{"id":"https://openalex.org/W4416250423","doi":"https://doi.org/10.1109/ijcnn64981.2025.11229384","title":"XGBoost6mA: A Framework for 6mA Site Prediction Based on Deep Learning and XGBoost","display_name":"XGBoost6mA: A Framework for 6mA Site Prediction Based on Deep Learning and XGBoost","publication_year":2025,"publication_date":"2025-06-30","ids":{"openalex":"https://openalex.org/W4416250423","doi":"https://doi.org/10.1109/ijcnn64981.2025.11229384"},"language":null,"primary_location":{"id":"doi:10.1109/ijcnn64981.2025.11229384","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn64981.2025.11229384","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 International Joint Conference on Neural Networks (IJCNN)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100820808","display_name":"Zhixiang Xu","orcid":"https://orcid.org/0000-0003-4713-5124"},"institutions":[{"id":"https://openalex.org/I107982497","display_name":"Dalian Ocean University","ror":"https://ror.org/0523b6g79","country_code":"CN","type":"education","lineage":["https://openalex.org/I107982497"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhixiang Xu","raw_affiliation_strings":["Dalian University of Technology,School of Chemical Engineering Ocean and Life Sciences,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Chemical Engineering Ocean and Life Sciences,Dalian,China","institution_ids":["https://openalex.org/I107982497"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113976548","display_name":"Jiaxin Zhong","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxin Zhong","raw_affiliation_strings":["Dalian University of Technology,School of Software,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Software,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108046713","display_name":"Wen Wen","orcid":"https://orcid.org/0009-0004-5309-6373"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen Wen","raw_affiliation_strings":["Dalian University of Technology,School of Software,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Software,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111196692","display_name":"Yufei Bao","orcid":null},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yufei Bao","raw_affiliation_strings":["The University of Sydney,Sydney,Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Sydney,Sydney,Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055305202","display_name":"Xiaoya Fan","orcid":"https://orcid.org/0000-0002-5002-6968"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoya Fan","raw_affiliation_strings":["Dalian University of Technology,School of Software,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Software,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113094343","display_name":"Xiangtao Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I154093214","display_name":"Xinjiang Medical University","ror":"https://ror.org/01p455v08","country_code":"CN","type":"education","lineage":["https://openalex.org/I154093214"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtao Liu","raw_affiliation_strings":["Xinjiang Medical University,College of Medical Engineering and Technology,Ürümqi,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xinjiang Medical University,College of Medical Engineering and Technology,Ürümqi,China","institution_ids":["https://openalex.org/I154093214"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100435261","display_name":"Zhong Wang","orcid":"https://orcid.org/0000-0001-8399-2575"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhong Wang","raw_affiliation_strings":["Dalian University of Technology,School of Software,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Software,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.7046999931335449,"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":0.7046999931335449,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.1242000013589859,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.03200000151991844,"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/interpretability","display_name":"Interpretability","score":0.910099983215332},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6833999752998352},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6646000146865845},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4797999858856201},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4690000116825104},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.45190000534057617},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.4106999933719635},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.40149998664855957}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.910099983215332},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7782999873161316},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6912999749183655},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6833999752998352},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6646000146865845},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6261000037193298},