{"id":"https://openalex.org/W4412785638","doi":"https://doi.org/10.1093/bioinformatics/btaf427","title":"Deep generative model of RNAs based on variational autoencoder with context-free grammar","display_name":"Deep generative model of RNAs based on variational autoencoder with context-free grammar","publication_year":2025,"publication_date":"2025-07-29","ids":{"openalex":"https://openalex.org/W4412785638","doi":"https://doi.org/10.1093/bioinformatics/btaf427","pmid":"https://pubmed.ncbi.nlm.nih.gov/40728942"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf427","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf427","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf427","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078752284","display_name":"Goro Terai","orcid":"https://orcid.org/0000-0002-1059-2519"},"institutions":[{"id":"https://openalex.org/I14396692","display_name":"Tokyo University of Information Sciences","ror":"https://ror.org/044bdx604","country_code":"JP","type":"education","lineage":["https://openalex.org/I14396692"]},{"id":"https://openalex.org/I159385669","display_name":"Chiba University","ror":"https://ror.org/01hjzeq58","country_code":"JP","type":"education","lineage":["https://openalex.org/I159385669"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Goro Terai","raw_affiliation_strings":["Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo , Chiba 277-8561,","Department of Computational Biology and Medical Sciences, University of Tokyo, Chiba, 277-8561, Japan","Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo , Chiba 277-8561,","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, University of Tokyo, Chiba, 277-8561, Japan","institution_ids":["https://openalex.org/I159385669","https://openalex.org/I14396692"]},{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan","institution_ids":["https://openalex.org/I159385669","https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082068847","display_name":"Kiyoshi Asai","orcid":"https://orcid.org/0000-0003-0909-4982"},"institutions":[{"id":"https://openalex.org/I14396692","display_name":"Tokyo University of Information Sciences","ror":"https://ror.org/044bdx604","country_code":"JP","type":"education","lineage":["https://openalex.org/I14396692"]},{"id":"https://openalex.org/I159385669","display_name":"Chiba University","ror":"https://ror.org/01hjzeq58","country_code":"JP","type":"education","lineage":["https://openalex.org/I159385669"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyoshi Asai","raw_affiliation_strings":["Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo , Chiba 277-8561,","Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan","Department of Computational Biology and Medical Sciences, University of Tokyo, Chiba, 277-8561, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo , Chiba 277-8561,","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan","institution_ids":["https://openalex.org/I159385669","https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, University of Tokyo, Chiba, 277-8561, Japan","institution_ids":["https://openalex.org/I159385669","https://openalex.org/I14396692"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5078752284"],"corresponding_institution_ids":["https://openalex.org/I14396692","https://openalex.org/I159385669","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16890985,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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":0.9980000257492065,"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":0.9979000091552734,"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":0.6891493797302246},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.629479706287384},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.6263784170150757},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.6188892722129822},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6147486567497253},{"id":"https://openalex.org/keywords/context-free-grammar","display_name":"Context-free grammar","score":0.5511101484298706},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.547512948513031},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.5256532430648804},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5205058455467224},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.48651355504989624},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4653511643409729},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.46103715896606445},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45652925968170166},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4407612085342407},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4210800528526306},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.32540833950042725},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21593645215034485},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1603480875492096}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6891493797302246},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.629479706287384},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.6263784170150757},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6188892722129822},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6147486567497253},{"id":"https://openalex.org/C97212296","wikidata":"https://www.wikidata.org/wiki/Q338047","display_name":"Context-free grammar","level":3,"score":0.5511101484298706},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.547512948513031},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.5256532430648804},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5205058455467224},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.48651355504989624},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4653511643409729},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.46103715896606445},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45652925968170166},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4407612085342407},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4210800528526306},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.32540833950042725},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21593645215034485},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1603480875492096},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"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":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf427","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf427","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40728942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40728942","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12342829","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12342829","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf427","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf427","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.7200000286102295,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G4709092590","display_name":null,"funder_award_id":"JP22H04925","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5488295451","display_name":null,"funder_award_id":"JP24H00737","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1861164398","https://openalex.org/W1929414144","https://openalex.org/W2052611179","https://openalex.org/W2067258168","https://openalex.org/W2076591428","https://openalex.org/W2104095017","https://openalex.org/W2141152740","https://openalex.org/W2148419405","https://openalex.org/W2339766289","https://openalex.org/W2489381017","https://openalex.org/W2529996553","https://openalex.org/W2561599208","https://openalex.org/W2607077817","https://openalex.org/W2794067415","https://openalex.org/W3098269892","https://openalex.org/W3100348855","https://openalex.org/W3126773939","https://openalex.org/W4383957026","https://openalex.org/W4390975839","https://openalex.org/W4404112650","https://openalex.org/W6731351848"],"related_works":["https://openalex.org/W2036643266","https://openalex.org/W1583489351","https://openalex.org/W1999060916","https://openalex.org/W3047450301","https://openalex.org/W2280924737","https://openalex.org/W2558432341","https://openalex.org/W2159621058","https://openalex.org/W4225160382","https://openalex.org/W2059090778","https://openalex.org/W2039746015"],"abstract_inverted_index":{"https://github.com/gterai/RNAgg":[0],"(archived":[1],"at":[2],"Zenodo:":[3],"https://doi.org/10.5281/zenodo.15354990).":[4]},"counts_by_year":[],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}