{"id":"https://openalex.org/W7126024356","doi":"https://doi.org/10.1109/bibm66473.2025.11356417","title":"Retrieval-Augmented Generation for Biomedical Question Answering Based on Hierarchical Knowledge Tree","display_name":"Retrieval-Augmented Generation for Biomedical Question Answering Based on Hierarchical Knowledge Tree","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126024356","doi":"https://doi.org/10.1109/bibm66473.2025.11356417"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356417","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356417","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":"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/A5124252454","display_name":"Ning Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]},{"id":"https://openalex.org/I4210123021","display_name":"Chongqing Institute of Green and Intelligent Technology","ror":"https://ror.org/031npqv35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210123021"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ning Wang","raw_affiliation_strings":["Chongqing University of Posts and Telecommunications, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences,Chongqing,China"],"affiliations":[{"raw_affiliation_string":"Chongqing University of Posts and Telecommunications, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences,Chongqing,China","institution_ids":["https://openalex.org/I4210123021","https://openalex.org/I10535382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103044463","display_name":"Xueliang Zhao","orcid":"https://orcid.org/0000-0001-9418-8881"},"institutions":[{"id":"https://openalex.org/I4210123021","display_name":"Chongqing Institute of Green and Intelligent Technology","ror":"https://ror.org/031npqv35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210123021"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueliang Zhao","raw_affiliation_strings":["Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China"],"affiliations":[{"raw_affiliation_string":"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China","institution_ids":["https://openalex.org/I4210123021"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064680400","display_name":"Xiaoguang Lin","orcid":"https://orcid.org/0000-0001-9533-0931"},"institutions":[{"id":"https://openalex.org/I4210123021","display_name":"Chongqing Institute of Green and Intelligent Technology","ror":"https://ror.org/031npqv35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210123021"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoguang Lin","raw_affiliation_strings":["Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China"],"affiliations":[{"raw_affiliation_string":"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China","institution_ids":["https://openalex.org/I4210123021"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036277468","display_name":"Xinyu Liu","orcid":"https://orcid.org/0009-0001-5571-5826"},"institutions":[{"id":"https://openalex.org/I4210123021","display_name":"Chongqing Institute of Green and Intelligent Technology","ror":"https://ror.org/031npqv35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210123021"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyu Liu","raw_affiliation_strings":["Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China"],"affiliations":[{"raw_affiliation_string":"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China","institution_ids":["https://openalex.org/I4210123021"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090273013","display_name":"Qingping Sun","orcid":"https://orcid.org/0000-0002-1032-766X"},"institutions":[{"id":"https://openalex.org/I4210123021","display_name":"Chongqing Institute of Green and Intelligent Technology","ror":"https://ror.org/031npqv35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210123021"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qilong Sun","raw_affiliation_strings":["Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China"],"affiliations":[{"raw_affiliation_string":"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences Chongqing,Chongqing,China","institution_ids":["https://openalex.org/I4210123021"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5124252454"],"corresponding_institution_ids":["https://openalex.org/I10535382","https://openalex.org/I4210123021"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.87335213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"7438","last_page":"7444"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.6100000143051147,"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":0.6100000143051147,"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":0.22280000150203705,"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/T10286","display_name":"Information Retrieval and Search Behavior","score":0.054099999368190765,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/question-answering","display_name":"Question answering","score":0.6247000098228455},{"id":"https://openalex.org/keywords/automatic-summarization","display_name":"Automatic