{"id":"https://openalex.org/W7171503003","doi":"https://doi.org/10.1145/3807503.3819502","title":"Evaluating Retrieval\u2011Augmented Open\u2011Source LLMs for Generating Context\u2011Rich Gene Sets","display_name":"Evaluating Retrieval\u2011Augmented Open\u2011Source LLMs for Generating Context\u2011Rich Gene Sets","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171503003","doi":"https://doi.org/10.1145/3807503.3819502"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819502","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819502","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819502","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5094096987","display_name":"Ebunoluwa Makinde","orcid":null},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ebunoluwa Makinde","raw_affiliation_strings":["Computer Science, University of Calgary, Calgary, Alberta, Canada"],"raw_orcid":"https://orcid.org/0009-0002-1873-0266","affiliations":[{"raw_affiliation_string":"Computer Science, University of Calgary, Calgary, Alberta, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033210702","display_name":"Farhad Maleki","orcid":"https://orcid.org/0000-0002-5673-8210"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Farhad Maleki","raw_affiliation_strings":["Computer Science, University of Calgary, Calgary, Alberta, Canada"],"raw_orcid":"https://orcid.org/0000-0002-5673-8210","affiliations":[{"raw_affiliation_string":"Computer Science, University of Calgary, Calgary, Alberta, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086014360","display_name":"Alan Rosenberg","orcid":"https://orcid.org/0000-0002-0109-1595"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alan Rosenberg","raw_affiliation_strings":["Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan, Canada"],"raw_orcid":"https://orcid.org/0000-0002-0109-1595","affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073425263","display_name":"Katie Ovens","orcid":"https://orcid.org/0000-0001-5956-7739"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Katie Ovens","raw_affiliation_strings":["Computer Science, University of Calgary, Calgary, Alberta, Canada"],"raw_orcid":"https://orcid.org/0000-0001-5956-7739","affiliations":[{"raw_affiliation_string":"Computer Science, University of Calgary, Calgary, Alberta, Canada","institution_ids":["https://openalex.org/I168635309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"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":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3589000105857849},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.2890999913215637},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.25029999017715454},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.243599995970726}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3853999972343445},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3628000020980835},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3589000105857849},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34310001134872437},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2890999913215637},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.27869999408721924},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.25029999017715454},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.243599995970726},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.23589999973773956},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.22759999334812164}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819502","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819502","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819502","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819502","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1554161009","https://openalex.org/W2010457001","https://openalex.org/W2066351138","https://openalex.org/W2127119915","https://openalex.org/W2136410628","https://openalex.org/W2170282111","https://openalex.org/W2214074259","https://openalex.org/W2557385283","https://openalex.org/W2973131311","https://openalex.org/W3039150496","https://openalex.org/W3106811464","https://openalex.org/W4393936594","https://openalex.org/W4404824622","https://openalex.org/W4408389039","https://openalex.org/W4409906005"],"related_works":[],"abstract_inverted_index":{"Gene":[0],"sets":[1,27],"are":[2,16,71],"collections":[3],"of":[4],"genes":[5],"that":[6,70],"share":[7],"a":[8],"common":[9],"biological":[10,58],"function,":[11],"process,":[12],"or":[13],"component":[14],"and":[15,36,50,67],"widely":[17],"used":[18],"to":[19,77,82],"interpret":[20],"genomic":[21],"data.":[22],"Databases":[23],"containing":[24],"these":[25],"gene":[26,33,38,44,86],"support":[28],"many":[29],"analytical":[30],"methods,":[31],"including":[32],"set":[34,45],"analysis":[35],"phenotype-based":[37],"prioritization,":[39],"whose":[40],"results":[41],"depend":[42],"on":[43,63],"quality.":[46],"Despite":[47],"extensive":[48],"literature":[49,81],"genetic":[51],"data,":[52],"existing":[53],"resources":[54],"often":[55],"lack":[56],"sufficient":[57],"context.":[59],"Current":[60],"curation":[61],"relies":[62],"labour\u2011intensive":[64],"expert":[65],"review":[66],"automated":[68],"methods":[69],"not":[72],"context\u2011aware,":[73],"leaving":[74],"an":[75],"opportunity":[76],"use":[78],"publicly":[79],"available":[80],"construct":[83],"more":[84,104],"precise":[85],"sets.":[87],"With":[88],"advances":[89],"in":[90],"natural":[91],"language":[92,96],"processing,":[93],"particularly":[94],"large":[95],"models":[97],"(LLMs),":[98],"this":[99],"task":[100],"can":[101],"be":[102],"performed":[103],"efficiently.":[105]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}