{"id":"https://openalex.org/W7151757201","doi":"https://doi.org/10.48550/arxiv.2604.05774","title":"GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding","display_name":"GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding","publication_year":2026,"publication_date":"2026-04-07","ids":{"openalex":"https://openalex.org/W7151757201","doi":"https://doi.org/10.48550/arxiv.2604.05774"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.05774","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.05774","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":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.2604.05774","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034040709","display_name":"Weicai Long","orcid":"https://orcid.org/0009-0009-3205-9537"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Long, Weicai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109627184","display_name":"Yusen Hou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hou, Yusen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124723523","display_name":"Junning Feng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Feng, Junning","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126507911","display_name":"H. Su","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Su, Houcheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133198882","display_name":"Shuo Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Shuo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133232798","display_name":"Donglin Xie","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xie, Donglin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5133236066","display_name":"Yanlin Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Yanlin","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/T11642","display_name":"Genomics and Rare Diseases","score":0.2599000036716461,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.2599000036716461,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.2004999965429306,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.08959999680519104,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6057000160217285},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5446000099182129},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5383999943733215},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.48159998655319214},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4498000144958496},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.44269999861717224},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.427700012922287},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.41100001335144043},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4090999960899353}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6057000160217285},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5907999873161316},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5446000099182129},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5383999943733215},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5232999920845032},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.48159998655319214},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4498000144958496},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.44269999861717224},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.427700012922287},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.41100001335144043},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4090999960899353},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3781000077724457},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36719998717308044},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.35089999437332153},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.35040000081062317},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.3481000065803528},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.33320000767707825},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.31060001254081726},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3073999881744385},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.30480000376701355},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30469998717308044},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.30219998955726624},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.29809999465942383},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.2964000105857849},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.29440000653266907},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.29190000891685486},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.28780001401901245},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.2827000021934509},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.2793999910354614},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.26429998874664307},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.25290000438690186},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.25270000100135803},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.2515999972820282}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.05774","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.05774","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":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.05774","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.05774","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":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.8250795006752014,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Large":[0],"Language":[1],"Models":[2],"(LLMs)":[3],"are":[4,14],"increasingly":[5],"adopted":[6],"as":[7,148],"conversational":[8],"assistants":[9],"in":[10],"genomics,":[11],"where":[12],"they":[13],"mainly":[15],"used":[16],"to":[17,59,70,99],"reason":[18],"over":[19,166],"biological":[20,45,91],"knowledge,":[21],"annotations,":[22],"and":[23,109,125,141,151,176],"analysis":[24],"outputs":[25],"through":[26],"natural":[27],"language":[28],"interfaces.":[29],"However,":[30],"existing":[31],"benchmarks":[32],"either":[33],"focus":[34],"on":[35,79,157,183],"specialized":[36],"DNA":[37],"models":[38,136],"trained":[39],"for":[40,76,174],"sequence":[41,94,145,167],"prediction":[42],"or":[43,163],"evaluate":[44],"knowledge":[46],"using":[47],"text-only":[48],"questions,":[49],"leaving":[50],"the":[51,178],"behavior":[52],"of":[53,180],"general-purpose":[54,77,181],"LLMs":[55,78,182],"when":[56],"directly":[57],"exposed":[58],"raw":[60,184],"genome":[61,81],"sequences":[62],"underexplored.":[63],"We":[64],"introduce":[65],"GenomeQA,":[66],"a":[67,72,171],"benchmark":[68,173],"designed":[69],"provide":[71],"controlled":[73],"evaluation":[74],"setting":[75],"sequence-based":[80],"inference":[82,165],"tasks.":[83],"GenomeQA":[84,169],"comprises":[85],"5,200":[86],"samples":[87],"drawn":[88],"from":[89,97],"multiple":[90],"databases,":[92],"with":[93],"lengths":[95],"ranging":[96],"6":[98],"1,000":[100],"base":[101],"pairs":[102],"(bp),":[103],"spanning":[104],"six":[105,130],"task":[106],"families:":[107],"Enhancer":[108],"Promoter":[110],"Identification,":[111,114],"Splice":[112],"Site":[113,123],"Taxonomic":[115],"Classification,":[116],"Histone":[117],"Mark":[118],"Prediction,":[119,124],"Transcription":[120],"Factor":[121],"Binding":[122],"TF":[126],"Motif":[127],"Prediction.":[128],"Across":[129],"frontier":[131],"LLMs,":[132],"we":[133],"find":[134],"that":[135,159],"consistently":[137],"outperform":[138],"random":[139],"baselines":[140],"can":[142],"exploit":[143],"local":[144],"signals":[146],"such":[147],"GC":[149],"content":[150],"short":[152],"motifs,":[153],"while":[154],"performance":[155],"degrades":[156],"tasks":[158],"require":[160],"more":[161],"indirect":[162],"multi-step":[164],"patterns.":[168],"establishes":[170],"diagnostic":[172],"studying":[175],"improving":[177],"use":[179],"genomic":[185],"sequences.":[186]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-04-09T00:00:00"}
