{"id":"https://openalex.org/W4411464978","doi":"https://doi.org/10.1145/3703412.3703425","title":"Trans-ARG: Predicting Antibiotic Resistance Genes with a Transformer-Based Model and Pretrained Protein Language Model","display_name":"Trans-ARG: Predicting Antibiotic Resistance Genes with a Transformer-Based Model and Pretrained Protein Language Model","publication_year":2024,"publication_date":"2024-10-08","ids":{"openalex":"https://openalex.org/W4411464978","doi":"https://doi.org/10.1145/3703412.3703425"},"language":"en","primary_location":{"id":"doi:10.1145/3703412.3703425","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3703412.3703425","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 4th International Conference on AI-ML Systems","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3703412.3703425","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109841647","display_name":"Mohd Abbas","orcid":null},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mohd Manzar Abbas","raw_affiliation_strings":["Louisiana State University, Baton Rouge, United States of America"],"affiliations":[{"raw_affiliation_string":"Louisiana State University, Baton Rouge, United States of America","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075138847","display_name":"Amit Ranjan","orcid":"https://orcid.org/0000-0002-7940-5865"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amit Ranjan","raw_affiliation_strings":["Louisiana State University, Baton Rouge, United States of America"],"affiliations":[{"raw_affiliation_string":"Louisiana State University, Baton Rouge, United States of America","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050733500","display_name":"Aixin Hou","orcid":"https://orcid.org/0000-0002-2727-6678"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aixin Hou","raw_affiliation_strings":["Louisiana State University, Baton Rouge, United States of America"],"affiliations":[{"raw_affiliation_string":"Louisiana State University, Baton Rouge, United States of America","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101963514","display_name":"Supratik Mukhopadhyay","orcid":"https://orcid.org/0000-0003-0839-1133"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Supratik Mukhopadhyay","raw_affiliation_strings":["Louisiana State University, Baton Rouge, United States of America"],"affiliations":[{"raw_affiliation_string":"Louisiana State University, Baton Rouge, United States of America","institution_ids":["https://openalex.org/I121820613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5109841647"],"corresponding_institution_ids":["https://openalex.org/I121820613"],"apc_list":null,"apc_paid":null,"fwci":0.5001,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.67917451,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9976999759674072,"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":0.9976999759674072,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9937000274658203,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9890000224113464,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/transformer","display_name":"Transformer","score":0.675503134727478},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.6120390892028809},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4850958585739136},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"Antibiotic resistance","score":0.4540967345237732},{"id":"https://openalex.org/keywords/antibiotics","display_name":"Antibiotics","score":0.4522536098957062},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.427035927772522},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3757858872413635},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3042471706867218},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.21245518326759338},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19989868998527527},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19048845767974854},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.15208670496940613},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.07231748104095459},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.062371253967285156}],"concepts":[{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.675503134727478},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.6120390892028809},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4850958585739136},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.4540967345237732},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.4522536098957062},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.427035927772522},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3757858872413635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3042471706867218},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.21245518326759338},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19989868998527527},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19048845767974854},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.15208670496940613},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.07231748104095459},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.062371253967285156}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3703412.3703425","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3703412.3703425","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 4th International Conference on AI-ML Systems","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.lsu.edu:enviro_sciences_pubs-1147","is_oa":true,"landing_page_url":"https://repository.lsu.edu/enviro_sciences_pubs/148","pdf_url":null,"source":{"id":"https://openalex.org/S4210169993","display_name":"Civil