{"id":"https://openalex.org/W4411327294","doi":"https://doi.org/10.1093/bib/bbaf274","title":"MultiPep-DLCL: recognition of multifunctional therapeutic peptides through deep learning with label-sequence contrastive learning","display_name":"MultiPep-DLCL: recognition of multifunctional therapeutic peptides through deep learning with label-sequence contrastive learning","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4411327294","doi":"https://doi.org/10.1093/bib/bbaf274","pmid":"https://pubmed.ncbi.nlm.nih.gov/40518951"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf274","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf274","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf274","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110489737","display_name":"Ting Li","orcid":"https://orcid.org/0009-0007-7236-6203"},"institutions":[{"id":"https://openalex.org/I96908189","display_name":"Xinjiang University","ror":"https://ror.org/059gw8r13","country_code":"CN","type":"education","lineage":["https://openalex.org/I96908189"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ting Li","raw_affiliation_strings":["College of Mathematics and Systems Science , Xinjiang University, No. 777 Huarui Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region 830046 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mathematics and Systems Science , Xinjiang University, No. 777 Huarui Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region 830046 ,","institution_ids":["https://openalex.org/I96908189"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103163068","display_name":"Henghui Fan","orcid":"https://orcid.org/0000-0002-8150-9954"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Henghui Fan","raw_affiliation_strings":["Institutes of Physical Science and Information Technology , Anhui University, No. 111 Jiulong Road, Economic and Technological Development Zone, Hefei, Anhui Province 230601 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institutes of Physical Science and Information Technology , Anhui University, No. 111 Jiulong Road, Economic and Technological Development Zone, Hefei, Anhui Province 230601 ,","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101592781","display_name":"Jianping Zhao","orcid":"https://orcid.org/0000-0002-4080-8448"},"institutions":[{"id":"https://openalex.org/I96908189","display_name":"Xinjiang University","ror":"https://ror.org/059gw8r13","country_code":"CN","type":"education","lineage":["https://openalex.org/I96908189"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianping Zhao","raw_affiliation_strings":["College of Mathematics and Systems Science , Xinjiang University, No. 777 Huarui Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region 830046 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mathematics and Systems Science , Xinjiang University, No. 777 Huarui Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region 830046 ,","institution_ids":["https://openalex.org/I96908189"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034704065","display_name":"Xiaomei Yang","orcid":"https://orcid.org/0000-0003-1711-3004"},"institutions":[{"id":"https://openalex.org/I96908189","display_name":"Xinjiang University","ror":"https://ror.org/059gw8r13","country_code":"CN","type":"education","lineage":["https://openalex.org/I96908189"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaomei Yang","raw_affiliation_strings":["College of Mathematics and Systems Science , Xinjiang University, No. 777 Huarui Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region 830046 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mathematics and Systems Science , Xinjiang University, No. 777 Huarui Road, Shuimogou District, Urumqi, Xinjiang Uygur Autonomous Region 830046 ,","institution_ids":["https://openalex.org/I96908189"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Institutes of Physical Science and Information Technology , Anhui University, No. 111 Jiulong Road, Economic and Technological Development Zone, Hefei, Anhui Province 230601 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institutes of Physical Science and Information Technology , Anhui University, No. 111 Jiulong Road, Economic and Technological Development Zone, Hefei, Anhui Province 230601 ,","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.9472,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.85803069,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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":0.9997000098228455,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9991999864578247,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9991999864578247,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6709766387939453},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6636201739311218},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5663026571273804},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5350649952888489},{"id":"https://openalex.org/keywords/cross-entropy","display_name":"Cross entropy","score":0.4487270414829254},{"id":"https://openalex.org/keywords/sequence-learning","display_name":"Sequence learning","score":0.4399130046367645},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3820430636405945},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35822150111198425},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.29472577571868896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1345091462135315}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6709766387939453},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6636201739311218},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5663026571273804},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5350649952888489},{"id":"https://openalex.org/C167981619","wikidata":"https://www.wikidata.org/wiki/Q1685498","display_name":"Cross