{"id":"https://openalex.org/W4415152219","doi":"https://doi.org/10.48550/arxiv.2504.08768","title":"Accelerating Causal Network Discovery of Alzheimer Disease Biomarkers via Scientific Literature-based Retrieval Augmented Generation","display_name":"Accelerating Causal Network Discovery of Alzheimer Disease Biomarkers via Scientific Literature-based Retrieval Augmented Generation","publication_year":2025,"publication_date":"2025-04-01","ids":{"openalex":"https://openalex.org/W4415152219","doi":"https://doi.org/10.48550/arxiv.2504.08768"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2504.08768","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2504.08768","pdf_url":"https://arxiv.org/pdf/2504.08768","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2504.08768","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082973092","display_name":"Xiaofan Zhou","orcid":"https://orcid.org/0000-0002-2879-6317"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Zhou, Xiaofan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119013469","display_name":"Lv Huang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huang, Liangjie","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012637338","display_name":"Peng Cheng","orcid":"https://orcid.org/0000-0003-2351-2060"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cheng, Pinyang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038386528","display_name":"Wenpeng Yin","orcid":"https://orcid.org/0000-0002-3154-1139"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yin, Wenpen","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110537181","display_name":"Rui Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Rui","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032431412","display_name":"Wenrui Hao","orcid":"https://orcid.org/0000-0002-6925-7424"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hao, Wenrui","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5101409622","display_name":"Cheng Lu","orcid":"https://orcid.org/0000-0002-8577-4288"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cheng, Lu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5082973092"],"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":0.9883000254631042,"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":0.9883000254631042,"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/T10538","display_name":"Data Mining Algorithms and Applications","score":0.9301999807357788,"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"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9017999768257141,"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/disease","display_name":"Disease","score":0.6348000168800354},{"id":"https://openalex.org/keywords/causality","display_name":"Causality (physics)","score":0.5042999982833862},{"id":"https://openalex.org/keywords/causal-model","display_name":"Causal model","score":0.4927000105381012},{"id":"https://openalex.org/keywords/causal-inference","display_name":"Causal inference","score":0.4147000014781952},{"id":"https://openalex.org/keywords/causal-reasoning","display_name":"Causal reasoning","score":0.40470001101493835},{"id":"https://openalex.org/keywords/medical-research","display_name":"Medical research","score":0.361299991607666},{"id":"https://openalex.org/keywords/causal-structure","display_name":"Causal structure","score":0.35679998993873596},{"id":"https://openalex.org/keywords/alzheimers-disease","display_name":"Alzheimer's disease","score":0.33820000290870667}],"concepts":[{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6348000168800354},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5220999717712402},{"id":"https://openalex.org/C64357122","wikidata":"https://www.wikidata.org/wiki/Q1149766","display_name":"Causality (physics)","level":2,"score":0.5042999982833862},{"id":"https://openalex.org/C11671645","wikidata":"https://www.wikidata.org/wiki/Q5054567","display_name":"Causal model","level":2,"score":0.4927000105381012},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4869000017642975},{"id":"https://openalex.org/C158600405","wikidata":"https://www.wikidata.org/wiki/Q5054566","display_name":"Causal inference","level":2,"score":0.4147000014781952},{"id":"https://openalex.org/C115086926","wikidata":"https://www.wikidata.org/wiki/Q17004651","display_name":"Causal reasoning","level":3,"score":0.40470001101493835},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3682999908924103},{"id":"https://openalex.org/C106977388","wikidata":"https://www.wikidata.org/wiki/Q2752427","display_name":"Medical research","level":2,"score":0.361299991607666},{"id":"https://openalex.org/C163504300","wikidata":"https://www.wikidata.org/wiki/Q2364925","display_name":"Causal structure","level":2,"score":0.35679998993873596},{"id":"https://openalex.org/C502032728","wikidata":"https://www.wikidata.org/wiki/Q11081","display_name":"Alzheimer's