{"id":"https://openalex.org/W7129021560","doi":"https://doi.org/10.1093/bioinformatics/btag077","title":"A dual diffusion model-based representation learning framework for antimicrobial peptides classification","display_name":"A dual diffusion model-based representation learning framework for antimicrobial peptides classification","publication_year":2026,"publication_date":"2026-02-11","ids":{"openalex":"https://openalex.org/W7129021560","doi":"https://doi.org/10.1093/bioinformatics/btag077","pmid":"https://pubmed.ncbi.nlm.nih.gov/41692989"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag077","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag077","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111863642","display_name":"Wen Kong","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen Kong","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126157173","display_name":"Lingling Fu","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingling Fu","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126075749","display_name":"Xingpeng Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xingpeng Jiang","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,","National Language Resources Monitoring & Research Center for Network Media, Central China Normal University , Wuhan, Hubei 430089,","School of Computer, Central China Normal University , Wuhan, Hubei 430089,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"National Language Resources Monitoring & Research Center for Network Media, Central China Normal University , Wuhan, Hubei 430089,","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"School of Computer, Central China Normal University , Wuhan, Hubei 430089,","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5121420414","display_name":"Weizhong Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Weizhong Zhao","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,","National Language Resources Monitoring & Research Center for Network Media, Central China Normal University , Wuhan, Hubei 430089,","School of Computer, Central China Normal University , Wuhan, Hubei 430089,"],"raw_orcid":"https://orcid.org/0000-0001-8552-6084","affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079,","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"National Language Resources Monitoring & Research Center for Network Media, Central China Normal University , Wuhan, Hubei 430089,","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"School of Computer, Central China Normal University , Wuhan, Hubei 430089,","institution_ids":["https://openalex.org/I40963666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5121420414","https://openalex.org/A5126075749"],"corresponding_institution_ids":["https://openalex.org/I40963666"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.15970904,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","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":0.9805999994277954,"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":0.9805999994277954,"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":0.003700000001117587,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.0026000000070780516,"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/representation","display_name":"Representation (politics)","score":0.6412000060081482},{"id":"https://openalex.org/keywords/dual","display_name":"Dual (grammatical number)","score":0.6218000054359436},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.4138000011444092},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3650999963283539},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3626999855041504},{"id":"https://openalex.org/keywords/external-data-representation","display_name":"External Data Representation","score":0.3034999966621399}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.737500011920929},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6412000060081482},{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.6218000054359436},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5616999864578247},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.4138000011444092},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39250001311302185},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3650999963283539},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3626999855041504},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3513000011444092},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3224000036716461},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.31209999322891235},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.3034999966621399},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.29190000891685486},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.2849000096321106},{"id":"https://openalex.org/C84750791","wikidata":"https://www.wikidata.org/wiki/Q3427408","display_name":"Dual representation","level":3,"score":0.27559998631477356},{"id":"https://openalex.org/C2982736386","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Statistical learning","level":2,"score":0.271699994802475}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000089882","descriptor_name":"Antimicrobial Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000098409","descriptor_name":"Representation Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098409","descriptor_name":"Representation Machine Learning","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag077","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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:41692989","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41692989","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:12960902","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12960902/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12960902/pdf/btag077.pdf","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/btag077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag077","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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":[],"awards":[{"id":"https://openalex.org/G2235372276","display_name":null,"funder_award_id":"62472192","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G235156935","display_name":null,"funder_award_id":"62372205","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1973742248","https://openalex.org/W2043338013","https://openalex.org/W2053069893","https://openalex.org/W2118020555","https://openalex.org/W2133056039","https://openalex.org/W2143210482","https://openalex.org/W3094708881","https://openalex.org/W3214417866","https://openalex.org/W4205773061","https://openalex.org/W4225665657","https://openalex.org/W4285597312","https://openalex.org/W4308370073","https://openalex.org/W4310641985","https://openalex.org/W4322718303","https://openalex.org/W4383273076","https://openalex.org/W4386590253","https://openalex.org/W4389450648","https://openalex.org/W4392405811","https://openalex.org/W4399328472","https://openalex.org/W4400060951","https://openalex.org/W4400520514","https://openalex.org/W4400834721","https://openalex.org/W4405290485","https://openalex.org/W4405622764"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,176],"increasing":[2],"prevalence":[3],"of":[4,34,145,158,169],"antibiotic-resistant":[5],"bacteria":[6],"has":[7],"intensified":[8],"the":[9,32,75,107,141,156,167],"demand":[10],"for":[11,58,74,114,155],"novel":[12,170],"antimicrobial":[13,171],"agents.":[14,172],"Antimicrobial":[15],"peptides":[16],"(AMPs)":[17],"have":[18],"emerged":[19],"as":[20],"promising":[21],"alternatives,":[22],"yet":[23],"their":[24],"identification":[25],"or":[26],"classification":[27],"remains":[28],"challenging":[29],"due":[30],"to":[31,70,120,138,165],"lack":[33],"multi-perspective":[35],"information,":[36],"insufficient":[37],"feature":[38,83,97],"representation":[39,55,105,142],"learning,":[40,106],"and":[41,67,90,116,132,178],"monocular":[42],"data":[43,177],"modalities.":[44,127],"RESULTS:":[45],"In":[46,128],"this":[47],"paper,":[48],"we":[49],"propose":[50],"a":[51,81,162],"dual":[52,126],"diffusion":[53,112],"model-based":[54],"learning":[56,135],"framework":[57,109],"classifying":[59],"AMPs,":[60],"which":[61,86],"effectively":[62,121],"integrates":[63],"both":[64,111,130],"peptide":[65,88],"sequence":[66,115],"structure":[68,117],"information":[69,118],"address":[71],"existing":[72,153],"issues":[73],"task.":[76],"Specifically,":[77],"our":[78,150],"approach":[79],"utilizes":[80],"multi-view":[82],"construction":[84],"module,":[85],"encodes":[87],"sequences":[89],"structures":[91],"from":[92,125],"distinctive":[93],"perspectives,":[94],"deriving":[95],"initial":[96],"representations":[98],"with":[99],"enriched":[100],"biological":[101],"semantics.":[102],"To":[103],"enhance":[104],"proposed":[108],"leverages":[110],"models":[113],"respectively":[119],"capture":[122],"complex":[123],"semantics":[124],"addition,":[129],"single-modal":[131],"dual-modal":[133],"contrastive":[134],"are":[136,181],"used":[137],"further":[139],"advance":[140],"learning.":[143],"Results":[144],"comprehensive":[146],"experiments":[147],"demonstrate":[148],"that":[149],"model":[151],"outperforms":[152],"methods":[154],"task":[157],"AMPs":[159],"classification,":[160],"providing":[161],"feasible":[163],"solution":[164],"accelerating":[166],"discovery":[168],"AVAILABILITY":[173],"OF":[174],"IMPLEMENTATION:":[175],"source":[179],"codes":[180],"available":[182],"in":[183],"GitHub":[184],"at":[185],"https://github.com/kww567upup/DDM.":[186]},"counts_by_year":[],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2026-02-17T00:00:00"}
