{"id":"https://openalex.org/W2124339012","doi":null,"title":"Marginalized kernels for RNA sequence data analysis.","display_name":"Marginalized kernels for RNA sequence data analysis.","publication_year":2002,"publication_date":"2002-01-01","ids":{"openalex":"https://openalex.org/W2124339012","mag":"2124339012","pmid":"https://pubmed.ncbi.nlm.nih.gov/14571380"},"language":"en","primary_location":{"id":"pmid:14571380","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14571380","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,"listed_in":[],"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":"Genome informatics. International Conference on Genome Informatics","raw_type":"Journal Article"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":["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/A5109004340","display_name":"Taishin Kin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Taishin Kin","raw_affiliation_strings":["Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan. taishin@cbrc.jp"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan. taishin@cbrc.jp","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070597006","display_name":"Koji Tsuda","orcid":"https://orcid.org/0000-0002-4288-1606","observed_orcids":["https://orcid.org/0000-0002-4288-1606"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Koji Tsuda","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5082068847","display_name":"Kiyoshi Asai","orcid":"https://orcid.org/0000-0003-0909-4982","observed_orcids":["https://orcid.org/0000-0003-0909-4982"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kiyoshi Asai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.3467,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.92972392,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"13","issue":null,"first_page":"112","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9042999744415283,"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":0.9042999744415283,"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":0.0348999984562397,"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":0.025200000032782555,"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-secondary-structure","display_name":"RNA secondary structure","score":0.9480000138282776},{"id":"https://openalex.org/keywords/probabilistic-context-free-grammars","display_name":"probabilistic context-free grammars","score":0.9559999704360962},{"id":"https://openalex.org/keywords/trna","display_name":"tRNA","score":0.6200000047683716},{"id":"https://openalex.org/keywords/kernel-pca","display_name":"kernel principal component analysis","score":0.7960000038146973},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"support vector machine","score":0.9670000076293945},{"id":"https://openalex.org/keywords/sequence-similarity","display_name":"sequence similarity","score":0.6349999904632568}],"concepts":[{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6377561688423157},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5980639457702637},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5902379751205444},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5857205390930176},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5838812589645386},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5734596252441406},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5446365475654602},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.5410342216491699},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5382328629493713},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.44630828499794006},{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.43131959438323975},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4252457618713379},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.42415574193000793},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34827059507369995},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3310166895389557},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29401975870132446},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14185082912445068},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.13589826226234436},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11060243844985962},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07774165272712708},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","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}],"mesh":[{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"pmid:14571380","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14571380","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,"listed_in":[],"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":"Genome informatics. International Conference on Genome Informatics","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.12.3060","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.12.3060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cbrc.jp/~tsuda/./giw02.ps.gz","raw_type":"text"},{"id":"pmh:oai:pure.mpg.de:item_1793007","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0013-E0ED-6","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"mag:2124339012","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14571380","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,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1526127001","https://openalex.org/W1978470410","https://openalex.org/W2017313617","https://openalex.org/W2020816856","https://openalex.org/W2025763720","https://openalex.org/W2054931730","https://openalex.org/W2079316064","https://openalex.org/W2081264480","https://openalex.org/W2088938573","https://openalex.org/W2093989924","https://openalex.org/W2107427637","https://openalex.org/W2123241418","https://openalex.org/W2132005946","https://openalex.org/W2149429041","https://openalex.org/W2173626280","https://openalex.org/W2283504545","https://openalex.org/W3214380909"],"related_works":["https://openalex.org/W7095851045","https://openalex.org/W7097600611","https://openalex.org/W1601317078","https://openalex.org/W2156717698","https://openalex.org/W1509279450","https://openalex.org/W2016614259","https://openalex.org/W2094440264","https://openalex.org/W2803452209","https://openalex.org/W306611029","https://openalex.org/W1000189836"],"abstract_inverted_index":{"We":[0,52,61],"present":[1],"novel":[2],"kernels":[3,20],"that":[4],"measure":[5],"similarity":[6],"of":[7,13,19,70,95],"two":[8],"RNA":[9,26],"sequences,":[10],"taking":[11],"account":[12],"their":[14],"secondary":[15,30,38,50],"structures.":[16,39],"Two":[17],"types":[18,94],"are":[21],"presented.":[22],"One":[23],"is":[24],"for":[25,34,47,65,81,100],"sequences":[27],"with":[28,88],"known":[29,37],"structures,":[31],"the":[32,49,54,56],"other":[33],"those":[35],"without":[36],"The":[40],"latter":[41,55],"employs":[42],"stochastic":[43],"context-free":[44],"grammar":[45],"(SCFG)":[46],"estimating":[48],"structure.":[51],"call":[53],"marginalized":[57],"count":[58],"kernel":[59,76],"(MCK).":[60],"show":[62,97],"computational":[63],"experiments":[64],"MCK":[66],"using":[67],"74":[68],"sets":[69],"human":[71],"tRNA":[72,83],"sequence":[73],"data:":[74],"(i)":[75],"principal":[77],"component":[78],"analysis":[79],"(PCA)":[80],"visualizing":[82],"similarities,":[84],"(ii)":[85],"supervised":[86],"classification":[87],"support":[89],"vector":[90],"machines":[91],"(SVMs).":[92],"Both":[93],"experiment":[96],"promising":[98],"results":[99],"MCKs.":[101]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}