disease","level":3,"score":0.33820000290870667},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.3278999924659729},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.314300000667572},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.3124000132083893},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.3046000003814697},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.3009999990463257},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.29980000853538513},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.2937999963760376},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.29269999265670776},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2921000123023987},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.29170000553131104},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.2858000099658966},{"id":"https://openalex.org/C180747234","wikidata":"https://www.wikidata.org/wiki/Q23373","display_name":"Cognitive psychology","level":1,"score":0.28540000319480896},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2809999883174896},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.2711000144481659},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.26969999074935913},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26669999957084656},{"id":"https://openalex.org/C169900460","wikidata":"https://www.wikidata.org/wiki/Q2200417","display_name":"Cognition","level":2,"score":0.2605000138282776},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.2556000053882599}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2504.08768","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2504.08768","pdf_url":"https://arxiv.org/pdf/2504.08768","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2504.08768","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2504.08768","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2504.08768","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2504.08768","pdf_url":"https://arxiv.org/pdf/2504.08768","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"The":[0],"causal":[1,48,59,109,145,168,198,211,234],"relationships":[2,49],"between":[3],"biomarkers":[4,24,62,84,112,142,215,233],"are":[5],"essential":[6],"for":[7,113],"disease":[8,19,35,43],"diagnosis":[9],"and":[10,39,52,78,85,132,143,170,174,182],"medical":[11,115,155],"treatment":[12],"planning.":[13],"One":[14],"notable":[15],"application":[16],"is":[17,50,216],"Alzheimer's":[18],"(AD)":[20],"diagnosis,":[21,156],"where":[22],"certain":[23],"may":[25],"influence":[26],"the":[27,128,150,154,163,166,172,190,204],"presence":[28],"of":[29,42,61,75,111,153,165,176,192,207,213,231],"others,":[30],"enabling":[31],"early":[32],"detection,":[33],"precise":[34],"staging,":[36],"targeted":[37],"treatments,":[38],"improved":[40],"monitoring":[41],"progression.":[44],"However,":[45,203],"understanding":[46,82],"these":[47],"complex":[51],"requires":[53],"extensive":[54],"research.":[55],"Constructing":[56],"a":[57,72],"comprehensive":[58],"network":[60,235],"demands":[63],"significant":[64],"effort":[65],"from":[66,200],"human":[67,183],"experts,":[68],"who":[69],"must":[70],"analyze":[71],"vast":[73],"number":[74],"research":[76,124,227],"papers,":[77],"have":[79],"bias":[80],"in":[81,107,209],"diseases'":[83],"their":[86],"relation.":[87],"This":[88],"raises":[89],"an":[90],"important":[91],"question:":[92],"Can":[93],"advanced":[94],"large":[95],"language":[96],"models":[97],"(LLMs),":[98],"such":[99],"as":[100],"those":[101],"utilizing":[102],"retrieval-augmented":[103],"generation":[104],"(RAG),":[105],"assist":[106],"building":[108],"networks":[110,199],"further":[114,225],"analysis?":[116],"To":[117],"explore":[118],"this,":[119],"we":[120,157],"collected":[121],"200":[122],"AD-related":[123],"papers":[125],"published":[126],"over":[127],"past":[129],"25":[130],"years":[131],"then":[133],"integrated":[134],"scientific":[135,201],"literature":[136],"with":[137],"RAG":[138,188],"to":[139,161,194],"extract":[140],"AD":[141,214,232],"generate":[144,195],"relations":[146,212],"among":[147],"them.":[148],"Given":[149],"high-risk":[151],"nature":[152],"applied":[158],"uncertainty":[159],"estimation":[160],"assess":[162],"reliability":[164],"generated":[167],"edges":[169],"examined":[171],"faithfulness":[173],"scientificness":[175],"LLM":[177],"reasoning":[178],"using":[179],"both":[180],"automatic":[181],"evaluation.":[184],"We":[185,219],"find":[186],"that":[187],"enhances":[189],"ability":[191],"LLMs":[193,208],"more":[196],"accurate":[197],"papers.":[202],"overall":[205],"performance":[206],"identifying":[210],"still":[217],"limited.":[218],"hope":[220],"this":[221],"study":[222],"will":[223],"inspire":[224],"foundational":[226],"on":[228],"AI-driven":[229],"analysis":[230],"discovery.":[236]},"counts_by_year":[],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-14T00:00:00"}