{"id":"https://openalex.org/W7164855553","doi":"https://doi.org/10.1021/acs.jcim.6c01274","title":"An Interpretable Deep Learning Framework Leveraging RNA Foundation Model and Capsule Networks for Accurate Prediction of RNA 2\u2032-O-Methylation Sites","display_name":"An Interpretable Deep Learning Framework Leveraging RNA Foundation Model and Capsule Networks for Accurate Prediction of RNA 2\u2032-O-Methylation Sites","publication_year":2026,"publication_date":"2026-06-15","ids":{"openalex":"https://openalex.org/W7164855553","doi":"https://doi.org/10.1021/acs.jcim.6c01274","pmid":"https://pubmed.ncbi.nlm.nih.gov/42296393"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6c01274","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c01274","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100741399","display_name":"Feng Wang","orcid":"https://orcid.org/0000-0002-7547-3115"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"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"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Wang","raw_affiliation_strings":["The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","Xiamen University , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","institution_ids":["https://openalex.org/I4210116924"]},{"raw_affiliation_string":"Xiamen University , , ,","institution_ids":["https://openalex.org/I191208505","https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134150285","display_name":"Bowen Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bowen Shi","raw_affiliation_strings":["Xiamen University , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xiamen University , , ,","institution_ids":["https://openalex.org/I191208505","https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138680782","display_name":"Yuxuan Gu","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuxuan Gu","raw_affiliation_strings":["Xiamen University , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xiamen University , , ,","institution_ids":["https://openalex.org/I191208505","https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138678160","display_name":"Fangyi Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangyi Liu","raw_affiliation_strings":["Xiamen University , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xiamen University , , ,","institution_ids":["https://openalex.org/I191208505","https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138669453","display_name":"Zhihao Zhao","orcid":null},"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":"Zhihao Zhao","raw_affiliation_strings":["The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100644710","display_name":"Xingchen Liu","orcid":"https://orcid.org/0000-0002-5638-4053"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"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"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xingchen Liu","raw_affiliation_strings":["The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","Xiamen University , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","institution_ids":["https://openalex.org/I4210116924"]},{"raw_affiliation_string":"Xiamen University , , ,","institution_ids":["https://openalex.org/I191208505","https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006150874","display_name":"X Y Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"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"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangrong Liu","raw_affiliation_strings":["The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","Xiamen University , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","institution_ids":["https://openalex.org/I4210116924"]},{"raw_affiliation_string":"Xiamen University , , ,","institution_ids":["https://openalex.org/I191208505","https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002567070","display_name":"Tzong-Yi Lee","orcid":"https://orcid.org/0009-0002-0283-7712"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzong-Yi Lee","raw_affiliation_strings":["National Yang Ming Chiao Tung University , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Yang Ming Chiao Tung University , , ,","institution_ids":["https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033232360","display_name":"Leyi Wei","orcid":"https://orcid.org/0000-0003-1444-190X"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Leyi Wei","raw_affiliation_strings":["Macao Polytechnic University , , R. de Lui\u0301s Gonzaga Gomes , ,"],"raw_orcid":"https://orcid.org/0000-0003-1444-190X","affiliations":[{"raw_affiliation_string":"Macao Polytechnic University , , R. de Lui\u0301s Gonzaga Gomes , ,","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100597582","display_name":"Jiahui Guan","orcid":"https://orcid.org/0009-0007-2839-2199"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiahui Guan","raw_affiliation_strings":["The University of Hong Kong , , ,"],"raw_orcid":"https://orcid.org/0009-0001-0584-0637","affiliations":[{"raw_affiliation_string":"The University of Hong Kong , , ,","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101189636","display_name":"Peilin Xie","orcid":null},"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":"Peilin Xie","raw_affiliation_strings":["The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","institution_ids":["https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001619694","display_name":"Jijun Tang","orcid":"https://orcid.org/0000-0002-6377-536X"},"institutions":[{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jijun Tang","raw_affiliation_strings":["Shenzhen University of Advanced Technology , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen University of Advanced Technology , , ,","institution_ids":["https://openalex.org/I4210152380"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078222868","display_name":"Lantian Yao","orcid":"https://orcid.org/0000-0003-4554-6827"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lantian Yao","raw_affiliation_strings":["Shenzhen University of Advanced Technology , , ,","Xiamen University , , ,"],"raw_orcid":"https://orcid.org/0000-0003-4554-6827","affiliations":[{"raw_affiliation_string":"Shenzhen University of Advanced Technology , , ,","institution_ids":["https://openalex.org/I4210152380"]},{"raw_affiliation_string":"Xiamen University , , ,","institution_ids":["https://openalex.org/I191208505","https://openalex.org/I75867142"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5001619694","https://openalex.org/A5078222868","https://openalex.org/A5101189636"],"corresponding_institution_ids":["https://openalex.org/I191208505","https://openalex.org/I4210116924","https://openalex.org/I4210152380","https://openalex.org/I75867142"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.54899159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"15","first_page":"9651","last_page":"9662"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.4668000042438507,"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":0.4668000042438507,"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/T11482","display_name":"RNA modifications and cancer","score":0.2705000042915344,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.11240000277757645,"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/deep-learning","display_name":"Deep