{"id":"https://openalex.org/W4406783055","doi":"https://doi.org/10.1093/bioinformatics/btaf031","title":"ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning","display_name":"ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning","publication_year":2025,"publication_date":"2025-01-22","ids":{"openalex":"https://openalex.org/W4406783055","doi":"https://doi.org/10.1093/bioinformatics/btaf031","pmid":"https://pubmed.ncbi.nlm.nih.gov/39842860"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf031","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf031/61561980/btaf031.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf031/61561980/btaf031.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054144186","display_name":"Nicholas Matsumoto","orcid":"https://orcid.org/0000-0002-3280-9678"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Matsumoto","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101864277","display_name":"Hyun\u2010Jun Choi","orcid":"https://orcid.org/0000-0003-4487-0799"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyunjun Choi","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111219334","display_name":"Jay Moran","orcid":null},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jay Moran","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101646780","display_name":"Miguel Hernandez","orcid":"https://orcid.org/0000-0003-4483-7964"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Miguel E Hernandez","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058539869","display_name":"Mythreye Venkatesan","orcid":"https://orcid.org/0000-0001-9946-0688"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mythreye Venkatesan","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407710","display_name":"Xi Li","orcid":"https://orcid.org/0000-0001-9565-328X"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xi Li","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068201313","display_name":"Jui-Hsuan Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jui-Hsuan Chang","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042224273","display_name":"Paul P. Wang","orcid":"https://orcid.org/0000-0002-9602-5979"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Wang","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032971510","display_name":"Jason H. Moore","orcid":"https://orcid.org/0000-0002-5015-1099"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason H Moore","raw_affiliation_strings":["Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-5015-1099","affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center , West Hollywood, CA 90069,","institution_ids":["https://openalex.org/I1282927834"]},{"raw_affiliation_string":"Department of Computational Biomedicine, Center for Artificial Intelligence Research and Education, Cedars Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G-541H, West Hollywood, 90069, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5032971510"],"corresponding_institution_ids":["https://openalex.org/I1282927834"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":28.5719,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.99534608,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"41","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.32409998774528503,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.32409998774528503,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.25130000710487366,"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/T10028","display_name":"Topic Modeling","score":0.18160000443458557,"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/computer-science","display_name":"Computer science","score":0.6831387877464294},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5208104848861694},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4327487349510193},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16342735290527344}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6831387877464294},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5208104848861694},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4327487349510193},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16342735290527344},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf031","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf031/61561980/btaf031.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39842860","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39842860","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11796095","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11796095","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11796095/pdf/btaf031.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf031","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf031/61561980/btaf031.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2866775907","display_name":null,"funder_award_id":"AG066833","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G350679715","display_name":null,"funder_award_id":"U01 AG066833","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4706438170","display_name":null,"funder_award_id":"R01 LM010098","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6682602594","display_name":null,"funder_award_id":"LM010098","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8791895767","display_name":null,"funder_award_id":"R01 LM014572","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320313996","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4406783055.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W4285227295","https://openalex.org/W4309674289","https://openalex.org/W4388467895","https://openalex.org/W4393160302","https://openalex.org/W4399305008","https://openalex.org/W6777615688","https://openalex.org/W6809646742","https://openalex.org/W6851275496"],"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":{"MOTIVATION:":[0],"LLMs":[1,51],"like":[2],"GPT-4,":[3],"despite":[4],"their":[5],"advancements,":[6],"often":[7],"produce":[8],"hallucinations":[9],"and":[10,38,58,65,99,123],"struggle":[11],"with":[12,52],"integrating":[13],"external":[14,27],"knowledge":[15,60,100],"effectively.":[16],"While":[17],"Retrieval-Augmented":[18],"Generation":[19],"(RAG)":[20],"attempts":[21],"to":[22,45,104],"address":[23],"this":[24],"by":[25,49],"incorporating":[26],"information,":[28],"it":[29],"faces":[30],"significant":[31],"challenges":[32],"such":[33],"as":[34,119],"context":[35],"length":[36],"limitations":[37],"imprecise":[39],"vector":[40],"similarity":[41],"search.":[42],"ESCARGOT":[43,69,83,116],"aims":[44],"overcome":[46],"these":[47],"issues":[48],"combining":[50],"a":[53,120],"dynamic":[54],"Graph":[55],"of":[56,96,108],"Thoughts":[57],"biomedical":[59],"graphs,":[61],"improving":[62],"output":[63],"reliability,":[64],"reducing":[66],"hallucinations.":[67],"RESULT:":[68],"significantly":[70],"outperforms":[71],"industry-standard":[72],"RAG":[73],"methods,":[74],"particularly":[75],"in":[76,88,102],"open-ended":[77],"questions":[78],"that":[79],"demand":[80],"high":[81],"precision.":[82],"also":[84],"offers":[85],"greater":[86],"transparency":[87],"its":[89],"reasoning":[90],"process,":[91],"allowing":[92],"for":[93],"the":[94,105],"vetting":[95],"both":[97],"code":[98],"requests,":[101],"contrast":[103],"black-box":[106],"nature":[107],"LLM-only":[109],"or":[110],"RAG-based":[111],"approaches.":[112],"AVAILABILITY":[113],"AND":[114],"IMPLEMENTATION:":[115],"is":[117],"available":[118],"pip":[121],"package":[122],"on":[124],"GitHub":[125],"at:":[126],"https://github.com/EpistasisLab/ESCARGOT.":[127]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":11}],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}
