{"id":"https://openalex.org/W7160251884","doi":"https://doi.org/10.3837/tiis.2026.04.021","title":"HG-RAG: Hierarchical Graph-Based Retrieval-Augmented Generation for Metabolomics","display_name":"HG-RAG: Hierarchical Graph-Based Retrieval-Augmented Generation for Metabolomics","publication_year":2026,"publication_date":"2026-04-30","ids":{"openalex":"https://openalex.org/W7160251884","doi":"https://doi.org/10.3837/tiis.2026.04.021"},"language":null,"primary_location":{"id":"doi:10.3837/tiis.2026.04.021","is_oa":true,"landing_page_url":"https://doi.org/10.3837/tiis.2026.04.021","pdf_url":"https://itiis.org/digital-library/manuscript/file/106292/TIIS Vol 20, No 4-21.pdf","source":{"id":"https://openalex.org/S204131793","display_name":"KSII Transactions on Internet and Information Systems","issn_l":"1976-7277","issn":["1976-7277","2288-1468"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4323966148","host_organization_name":"Korea Society of Internet Information","host_organization_lineage":["https://openalex.org/P4323966148"],"host_organization_lineage_names":["Korea Society of Internet Information"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"KSII Transactions on Internet and Information Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://itiis.org/digital-library/manuscript/file/106292/TIIS Vol 20, No 4-21.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5128336399","display_name":"Jifei Cheng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jifei Cheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135335294","display_name":"Donghui Shi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Donghui Shi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135286540","display_name":"Yakun Sun","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yakun Sun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5135398257","display_name":"Jozef Zurada","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jozef Zurada","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.51366736,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"20","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.32409998774528503,"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":0.32409998774528503,"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":0.23000000417232513,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.20819999277591705,"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/context","display_name":"Context (archaeology)","score":0.5037999749183655},{"id":"https://openalex.org/keywords/hierarchical-database-model","display_name":"Hierarchical database model","score":0.47609999775886536},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.43149998784065247},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.4212999939918518},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.3991999924182892},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.39660000801086426},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.38109999895095825},{"id":"https://openalex.org/keywords/coherence","display_name":"Coherence (philosophical gambling strategy)","score":0.36970001459121704}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8952999711036682},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5037999749183655},{"id":"https://openalex.org/C144986985","wikidata":"https://www.wikidata.org/wiki/Q871236","display_name":"Hierarchical database model","level":2,"score":0.47609999775886536},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43149998784065247},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.4212999939918518},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.3991999924182892},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.39660000801086426},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3882000148296356},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.38109999895095825},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3799999952316284},{"id":"https://openalex.org/C2781181686","wikidata":"https://www.wikidata.org/wiki/Q4226068","display_name":"Coherence (philosophical gambling strategy)","level":2,"score":0.36970001459121704},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3637999892234802},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.34360000491142273},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.33090001344680786},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3125},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3107999861240387},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.30410000681877136},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.2994999885559082},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.29809999465942383},{"id":"https://openalex.org/C135870905","wikidata":"https://www.wikidata.org/wiki/Q903667","display_name":"Metabolome","level":3,"score":0.2757999897003174},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C33762810","wikidata":"https://www.wikidata.org/wiki/Q461671","display_name":"Data