summarization","score":0.6190000176429749},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.5320000052452087},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4401000142097473},{"id":"https://openalex.org/keywords/coherence","display_name":"Coherence (philosophical gambling strategy)","score":0.40639999508857727},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.38420000672340393},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.3635999858379364},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.35589998960494995}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8152999877929688},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.6247000098228455},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.6190000176429749},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.5320000052452087},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.45969998836517334},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4571000039577484},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4401000142097473},{"id":"https://openalex.org/C2781181686","wikidata":"https://www.wikidata.org/wiki/Q4226068","display_name":"Coherence (philosophical gambling strategy)","level":2,"score":0.40639999508857727},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.38420000672340393},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.3635999858379364},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.35589998960494995},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.32339999079704285},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.32010000944137573},{"id":"https://openalex.org/C203357204","wikidata":"https://www.wikidata.org/wiki/Q1089605","display_name":"Chunking (psychology)","level":2,"score":0.3052000105381012},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.28690001368522644},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.28540000319480896},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.2793000042438507},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.2745000123977661},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2703999876976013},{"id":"https://openalex.org/C186625053","wikidata":"https://www.wikidata.org/wiki/Q1130191","display_name":"Information overload","level":2,"score":0.26919999718666077},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.2687999904155731},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.26510000228881836},{"id":"https://openalex.org/C144986985","wikidata":"https://www.wikidata.org/wiki/Q871236","display_name":"Hierarchical database model","level":2,"score":0.26330000162124634}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356417","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356417","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","score":0.6740813255310059,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W151377110","https://openalex.org/W1981208470","https://openalex.org/W2911489562","https://openalex.org/W2970641574","https://openalex.org/W3099700870","https://openalex.org/W3100107515","https://openalex.org/W4309674289","https://openalex.org/W4385565351","https://openalex.org/W4391876619","https://openalex.org/W4391940656","https://openalex.org/W4402671321","https://openalex.org/W4404782883"],"related_works":[],"abstract_inverted_index":{"Biomedical":[0],"literature":[1],"is":[2],"characterized":[3],"by":[4],"vast,":[5],"structurally":[6],"complex,":[7],"and":[8,34,68,82,101,129],"rapidly":[9],"evolving":[10],"knowledge":[11],"that":[12,30,122],"poses":[13],"significant":[14],"challenges":[15],"for":[16],"conventional":[17],"retrieval-augmented":[18],"generation":[19],"(RAG)":[20],"methods.":[21],"Existing":[22],"approaches":[23],"typically":[24],"rely":[25],"on":[26,116],"fixed-length":[27],"chunking":[28],"strategies":[29],"disrupt":[31],"semantic":[32,76,89],"coherence":[33],"fail":[35],"to":[36,63,85,106],"capture":[37],"hierarchical":[38,58,83],"relationships":[39],"in":[40,46,134],"biomedical":[41,71,92,118,136],"texts,":[42],"limiting":[43],"their":[44],"effectiveness":[45],"multi-hop":[47],"reasoning":[48],"tasks.":[49],"To":[50],"address":[51],"these":[52],"limitations,":[53],"we":[54,96],"propose":[55],"Bio-RAPTOR,":[56],"a":[57],"RAG":[59,128],"framework":[60,133],"specifically":[61],"designed":[62],"accommodate":[64],"the":[65,130,135],"distinct":[66],"structure":[67],"semantics":[69],"of":[70],"texts.":[72],"Our":[73],"approach":[74],"integrates":[75],"chunking,":[77],"recursive":[78],"clustering":[79],"with":[80,104],"HDBSCAN,":[81],"summarization":[84],"construct":[86],"hierarchically":[87],"organized":[88],"structures":[90],"from":[91],"documents.":[93],"During":[94],"inference,":[95],"employ":[97],"HyDE-based":[98],"query":[99],"expansion":[100],"hybrid":[102],"retrieval":[103],"reranking":[105],"retrieve":[107],"relevant":[108],"information":[109],"across":[110],"different":[111],"abstraction":[112],"levels.":[113],"Experimental":[114],"results":[115],"authoritative":[117],"QA":[119],"datasets":[120],"demonstrate":[121],"Bio-RAPTOR":[123],"significantly":[124],"outperforms":[125],"both":[126],"standard":[127],"original":[131],"RAPTOR":[132],"question":[137],"answering.":[138]},"counts_by_year":[],"updated_date":"2026-02-01T03:34:12.195049","created_date":"2026-01-30T00:00:00"}