learning","score":0.758400022983551},{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.6288999915122986},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5139999985694885},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.3605000078678131},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.3061000108718872},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.30230000615119934}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.758400022983551},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.728600025177002},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.6288999915122986},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5860999822616577},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5139999985694885},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4065000116825104},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3605000078678131},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32199999690055847},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3061000108718872},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.30230000615119934},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29679998755455017},{"id":"https://openalex.org/C97385483","wikidata":"https://www.wikidata.org/wiki/Q16954980","display_name":"Deep belief network","level":3,"score":0.27219998836517334},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.2712000012397766},{"id":"https://openalex.org/C2778778583","wikidata":"https://www.wikidata.org/wiki/Q147768","display_name":"Capsule","level":2,"score":0.2644999921321869},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.25440001487731934},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.251800000667572}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000097906","descriptor_name":"RNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6c01274","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c01274","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:42296393","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42296393","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":"Journal of chemical information and modeling","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1951464544","display_name":null,"funder_award_id":"JCYJ20241202130212016","funder_id":"https://openalex.org/F4320317337","funder_display_name":"Science and Technology Foundation of Shenzhen City"},{"id":"https://openalex.org/G3021355719","display_name":null,"funder_award_id":"12426303","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3075931670","display_name":null,"funder_award_id":"U24A20257","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4009424769","display_name":null,"funder_award_id":"62272449","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5833155303","display_name":null,"funder_award_id":"20720250172","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G6093574916","display_name":null,"funder_award_id":"CKL075","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"}],"funders":[{"id":"https://openalex.org/F4320317337","display_name":"Science and Technology Foundation of Shenzhen City","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320325434","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785"},{"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":39,"referenced_works":["https://openalex.org/W1935366897","https://openalex.org/W2098475202","https://openalex.org/W2099866950","https://openalex.org/W2132866668","https://openalex.org/W2156125289","https://openalex.org/W2379683068","https://openalex.org/W2546967042","https://openalex.org/W2608271600","https://openalex.org/W2612024267","https://openalex.org/W2612631240","https://openalex.org/W2627064270","https://openalex.org/W2794905676","https://openalex.org/W2886373325","https://openalex.org/W2900837507","https://openalex.org/W2906046752","https://openalex.org/W2950270741","https://openalex.org/W2976711440","https://openalex.org/W2997945489","https://openalex.org/W3162235259","https://openalex.org/W3213133098","https://openalex.org/W3217082130","https://openalex.org/W4225725937","https://openalex.org/W4229801112","https://openalex.org/W4306793037","https://openalex.org/W4308697814","https://openalex.org/W4317033517","https://openalex.org/W4361276057","https://openalex.org/W4380591223","https://openalex.org/W4386209832","https://openalex.org/W4386766251","https://openalex.org/W4388622785","https://openalex.org/W4390621086","https://openalex.org/W4393384192","https://openalex.org/W4400060796","https://openalex.org/W4402623328","https://openalex.org/W4404595545","https://openalex.org/W4411388993","https://openalex.org/W4411886797","https://openalex.org/W4412712644"],"related_works":[],"abstract_inverted_index":{"RNA":[0,10,194],"2'-O-methylation":[1],"(2OMe)":[2],"is":[3],"a":[4,49,84,126,146,185],"widespread":[5],"post-transcriptional":[6],"modification":[7],"that":[8,47,154],"influences":[9],"stability,":[11],"translation,":[12],"and":[13,33,58,71,81,98,117,145,176,183,196],"immune":[14],"recognition.":[15],"Yet,":[16],"accurate":[17,175],"computational":[18,110,191],"identification":[19],"of":[20,96,101,129,193],"2OMe":[21,89,180],"sites":[22],"remains":[23],"challenging":[24],"because":[25],"conventional":[26],"sequence":[27,35,60,69,138,149],"encodings":[28],"incompletely":[29],"capture":[30,67],"contextual":[31],"dependencies":[32],"higher-order":[34],"patterns.":[36],"Here,":[37],"we":[38],"present":[39],"Caps-2OMe,":[40],"an":[41,63,94,99,141,174],"interpretable":[42,177],"multimodal":[43],"deep":[44],"learning":[45],"framework":[46,178,187],"combines":[48],"Chaos":[50],"Game":[51],"Representation":[52],"(CGR)":[53],"branch":[54,65],"to":[55,66],"encode":[56],"positional":[57],"compositional":[59],"patterns":[61],"with":[62],"RNA-FM":[64],"context-aware":[68],"representations":[70],"long-range":[72],"dependencies.":[73],"The":[74],"two":[75],"feature":[76],"streams":[77],"are":[78],"adaptively":[79],"fused":[80],"decoded":[82],"by":[83],"capsule-based":[85],"architecture":[86],"for":[87,179,188],"robust":[88],"site":[90,181],"prediction.":[91],"Caps-2OMe":[92,172],"achieved":[93],"accuracy":[95],"0.936":[97],"AUC":[100],"0.987":[102],"on":[103],"the":[104,155,190],"independent":[105],"test":[106],"set,":[107],"outperforming":[108],"existing":[109],"predictors.":[111],"Capsule-level":[112],"analyses":[113],"further":[114,134],"revealed":[115,135],"sparse":[116],"class-specific":[118],"routing":[119],"patterns,":[120],"while":[121],"digit":[122],"capsule":[123],"length":[124],"provided":[125],"meaningful":[127,137],"estimate":[128],"prediction":[130,182],"confidence.":[131],"Motif":[132],"analysis":[133],"biologically":[136],"signatures,":[139],"including":[140],"AGAUC-like":[142],"dominant":[143],"motif":[144],"CU-enriched":[147],"local":[148],"context.":[150],"Cross-nucleotide":[151],"evaluation":[152],"showed":[153],"general":[156],"model":[157],"remained":[158],"stable":[159],"across":[160],"four":[161],"subsets,":[162],"whereas":[163],"subtype-specific":[164],"models":[165],"exhibited":[166],"limited":[167],"transferability.":[168],"These":[169],"results":[170],"establish":[171],"as":[173],"provide":[184],"useful":[186],"advancing":[189],"study":[192],"modifications":[195],"their":[197],"regulatory":[198],"roles.":[199]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-16T00:00:00"}