{"id":"https://openalex.org/W4362657509","doi":"https://doi.org/10.1093/bib/bbad135","title":"UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity","display_name":"UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity","publication_year":2023,"publication_date":"2023-04-05","ids":{"openalex":"https://openalex.org/W4362657509","doi":"https://doi.org/10.1093/bib/bbad135","pmid":"https://pubmed.ncbi.nlm.nih.gov/37020337"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad135","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad135","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad135/50410977/bbad135.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad135/50410977/bbad135.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022574661","display_name":"Zhenjiao Du","orcid":"https://orcid.org/0000-0002-8492-4328"},"institutions":[{"id":"https://openalex.org/I189590672","display_name":"Kansas State University","ror":"https://ror.org/05p1j8758","country_code":"US","type":"education","lineage":["https://openalex.org/I189590672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhenjiao Du","raw_affiliation_strings":["Department of Grain Science and Industry, Kansas State University , Manhattan, KS 66506, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Grain Science and Industry, Kansas State University , Manhattan, KS 66506, USA","institution_ids":["https://openalex.org/I189590672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021789231","display_name":"Xingjian Ding","orcid":"https://orcid.org/0000-0001-8866-4941"},"institutions":[{"id":"https://openalex.org/I189590672","display_name":"Kansas State University","ror":"https://ror.org/05p1j8758","country_code":"US","type":"education","lineage":["https://openalex.org/I189590672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xingjian Ding","raw_affiliation_strings":["Department of Computer Science, Kansas State University , Manhattan, KS 66506, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Kansas State University , Manhattan, KS 66506, USA","institution_ids":["https://openalex.org/I189590672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079122598","display_name":"Yixiang Xu","orcid":"https://orcid.org/0000-0003-3122-6101"},"institutions":[{"id":"https://openalex.org/I4210140558","display_name":"Western Regional Research Center","ror":"https://ror.org/03x7fn667","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210094889","https://openalex.org/I4210140558"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yixiang Xu","raw_affiliation_strings":["Healthy Processed Foods Research Unit, Western Regional Research Center USDA-ARS , 800 Buchanan Street, Albany, CA 94710, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Healthy Processed Foods Research Unit, Western Regional Research Center USDA-ARS , 800 Buchanan Street, Albany, CA 94710, USA","institution_ids":["https://openalex.org/I4210140558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059420555","display_name":"Yonghui Li","orcid":"https://orcid.org/0000-0003-4320-0806"},"institutions":[{"id":"https://openalex.org/I189590672","display_name":"Kansas State University","ror":"https://ror.org/05p1j8758","country_code":"US","type":"education","lineage":["https://openalex.org/I189590672"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yonghui Li","raw_affiliation_strings":["Department of Grain Science and Industry, Kansas State University , Manhattan, KS 66506, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Grain Science and Industry, Kansas State University , Manhattan, KS 66506, USA","institution_ids":["https://openalex.org/I189590672"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5059420555"],"corresponding_institution_ids":["https://openalex.org/I189590672"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":20.1593,"has_fulltext":true,"cited_by_count":126,"citation_normalized_percentile":{"value":0.99751378,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9987000226974487,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983000159263611,"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/computer-science","display_name":"Computer science","score":0.726341962814331},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6656871438026428},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6407710909843445},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5692781805992126},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.536311686038971},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.4703393578529358},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.44211235642433167},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4372761845588684},{"id":"https://openalex.org/keywords/model-selection","display_name":"Model selection","score":0.4249185621738434},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.35634493827819824},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12855523824691772}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.726341962814331},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6656871438026428},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6407710909843445},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5692781805992126},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.536311686038971},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.4703393578529358},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44211235642433167},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4372761845588684},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.4249185621738434},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35634493827819824},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12855523824691772},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad135","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad135","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad135/50410977/bbad135.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37020337","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37020337","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad135","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad135","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad135/50410977/bbad135.