entropy","level":3,"score":0.4487270414829254},{"id":"https://openalex.org/C40506919","wikidata":"https://www.wikidata.org/wiki/Q7452469","display_name":"Sequence learning","level":2,"score":0.4399130046367645},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3820430636405945},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35822150111198425},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.29472577571868896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1345091462135315},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf274","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf274","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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:40518951","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40518951","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12167766","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12167766","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf274","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf274","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":[],"awards":[{"id":"https://openalex.org/G4784360784","display_name":null,"funder_award_id":"2020YFA0908700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7779363393","display_name":null,"funder_award_id":"62362062","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1832693441","https://openalex.org/W2064675550","https://openalex.org/W2168812241","https://openalex.org/W2265788075","https://openalex.org/W2781871595","https://openalex.org/W2794956775","https://openalex.org/W2914304175","https://openalex.org/W2918929658","https://openalex.org/W2924750018","https://openalex.org/W2971296908","https://openalex.org/W2996244073","https://openalex.org/W3047310964","https://openalex.org/W3082499071","https://openalex.org/W3119003488","https://openalex.org/W3156636935","https://openalex.org/W3164941572","https://openalex.org/W3174855653","https://openalex.org/W3175613352","https://openalex.org/W3177500196","https://openalex.org/W3205925781","https://openalex.org/W4200133092","https://openalex.org/W4212959738","https://openalex.org/W4224284938","https://openalex.org/W4225983992","https://openalex.org/W4226320060","https://openalex.org/W4282039921","https://openalex.org/W4282976570","https://openalex.org/W4286251201","https://openalex.org/W4289526583","https://openalex.org/W4291994084","https://openalex.org/W4295136274","https://openalex.org/W4295879738","https://openalex.org/W4301409532","https://openalex.org/W4310631727","https://openalex.org/W4312747027","https://openalex.org/W4313421210","https://openalex.org/W4313453841","https://openalex.org/W4321071737","https://openalex.org/W4377223989","https://openalex.org/W4380875839","https://openalex.org/W4382198814","https://openalex.org/W4385339003","https://openalex.org/W4386220612","https://openalex.org/W4388035706","https://openalex.org/W4390558569","https://openalex.org/W6739901393","https://openalex.org/W6742348326","https://openalex.org/W6743573349","https://openalex.org/W6765939562","https://openalex.org/W6840822713","https://openalex.org/W6843345451","https://openalex.org/W6852262732","https://openalex.org/W6856839813"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W2731899572","https://openalex.org/W4230611425","https://openalex.org/W4294635752","https://openalex.org/W2883195674","https://openalex.org/W2072736607","https://openalex.org/W3080374445","https://openalex.org/W3046682795","https://openalex.org/W2964790801"],"abstract_inverted_index":{"Identifying":[0],"multifunctional":[1,93],"therapeutic":[2,94],"peptides":[3],"(MFTP)":[4],"is":[5,102,126],"an":[6],"important":[7],"yet":[8],"complex":[9],"challenge":[10],"in":[11,160],"the":[12,39,50,87,98,118,145,154],"realm":[13],"of":[14,42,92],"peptide":[15,53,80,95,115],"recognition.":[16,162],"Unlike":[17],"monofunctional":[18],"peptides,":[19],"MFTP":[20,161],"classification":[21,66],"requires":[22],"discerning":[23],"fine-grained":[24],"labeling":[25],"information":[26,113],"associated":[27],"with":[28],"amino":[29],"acids,":[30],"making":[31],"it":[32],"more":[33],"intricate.":[34],"Existing":[35],"methods":[36,159],"often":[37],"ignore":[38],"nuanced":[40],"semantics":[41],"these":[43,60],"labels":[44],"and":[45,55,89,123],"fail":[46],"to":[47,78,104],"fully":[48],"explore":[49],"interplay":[51],"between":[52,120],"sequences":[54,81],"their":[56],"labels.":[57],"To":[58,132],"address":[59],"issues,":[61],"we":[62],"propose":[63],"a":[64,73,138],"multilabel":[65,139],"method":[67,71],"named":[68],"MultiPep-DLCL.":[69],"This":[70],"uses":[72],"deep":[74],"learning-based":[75],"model":[76],"architecture":[77],"translate":[79],"into":[82],"sequence":[83,121],"features":[84,122],"by":[85,110],"learning":[86],"local":[88],"global":[90],"dependencies":[91],"sequences.":[96,116],"Additionally,":[97],"Label-Sequence":[99],"Fusion":[100],"Transformer":[101],"employed":[103],"efficiently":[105],"learn":[106],"high-quality":[107],"label":[108,124],"embeddings":[109,125],"mining":[111],"effective":[112],"from":[114],"Finally,":[117],"correspondence":[119],"strengthened":[127],"through":[128],"label-sequence":[129],"contrastive":[130],"learning.":[131],"tackle":[133],"dataset":[134],"imbalance,":[135],"MultiPep-DLCL":[136,155],"integrates":[137],"focal":[140],"dice":[141],"loss":[142,148],"function":[143],"alongside":[144],"traditional":[146],"cross-entropy":[147],"function.":[149],"Experimental":[150],"results":[151],"demonstrate":[152],"that":[153],"significantly":[156],"outperforms":[157],"existing":[158]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}