{"id":"https://openalex.org/W4402975031","doi":"https://doi.org/10.1186/s12859-024-05916-1","title":"Predicting RNA sequence-structure likelihood via structure-aware deep learning","display_name":"Predicting RNA sequence-structure likelihood via structure-aware deep learning","publication_year":2024,"publication_date":"2024-09-30","ids":{"openalex":"https://openalex.org/W4402975031","doi":"https://doi.org/10.1186/s12859-024-05916-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/39350066"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05916-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05916-1","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05916-1.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05916-1.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088280950","display_name":"You Zhou","orcid":"https://orcid.org/0009-0002-2095-3282"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"You Zhou","raw_affiliation_strings":["ASU-Mayo Center for Innovative Imaging, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA","School of Computing and Augmented Intelligence, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ASU-Mayo Center for Innovative Imaging, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Computing and Augmented Intelligence, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049158387","display_name":"Giulia Pedrielli","orcid":"https://orcid.org/0000-0001-6726-9790"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Giulia Pedrielli","raw_affiliation_strings":["ASU-Mayo Center for Innovative Imaging, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA. Giulia.Pedrielli@asu.edu","School of Computing and Augmented Intelligence, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA. Giulia.Pedrielli@asu.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ASU-Mayo Center for Innovative Imaging, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA. Giulia.Pedrielli@asu.edu","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Computing and Augmented Intelligence, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA. Giulia.Pedrielli@asu.edu","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100412172","display_name":"Fei Zhang","orcid":"https://orcid.org/0000-0002-3177-7547"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fei Zhang","raw_affiliation_strings":["Department of Chemistry, Rutgers University, 73 Warren St, Newark, NJ, 07102, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Rutgers University, 73 Warren St, Newark, NJ, 07102, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069823101","display_name":"Teresa Wu","orcid":"https://orcid.org/0000-0002-0529-7048"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Teresa Wu","raw_affiliation_strings":["ASU-Mayo Center for Innovative Imaging, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA","School of Computing and Augmented Intelligence, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ASU-Mayo Center for Innovative Imaging, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Computing and Augmented Intelligence, Arizona State University, 699\u00a0S Mill Ave, Tempe, AZ, 85281, USA","institution_ids":["https://openalex.org/I55732556"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5088280950"],"corresponding_institution_ids":["https://openalex.org/I55732556"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6554,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.69365459,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"25","issue":"1","first_page":"316","last_page":"316"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9456999897956848,"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":0.9456999897956848,"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":0.010900000110268593,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.00839999970048666,"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/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.6491050124168396},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6472423076629639},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5436230897903442},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5284155607223511},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5028225779533386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4918632507324219},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.44106942415237427},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36850446462631226},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3453678488731384},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33813947439193726},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1728556752204895},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11830711364746094}],"concepts":[{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.6491050124168396},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6472423076629639},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5436230897903442},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5284155607223511},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5028225779533386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4918632507324219},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.44106942415237427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36850446462631226},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3453678488731384},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33813947439193726},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1728556752204895},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11830711364746094}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"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":"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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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},{"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":4,"locations":[{"id":"doi:10.1186/s12859-024-05916-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05916-1","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05916-1.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39350066","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39350066","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11443715","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11443715","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11443715/pdf/12859_2024_Article_5916.