War Book Review","issn_l":"1528-6592","issn":["1528-6592"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310315936","host_organization_name":"Louisiana State University","host_organization_lineage":["https://openalex.org/P4310315936"],"host_organization_lineage_names":["Louisiana State University"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1145/3703412.3703425","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3703412.3703425","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 4th International Conference on AI-ML Systems","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.6899999976158142}],"awards":[{"id":"https://openalex.org/G5372659370","display_name":null,"funder_award_id":"1636933","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1498436455","https://openalex.org/W1874122563","https://openalex.org/W1964640602","https://openalex.org/W2094722405","https://openalex.org/W2110118677","https://openalex.org/W2134852597","https://openalex.org/W2156125289","https://openalex.org/W2172154910","https://openalex.org/W2295598076","https://openalex.org/W2300972769","https://openalex.org/W2528705988","https://openalex.org/W2557776122","https://openalex.org/W2763934038","https://openalex.org/W2911964244","https://openalex.org/W2921872415","https://openalex.org/W2951274106","https://openalex.org/W2963592600","https://openalex.org/W2967125766","https://openalex.org/W2979939041","https://openalex.org/W2999309192","https://openalex.org/W3037888463","https://openalex.org/W3100541926","https://openalex.org/W3128120098","https://openalex.org/W3171788996","https://openalex.org/W3191207131","https://openalex.org/W4313525374","https://openalex.org/W4313595375","https://openalex.org/W4320037231","https://openalex.org/W4327550249","https://openalex.org/W4396773428","https://openalex.org/W4400234633","https://openalex.org/W4400444117"],"related_works":["https://openalex.org/W2955020749","https://openalex.org/W2029063045","https://openalex.org/W2507683919","https://openalex.org/W2076505260","https://openalex.org/W4320037900","https://openalex.org/W4226193097","https://openalex.org/W4297123388","https://openalex.org/W3032187068","https://openalex.org/W4221083638","https://openalex.org/W3152803520"],"abstract_inverted_index":{"Antibiotic":[0],"resistance":[1,25,252],"presents":[2],"an":[3,186,191],"emerging":[4],"challenge":[5],"to":[6,16,47,65,76,116,151,167,207,227,249],"global":[7],"health":[8],"by":[9],"reducing":[10],"the":[11,40,72,98,110,139,145,155,197,213,220],"efficacy":[12],"of":[13,141,188,194,203,258],"antibiotics":[14],"administered":[15],"treat":[17],"bacterial":[18],"infections.":[19],"Traditional":[20],"approaches":[21],"for":[22,42,239],"detecting":[23],"antibiotic":[24,251,259],"genes":[26],"(ARGs)":[27],"involve":[28],"alignment-based":[29],"sequence":[30],"similarity":[31],"techniques,":[32],"which":[33],"are":[34],"time-consuming":[35],"and":[36,85,134,138,190,217],"resource-intensive.":[37],"This":[38,223],"signifies":[39],"necessity":[41],"developing":[43],"advanced":[44],"computational":[45],"methods":[46],"detect":[48],"ARGs":[49],"early.":[50],"To":[51],"address":[52],"this":[53,247],"challenge,":[54],"we":[55,161],"introduce":[56],"Trans-ARG,":[57],"a":[58,105,163,236],"novel":[59],"multi-head":[60,142],"attention":[61,143],"transformer-based":[62],"model":[63,75,119,216],"designed":[64],"predict":[66,250],"potential":[67],"ARGs.":[68,124],"Our":[69,173],"approach":[70,248],"leverages":[71],"pretrained":[73,214],"ESMFold":[74,215],"extract":[77],"embeddings":[78,112],"from":[79,157,212],"protein":[80,232],"sequences,":[81,233],"capturing":[82,135],"intricate":[83],"structural":[84],"functional":[86],"information.":[87],"Protein":[88],"sequences":[89],"labelled":[90],"as":[91,97,104,114],"ARG":[92,240],"or":[93],"non-ARG":[94],"were":[95],"used":[96],"dataset.":[99,199],"We":[100],"formulate":[101],"our":[102,117,256],"problem":[103],"binary":[106],"classification":[107],"task,":[108],"where":[109],"extracted":[111],"serve":[113],"inputs":[115],"transformer":[118,126],"with":[120],"output":[121],"results":[122,175],"predicting":[123],"The":[125,200],"network":[127,146],"is":[128,205],"excellent":[129],"at":[130],"handling":[131],"sequential":[132],"data":[133,156],"long-range":[136],"dependencies,":[137],"use":[140],"within":[144,154],"improves":[147],"he":[148],"model\u2019s":[149],"capacity":[150],"comprehend":[152],"relationships":[153],"various":[158],"perspectives.":[159],"Additionally,":[160],"implemented":[162],"five-fold":[164],"cross-validation":[165],"strategy":[166],"ensure":[168],"robust":[169],"performance":[170,202],"during":[171],"training.":[172],"experimental":[174],"demonstrate":[176],"that":[177],"Trans-ARG":[178,204,226],"significantly":[179],"outperforms":[180],"standard":[181],"existing":[182],"baseline":[183],"methods,":[184],"presenting":[185],"accuracy":[187],"90.96%":[189],"AUC":[192],"score":[193],"97.08%":[195],"on":[196],"test":[198],"high-efficiency":[201],"attributed":[206],"integrating":[208],"embedding":[209],"features":[210],"obtained":[211],"effectively":[218],"utilizing":[219],"transformer\u2019s":[221],"architecture.":[222],"integration":[224],"allows":[225],"generalize":[228],"well":[229],"across":[230],"diverse":[231],"making":[234],"it":[235],"valuable":[237],"tool":[238],"prediction.":[241],"Future":[242],"research":[243],"may":[244],"explore":[245],"applying":[246],"categories,":[253],"further":[254],"enhancing":[255],"understanding":[257],"resistance.":[260]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2025-12-21T01:58:51.020947","created_date":"2025-10-10T00:00:00"}