{"id":"https://openalex.org/W4406238035","doi":"https://doi.org/10.1109/bibm62325.2024.10821865","title":"RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs","display_name":"RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238035","doi":"https://doi.org/10.1109/bibm62325.2024.10821865"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10821865","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821865","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5100391240","display_name":"Li Y","orcid":"https://orcid.org/0000-0003-3842-475X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yichong Li","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Computer Science and Engineering,Shanghai,China,200240"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Computer Science and Engineering,Shanghai,China,200240","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103236916","display_name":"Xiaojian Liu","orcid":"https://orcid.org/0000-0002-4151-7466"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaojian Liu","raw_affiliation_strings":["Shanghai Jiao Tong University,Institute of Image Processing and Pattern Recognition,Shanghai,China,200240"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Institute of Image Processing and Pattern Recognition,Shanghai,China,200240","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100322080","display_name":"Cheng Fan","orcid":"https://orcid.org/0000-0002-3471-6221"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Cheng","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Computer Science and Engineering,Shanghai,China,200240"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Computer Science and Engineering,Shanghai,China,200240","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091365447","display_name":"Xiaoyong Pan","orcid":"https://orcid.org/0000-0001-5010-464X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyong Pan","raw_affiliation_strings":["Shanghai Jiao Tong University,Institute of Image Processing and Pattern Recognition,Shanghai,China,200240"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Institute of Image Processing and Pattern Recognition,Shanghai,China,200240","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100397510","display_name":"Yang Yang","orcid":"https://orcid.org/0000-0002-1163-2359"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Yang","raw_affiliation_strings":["Shanghai Jiao Tong University,Department of Computer Science and Engineering,Shanghai,China,200240"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Department of Computer Science and Engineering,Shanghai,China,200240","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I183067930"],"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":"48","last_page":"53"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9975000023841858,"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":0.9975000023841858,"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":0.9950000047683716,"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":0.9943000078201294,"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-binding-protein","display_name":"RNA-binding protein","score":0.6978964805603027},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5543333292007446},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5512347221374512},{"id":"https://openalex.org/keywords/joint","display_name":"Joint (building)","score":0.5197174549102783},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4611317217350006},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3179507255554199},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2591550946235657},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23228654265403748},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1094103455543518}],"concepts":[{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.6978964805603027},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5543333292007446},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5512347221374512},{"id":"https://openalex.org/C18555067","wikidata":"https://www.wikidata.org/wiki/Q8375051","display_name":"Joint (building)","level":2,"score":0.5197174549102783},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4611317217350006},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3179507255554199},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2591550946235657},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23228654265403748},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1094103455543518},{"id":"https://openalex.org/C170154142","wikidata":"https://www.wikidata.org/wiki/Q150737","display_name":"Architectural engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10821865","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821865","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","score":0.5600000023841858,"display_name":"Zero hunger"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1984574291","https://openalex.org/W2307041907","https://openalex.org/W2378703660","https://openalex.org/W2474507425","https://openalex.org/W2573587735","https://openalex.org/W2951748044","https://openalex.org/W3003684254","https://openalex.org/W3099409512","https://openalex.org/W3106930452","https://openalex.org/W3112745729","https://openalex.org/W3127145950","https://openalex.org/W3196282583","https://openalex.org/W3203588026","https://openalex.org/W3211440389","https://openalex.org/W4225917625","https://openalex.org/W4283693600","https://openalex.org/W4368356090","https://openalex.org/W4386209142","https://openalex.org/W6632100814","https://openalex.org/W6726873649","https://openalex.org/W6792439368"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W4379233576","https://openalex.org/W2753172052","https://openalex.org/W3080365360","https://openalex.org/W1935063092"],"abstract_inverted_index":{"RNA-binding":[0],"proteins":[1],"(RBPs)":[2],"are":[3],"essential":[4],"for":[5,33,81,89,138],"gene":[6],"expression,":[7],"and":[8,37,64,99,107,148],"the":[9],"complex":[10],"RNA-protein":[11],"interaction":[12],"mechanisms":[13,36],"require":[14],"analysis":[15],"of":[16,23],"global":[17],"RNA":[18,29,51,83,136],"information.":[19],"Therefore,":[20],"accurate":[21],"prediction":[22,77],"RBP":[24,48],"binding":[25,49,74,132],"sites":[26,133],"on":[27,122,134],"full-length":[28,56,82,135],"transcripts":[30,57,84,137],"is":[31],"crucial":[32],"understanding":[34],"these":[35],"their":[38],"roles":[39],"in":[40,130,144],"diseases.":[41],"While":[42],"machine":[43],"learning":[44,117],"methods":[45,129],"can":[46,86],"predict":[47],"to":[50,55,61,102],"fragments,":[52],"extending":[53],"this":[54,68],"presents":[58],"challenges":[59],"due":[60],"sequence":[62,105],"length":[63],"data":[65,106],"imbalance.":[66],"In":[67],"paper,":[69],"we":[70],"introduce":[71],"RBP-Former,":[72],"a":[73],"site":[75],"joint":[76],"model":[78,93],"designed":[79],"specifically":[80],"that":[85],"be":[87],"used":[88],"multiple":[90,111,139],"RBPs.":[91,112],"This":[92],"processes":[94],"information":[95],"at":[96],"both":[97],"coarse":[98],"fine-grained":[100],"levels":[101],"fully":[103],"exploit":[104],"its":[108,142],"interactions":[109],"with":[110],"We":[113],"develop":[114],"multi-level":[115],"imbalance":[116],"strategies,":[118],"achieving":[119],"favorable":[120],"results":[121],"imbalanced":[123,146],"data.":[124],"Our":[125],"method":[126],"outperforms":[127],"existing":[128],"predicting":[131],"RBPs,":[140],"demonstrating":[141],"effectiveness":[143],"handling":[145],"label":[147],"sample":[149],"distributions.":[150]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
