{"id":"https://openalex.org/W7163207511","doi":"https://doi.org/10.48550/arxiv.2606.01394","title":"UniD$^3$: A Knowledge Graph-Enhanced RAG Framework for Drug-Disease Discovery and Reasoning","display_name":"UniD$^3$: A Knowledge Graph-Enhanced RAG Framework for Drug-Disease Discovery and Reasoning","publication_year":2026,"publication_date":"2026-05-31","ids":{"openalex":"https://openalex.org/W7163207511","doi":"https://doi.org/10.48550/arxiv.2606.01394"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.01394","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.01394","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2606.01394","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5137626534","display_name":"Qing Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Qing","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134497025","display_name":"Tianshi Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Tianshi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137674830","display_name":"Minghao Zhou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Minghao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137680875","display_name":"Jialu Liang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liang, Jialu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101974773","display_name":"Sen Guo","orcid":"https://orcid.org/0000-0002-8732-7422"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guo, Sen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137688796","display_name":"Guangyu Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Guangyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137620876","display_name":"Jing Su","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Su, Jing","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5137630777","display_name":"Qianqian Song","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Song, Qianqian","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":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.3605000078678131,"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":0.3605000078678131,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.23350000381469727,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.1517000049352646,"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/knowledge-graph","display_name":"Knowledge graph","score":0.4871000051498413},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4794999957084656},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.46970000863075256},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.4293000102043152},{"id":"https://openalex.org/keywords/question-answering","display_name":"Question answering","score":0.40610000491142273},{"id":"https://openalex.org/keywords/fuzzy-logic","display_name":"Fuzzy logic","score":0.3734000027179718},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.32839998602867126},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.32269999384880066}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7592999935150146},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.4871000051498413},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4794999957084656},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.46970000863075256},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4375999867916107},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.4293000102043152},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41130000352859497},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.40610000491142273},{"id":"https://openalex.org/C58166","wikidata":"https://www.wikidata.org/wiki/Q224821","display_name":"Fuzzy logic","level":2,"score":0.3734000027179718},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3716000020503998},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32910001277923584},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.32839998602867126},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.32269999384880066},{"id":"https://openalex.org/C2777220311","wikidata":"https://www.wikidata.org/wiki/Q6423340","display_name":"Knowledge acquisition","level":2,"score":0.3091000020503998},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3084999918937683},{"id":"https://openalex.org/C115925183","wikidata":"https://www.wikidata.org/wiki/Q1412694","display_name":"Knowledge-based systems","level":2,"score":0.3061000108718872},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.3001999855041504},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.2799000144004822},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2615000009536743},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.2614000141620636},{"id":"https://openalex.org/C234837","wikidata":"https://www.wikidata.org/wiki/Q1420493","display_name":"Conceptual graph","level":3,"score":0.25999999046325684},{"id":"https://openalex.org/C84685590","wikidata":"https://www.wikidata.org/wiki/Q1540472","display_name":"Knowledge engineering","level":2,"score":0.2531999945640564},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.2524000108242035}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.01394","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.01394","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.01394","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.01394","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Systematic":[0],"characterization":[1],"of":[2,21,113,181],"drug-disease":[3,66,182,198],"relationships":[4],"is":[5,13],"essential":[6],"for":[7,154,157,190],"drug":[8,104],"discovery":[9],"and":[10,18,30,40,64,76,88,105,125,133,141,173,204],"repurposing,":[11,203],"yet":[12],"hindered":[14],"by":[15],"the":[16,174],"heterogeneity":[17],"rapid":[19],"growth":[20],"biomedical":[22,193],"literature.":[23],"Existing":[24],"datasets":[25],"rely":[26],"on":[27,103],"labor-intensive":[28],"curation":[29],"are":[31],"often":[32],"incomplete,":[33],"while":[34],"LLM-only":[35],"approaches":[36],"suffer":[37],"from":[38],"hallucination":[39],"weak":[41],"evidence":[42],"grounding.":[43],"We":[44],"introduce":[45],"UniD$^3$,":[46],"a":[47,93,186],"unified":[48],"framework":[49,189],"that":[50],"integrates":[51],"Large":[52],"Language":[53],"Models":[54],"with":[55,85,99,122,159],"Knowledge":[56],"Graph-enhanced":[57],"Retrieval-Augmented":[58],"Generation":[59],"(KG-RAG)":[60],"to":[61],"extract,":[62],"organize,":[63],"validate":[65],"knowledge":[67,90,131],"across":[68],"Drug-Disease":[69],"Matching":[70],"(DDM),":[71],"Drug":[72],"Effectiveness":[73],"Assessment":[74],"(DEA),":[75],"Drug-Target":[77],"Analysis":[78],"(DTA).":[79],"UniD$^3$":[80,128,175,184],"processes":[81],"157,849":[82],"PubMed":[83],"articles":[84],"Llama":[86],"3.3-70B":[87],"constructs":[89],"graphs":[91,109,132],"via":[92],"dual-stage":[94],"strategy":[95],"combining":[96],"paper-level":[97],"extraction":[98],"KG-level":[100],"consolidation":[101],"centered":[102],"disease":[106],"entities.":[107],"These":[108],"support":[110],"KG-RAG-based":[111],"generation":[112],"structured":[114,197],"datasets,":[115,135],"evaluated":[116],"through":[117],"external":[118],"benchmarks,":[119],"fuzzy":[120],"matching":[121],"curated":[123],"resources,":[124],"clinician":[126,160],"review.":[127],"produces":[129],"six":[130],"large-scale":[134],"including":[136],"28,915":[137],"DDM,":[138],"15,042":[139],"DEA,":[140],"over":[142],"4,000":[143],"DTA":[144],"QA":[145],"pairs.":[146],"External":[147],"validation":[148],"shows":[149],"strong":[150],"performance":[151],"(F1:":[152],"0.85-0.87":[153],"DDM/DEA;":[155],"0.82":[156],"DTA),":[158],"review":[161],"confirming":[162],"high":[163],"reliability":[164],"(AUROC":[165],"=":[166],"0.90).":[167],"KG-RAG-augmented":[168],"models":[169],"outperform":[170],"standalone":[171],"LLMs,":[172],"chatbot":[176],"enables":[177],"interpretable,":[178],"citation-supported":[179],"exploration":[180],"relationships.":[183],"provides":[185],"scalable,":[187],"extensible":[188],"transforming":[191],"unstructured":[192],"literature":[194],"into":[195],"high-quality,":[196],"knowledge,":[199],"supporting":[200],"AI-driven":[201],"discovery,":[202],"precision":[205],"medicine.":[206]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-06-03T00:00:00"}
