{"id":"https://openalex.org/W4387910306","doi":"https://doi.org/10.46793/match.91-1.109z","title":"AMP-EF: An Ensemble Framework of Extreme Gradient Boosting and Bidirectional Long Short-Term Memory Network for Identifying Antimicrobial Peptides","display_name":"AMP-EF: An Ensemble Framework of Extreme Gradient Boosting and Bidirectional Long Short-Term Memory Network for Identifying Antimicrobial Peptides","publication_year":2023,"publication_date":"2023-10-01","ids":{"openalex":"https://openalex.org/W4387910306","doi":"https://doi.org/10.46793/match.91-1.109z"},"language":"en","primary_location":{"id":"doi:10.46793/match.91-1.109z","doi":"https://doi.org/10.46793/match.91-1.109z","is_oa":true,"landing_page_url":"https://doi.org/10.46793/match.91-1.109z","pdf_url":"https://match.pmf.kg.ac.rs/electronic_versions/Match91/n1/match91n1_109-131.pdf","source":{"id":"https://openalex.org/S4210170887","display_name":"match Communications in Mathematical and in Computer Chemistry","issn_l":"0340-6253","issn":["0340-6253","3009-4399"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310321452","host_organization_name":"University of Kragujevac","host_organization_lineage":["https://openalex.org/P4310321452"],"host_organization_lineage_names":["University of Kragujevac"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Match - Communications in Mathematical and in Computer Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://match.pmf.kg.ac.rs/electronic_versions/Match91/n1/match91n1_109-131.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100413412","display_name":"Shengli Zhang","orcid":"https://orcid.org/0000-0001-8786-0940","observed_orcids":["https://orcid.org/0000-0001-8786-0940"]},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]},{"id":"https://openalex.org/I27599042","display_name":"Xi'an Polytechnic University","ror":"https://ror.org/03442p831","country_code":"CN","type":"education","lineage":["https://openalex.org/I27599042"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shengli Zhang","raw_affiliation_strings":["Application of Hainan Province, Haikou, 571158, China","\ud835\udc4e School of Mathematics and Statistics, Xidian University, Xi'an 710071, P. R. China \ud835\udc4f Key Laboratory of Computational Science and","\ud835\udc50 School of Science, Xi'an Polytechnic University, Xi'an 710048, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Application of Hainan Province, Haikou, 571158, China","institution_ids":[]},{"raw_affiliation_string":"\ud835\udc4e School of Mathematics and Statistics, Xidian University, Xi'an 710071, P. R. China \ud835\udc4f Key Laboratory of Computational Science and","institution_ids":["https://openalex.org/I149594827"]},{"raw_affiliation_string":"\ud835\udc50 School of Science, Xi'an Polytechnic University, Xi'an 710048, P. R. China","institution_ids":["https://openalex.org/I27599042"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101259241","display_name":"Ya Zhao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]},{"id":"https://openalex.org/I27599042","display_name":"Xi'an Polytechnic University","ror":"https://ror.org/03442p831","country_code":"CN","type":"education","lineage":["https://openalex.org/I27599042"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ya Zhao","raw_affiliation_strings":["Key Laboratory of Computational Science and Application of Hainan Province , Haikou , 571158 , China","\ud835\udc4e School of Mathematics and Statistics , Xidian University , Xi'an 710071 , P. R. China \ud835\udc4f","Application of Hainan Province, Haikou, 571158, China","\ud835\udc4e School of Mathematics and Statistics, Xidian University, Xi'an 710071, P. R. China \ud835\udc4f Key Laboratory of Computational Science and","\ud835\udc50 School of Science, Xi'an Polytechnic University, Xi'an 710048, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Computational Science and Application of Hainan Province , Haikou , 571158 , China","institution_ids":[]},{"raw_affiliation_string":"\ud835\udc4e School of Mathematics and Statistics , Xidian University , Xi'an 710071 , P. R. China \ud835\udc4f","institution_ids":["https://openalex.org/I149594827"]},{"raw_affiliation_string":"Application of Hainan Province, Haikou, 571158, China","institution_ids":[]},{"raw_affiliation_string":"\ud835\udc4e School of Mathematics and Statistics, Xidian University, Xi'an 710071, P. R. China \ud835\udc4f Key Laboratory of Computational Science and","institution_ids":["https://openalex.org/I149594827"]},{"raw_affiliation_string":"\ud835\udc50 School of Science, Xi'an Polytechnic University, Xi'an 710048, P. R. China","institution_ids":["https://openalex.org/I27599042"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008784102","display_name":"Yunyun Liang","orcid":"https://orcid.org/0000-0002-1749-564X","observed_orcids":["https://orcid.org/0000-0002-1749-564X"]},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]},{"id":"https://openalex.org/I27599042","display_name":"Xi'an Polytechnic University","ror":"https://ror.org/03442p831","country_code":"CN","type":"education","lineage":["https://openalex.org/I27599042"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunyun Liang","raw_affiliation_strings":["School of Science , Xi'an Polytechnic