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4797999858856201},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4690000116825104},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.45190000534057617},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.4106999933719635},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.40149998664855957},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3546999990940094},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.31619998812675476},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.3156999945640564},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3028999865055084},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.2976999878883362},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2964000105857849},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.29159998893737793},{"id":"https://openalex.org/C110332635","wikidata":"https://www.wikidata.org/wiki/Q629498","display_name":"Genetic programming","level":2,"score":0.2831000089645386},{"id":"https://openalex.org/C2779585090","wikidata":"https://www.wikidata.org/wiki/Q3457762","display_name":"Resilience (materials science)","level":2,"score":0.2809000015258789},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.28049999475479126},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.25999999046325684}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/ijcnn64981.2025.11229384","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn64981.2025.11229384","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 International Joint Conference on Neural Networks (IJCNN)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1974527579","https://openalex.org/W1984783889","https://openalex.org/W1987735941","https://openalex.org/W2084200091","https://openalex.org/W2102589447","https://openalex.org/W2129329277","https://openalex.org/W2132341951","https://openalex.org/W2414319411","https://openalex.org/W2564664392","https://openalex.org/W2737196618","https://openalex.org/W2898871895","https://openalex.org/W2910591656","https://openalex.org/W2944682099","https://openalex.org/W2979999916","https://openalex.org/W2999309192","https://openalex.org/W3011537067","https://openalex.org/W3011553090","https://openalex.org/W3034527519","https://openalex.org/W3084754935","https://openalex.org/W3128244560","https://openalex.org/W3130800274","https://openalex.org/W3204213738","https://openalex.org/W3216660278","https://openalex.org/W4210371902","https://openalex.org/W4220924661","https://openalex.org/W4313530678","https://openalex.org/W4318985501"],"related_works":[],"abstract_inverted_index":{"N6-methyladenine":[0],"(6mA)":[1],"is":[2,169],"a":[3,43,157],"crucial":[4],"epigenetic":[5],"regulator":[6],"involved":[7],"in":[8,110,150],"various":[9],"biological":[10,138],"processes.":[11],"Existing":[12],"high-throughput":[13],"methods":[14],"like":[15],"6mA-DIP-seq,":[16],"ChIP-exo/6mACE-seq,":[17],"SMRT-seq,":[18],"and":[19,30,36,49,64,74,92,133,153],"nanopore":[20],"sequencing":[21],"offer":[22],"high":[23],"accuracy":[24],"but":[25],"are":[26],"typically":[27],"time-consuming,":[28],"labor-intensive,":[29],"expensive.":[31],"To":[32,98,162],"address":[33],"these":[34],"limitations":[35],"promote":[37],"6mA":[38,151],"research,":[39,165],"we":[40,102],"introduce":[41],"XGBoost6mA,":[42],"predictive":[44],"framework":[45,71],"integrating":[46],"deep":[47,56],"learning":[48],"XGBoost.":[50],"XGBoost6mA":[51,87,104,126,149],"utilizes":[52],"XGBoost":[53],"to":[54,121],"classify":[55],"learning-derived":[57],"sequence":[58,123],"features,":[59],"effectively":[60],"capturing":[61],"nonlinear":[62],"patterns":[63],"improving":[65],"classification":[66],"performance.":[67],"We":[68],"evaluated":[69],"the":[70,137,146],"using":[72],"BERT6mA":[73,91],"CNN6mA":[75,93],"feature":[76],"extractors":[77],"on":[78],"benchmark":[79],"datasets":[80],"from":[81],"11":[82],"species.":[83,97],"Results":[84],"showed":[85],"that":[86],"consistently":[88],"outperformed":[89],"both":[90],"across":[94],"all":[95],"tested":[96,103],"validate":[99],"its":[100,141,154],"robustness,":[101],"by":[105,129],"introducing":[106],"random":[107],"nucleotide":[108],"mutations":[109],"test":[111],"sequences.":[112],"The":[113],"model":[114],"maintained":[115],"stable":[116],"accuracy,":[117],"indicating":[118],"strong":[119],"resilience":[120],"small":[122],"variations.":[124],"Additionally,":[125],"offers":[127],"interpretability":[128],"pinpointing":[130],"key":[131],"k-mers":[132],"positional":[134],"factors,":[135],"enhancing":[136],"significance":[139],"of":[140,148],"predictions.":[142],"These":[143],"findings":[144],"underscore":[145],"advantages":[147],"prediction":[152],"promise":[155],"as":[156],"widely":[158],"applicable":[159],"bioinformatics":[160],"tool.":[161],"support":[163],"future":[164],"XGBoost6mA\u2019s":[166],"source":[167],"code":[168],"publicly":[170],"available":[171],"at":[172],"https://github.com/xzx0554/xgboost6ma.":[173]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-11-14T00:00:00"}