{"id":"https://openalex.org/W4406260738","doi":"https://doi.org/10.1109/bibm62325.2024.10822781","title":"Document Embeddings Enhance Biomedical Retrieval-Augmented Generation","display_name":"Document Embeddings Enhance Biomedical Retrieval-Augmented Generation","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406260738","doi":"https://doi.org/10.1109/bibm62325.2024.10822781"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822781","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822781","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 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/A5119660492","display_name":"Yongle Kong","orcid":"https://orcid.org/0000-0003-4732-1357"},"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":"Yongle Kong","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and 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":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100619435","display_name":"Ling Luo","orcid":"https://orcid.org/0000-0002-5141-0259"},"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":"Ling Luo","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057983414","display_name":"Zeyuan Ding","orcid":"https://orcid.org/0000-0002-4969-6200"},"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":"Zeyuan Ding","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100736263","display_name":"Lei Wang","orcid":"https://orcid.org/0000-0002-8420-6860"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Wang","raw_affiliation_strings":["Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100641142","display_name":"Wei Liu","orcid":"https://orcid.org/0000-0002-7409-0948"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Liu","raw_affiliation_strings":["Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102013621","display_name":"Yin Zhang","orcid":"https://orcid.org/0000-0002-4429-6806"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yin Zhang","raw_affiliation_strings":["Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022604762","display_name":"Bo Xu","orcid":"https://orcid.org/0000-0003-4135-0683"},"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":"Bo Xu","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066719472","display_name":"Jian Wang","orcid":"https://orcid.org/0000-0001-9729-6052"},"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":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101472979","display_name":"Yuanyuan Sun","orcid":"https://orcid.org/0000-0003-2805-5911"},"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":"Yuanyuan Sun","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042620633","display_name":"Zhehuan Zhao","orcid":"https://orcid.org/0000-0002-5001-1352"},"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":"Zhehuan Zhao","raw_affiliation_strings":["Dalian University of Technology,School of Software,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Software,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":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and 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":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"962","last_page":"967"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9430000185966492,"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"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9430000185966492,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9388999938964844,"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":0.679804265499115},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5087924599647522},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38964611291885376}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.679804265499115},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5087924599647522},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38964611291885376}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822781","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822781","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W3035324702","https://openalex.org/W3046375318","https://openalex.org/W3099700870","https://openalex.org/W3162922479","https://openalex.org/W4252076394","https://openalex.org/W4309674289","https://openalex.org/W4388409299","https://openalex.org/W4389523675","https://openalex.org/W4389523807","https://openalex.org/W4394782456","https://openalex.org/W4402670290","https://openalex.org/W4402727764","https://openalex.org/W6777615688","https://openalex.org/W6782879696","https://openalex.org/W6810108873","https://openalex.org/W6810334672","https://openalex.org/W6849177959","https://openalex.org/W6849921291","https://openalex.org/W6852016728","https://openalex.org/W6854866820","https://openalex.org/W6856223801","https://openalex.org/W6856736072","https://openalex.org/W6859002407","https://openalex.org/W6862483598"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Large":[0],"language":[1],"models":[2],"(LLMs)":[3],"perform":[4],"well":[5],"in":[6,15,48,54,193],"many":[7],"NLP":[8],"tasks":[9],"but":[10],"frequently":[11],"generate":[12,128],"inaccurate":[13],"information":[14,68],"the":[16,38,72,81,91,120,138,178,187],"biomedical":[17,154,183,194],"domain,":[18],"due":[19,94],"to":[20,29,62,86,95,127,176],"hallucination":[21],"issues.":[22],"Retrieval-Augmented":[23],"Generation":[24],"(RAG)":[25],"has":[26],"been":[27],"introduced":[28],"address":[30],"this":[31],"issue":[32],"by":[33],"integrating":[34],"external":[35],"knowledge,":[36],"enhancing":[37,186],"factual":[39],"accuracy":[40],"of":[41,167,180,191],"outputs.":[42],"However,":[43],"naive":[44,170],"RAG":[45,110],"encounters":[46],"challenges":[47,179],"effectively":[49],"utilizing":[50,181],"retrieved":[51,64,122],"content,":[52],"particularly":[53],"specialized":[55],"domains":[56],"like":[57],"biomedicine.":[58],"LLMs":[59,192],"often":[60],"struggle":[61],"integrate":[63],"content":[65],"as":[66],"irrelevant":[67],"can":[69],"interfere":[70],"with":[71,119,137,162],"model\u2019s":[73],"judgment.":[74],"Even":[75],"if":[76],"relevant":[77],"documents":[78],"are":[79,134],"retrieved,":[80],"model":[82],"may":[83],"be":[84],"unable":[85],"accurately":[87],"comprehend":[88],"and":[89,131,189],"utilize":[90],"domain-specific":[92],"features":[93],"its":[96],"inherent":[97],"knowledge":[98],"limitations.":[99],"To":[100],"overcome":[101],"these":[102,132],"limitations,":[103],"we":[104],"propose":[105],"Document":[106],"Embeddings":[107],"Enhanced":[108],"Biomedical":[109],"(DEEB-RAG),":[111],"a":[112,143,148],"framework":[113],"that":[114,158],"incorporates":[115],"document":[116,129],"embeddings":[117,130,133],"along":[118],"original":[121],"text.":[123],"DEEB-RAG":[124,159],"uses":[125],"MedCPT":[126],"then":[135],"aligned":[136],"LLM\u2019s":[139],"semantic":[140],"space":[141],"using":[142],"two-stage":[144],"training":[145],"process":[146],"on":[147,153],"simple":[149],"projector.":[150],"Experimental":[151],"results":[152],"QA":[155],"datasets":[156],"show":[157],"improves":[160],"accuracy,":[161],"an":[163],"average":[164],"performance":[165],"increase":[166],"2.3%":[168],"over":[169],"RAG.":[171],"This":[172],"demonstrates":[173],"DEEB-RAG\u2019s":[174],"ability":[175],"mitigate":[177],"complex":[182],"information,":[184],"thereby":[185],"reliability":[188],"effectiveness":[190],"domain.":[195]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
