85],"Retrieval-augmented":[86],"generation":[87],"supplements":[88],"external":[92],"evidence":[94],"to":[95],"support":[96],"inference;":[98],"(3)":[100],"Chain-of-Thought":[101],"prompting":[102],"few-shot":[104],"learning":[105],"improve":[106],"reasoning":[107],"accuracy,":[108],"while":[109],"Low-Rank":[110],"Adaptation":[111],"fine-tuning":[112],"domain":[114],"adaptation.":[115],"Experiments":[116],"CDR":[119],"GDA":[121],"benchmarks":[122],"demonstrate":[123],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$\\mathbf{R}^{\\mathbf{3}}$</tex>":[128],"significantly":[129],"outperforms":[130],"methods,":[132],"demonstrating":[133],"its":[134],"effectiveness":[135],"of":[139],"relations.":[142]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2026-01-30T00:00:00"}