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2196763611","display_name":null,"funder_award_id":"2020-68008-31408","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G285035018","display_name":null,"funder_award_id":"23-192-J","funder_id":"https://openalex.org/F4320332529","funder_display_name":"Arkansas Agricultural Experiment Station"},{"id":"https://openalex.org/G5620962805","display_name":null,"funder_award_id":"67021","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G5927253622","display_name":null,"funder_award_id":"2021-67021-34495","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"},{"id":"https://openalex.org/F4320332529","display_name":"Arkansas Agricultural Experiment Station","ror":"https://ror.org/04q7j9m29"},{"id":"https://openalex.org/F4320332605","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4362657509.pdf","grobid_xml":"https://content.openalex.org/works/W4362657509.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1976309152","https://openalex.org/W2104817695","https://openalex.org/W2163316049","https://openalex.org/W2187089797","https://openalex.org/W2521200999","https://openalex.org/W2791848964","https://openalex.org/W2796531554","https://openalex.org/W2800668197","https://openalex.org/W2884561390","https://openalex.org/W2905629607","https://openalex.org/W2913961829","https://openalex.org/W2963923670","https://openalex.org/W2964614970","https://openalex.org/W2980789587","https://openalex.org/W2982358220","https://openalex.org/W2985778816","https://openalex.org/W2989775272","https://openalex.org/W2996238637","https://openalex.org/W3013552211","https://openalex.org/W3020081556","https://openalex.org/W3035032764","https://openalex.org/W3047310964","https://openalex.org/W3048086963","https://openalex.org/W3084375074","https://openalex.org/W3088459654","https://openalex.org/W3093729849","https://openalex.org/W3111174583","https://openalex.org/W3112842176","https://openalex.org/W3113134891","https://openalex.org/W3119003488","https://openalex.org/W3127712659","https://openalex.org/W3131121088","https://openalex.org/W3145990216","https://openalex.org/W3146944767","https://openalex.org/W3157437194","https://openalex.org/W3164698295","https://openalex.org/W3186261494","https://openalex.org/W3194214681","https://openalex.org/W3203053846","https://openalex.org/W3204123970","https://openalex.org/W3214908333","https://openalex.org/W4221099083","https://openalex.org/W4225081553","https://openalex.org/W4280645232","https://openalex.org/W4285493717","https://openalex.org/W4287724045","https://openalex.org/W4289528622","https://openalex.org/W4292676375","https://openalex.org/W4293713156","https://openalex.org/W4294087001","https://openalex.org/W4307922460","https://openalex.org/W4308052938","https://openalex.org/W4308545215","https://openalex.org/W4362677280","https://openalex.org/W6748816842","https://openalex.org/W6755207826","https://openalex.org/W6759104856","https://openalex.org/W6780145172","https://openalex.org/W6802197100","https://openalex.org/W6839893107","https://openalex.org/W6840065848","https://openalex.org/W6841227837"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W4293226380","https://openalex.org/W4375867731","https://openalex.org/W2037549926","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983","https://openalex.org/W3029198973"],"abstract_inverted_index":{"Identification":[0],"of":[1,17,116,144,181,209,228],"potent":[2],"peptides":[3],"through":[4,141,153],"model":[5,18,35,73,94,130,149],"prediction":[6,186,235],"can":[7,20,85],"reduce":[8],"benchwork":[9],"in":[10,78,89,107],"wet":[11],"experiments.":[12],"However,":[13],"the":[14,105,114,122,162,174,196,212],"conventional":[15],"process":[16],"buildings":[19],"be":[21],"complex":[22],"and":[23,37,55,59,99,136,157,193,201,217,226,234],"time":[24,124],"consuming":[25],"due":[26],"to":[27,57,103],"challenges":[28],"such":[29],"as":[30],"peptide":[31,80,111,134,139,146],"representation,":[32],"feature":[33],"selection,":[34],"selection":[36],"hyperparameter":[38],"tuning.":[39],"Recently,":[40],"advanced":[41],"pretrained":[42,127],"deep":[43],"learning-based":[44],"language":[45,129],"models":[46,177],"(LMs)":[47],"have":[48,67],"been":[49],"released":[50],"for":[51,75,133,178,211,230],"protein":[52],"sequence":[53],"embedding":[54],"applied":[56],"structure":[58],"function":[60],"prediction.":[61],"Based":[62],"on":[63],"these":[64],"developments,":[65],"we":[66],"developed":[68],"UniDL4BioPep,":[69],"a":[70,91,96,126,165],"universal":[71],"deep-learning":[72,93],"architecture":[74,98],"transfer":[76],"learning":[77],"bioactive":[79,110],"binary":[81],"classification":[82],"modeling.":[83],"It":[84],"directly":[86],"assist":[87],"users":[88],"training":[90],"high-performance":[92],"with":[95,164],"fixed":[97],"achieve":[100],"cutting-edge":[101],"performance":[102],"meet":[104],"demands":[106],"efficiently":[108],"novel":[109],"discovery.":[112],"To":[113],"best":[115,118],"our":[117],"knowledge,":[119],"this":[120],"is":[121,131,215],"first":[123],"that":[125],"biological":[128],"utilized":[132],"embeddings":[135],"successfully":[137],"predicts":[138],"bioactivities":[140,214],"large-scale":[142],"evaluations":[143],"those":[145],"embeddings.":[147],"The":[148,188,222],"was":[150],"also":[151],"validated":[152],"uniform":[154],"manifold":[155],"approximation":[156],"projection":[158],"analysis.":[159],"By":[160],"combining":[161],"LM":[163],"convolutional":[166],"neural":[167],"network,":[168],"UniDL4BioPep":[169,210,229],"achieved":[170],"greater":[171],"performances":[172],"than":[173],"respective":[175],"state-of-the-art":[176],"15":[179],"out":[180],"20":[182],"different":[183],"bioactivity":[184,232],"dataset":[185],"tasks.":[187],"accuracy,":[189],"Mathews":[190],"correlation":[191],"coefficient":[192],"area":[194],"under":[195],"curve":[197],"were":[198],"0.7-7,":[199],"1.23-26.7":[200],"0.3-25.6%":[202],"higher,":[203],"respectively.":[204],"A":[205],"user-friendly":[206],"web":[207],"server":[208],"tested":[213],"established":[216],"freely":[218],"accessible":[219],"at":[220,239],"https://nepc2pvmzy.us-east-1.awsapprunner.com.":[221],"source":[223],"codes,":[224],"datasets":[225],"templates":[227],"other":[231],"fitting":[233],"tasks":[236],"are":[237],"available":[238],"https://github.com/dzjxzyd/UniDL4BioPep.":[240]},"counts_by_year":[{"year":2026,"cited_by_count":18},{"year":2025,"cited_by_count":57},{"year":2024,"cited_by_count":39},{"year":2023,"cited_by_count":11}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}