{"id":"https://openalex.org/W4390992007","doi":"https://doi.org/10.1109/bibm58861.2023.10385694","title":"DARE: Sequence-Structure Dual-Aware Encoder for RNA-Protein Binding Prediction","display_name":"DARE: Sequence-Structure Dual-Aware Encoder for RNA-Protein Binding Prediction","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992007","doi":"https://doi.org/10.1109/bibm58861.2023.10385694"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385694","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385694","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pure.ulster.ac.uk/ws/files/135696597/BIBM2023-B2106.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102606311","display_name":"Luhan Shen","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Luhan Shen","raw_affiliation_strings":["Sichuan University,School of Computer Science,Chengdu,China","School of Computer Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sichuan University,School of Computer Science,Chengdu,China","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"School of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039550320","display_name":"Chengxin He","orcid":"https://orcid.org/0000-0003-3759-3914"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chengxin He","raw_affiliation_strings":["Sichuan University,School of Computer Science,Chengdu,China","School of Computer Science, Sichuan University, Chengdu, China","Med-X Center for Informatics, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sichuan University,School of Computer Science,Chengdu,China","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"School of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]},{"raw_affiliation_string":"Med-X Center for Informatics, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100379058","display_name":"Haiying Wang","orcid":"https://orcid.org/0000-0001-8358-9065"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Haiying Wang","raw_affiliation_strings":["Ulster University,School of Computing,United Kingdom","School of Computing, Ulster University, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ulster University,School of Computing,United Kingdom","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Computing, Ulster University, United Kingdom","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042699641","display_name":"Yuening Qu","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuening Qu","raw_affiliation_strings":["Sichuan University,School of Computer Science,Chengdu,China","School of Computer Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sichuan University,School of Computer Science,Chengdu,China","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"School of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103153652","display_name":"Lei Duan","orcid":"https://orcid.org/0000-0001-7254-1832"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Duan","raw_affiliation_strings":["Sichuan University,School of Computer Science,Chengdu,China","Med-X Center for Informatics, Sichuan University, Chengdu, China","School of Computer Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sichuan University,School of Computer Science,Chengdu,China","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"Med-X Center for Informatics, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"School of Computer Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"128","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9994999766349792,"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":0.9990000128746033,"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/computer-science","display_name":"Computer science","score":0.687680184841156},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5784786343574524},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.563206672668457},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5538095235824585},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.5430885553359985},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5396326780319214},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5359585881233215},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.4817942976951599},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.47737953066825867},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.4493013024330139},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40230679512023926},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3400803804397583},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33206266164779663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11918208003044128},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0732046365737915},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07028847932815552}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.687680184841156},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5784786343574524},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.563206672668457},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5538095235824585},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.5430885553359985},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5396326780319214},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5359585881233215},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.4817942976951599},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.47737953066825867},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.4493013024330139},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40230679512023926},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3400803804397583},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33206266164779663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11918208003044128},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0732046365737915},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07028847932815552},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385694","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385694","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.atira.dk:openaire/4f024dd4-a968-4994-95ce-6c77bd5e7702","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/4f024dd4-a968-4994-95ce-6c77bd5e7702","pdf_url":"https://pure.ulster.ac.uk/ws/files/135696597/BIBM2023-B2106.pdf","source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"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":"Shen, L, He, C, Wang, H, Qu, Y & Duan, L 2024, DARE: Sequence-Structure Dual-Aware Encoder for RNA-Protein Binding Prediction. in 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, pp. 1-4, 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Istanbul, Turkey, 5/12/23. https://doi.org/10.1109/bibm58861.2023.10385694","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:pure.atira.dk:openaire/4f024dd4-a968-4994-95ce-6c77bd5e7702","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/4f024dd4-a968-4994-95ce-6c77bd5e7702","pdf_url":"https://pure.ulster.ac.uk/ws/files/135696597/BIBM2023-B2106.pdf","source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"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":"Shen, L, He, C, Wang, H, Qu, Y & Duan, L 2024, DARE: Sequence-Structure Dual-Aware Encoder for RNA-Protein Binding Prediction. in 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, pp. 1-4, 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Istanbul, Turkey, 5/12/23. https://doi.org/10.1109/bibm58861.2023.10385694","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390992007.pdf","grobid_xml":"https://content.openalex.org/works/W4390992007.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1951403192","https://openalex.org/W1997535872","https://openalex.org/W2086561953","https://openalex.org/W2092896180","https://openalex.org/W2103375140","https://openalex.org/W2105694586","https://openalex.org/W2108191354","https://openalex.org/W2799487719","https://openalex.org/W2949563963","https://openalex.org/W3176811232","https://openalex.org/W3211726303","https://openalex.org/W4283693600","https://openalex.org/W4285078464"],"related_works":["https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983","https://openalex.org/W3167935049","https://openalex.org/W3029198973","https://openalex.org/W3047450301","https://openalex.org/W2558432341","https://openalex.org/W1975806245"],"abstract_inverted_index":{"Predicting":[0],"RNA-protein":[1,25,112],"binding":[2,26,113],"sites":[3,114],"helps":[4],"to":[5,23,82,133,161],"explore":[6],"the":[7,10,43,55,89,92,127,135,138,144,163,172,187,192],"mechanisms":[8],"of":[9,29,51,91,123,137,166,174,186,194],"interaction":[11],"between":[12],"RNA":[13,139],"and":[14,119,142,155],"proteins.":[15],"Numerous":[16],"deep":[17,67,106],"learning":[18,68,107],"methods":[19,31,69,96],"have":[20],"been":[21],"applied":[22],"predict":[24],"sites.":[27],"Some":[28],"these":[30],"use":[32],"only":[33],"sequence":[34,118],"information":[35,41,53,90,122,165],"for":[36,77,88,111],"prediction":[37,115],"which":[38,80],"could":[39],"lose":[40],"about":[42],"topology.":[44],"And":[45],"there":[46],"may":[47],"be":[48],"a":[49,104,150,156],"loss":[50],"important":[52],"if":[54],"secondary":[56,120,128,140],"structure":[57,121,129,141],"features":[58,136],"are":[59,70],"simply":[60],"represented":[61],"as":[62],"one-hot":[63],"matrices.":[64],"Furthermore,":[65],"existing":[66,95],"usually":[71,97],"based":[72],"on":[73,84],"convolutional":[74],"neural":[75],"networks":[76],"feature":[78,130,152,158],"extraction,":[79],"tend":[81],"focus":[83],"local":[85,151],"features.":[86,100],"As":[87],"whole":[93,164],"sequence,":[94],"ignore":[98],"global":[99,157],"Therefore,":[101,147],"we":[102,148,169],"propose":[103],"novel":[105],"model":[108],"called":[109],"DARE":[110,125,181],"using":[116],"both":[117],"RNA.":[124,167],"employs":[126],"extraction":[131,153],"module":[132,154,160],"capture":[134,162],"learn":[143],"topological":[145],"information.":[146,176],"design":[149],"integration":[159],"Thus":[168],"can":[170],"achieve":[171],"purpose":[173],"complementary":[175],"Extensive":[177],"experiments":[178],"demonstrate":[179],"that":[180],"outperforms":[182],"baselines.":[183],"Our":[184],"analysis":[185],"case":[188],"study":[189],"further":[190],"confirm":[191],"effectiveness":[193],"DARE.":[195]},"counts_by_year":[],"updated_date":"2026-07-25T15:57:00.446498","created_date":"2025-10-10T00:00:00"}
