{"id":"https://openalex.org/W4308052938","doi":"https://doi.org/10.1093/bioinformatics/btac711","title":"Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities","display_name":"Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities","publication_year":2022,"publication_date":"2022-11-02","ids":{"openalex":"https://openalex.org/W4308052938","doi":"https://doi.org/10.1093/bioinformatics/btac711","pmid":"https://pubmed.ncbi.nlm.nih.gov/36326438"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac711","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac711","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5368/47886933/btac711.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5368/47886933/btac711.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070743854","display_name":"Yuxuan Pang","orcid":"https://orcid.org/0000-0002-6778-7034"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuxuan Pang","raw_affiliation_strings":["School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China"],"raw_orcid":"https://orcid.org/0000-0002-6778-7034","affiliations":[{"raw_affiliation_string":"School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]},{"raw_affiliation_string":"Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078222868","display_name":"Lantian Yao","orcid":"https://orcid.org/0000-0003-4554-6827"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lantian Yao","raw_affiliation_strings":["School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China"],"raw_orcid":"https://orcid.org/0000-0003-4554-6827","affiliations":[{"raw_affiliation_string":"School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]},{"raw_affiliation_string":"Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100610905","display_name":"Jingyi Xu","orcid":"https://orcid.org/0000-0001-7608-2354"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingyi Xu","raw_affiliation_strings":["School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100446592","display_name":"Zhuo Wang","orcid":"https://orcid.org/0000-0002-7076-8432"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhuo Wang","raw_affiliation_strings":["Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China"],"raw_orcid":"https://orcid.org/0000-0002-7076-8432","affiliations":[{"raw_affiliation_string":"Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045675277","display_name":"Tzong-Yi Lee","orcid":"https://orcid.org/0000-0001-8475-7868"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tzong-Yi Lee","raw_affiliation_strings":["School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China"],"raw_orcid":"https://orcid.org/0000-0001-8475-7868","affiliations":[{"raw_affiliation_string":"School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]},{"raw_affiliation_string":"Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen , Shenzhen 518172, China","institution_ids":["https://openalex.org/I4210116924"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045675277","https://openalex.org/A5100446592"],"corresponding_institution_ids":["https://openalex.org/I4210116924"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.0323,"has_fulltext":false,"cited_by_count":56,"citation_normalized_percentile":{"value":0.97384306,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"38","issue":"24","first_page":"5368","last_page":"5374"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.7479000091552734,"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":0.7479000091552734,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0934000015258789,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.05649999901652336,"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":0.6849151253700256},{"id":"https://openalex.org/keywords/antimicrobial-peptides","display_name":"Antimicrobial peptides","score":0.6835250854492188},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6401271820068359},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5811522006988525},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5560554265975952},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5334314107894897},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5102729797363281},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5049763321876526},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.4802858531475067},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.41962963342666626},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41273680329322815},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2999686002731323},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.29376763105392456},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2487950623035431},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08712482452392578}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6849151253700256},{"id":"https://openalex.org/C540938839","wikidata":"https://www.wikidata.org/wiki/Q1201508","display_name":"Antimicrobial peptides","level":3,"score":0.6835250854492188},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6401271820068359},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5811522006988525},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5560554265975952},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5334314107894897},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5102729797363281},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5049763321876526},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.4802858531475067},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.41962963342666626},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41273680329322815},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2999686002731323},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.29376763105392456},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2487950623035431},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08712482452392578},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac711","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac711","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5368/47886933/btac711.