{"id":"https://openalex.org/W4406259856","doi":"https://doi.org/10.1109/bibm62325.2024.10822720","title":"CodonT5: A Multi-task Codon Language Model to Perform Generative Codon Optimization","display_name":"CodonT5: A Multi-task Codon Language Model to Perform Generative Codon Optimization","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406259856","doi":"https://doi.org/10.1109/bibm62325.2024.10822720"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822720","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822720","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045156137","display_name":"Ashley Babjac","orcid":"https://orcid.org/0000-0002-0991-7726"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ashley Babjac","raw_affiliation_strings":["University of Tennessee,Department of Computer Science,Knoxville,USA"],"affiliations":[{"raw_affiliation_string":"University of Tennessee,Department of Computer Science,Knoxville,USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019857186","display_name":"Scott Emrich","orcid":"https://orcid.org/0000-0002-5741-4517"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott J. Emrich","raw_affiliation_strings":["University of Tennessee,Department of Computer Science,Knoxville,USA"],"affiliations":[{"raw_affiliation_string":"University of Tennessee,Department of Computer Science,Knoxville,USA","institution_ids":["https://openalex.org/I75027704"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045156137"],"corresponding_institution_ids":["https://openalex.org/I75027704"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23241989,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"12","last_page":"18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9743000268936157,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9743000268936157,"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":0.7142000198364258},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.6130340695381165},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5892307758331299},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4175463318824768},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.4133811593055725},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.34005576372146606},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.061705708503723145}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7142000198364258},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.6130340695381165},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5892307758331299},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4175463318824768},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.4133811593055725},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34005576372146606},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.061705708503723145},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822720","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822720","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1760665500","https://openalex.org/W2006607348","https://openalex.org/W2018590530","https://openalex.org/W2096160166","https://openalex.org/W2168036974","https://openalex.org/W2611528178","https://openalex.org/W2949205269","https://openalex.org/W3004726194","https://openalex.org/W3111451490","https://openalex.org/W3164045210","https://openalex.org/W3177500196","https://openalex.org/W3208689379","https://openalex.org/W4205425368","https://openalex.org/W4205773061","https://openalex.org/W4290189484","https://openalex.org/W4327550249","https://openalex.org/W4362601885","https://openalex.org/W4387346412","https://openalex.org/W4392095606","https://openalex.org/W4399384112","https://openalex.org/W6769627184","https://openalex.org/W6782889966","https://openalex.org/W6796581206","https://openalex.org/W6849932668","https://openalex.org/W6856555777"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4391584540","https://openalex.org/W3204019825","https://openalex.org/W4380551139","https://openalex.org/W4317695495","https://openalex.org/W4395044357","https://openalex.org/W4287117424","https://openalex.org/W4387506531","https://openalex.org/W4385572368"],"abstract_inverted_index":{"Codon":[0,41],"language":[1],"modeling":[2,134],"is":[3,89,123],"an":[4],"emerging":[5],"area":[6],"of":[7,47,71,79,119],"research":[8],"interest.":[9],"Prior":[10],"efforts":[11],"in":[12,139,147],"codon":[13,21,81,100,120],"optimization":[14],"have":[15,23],"mostly":[16],"focused":[17],"on":[18,24,57,115],"the":[19,69,76,108,128],"effect":[20],"preferences":[22],"protein":[25,146],"translation":[26],"speed":[27],"either":[28],"at":[29,68],"single":[30],"codons":[31],"(e.g.,":[32,40,150],"selection":[33],"preference":[34],"measures)":[35],"or":[36],"entire":[37],"gene":[38,48],"sequences":[39,110],"Adaptation":[42],"Index":[43],"and":[44,97],"related":[45],"estimates":[46],"expression).":[49],"Model":[50],"parameters":[51],"are":[52],"almost":[53],"always":[54],"trained":[55],"based":[56],"a":[58,64,144,148],"specific":[59],"organism/task.":[60],"Here":[61],"we":[62],"explore":[63],"first":[65],"ever":[66],"look":[67],"impact":[70],"multi-task":[72],"model":[73],"pre-training":[74],"with":[75],"end":[77],"goal":[78],"performing":[80],"\"translations\"":[82],"between":[83],"species.":[84],"Significantly,":[85],"our":[86],"model,":[87],"CodonT5,":[88],"able":[90],"to":[91,102],"accurately":[92],"predict":[93],"across":[94],"multiple":[95],"tasks":[96],"generate":[98],"comparable":[99],"optimizations":[101],"previously":[103],"established":[104],"methods":[105],"using":[106],"only":[107],"reference":[109,145],"without":[111],"being":[112],"necessarily":[113],"dependent":[114],"any":[116],"pre-computed":[117],"metrics":[118],"preference.":[121],"This":[122],"important":[124],"as":[125],"it":[126],"paves":[127],"way":[129],"for":[130],"more":[131],"diverse":[132],"sequence-to-sequence":[133],"that":[135],"will":[136],"be":[137],"necessary":[138],"many":[140],"applications":[141],"involving":[142],"replicating":[143],"host":[149],"mRNA":[151],"vaccines).":[152]},"counts_by_year":[],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-10-10T00:00:00"}