University , Xi'an 710048 , P. R. China","Application of Hainan Province, Haikou, 571158, China","\ud835\udc4e School of Mathematics and Statistics, Xidian University, Xi'an 710071, P. R. China \ud835\udc4f Key Laboratory of Computational Science and","\ud835\udc50 School of Science, Xi'an Polytechnic University, Xi'an 710048, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science , Xi'an Polytechnic University , Xi'an 710048 , P. R. China","institution_ids":["https://openalex.org/I27599042"]},{"raw_affiliation_string":"Application of Hainan Province, Haikou, 571158, China","institution_ids":[]},{"raw_affiliation_string":"\ud835\udc4e School of Mathematics and Statistics, Xidian University, Xi'an 710071, P. R. China \ud835\udc4f Key Laboratory of Computational Science and","institution_ids":["https://openalex.org/I149594827"]},{"raw_affiliation_string":"\ud835\udc50 School of Science, Xi'an Polytechnic University, Xi'an 710048, P. R. China","institution_ids":["https://openalex.org/I27599042"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100413412"],"corresponding_institution_ids":["https://openalex.org/I149594827","https://openalex.org/I27599042"],"apc_list":null,"apc_paid":null,"fwci":1.4011,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.76085392,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"91","issue":"1","first_page":"109","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.948199987411499,"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":0.948199987411499,"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":0.03689999878406525,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0015999999595806003,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/antimicrobial-peptides","display_name":"antimicrobial peptides","score":0.9919999837875366},{"id":"https://openalex.org/keywords/peptide-sequence-classification","display_name":"peptide sequence classification","score":0.6000000238418579},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"ensemble learning","score":0.8059999942779541},{"id":"https://openalex.org/keywords/xgboost","display_name":"XGBoost","score":0.8510000109672546},{"id":"https://openalex.org/keywords/bidirectional-lstm","display_name":"bidirectional LSTM","score":0.9940000176429749},{"id":"https://openalex.org/keywords/attention-mechanism","display_name":"attention mechanism","score":0.9990000128746033},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"antibiotic resistance","score":0.699999988079071},{"id":"https://openalex.org/keywords/k-mer-features","display_name":"k-mer features","score":0.5730000138282776}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6223335862159729},{"id":"https://openalex.org/C540938839","wikidata":"https://www.wikidata.org/wiki/Q1201508","display_name":"Antimicrobial peptides","level":3,"score":0.5727939605712891},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5572272539138794},{"id":"https://openalex.org/C119898033","wikidata":"https://www.wikidata.org/wiki/Q3433888","display_name":"Ensemble forecasting","level":2,"score":0.5261568427085876},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.4919581115245819},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.46431446075439453},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.44498211145401},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41478702425956726},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32379865646362305},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.28284013271331787},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19306862354278564},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15809258818626404},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07664540410041809},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.46793/match.91-1.109z","doi":"https://doi.org/10.46793/match.91-1.109z","is_oa":true,"landing_page_url":"https://doi.org/10.46793/match.91-1.109z","pdf_url":"https://match.pmf.kg.ac.rs/electronic_versions/Match91/n1/match91n1_109-131.pdf","source":{"id":"https://openalex.org/S4210170887","display_name":"match Communications in Mathematical and in Computer Chemistry","issn_l":"0340-6253","issn":["0340-6253","3009-4399"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310321452","host_organization_name":"University of Kragujevac","host_organization_lineage":["https://openalex.org/P4310321452"],"host_organization_lineage_names":["University of Kragujevac"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Match - Communications in Mathematical and in Computer Chemistry","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.46793/match.91-1.109z","doi":"https://doi.org/10.46793/match.91-1.109z","is_oa":true,"landing_page_url":"https://doi.org/10.46793/match.91-1.109z","pdf_url":"https://match.pmf.kg.ac.rs/electronic_versions/Match91/n1/match91n1_109-131.pdf","source":{"id":"https://openalex.org/S4210170887","display_name":"match Communications in Mathematical and in Computer Chemistry","issn_l":"0340-6253","issn":["0340-6253","3009-4399"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310321452","host_organization_name":"University of Kragujevac","host_organization_lineage":["https://openalex.org/P4310321452"],"host_organization_lineage_names":["University of Kragujevac"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Match - Communications in Mathematical and in Computer Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1692094660","display_name":null,"funder_award_id":"12101480","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3713867002","display_name":null,"funder_award_id":"QTZX23002","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387910306.pdf","grobid_xml":"https://content.openalex.org/works/W4387910306.