{"id":"https://openalex.org/W4406864313","doi":"https://doi.org/10.3390/a18020067","title":"CSpredR: A Multi-Site mRNA Subcellular Localization Prediction Method Based on Fusion Encoding and Hybrid Neural Networks","display_name":"CSpredR: A Multi-Site mRNA Subcellular Localization Prediction Method Based on Fusion Encoding and Hybrid Neural Networks","publication_year":2025,"publication_date":"2025-01-26","ids":{"openalex":"https://openalex.org/W4406864313","doi":"https://doi.org/10.3390/a18020067"},"language":"en","primary_location":{"id":"doi:10.3390/a18020067","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a18020067","pdf_url":"https://www.mdpi.com/1999-4893/18/2/67/pdf","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/18/2/67/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100411464","display_name":"Xiao Wang","orcid":"https://orcid.org/0000-0002-3113-5149"},"institutions":[{"id":"https://openalex.org/I23171815","display_name":"Zhengzhou University of Light Industry","ror":"https://ror.org/05fwr8z16","country_code":"CN","type":"education","lineage":["https://openalex.org/I23171815"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiao Wang","raw_affiliation_strings":["Henan Provincial Key Laboratory of Data Intelligence for Food Safety, Zhengzhou University of Light Industry, Zhengzhou 450002, China","School of Computer Science and Technology, Zhengzhou University of Light Industry, Zhengzhou 450002, China"],"affiliations":[{"raw_affiliation_string":"Henan Provincial Key Laboratory of Data Intelligence for Food Safety, Zhengzhou University of Light Industry, Zhengzhou 450002, China","institution_ids":["https://openalex.org/I23171815"]},{"raw_affiliation_string":"School of Computer Science and Technology, Zhengzhou University of Light Industry, Zhengzhou 450002, China","institution_ids":["https://openalex.org/I23171815"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116048657","display_name":"Wenshuai Suo","orcid":null},"institutions":[{"id":"https://openalex.org/I23171815","display_name":"Zhengzhou University of Light Industry","ror":"https://ror.org/05fwr8z16","country_code":"CN","type":"education","lineage":["https://openalex.org/I23171815"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenshuai Suo","raw_affiliation_strings":["School of Computer Science and Technology, Zhengzhou University of Light Industry, Zhengzhou 450002, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Zhengzhou University of Light Industry, Zhengzhou 450002, China","institution_ids":["https://openalex.org/I23171815"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100324870","display_name":"Rong Wang","orcid":"https://orcid.org/0000-0001-6904-806X"},"institutions":[{"id":"https://openalex.org/I23171815","display_name":"Zhengzhou University of Light Industry","ror":"https://ror.org/05fwr8z16","country_code":"CN","type":"education","lineage":["https://openalex.org/I23171815"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rong Wang","raw_affiliation_strings":["School of Electronic Information, Zhengzhou University of Light Industry, Zhengzhou 450002, China"],"affiliations":[{"raw_affiliation_string":"School of Electronic Information, Zhengzhou University of Light Industry, Zhengzhou 450002, China","institution_ids":["https://openalex.org/I23171815"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100411464"],"corresponding_institution_ids":["https://openalex.org/I23171815"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.01500758,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":"2","first_page":"67","last_page":"67"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9911999702453613,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9819999933242798,"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/encoding","display_name":"Encoding (memory)","score":0.6760330200195312},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6446062326431274},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5789762139320374},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.5726537108421326},{"id":"https://openalex.org/keywords/subcellular-localization","display_name":"Subcellular localization","score":0.5546939969062805},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5214330554008484},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3601298928260803},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3525615334510803},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2407824695110321},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20846089720726013},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1420820951461792}],"concepts":[{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.6760330200195312},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6446062326431274},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5789762139320374},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.5726537108421326},{"id":"https://openalex.org/C2776879804","wikidata":"https://www.wikidata.org/wiki/Q7630919","display_name":"Subcellular