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e0a677c98588416b9d878cbcbf0a1891","is_oa":false,"landing_page_url":"https://doaj.org/article/e0a677c98588416b9d878cbcbf0a1891","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-26 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05916-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05916-1","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05916-1.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2862665411","display_name":"Collaborative Research: FET: Small: Hierarchical Computational Framework for large scale RNA Design Pathway Discovery through Data and Experiments","funder_award_id":"2007861","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309835","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402975031.pdf"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1514588745","https://openalex.org/W1543796220","https://openalex.org/W1578171303","https://openalex.org/W1974536306","https://openalex.org/W1981576666","https://openalex.org/W1984675364","https://openalex.org/W1988884185","https://openalex.org/W2009818318","https://openalex.org/W2013425283","https://openalex.org/W2025763720","https://openalex.org/W2036412199","https://openalex.org/W2051713039","https://openalex.org/W2063599852","https://openalex.org/W2078334480","https://openalex.org/W2086561953","https://openalex.org/W2098571862","https://openalex.org/W2111342151","https://openalex.org/W2122792293","https://openalex.org/W2125615424","https://openalex.org/W2131841865","https://openalex.org/W2134510195","https://openalex.org/W2140444174","https://openalex.org/W2140505514","https://openalex.org/W2143407915","https://openalex.org/W2146721220","https://openalex.org/W2158698691","https://openalex.org/W2162224067","https://openalex.org/W2164530723","https://openalex.org/W2165698076","https://openalex.org/W2194775991","https://openalex.org/W2618530766","https://openalex.org/W2772605365","https://openalex.org/W2954092143","https://openalex.org/W2990528340","https://openalex.org/W3043664941","https://openalex.org/W3126773939","https://openalex.org/W3135161193","https://openalex.org/W3161531818","https://openalex.org/W4213072029","https://openalex.org/W4224232193","https://openalex.org/W4283447041","https://openalex.org/W4300861274","https://openalex.org/W6634528131"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W3093937951","https://openalex.org/W2554722417","https://openalex.org/W2470187006","https://openalex.org/W2581348958","https://openalex.org/W2264054990","https://openalex.org/W2581888268","https://openalex.org/W2902683473","https://openalex.org/W1989561030","https://openalex.org/W2088051090"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,144],"active":[2],"functionalities":[3],"of":[4,60,118,126,183,212,237,250,314],"RNA":[5,28,87,100,119,128,140,162,256,267,287,304,330],"are":[6,81],"recognized":[7],"to":[8,45,70,108,121,198,276,302,328],"be":[9,32],"heavily":[10],"dependent":[11],"on":[12,78,203,215],"the":[13,58,67,82,123,127,156,181,186,210,224,235,247,277,312,325],"structure":[14,120,142,206,306,332],"and":[15,115,252,260,300],"sequence.":[16],"Therefore,":[17],"a":[18,24,33,149,166],"model":[19],"that":[20,104,112,154],"can":[21],"accurately":[22],"evaluate":[23,209,246,303],"design":[25,129],"by":[26,66,159],"giving":[27],"sequence-structure":[29,88,163],"pairs":[30],"would":[31],"valuable":[34],"tool":[35],"for":[36,85,138,317],"many":[37],"researchers.":[38],"Machine":[39],"learning":[40,62,94,136,297,318],"methods":[41,95],"have":[42],"been":[43],"explored":[44],"develop":[46,133],"such":[47],"tools,":[48],"showing":[49],"promising":[50],"results.":[51],"However,":[52],"two":[53,134,295,309,322],"key":[54],"issues":[55],"remain.":[56],"Firstly,":[57],"performance":[59,211,274],"machine":[61,93],"models":[63,137,214,222,225,264,271,278,310,323],"is":[64,75,106],"affected":[65],"features":[68,80,97,111],"used":[69],"characterize":[71,113],"RNA.":[72,319],"Currently,":[73],"there":[74],"no":[76],"consensus":[77],"which":[79],"most":[83,91],"effective":[84],"characterizing":[86],"pairs.":[89,143,307,333],"Secondly,":[90],"existing":[92],"extract":[96,199],"describing":[98],"entire":[99],"molecule.":[101],"We":[102,132,208],"argue":[103],"it":[105],"essential":[107],"define":[109],"additional":[110,177],"nucleotides":[114],"specific":[116],"sections":[117],"enhance":[122],"overall":[124],"efficacy":[125],"process.":[130],"RESULTS:":[131],"deep":[135,296],"evaluating":[139],"sequence-secondary":[141,305,331],"first":[145],"model,":[146,174],"NU-ResNet,":[147,171],"uses":[148],"convolutional":[150],"neural":[151],"network":[152],"architecture":[153],"solves":[155],"aforementioned":[157],"problems":[158],"explicitly":[160],"encoding":[161],"information":[164,178],"into":[165],"3D":[167],"matrix.":[168],"Building":[169],"upon":[170],"our":[172,238,262],"second":[173],"NUMO-ResNet,":[175,301],"incorporates":[176],"derived":[179],"from":[180,226,279],"characterizations":[182],"RNA,":[184],"specifically":[185],"2D":[187],"folding":[188],"motifs.":[189],"In":[190,290],"this":[191,229,291],"work,":[192],"we":[193,240,258,293],"introduce":[194],"an":[195,216],"automated":[196],"method":[197,327],"these":[200,321],"motifs":[201],"based":[202],"fundamental":[204],"secondary":[205],"descriptions.":[207],"both":[213],"independent":[217,230,286],"testing":[218,231],"dataset.":[219,232],"Our":[220,269],"proposed":[221,263,270],"outperform":[223],"literatures":[227,280],"in":[228,265],"To":[233,245],"assess":[234],"robustness":[236],"models,":[239,298],"conduct":[241],"10-fold":[242],"cross":[243],"validation.":[244],"generalization":[248],"ability":[249],"NU-ResNet":[251,299],"NUMO-ResNet":[253],"across":[254,284],"different":[255,266,285],"families,":[257],"train":[259],"test":[261],"families.":[268,288],"show":[272],"superior":[273],"compared":[275],"when":[281],"being":[282],"tested":[283],"CONCLUSIONS:":[289],"study,":[292],"propose":[294],"These":[308],"expand":[311],"field":[313],"data-driven":[315],"approaches":[316],"Furthermore,":[320],"provide":[324],"new":[326],"encode":[329]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}