{"id":"https://openalex.org/W2088346180","doi":"https://doi.org/10.1109/icmla.2013.37","title":"Variable-Length Protein Sequence Motif Extraction Using Hierarchically-Clustered Hidden Markov Models","display_name":"Variable-Length Protein Sequence Motif Extraction Using Hierarchically-Clustered Hidden Markov Models","publication_year":2013,"publication_date":"2013-12-01","ids":{"openalex":"https://openalex.org/W2088346180","doi":"https://doi.org/10.1109/icmla.2013.37","mag":"2088346180"},"language":"en","primary_location":{"id":"doi:10.1109/icmla.2013.37","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icmla.2013.37","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 12th International Conference on Machine Learning and Applications","raw_type":"proceedings-article"},"type":"article","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/A5067662566","display_name":"Cody Hudson","orcid":"https://orcid.org/0009-0001-3374-3754"},"institutions":[{"id":"https://openalex.org/I32038505","display_name":"University of Central Arkansas","ror":"https://ror.org/029bp0k25","country_code":"US","type":"education","lineage":["https://openalex.org/I32038505"]},{"id":"https://openalex.org/I4210152127","display_name":"Conway School of Landscape Design","ror":"https://ror.org/04q7y8a54","country_code":"US","type":"education","lineage":["https://openalex.org/I4210152127"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cody Hudson","raw_affiliation_strings":["Department of Computer Science, University of Central Arkansas, Conway, AR, USA","Dept. of Comput. Sci., Univ. of Central Arkansas, Conway, AR, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Arkansas, Conway, AR, USA","institution_ids":["https://openalex.org/I32038505","https://openalex.org/I4210152127"]},{"raw_affiliation_string":"Dept. of Comput. Sci., Univ. of Central Arkansas, Conway, AR, USA","institution_ids":["https://openalex.org/I32038505"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075234179","display_name":"Bernard Chen","orcid":"https://orcid.org/0000-0001-6556-1675"},"institutions":[{"id":"https://openalex.org/I32038505","display_name":"University of Central Arkansas","ror":"https://ror.org/029bp0k25","country_code":"US","type":"education","lineage":["https://openalex.org/I32038505"]},{"id":"https://openalex.org/I4210152127","display_name":"Conway School of Landscape Design","ror":"https://ror.org/04q7y8a54","country_code":"US","type":"education","lineage":["https://openalex.org/I4210152127"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernard Chen","raw_affiliation_strings":["Department of Computer Science, University of Central Arkansas, Conway, AR, USA","Dept. of Comput. Sci., Univ. of Central Arkansas, Conway, AR, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Arkansas, Conway, AR, USA","institution_ids":["https://openalex.org/I32038505","https://openalex.org/I4210152127"]},{"raw_affiliation_string":"Dept. of Comput. Sci., Univ. of Central Arkansas, Conway, AR, USA","institution_ids":["https://openalex.org/I32038505"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067662566"],"corresponding_institution_ids":["https://openalex.org/I32038505","https://openalex.org/I4210152127"],"apc_list":null,"apc_paid":null,"fwci":0.1462,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56574382,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"173","last_page":"178"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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":0.9986000061035156,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.7984057664871216},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.7913397550582886},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.6821987628936768},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6738516092300415},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.6279841661453247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5988302826881409},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5829553008079529},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.48935216665267944},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4817388355731964},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4365927278995514},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35256263613700867},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32521384954452515},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2082991898059845},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16611412167549133},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13734477758407593},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0882609486579895}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.7984057664871216},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7913397550582886},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.6821987628936768},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6738516092300415},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.6279841661453247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5988302826881409},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5829553008079529},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.48935216665267944},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4817388355731964},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4365927278995514},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35256263613700867},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32521384954452515},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2082991898059845},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16611412167549133},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13734477758407593},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0882609486579895},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/icmla.2013.37","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icmla.2013.37","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 12th International Conference on Machine Learning and Applications","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1550009289","https://openalex.org/W1589379007","https://openalex.org/W1970776980","https://openalex.org/W1984164188","https://openalex.org/W2008708467","https://openalex.org/W2015180542","https://openalex.org/W2019877779","https://openalex.org/W2052033556","https://openalex.org/W2073693914","https://openalex.org/W2099254366","https://openalex.org/W2107158607","https://openalex.org/W2124241917","https://openalex.org/W2153153865","https://openalex.org/W2157009395","https://openalex.org/W2158605937","https://openalex.org/W6632748434","https://openalex.org/W6655699678"],"related_works":["https://openalex.org/W2073661767","https://openalex.org/W2380185347","https://openalex.org/W2368410102","https://openalex.org/W2044328609","https://openalex.org/W2370034659","https://openalex.org/W2012993128","https://openalex.org/W3113308218","https://openalex.org/W3021477453","https://openalex.org/W2159636084","https://openalex.org/W2610941444"],"abstract_inverted_index":{"Primary":[0],"sequence":[1,135,172],"motif":[2,29,45,53,160],"extraction":[3,30,46,161],"from":[4],"protein":[5,41,134],"amino":[6],"sequences":[7],"is":[8,97],"a":[9,34,76,125],"field":[10],"of":[11,71,75,147,156],"growing":[12],"importance":[13],"in":[14,73],"bioinformatics":[15],"due":[16],"to":[17,20,43,132],"its":[18],"relevance":[19],"both":[21],"sequential":[22],"and":[23,50,69,81,94,189],"structural":[24,48],"analysis.":[25],"Many":[26,174],"approaches":[27],"for":[28,105,110,130,159],"include":[31],"two":[32,90],"limitations:":[33],"reliance":[35],"on":[36,112,144,162],"discovering":[37],"an":[38,51],"existing,":[39],"known":[40,99],"homologue":[42],"perform":[44],"or":[47],"analysis,":[49],"assumed":[52],"length.":[54],"This":[55,150],"work":[56],"would":[57],"propose":[58],"the":[59,67,145,148,154,184],"Hierarchically":[60],"Clustered-Hidden":[61],"Markov":[62,78,114],"Model":[63,79],"approach,":[64],"which":[65],"represents":[66],"behavior":[68],"structure":[70,93],"proteins":[72,165],"terms":[74],"Hidden":[77,113],"chain":[80,85],"hierarchically":[82],"clusters":[83],"each":[84],"by":[86,183],"minimizing":[87],"distance":[88],"between":[89],"given":[91],"chain's":[92],"behavior.":[95],"It":[96],"well":[98],"that":[100,137,166],"HMM":[101],"can":[102],"be":[103],"utilized":[104],"clustering":[106,111,127],"purpose,":[107],"however,":[108],"methods":[109],"Models":[115],"themselves":[116],"are":[117,177,187],"rarely":[118],"studied.":[119],"In":[120],"this":[121,157],"paper,":[122],"we":[123],"proposed":[124],"hierarchical":[126],"based":[128],"algorithm":[129],"HMMs":[131],"discover":[133],"motifs":[136,176,181],"transcend":[138],"family":[139],"boundaries":[140],"with":[141,191],"no":[142,168],"assumption":[143],"length":[146],"motif.":[149],"paper":[151],"carefully":[152],"examines":[153],"effectiveness":[155],"approach":[158,186],"2,":[163],"593":[164],"share":[167],"more":[169],"than":[170],"25%":[171],"identity.":[173],"interesting":[175],"generated.":[178],"Three":[179],"example":[180],"generated":[182],"HC-HMM":[185],"analyzed":[188],"visualized":[190],"their":[192],"tertiary":[193],"structure.":[194]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