integrity","level":2,"score":0.26910001039505005},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2680000066757202},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2646999955177307},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.2590999901294708}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3837/tiis.2026.04.021","is_oa":true,"landing_page_url":"https://doi.org/10.3837/tiis.2026.04.021","pdf_url":"https://itiis.org/digital-library/manuscript/file/106292/TIIS Vol 20, No 4-21.pdf","source":{"id":"https://openalex.org/S204131793","display_name":"KSII Transactions on Internet and Information Systems","issn_l":"1976-7277","issn":["1976-7277","2288-1468"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4323966148","host_organization_name":"Korea Society of Internet Information","host_organization_lineage":["https://openalex.org/P4323966148"],"host_organization_lineage_names":["Korea Society of Internet Information"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"KSII Transactions on Internet and Information Systems","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.3837/tiis.2026.04.021","is_oa":true,"landing_page_url":"https://doi.org/10.3837/tiis.2026.04.021","pdf_url":"https://itiis.org/digital-library/manuscript/file/106292/TIIS Vol 20, No 4-21.pdf","source":{"id":"https://openalex.org/S204131793","display_name":"KSII Transactions on Internet and Information Systems","issn_l":"1976-7277","issn":["1976-7277","2288-1468"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4323966148","host_organization_name":"Korea Society of Internet Information","host_organization_lineage":["https://openalex.org/P4323966148"],"host_organization_lineage_names":["Korea Society of Internet Information"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"KSII Transactions on Internet and Information Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5470966696739197,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7160251884.pdf","grobid_xml":"https://content.openalex.org/works/W7160251884.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Retrieval-Augmented":[0,71],"Generation":[1,72],"(RAG)":[2],"has":[3],"emerged":[4],"as":[5],"an":[6],"effective":[7],"method":[8],"for":[9,76],"enhancing":[10],"Large":[11],"Language":[12],"Models":[13],"(LLMs)":[14],"with":[15,121],"external":[16],"knowledge,":[17],"demonstrating":[18],"significant":[19],"potential":[20],"in":[21,61,161,180,187],"biomedical":[22],"question":[23],"answering.However,":[24],"existing":[25,155],"RAG":[26,29,156,159],"and":[27,95,103,109,128,157,166,177,183,191],"Graph-based":[28,70,158],"approaches":[30],"primarily":[31],"focus":[32],"on":[33,89,112],"flat":[34],"or":[35,47],"weakly":[36],"hierarchical":[37,175],"entity":[38],"relationships.They":[39],"are":[40,193],"often":[41],"limited":[42],"to":[43,54,100,124,142],"traversing":[44],"global":[45],"graphs":[46],"retrieving":[48],"local":[49],"subgraphs,":[50],"making":[51],"it":[52],"challenging":[53],"capture":[55],"the":[56,90,134,144,172],"complex":[57],"cross-hierarchical":[58],"dependencies":[59],"inherent":[60],"metabolomics.To":[62],"address":[63],"this,":[64,113],"we":[65],"propose":[66],"HG-RAG,":[67],"a":[68,83,97,116,137],"Hierarchical":[69],"framework":[73,81,135],"specifically":[74],"designed":[75],"metabolomics":[77],"Question":[78],"Answering":[79],"(QA).The":[80],"constructs":[82],"three-layer":[84],"\"Disease-Metabolite-Concentration\"":[85],"knowledge":[86],"graph":[87],"based":[88],"Human":[91],"Metabolome":[92],"Database":[93],"(HMDB)":[94],"employs":[96],"dual-vector":[98],"store":[99],"achieve":[101],"aligned":[102],"unified":[104],"modeling":[105,176],"of":[106,146,174],"both":[107],"structured":[108,178],"semantic":[110,129],"information.Building":[111],"HG-RAG":[114,152],"adopts":[115],"multi-stage":[117],"retrieval":[118,179],"strategy":[119,141],"combined":[120],"hierarchy-aware":[122],"expansion":[123],"ensure":[125],"structural":[126],"integrity":[127],"coherence":[130],"during":[131],"context":[132,162],"retrieval.Furthermore,":[133],"introduces":[136],"provenance":[138],"citation":[139],"constraint":[140],"enhance":[143],"reliability":[145],"generated":[147],"answers.Experimental":[148],"results":[149,170],"demonstrate":[150],"that":[151],"consistently":[153],"outperforms":[154],"baselines":[160],"recall,":[163],"answer":[164],"relevancy,":[165],"overall":[167],"reasoning":[168],"quality.These":[169],"highlight":[171],"effectiveness":[173],"achieving":[181],"accurate":[182],"reliable":[184],"knowledge-intensive":[185],"QA":[186],"metabolomics.The":[188],"source":[189],"code":[190],"data":[192],"available":[194],"at:":[195]},"counts_by_year":[],"updated_date":"2026-05-06T06:10:43.113611","created_date":"2026-05-06T00:00:00"}