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1978444624","https://openalex.org/W2015490529","https://openalex.org/W2128495797","https://openalex.org/W2129115651","https://openalex.org/W2152380569","https://openalex.org/W2156125289","https://openalex.org/W2163878064","https://openalex.org/W2175270296","https://openalex.org/W2252278563","https://openalex.org/W2295598076","https://openalex.org/W2339719866","https://openalex.org/W2774174188","https://openalex.org/W2791848964","https://openalex.org/W2807001312","https://openalex.org/W2898355747","https://openalex.org/W2899153547","https://openalex.org/W2905629607","https://openalex.org/W2965128681","https://openalex.org/W2981572887","https://openalex.org/W2984592028","https://openalex.org/W2998197489","https://openalex.org/W3013450562","https://openalex.org/W3025501158","https://openalex.org/W3036144909","https://openalex.org/W3043115370","https://openalex.org/W3080137602","https://openalex.org/W3087692915","https://openalex.org/W3094708881","https://openalex.org/W3136366652","https://openalex.org/W3139686515","https://openalex.org/W3150808126","https://openalex.org/W3204692337","https://openalex.org/W4206358548","https://openalex.org/W4210686463","https://openalex.org/W4212839884","https://openalex.org/W4213430678","https://openalex.org/W4226148785","https://openalex.org/W4295745509","https://openalex.org/W4296977048","https://openalex.org/W4308370073","https://openalex.org/W4309409056","https://openalex.org/W4322627134","https://openalex.org/W6601630192","https://openalex.org/W6603257565"],"related_works":["https://openalex.org/W4390828734","https://openalex.org/W4225373802","https://openalex.org/W4404620945","https://openalex.org/W3113147805","https://openalex.org/W3134555241","https://openalex.org/W7126060876","https://openalex.org/W4408147599","https://openalex.org/W4392966685","https://openalex.org/W4311594423","https://openalex.org/W4400396940"],"abstract_inverted_index":{"In":[0,46],"recent":[1],"years,":[2],"bacterial":[3],"resistance":[4],"becomes":[5],"a":[6,49,76],"serious":[7],"problem":[8],"due":[9],"to":[10,25,31,55,74,86,103,131,143,147],"the":[11,22,42,88,92,98,109,119,151,156,172,204],"abuse":[12],"of":[13,28,118,133,180],"antibiotics.":[14],"Antimicrobial":[15],"peptides":[16],"(AMPs)":[17],"have":[18],"rapidly":[19,32],"emerged":[20],"as":[21],"best":[23],"alternative":[24],"antibiotics":[26],"because":[27],"their":[29],"ability":[30],"target":[33],"bacteria,":[34],"fungi,":[35],"viruses,":[36],"and":[37,40,64,82,128,145,188,198,210,216],"cancer":[38],"cells":[39],"counteract":[41],"toxins":[43],"they":[44],"produce.":[45],"this":[47],"study,":[48],"two-branch":[50,205],"ensemble":[51,206],"framework":[52],"is":[53,154,208],"proposed":[54],"identify":[56],"AMPs,":[57],"which":[58],"integrates":[59],"extreme":[60],"gradient":[61],"boosting":[62],"(XGBoost)":[63],"bidirectional":[65],"long":[66],"short-term":[67],"memory":[68],"network":[69],"(Bi-LSTM)":[70],"with":[71],"attention":[72],"mechanism":[73],"form":[75],"stronger":[77],"model.":[78],"First,":[79],"one-hot":[80],"coding":[81],"-mer":[83],"are":[84,95,112,190,218],"used":[85],"represent":[87],"sequence":[89],"features.":[90],"Then,":[91],"feature":[93],"vectors":[94],"input":[96],"into":[97],"two":[99,105],"base":[100],"classifiers":[101],"respectively":[102],"obtain":[104],"predicted":[106],"values.":[107],"Finally,":[108],"prediction":[110],"results":[111,170],"obtained":[113],"by":[114],"compromise.":[115],"As":[116,150],"one":[117],"classical":[120],"machine":[121],"learning":[122],"methods,":[123],"XGBoost":[124],"has":[125,211],"strong":[126,212],"stability":[127],"can":[129,158],"adapt":[130],"datasets":[132,217],"different":[134],"sizes.":[135],"Bi-LSTM":[136],"recurses":[137],"for":[138],"each":[139],"peptide":[140],"from":[141],"N-terminal":[142],"C-terminal":[144,146],"N-terminal,":[148],"respectively.":[149,200],"context":[152],"information":[153],"provided,":[155],"model":[157],"make":[159],"more":[160],"accurate":[161],"prediction.":[162],"Our":[163],"method":[164],"achieves":[165],"higher":[166],"or":[167],"highly":[168],"comparable":[169],"across":[171],"eight":[173],"independent":[174],"test":[175],"datasets.":[176],"The":[177,214],"ACC":[178],"values":[179],"XUAMP,":[181],"YADAMP,":[182],"DRAMP,":[183],"CAMP,":[184],"LAMP,":[185],"APD3,":[186],"dbAMP,":[187],"DBAASP":[189],"77.9%,":[191],"98.5%,":[192],"72.5%,":[193],"99.8%,":[194],"83.0%,":[195],"92.4%,":[196],"87.5%,":[197],"84.6%,":[199],"This":[201],"shows":[202],"that":[203],"structure":[207],"feasible":[209],"generalization.":[213],"codes":[215],"accessible":[219],"at":[220],"https://github.com/z11code/AMP-EF.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2023-10-25T00:00:00"}