{"id":"https://openalex.org/W4313525374","doi":"https://doi.org/10.1109/bibm55620.2022.9995492","title":"LM-ARG: Identification & classification of antibiotic resistance genes leveraging pre-trained protein language models","display_name":"LM-ARG: Identification & classification of antibiotic resistance genes leveraging pre-trained protein language models","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313525374","doi":"https://doi.org/10.1109/bibm55620.2022.9995492"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9995492","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995492","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 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/A5058975650","display_name":"Shafayat Ahmed","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shafayat Ahmed","raw_affiliation_strings":["Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia"],"affiliations":[{"raw_affiliation_string":"Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051072835","display_name":"Muhit Islam Emon","orcid":"https://orcid.org/0000-0002-8190-4495"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Muhit Islam Emon","raw_affiliation_strings":["Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia"],"affiliations":[{"raw_affiliation_string":"Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079050999","display_name":"Nazifa Ahmed Moumi","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nazifa Ahmed Moumi","raw_affiliation_strings":["Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia"],"affiliations":[{"raw_affiliation_string":"Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100741571","display_name":"Liqing Zhang","orcid":"https://orcid.org/0000-0002-3936-4376"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liqing Zhang","raw_affiliation_strings":["Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia"],"affiliations":[{"raw_affiliation_string":"Virginia Polytechnic Institute and State University,Department of Computer Science,Blacksburg,Virginia","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5058975650"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":3.0864,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.92958861,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"3782","last_page":"3784"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9952999949455261,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9952999949455261,"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9904999732971191,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9876000285148621,"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/artificial-intelligence","display_name":"Artificial intelligence","score":0.6679970026016235},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6346839666366577},{"id":"https://openalex.org/keywords/margin","display_name":"Margin (machine learning)","score":0.6222795844078064},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5827493667602539},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5624969005584717},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5320103168487549},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.49821949005126953},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.46061965823173523},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1677180826663971},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08680951595306396}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6679970026016235},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6346839666366577},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.6222795844078064},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5827493667602539},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5624969005584717},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5320103168487549},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.49821949005126953},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.46061965823173523},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1677180826663971},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08680951595306396},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"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/bibm55620.2022.9995492","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995492","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8600000143051147,"display_name":"Good health and well-being"}],"awards":[],"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":7,"referenced_works":["https://openalex.org/W2138952930","https://openalex.org/W2761788747","https://openalex.org/W2951274106","https://openalex.org/W2982531601","https://openalex.org/W3128120098","https://openalex.org/W4287724045","https://openalex.org/W6780145172"],"related_works":["https://openalex.org/W3125011624","https://openalex.org/W1508631387","https://openalex.org/W2370917603","https://openalex.org/W2952760143","https://openalex.org/W2017776670","https://openalex.org/W2347897961","https://openalex.org/W2340870721","https://openalex.org/W2358318464","https://openalex.org/W2979236518","https://openalex.org/W3098003361"],"abstract_inverted_index":{"Antibiotic":[0,16],"resistance":[1,17,23],"is":[2,31,55],"a":[3,91,104,144],"silent":[4],"pandemic,":[5],"causing":[6],"700":[7],"thousand":[8],"human":[9],"deaths":[10],"across":[11],"the":[12,25,45,52,65,82,95,101,111,134,139],"world":[13],"every":[14],"year.":[15],"genes":[18,21],"(ARG)":[19],"are":[20,38],"conferring":[22],"for":[24,49,81],"bacteria":[26],"carrying":[27],"them.":[28],"Predicting":[29],"ARGs":[30,37],"an":[32],"important":[33],"computational":[34],"task.":[35],"Traditionally":[36],"predicted":[39],"using":[40],"alignment":[41],"based":[42],"methods.":[43],"However,":[44],"false":[46],"negative":[47],"rate":[48],"most":[50],"of":[51,86,103],"alignment-based":[53],"tools":[54],"very":[56],"high.":[57],"The":[58,130],"protein":[59,68,74,113],"language":[60,106,136],"models":[61],"(LM)":[62],"trained":[63],"on":[64,94,118],"huge":[66],"corpus":[67],"sequences":[69],"capture":[70],"distant":[71],"relations":[72],"among":[73],"sequences.":[75],"These":[76],"features":[77,132],"can":[78],"be":[79],"utilized":[80],"identification":[83],"and":[84,123],"classification":[85,121],"ARGs.":[87],"We":[88,109],"have":[89],"presented":[90],"self-supervised":[92],"model":[93,107,137,141],"largest":[96],"available":[97],"ARG":[98,120],"database":[99],"with":[100],"help":[102],"pre-trained":[105],"ProtAlbert.":[108],"used":[110],"raw":[112],"LM-embeddings":[114],"from":[115,133],"unlabeled":[116],"data":[117],"our":[119],"task":[122],"saw":[124],"it":[125],"outperform":[126],"state-of-the-art":[127],"prediction":[128],"algorithms.":[129],"extracted":[131],"pretrained":[135],"boosted":[138],"supervised":[140],"accuracy":[142],"to":[143],"great":[145],"margin.":[146]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}