{"id":"https://openalex.org/W2976217562","doi":"https://doi.org/10.1109/tcbb.2019.2943465","title":"Capsule Network for Predicting RNA-Protein Binding Preferences Using Hybrid Feature","display_name":"Capsule Network for Predicting RNA-Protein Binding Preferences Using Hybrid Feature","publication_year":2019,"publication_date":"2019-09-24","ids":{"openalex":"https://openalex.org/W2976217562","doi":"https://doi.org/10.1109/tcbb.2019.2943465","mag":"2976217562","pmid":"https://pubmed.ncbi.nlm.nih.gov/31562101"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2943465","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2943465","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5089051425","display_name":"Zhen Shen","orcid":"https://orcid.org/0000-0001-7572-9195"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhen Shen","raw_affiliation_strings":["Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-7572-9195","affiliations":[{"raw_affiliation_string":"Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010612686","display_name":"Su-Ping Deng","orcid":"https://orcid.org/0000-0001-6619-6497"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Su-Ping Deng","raw_affiliation_strings":["Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-6619-6497","affiliations":[{"raw_affiliation_string":"Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060381913","display_name":"De-Shuang Huang","orcid":"https://orcid.org/0000-0002-6759-2691"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"De-Shuang Huang","raw_affiliation_strings":["Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0002-6759-2691","affiliations":[{"raw_affiliation_string":"Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China","institution_ids":["https://openalex.org/I116953780"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5089051425"],"corresponding_institution_ids":["https://openalex.org/I116953780"],"apc_list":null,"apc_paid":null,"fwci":1.632,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.84214091,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"17","issue":"5","first_page":"1483","last_page":"1492"},"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":0.9994000196456909,"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":0.9987000226974487,"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/rna","display_name":"RNA","score":0.7274739146232605},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5991407036781311},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5773683190345764},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5428853034973145},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.49802112579345703},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4719476103782654},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.44987407326698303},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44294285774230957},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.389305055141449},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36528775095939636},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32687148451805115},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32090798020362854},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2080967128276825},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17771020531654358},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1055087149143219},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1007128655910492}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7274739146232605},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5991407036781311},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5773683190345764},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5428853034973145},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.49802112579345703},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4719476103782654},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.44987407326698303},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44294285774230957},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.389305055141449},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36528775095939636},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32687148451805115},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32090798020362854},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2080967128276825},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17771020531654358},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1055087149143219},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1007128655910492},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","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":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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2943465","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2943465","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31562101","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31562101","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1083522900","display_name":null,"funder_award_id":"61702371","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1307575636","display_name":null,"funder_award_id":"61932008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1596993240","display_name":null,"funder_award_id":"61772370","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3263865980","display_name":null,"funder_award_id":"61520106006","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G344637341","display_name":null,"funder_award_id":"61772357","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G710220644","display_name":null,"funder_award_id":"61672382","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7352770851","display_name":null,"funder_award_id":"2017M611619","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G74711194","display_name":null,"funder_award_id":"61732012","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8031058355","display_name":null,"funder_award_id":"61861146002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8417010444","display_name":null,"funder_award_id":"61672203","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8543904368","display_name":null,"funder_award_id":"61532008","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"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W394412225","https://openalex.org/W1019830208","https://openalex.org/W1964168965","https://openalex.org/W1973480874","https://openalex.org/W1976312746","https://openalex.org/W1984574291","https://openalex.org/W1987951943","https://openalex.org/W1988884185","https://openalex.org/W1997535872","https://openalex.org/W2007618103","https://openalex.org/W2016107719","https://openalex.org/W2018219462","https://openalex.org/W2028928739","https://openalex.org/W2043391289","https://openalex.org/W2047280022","https://openalex.org/W2052034930","https://openalex.org/W2074882547","https://openalex.org/W2090123586","https://openalex.org/W2091549056","https://openalex.org/W2103375140","https://openalex.org/W2105694586","https://openalex.org/W2127616922","https://openalex.org/W2129874158","https://openalex.org/W2131462431","https://openalex.org/W2132863465","https://openalex.org/W2136735223","https://openalex.org/W2147339185","https://openalex.org/W2156387975","https://openalex.org/W2158318580","https://openalex.org/W2164552612","https://openalex.org/W2166810745","https://openalex.org/W2198606573","https://openalex.org/W2247766769","https://openalex.org/W2285139619","https://openalex.org/W2294639133","https://openalex.org/W2295745415","https://openalex.org/W2502569966","https://openalex.org/W2517253711","https://openalex.org/W2593887162","https://openalex.org/W2613155248","https://openalex.org/W2734575741","https://openalex.org/W2752744122","https://openalex.org/W2753767186","https://openalex.org/W2757038198","https://openalex.org/W2789652838","https://openalex.org/W2810756255","https://openalex.org/W2885815722","https://openalex.org/W2919115771","https://openalex.org/W2951748044","https://openalex.org/W2963703618","https://openalex.org/W2964189376","https://openalex.org/W4232920930","https://openalex.org/W4294238563","https://openalex.org/W6682889407","https://openalex.org/W6734429903","https://openalex.org/W6743446608","https://openalex.org/W6744649695"],"related_works":["https://openalex.org/W2147993839","https://openalex.org/W1840103016","https://openalex.org/W54859794","https://openalex.org/W2064941026","https://openalex.org/W2057323302","https://openalex.org/W2359508303","https://openalex.org/W1983151649","https://openalex.org/W1966225171","https://openalex.org/W2028642547","https://openalex.org/W4295068701"],"abstract_inverted_index":{"RNA-Protein":[0,34],"binding":[1,35,77],"is":[2,62],"involved":[3],"in":[4,103,115],"many":[5,26],"different":[6,150,156],"biological":[7],"processes.":[8],"With":[9],"the":[10,57,116,121,136],"progress":[11],"of":[12,38,59,123,138,152],"technology,":[13],"more":[14,16],"and":[15,48,86,112,155],"data":[17],"are":[18],"available":[19],"for":[20,46,54],"research.":[21],"Based":[22],"on":[23,128,141],"these":[24,39,60],"data,":[25],"prediction":[27],"methods":[28,40,50,61,102],"have":[29],"been":[30],"proposed":[31,94,147],"to":[32,74],"predict":[33,75],"preference.":[36],"Some":[37],"use":[41,51,81],"only":[42],"RNA":[43,83,109],"sequence":[44,84,110],"features":[45,53,85,111,114],"prediction,":[47],"some":[49],"multiple":[52],"prediction.":[55],"But,":[56],"performance":[58,143],"not":[63],"satisfactory.":[64],"In":[65,131],"this":[66,104],"study,":[67],"we":[68,119,133],"propose":[69],"an":[70],"improved":[71],"capsule":[72,125],"network":[73],"RNA-protein":[76],"preferences,":[78],"which":[79],"can":[80],"both":[82,108],"structure":[87,113,140],"features.":[88],"Experimental":[89],"results":[90],"show":[91],"that":[92],"our":[93,146],"method":[95,148],"iCapsule":[96],"performs":[97],"better":[98],"than":[99],"three":[100],"baseline":[101],"field.":[105],"We":[106],"used":[107],"model,":[117],"so":[118],"tested":[120],"effect":[122],"primary":[124],"layer":[126],"changes":[127],"model":[129,139,142],"performance.":[130],"addition,":[132],"also":[134],"studied":[135],"impact":[137],"by":[144],"performing":[145],"with":[149],"number":[151],"convolution":[153],"layers":[154],"kernel":[157],"sizes.":[158]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