localization","level":3,"score":0.5546939969062805},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5214330554008484},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3601298928260803},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3525615334510803},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2407824695110321},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20846089720726013},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1420820951461792},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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:10.3390/a18020067","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a18020067","pdf_url":"https://www.mdpi.com/1999-4893/18/2/67/pdf","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:90a11f10b33e4758ad864fa9f0304454","is_oa":true,"landing_page_url":"https://doaj.org/article/90a11f10b33e4758ad864fa9f0304454","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 18, Iss 2, p 67 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/a18020067","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a18020067","pdf_url":"https://www.mdpi.com/1999-4893/18/2/67/pdf","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406864313.pdf","grobid_xml":"https://content.openalex.org/works/W4406864313.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W2036789528","https://openalex.org/W2047569375","https://openalex.org/W2082916462","https://openalex.org/W2145241906","https://openalex.org/W2156125289","https://openalex.org/W2158166500","https://openalex.org/W2198153867","https://openalex.org/W2336509392","https://openalex.org/W2522056448","https://openalex.org/W2618219849","https://openalex.org/W2625599729","https://openalex.org/W2806741085","https://openalex.org/W2908663744","https://openalex.org/W2943568678","https://openalex.org/W2962655813","https://openalex.org/W2971769670","https://openalex.org/W2987092090","https://openalex.org/W3004263072","https://openalex.org/W3026307143","https://openalex.org/W3047670845","https://openalex.org/W3080359515","https://openalex.org/W3118794840","https://openalex.org/W3124828689","https://openalex.org/W3144893534","https://openalex.org/W3174714560","https://openalex.org/W3176118617","https://openalex.org/W4281557145","https://openalex.org/W4286721853","https://openalex.org/W4308370554","https://openalex.org/W4312094581","https://openalex.org/W4322772305","https://openalex.org/W4381157939","https://openalex.org/W4391607533","https://openalex.org/W6649956883"],"related_works":["https://openalex.org/W2359834996","https://openalex.org/W2384565783","https://openalex.org/W2070256704","https://openalex.org/W4282922129","https://openalex.org/W1964033480","https://openalex.org/W2099701744","https://openalex.org/W2375119535","https://openalex.org/W2012210483","https://openalex.org/W4322772305","https://openalex.org/W2024189384"],"abstract_inverted_index":{"Current":[0],"research":[1],"widely":[2],"acknowledges":[3],"that":[4,235],"the":[5,31,35,46,63,78,83,97,101,105,124,130,134,140,144,152,157,165,196,214,219,242],"subcellular":[6,22,64,253],"localization":[7,23,65,254],"of":[8,34,66,96,107,126,156],"mRNA":[9,21,79,252],"is":[10,167,211],"crucial":[11],"for":[12,20,61,200,229,251],"understanding":[13],"its":[14],"biological":[15],"functions.":[16],"However,":[17],"current":[18],"methods":[19],"based":[24],"on":[25],"k-mer":[26,75,141],"frequency":[27],"features":[28,125],"may":[29,42],"overlook":[30],"sequential":[32,109],"information":[33,99,110,207],"sequence,":[36],"and":[37,111,119,132,183,194,217],"a":[38,52,92,169,201,238,247],"single":[39],"encoding":[40],"method":[41],"not":[43],"adequately":[44],"extract":[45,123],"sequence\u2019s":[47],"features.":[48],"This":[49],"paper":[50],"proposes":[51],"novel":[53],"deep":[54],"learning":[55],"prediction":[56,230],"method,":[57],"CSpredR,":[58],"specifically":[59],"designed":[60],"predicting":[62],"multi-site":[67],"mRNAs.":[68],"Unlike":[69],"previous":[70],"methods,":[71],"CSpredR":[72,236],"first":[73],"employs":[74],"to":[76,122,189],"tokenize":[77],"sequences,":[80],"then":[81],"converts":[82],"tokenized":[84],"sequences":[85],"into":[86,146,213,224],"de":[87],"Bruijn":[88],"graphs,":[89],"thereby":[90],"enabling":[91],"more":[93,248],"precise":[94],"capture":[95,113,190],"structural":[98],"within":[100],"sequences.":[102],"To":[103],"mitigate":[104],"impact":[106],"lost":[108],"better":[112],"sequence":[114,135,145,191],"features,":[115,192],"we":[116,177],"combine":[117],"word2vec":[118],"fasttext":[120],"models":[121],"each":[127,162],"node":[128,153,163,215],"in":[129,143,164],"graph":[131,166],"retain":[133],"order.":[136],"They":[137],"can":[138],"encode":[139],"units":[142],"word":[147],"vectors,":[148],"thus":[149],"serving":[150],"as":[151,198],"feature":[154,170],"vectors":[155],"graph.":[158],"In":[159],"this":[160],"way,":[161],"assigned":[168],"vector":[171],"containing":[172],"rich":[173],"semantic":[174],"information.":[175],"Subsequently,":[176],"utilize":[178],"multi-scale":[179],"convolutional":[180],"neural":[181],"networks":[182,188],"bidirectional":[184],"long":[185],"short-term":[186],"memory":[187],"respectively,":[193],"fuse":[195],"results":[197],"input":[199],"multi-head":[202],"attention":[203],"mechanism":[204],"model.":[205],"The":[206],"from":[208],"these":[209],"heads":[210],"integrated":[212],"representations,":[216],"finally,":[218],"attention-processed":[220],"data":[221],"are":[222],"fed":[223],"an":[225],"MLP":[226],"(Multi-Layer":[227],"Perceptron)":[228],"tasks.":[231],"Extensive":[232],"experiments":[233],"reveal":[234],"achieves":[237],"2%":[239],"improvement":[240],"over":[241],"best":[243],"existing":[244],"predictors,":[245],"offering":[246],"effective":[249],"tool":[250],"prediction.":[255]},"counts_by_year":[],"updated_date":"2026-03-09T07:00:12.390032","created_date":"2025-10-10T00:00:00"}