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36326438","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36326438","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9750108","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9750108","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac711","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac711","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/24/5368/47886933/btac711.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.5799999833106995,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G287154221","display_name":null,"funder_award_id":"32070659","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3176667179","display_name":null,"funder_award_id":"JCYJ20200109150003938","funder_id":"https://openalex.org/F4320326705","funder_display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322942","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48"},{"id":"https://openalex.org/F4320326705","display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W54887220","https://openalex.org/W1546047689","https://openalex.org/W1766594731","https://openalex.org/W1967541074","https://openalex.org/W1978444624","https://openalex.org/W2010979687","https://openalex.org/W2041942794","https://openalex.org/W2047438216","https://openalex.org/W2080614447","https://openalex.org/W2081697244","https://openalex.org/W2095705004","https://openalex.org/W2099153308","https://openalex.org/W2131275757","https://openalex.org/W2145957695","https://openalex.org/W2148143831","https://openalex.org/W2156125289","https://openalex.org/W2511835277","https://openalex.org/W2562261325","https://openalex.org/W2588467130","https://openalex.org/W2761599107","https://openalex.org/W2791765498","https://openalex.org/W2791848964","https://openalex.org/W2792378492","https://openalex.org/W2911964244","https://openalex.org/W2956569764","https://openalex.org/W2971227267","https://openalex.org/W3048086963","https://openalex.org/W3080137602","https://openalex.org/W3095583226","https://openalex.org/W3097405028","https://openalex.org/W3106094498","https://openalex.org/W3112376646","https://openalex.org/W3158777740","https://openalex.org/W3162422430","https://openalex.org/W3164453494","https://openalex.org/W3185903970","https://openalex.org/W3186424845","https://openalex.org/W3188372451","https://openalex.org/W3198303770","https://openalex.org/W3199352650","https://openalex.org/W3216979156","https://openalex.org/W4213072029","https://openalex.org/W4295312788","https://openalex.org/W4385245566","https://openalex.org/W6602203489","https://openalex.org/W6632634077","https://openalex.org/W6674330103","https://openalex.org/W6739901393","https://openalex.org/W6766978945","https://openalex.org/W6800693912"],"related_works":["https://openalex.org/W1973959357","https://openalex.org/W2360158017","https://openalex.org/W2159604840","https://openalex.org/W2126785046","https://openalex.org/W1982829397","https://openalex.org/W2114802749","https://openalex.org/W2140673944","https://openalex.org/W2911822841","https://openalex.org/W2258364789","https://openalex.org/W4205828568"],"abstract_inverted_index":{"MOTIVATION:":[0],"Antimicrobial":[1],"peptides":[2],"(AMPs)":[3],"have":[4],"the":[5,59,77,83,93,132,139,150,154,167],"potential":[6],"to":[7,14,70,86,102,130],"inhibit":[8],"multiple":[9],"types":[10],"of":[11,29,135,182,198],"pathogens":[12],"and":[13,32,92,115,160,196],"heal":[15],"infections.":[16],"Computational":[17],"strategies":[18,183],"can":[19],"assist":[20],"in":[21],"characterizing":[22],"novel":[23,54],"AMPs":[24,88,98],"from":[25,66,89],"proteome":[26],"or":[27,187],"collections":[28],"synthetic":[30],"sequences":[31],"discovering":[33],"their":[34],"functional":[35,99,176],"abilities":[36],"toward":[37],"different":[38,104],"microbial":[39],"targets":[40,105],"without":[41,184],"intensive":[42],"labor.":[43],"RESULTS:":[44],"Here,":[45],"we":[46],"present":[47],"a":[48,121,162],"deep":[49,188],"learning-based":[50],"method":[51,78],"for":[52,79,138,153,166],"computer-aided":[53],"AMP":[55],"discovery":[56],"that":[57,145,181],"utilizes":[58],"transformer":[60],"neural":[61],"network":[62],"architecture":[63],"with":[64,180],"knowledge":[65],"natural":[67],"language":[68],"processing":[69],"extract":[71],"peptide":[72],"sequence":[73],"information.":[74],"We":[75],"implemented":[76],"two":[80],"AMP-related":[81],"tasks:":[82],"first":[84,155],"is":[85,96,120],"discriminate":[87],"other":[90],"peptides,":[91],"second":[94,168],"task":[95,156,169],"identifying":[97],"activities":[100],"related":[101],"seven":[103],"(gram-negative":[106],"bacteria,":[107,109],"gram-positive":[108],"fungi,":[110],"viruses,":[111],"cancer":[112],"cells,":[113],"parasites":[114],"mammalian":[116],"cell":[117],"inhibition),":[118],"which":[119],"multi-label":[122,140],"problem.":[123],"In":[124],"addition,":[125],"asymmetric":[126],"loss":[127],"was":[128],"adopted":[129],"resolve":[131],"intrinsic":[133],"imbalance":[134],"dataset,":[136],"particularly":[137],"scenarios.":[141],"The":[142,193],"evaluation":[143],"showed":[144],"our":[146],"proposed":[147],"scheme":[148],"achieves":[149],"best":[151],"performance":[152],"(96.85%":[157],"balanced":[158,171],"accuracy)":[159],"has":[161],"more":[163],"unbiased":[164],"prediction":[165],"(79.83%":[170],"accuracy":[172],"averaged":[173],"across":[174],"all":[175],"activities)":[177],"when":[178],"compared":[179],"imbalanced":[185],"learning":[186],"learning.":[189],"AVAILABILITY":[190],"AND":[191],"IMPLEMENTATION:":[192],"source":[194],"code":[195],"data":[197,208],"this":[199],"study":[200],"are":[201,209],"available":[202,210],"at":[203,211],"https://github.com/BiOmicsLab/TransImbAMP.":[204],"SUPPLEMENTARY":[205],"INFORMATION:":[206],"Supplementary":[207],"Bioinformatics":[212],"online.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
