{"id":"https://openalex.org/W7138144658","doi":"https://doi.org/10.1609/aaai.v40i33.39980","title":"TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling","display_name":"TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling","publication_year":2026,"publication_date":"2026-03-14","ids":{"openalex":"https://openalex.org/W7138144658","doi":"https://doi.org/10.1609/aaai.v40i33.39980"},"language":null,"primary_location":{"id":"doi:10.1609/aaai.v40i33.39980","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i33.39980","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.1609/aaai.v40i33.39980","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Qirong Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Qirong Yang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Yucheng Guo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yucheng Guo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Zicheng Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zicheng Liu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Yujie Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yujie Yang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Qijin Yin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qijin Yin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Siyuan Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Siyuan Li","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Shaomin Ji","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shaomin Ji","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Linlin Chao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Linlin Chao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Xiaoming Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiaoming Zhang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.40860215,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"40","issue":"33","first_page":"27602","last_page":"27610"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.29269999265670776,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.29269999265670776,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.2793000042438507,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.17350000143051147,"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/complement","display_name":"Complement (music)","score":0.573199987411499},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5376999974250793},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5148000121116638},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5073000192642212},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.5056999921798706},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.47690001130104065},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.45969998836517334}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6316999793052673},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.573199987411499},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5376999974250793},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5148000121116638},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5131000280380249},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5073000192642212},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.5056999921798706},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.47690001130104065},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46959999203681946},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.45969998836517334},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4092000126838684},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.3422999978065491},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3391000032424927},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.3140000104904175},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3091999888420105},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3086000084877014},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.3061999976634979},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.2992999851703644},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.2922999858856201},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.28690001368522644},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2718000113964081}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1609/aaai.v40i33.39980","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i33.39980","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1609/aaai.v40i33.39980","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i33.39980","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"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":{"The":[0,46],"modeling":[1],"of":[2,70,89,153],"genomic":[3,117,154],"sequences":[4],"presents":[5],"unique":[6],"challenges":[7],"due":[8],"to":[9,20,42,65,84,86,102,116,166],"their":[10],"long":[11],"length":[12],"and":[13,24,60,92,105,113,130,143,171],"structural":[14,58],"complexity.":[15],"Traditional":[16],"sequence":[17,90,118],"models":[18],"struggle":[19],"capture":[21],"long-range":[22],"dependencies":[23],"biological":[25,144],"features":[26,59],"inherent":[27,68],"in":[28,123],"DNA.":[29],"In":[30],"this":[31],"work,":[32],"we":[33,74,157],"propose":[34],"TrinityDNA,":[35],"a":[36,76,110,159],"novel":[37],"DNA":[38,71,161],"foundational":[39],"model":[40,47,83,101,135],"designed":[41],"address":[43],"these":[44],"challenges.":[45],"integrates":[48],"biologically":[49],"informed":[50],"components,":[51],"including":[52],"Groove":[53],"Fusion":[54],"for":[55,149],"capturing":[56],"DNA's":[57],"Gated":[61],"Reverse":[62],"Complement":[63],"(GRC)":[64],"handle":[66],"the":[67,82,100,137,147],"symmetry":[69],"sequences.":[72],"Additionally,":[73,156],"introduce":[75],"multi-scale":[77],"attention":[78],"mechanism":[79,128],"that":[80,97],"allows":[81],"attend":[85],"varying":[87],"levels":[88],"dependencies,":[91],"an":[93],"evolutionary":[94],"training":[95],"strategy":[96],"progressively":[98],"adapts":[99],"both":[103],"prokaryotic":[104],"eukaryotic":[106],"genomes.":[107],"TrinityDNA":[108],"provides":[109],"more":[111,150,169],"accurate":[112],"efficient":[114],"approach":[115],"modeling,":[119],"offering":[120],"significant":[121],"improvements":[122],"gene":[124],"function":[125],"prediction,":[126],"regulatory":[127],"discovery,":[129],"other":[131],"genomics":[132],"applications.":[133,175],"Our":[134],"bridges":[136],"gap":[138],"between":[139],"machine":[140],"learning":[141],"techniques":[142],"insights,":[145],"paving":[146],"way":[148],"effective":[151],"analysis":[152],"data.":[155],"introduced":[158],"new":[160],"long-sequence":[162],"CDS":[163],"annotation":[164],"benchmark":[165],"make":[167],"evaluations":[168],"comprehensive":[170],"oriented":[172],"toward":[173],"practical":[174]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2026-03-11T00:00:00"}