{"id":"https://openalex.org/W2886471703","doi":"https://doi.org/10.1142/s0219720018500191","title":"Extending hidden Markov models to allow conditioning on previous observations","display_name":"Extending hidden Markov models to allow conditioning on previous observations","publication_year":2018,"publication_date":"2018-08-03","ids":{"openalex":"https://openalex.org/W2886471703","doi":"https://doi.org/10.1142/s0219720018500191","mag":"2886471703"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720018500191","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720018500191","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-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/A5074156910","display_name":"Ioannis Tamposis","orcid":"https://orcid.org/0000-0001-9247-6871"},"institutions":[{"id":"https://openalex.org/I145722265","display_name":"University of Thessaly","ror":"https://ror.org/04v4g9h31","country_code":"GR","type":"education","lineage":["https://openalex.org/I145722265"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Ioannis A. Tamposis","raw_affiliation_strings":["Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece","institution_ids":["https://openalex.org/I145722265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080412387","display_name":"Margarita C. Theodoropoulou","orcid":null},"institutions":[{"id":"https://openalex.org/I145722265","display_name":"University of Thessaly","ror":"https://ror.org/04v4g9h31","country_code":"GR","type":"education","lineage":["https://openalex.org/I145722265"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Margarita C. Theodoropoulou","raw_affiliation_strings":["Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece","institution_ids":["https://openalex.org/I145722265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087868319","display_name":"Konstantinos D. Tsirigos","orcid":"https://orcid.org/0000-0001-5280-1107"},"institutions":[{"id":"https://openalex.org/I145722265","display_name":"University of Thessaly","ror":"https://ror.org/04v4g9h31","country_code":"GR","type":"education","lineage":["https://openalex.org/I145722265"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Konstantinos D. Tsirigos","raw_affiliation_strings":["Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece","institution_ids":["https://openalex.org/I145722265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035334094","display_name":"Pantelis G. Bagos","orcid":"https://orcid.org/0000-0003-4935-2325"},"institutions":[{"id":"https://openalex.org/I145722265","display_name":"University of Thessaly","ror":"https://ror.org/04v4g9h31","country_code":"GR","type":"education","lineage":["https://openalex.org/I145722265"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Pantelis G. Bagos","raw_affiliation_strings":["Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece"],"raw_orcid":"https://orcid.org/0000-0003-4935-2325","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, 35100 Lamia, Greece","institution_ids":["https://openalex.org/I145722265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5035334094"],"corresponding_institution_ids":["https://openalex.org/I145722265"],"apc_list":null,"apc_paid":null,"fwci":0.5585,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.66187772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"16","issue":"05","first_page":"1850019","last_page":"1850019"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9988999962806702,"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":0.995199978351593,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.8724930286407471},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6902227401733398},{"id":"https://openalex.org/keywords/markov-model","display_name":"Markov model","score":0.5404875874519348},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.49306222796440125},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4863291382789612},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48321664333343506},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4726528227329254},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.466838002204895},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4599458575248718},{"id":"https://openalex.org/keywords/symbol","display_name":"Symbol (formal)","score":0.43952250480651855},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4253196716308594},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3964962065219879}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.8724930286407471},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6902227401733398},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.5404875874519348},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.49306222796440125},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4863291382789612},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48321664333343506},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4726528227329254},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.466838002204895},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4599458575248718},{"id":"https://openalex.org/C134400042","wikidata":"https://www.wikidata.org/wiki/Q2372244","display_name":"Symbol (formal)","level":2,"score":0.43952250480651855},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4253196716308594},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3964962065219879},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720018500191","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720018500191","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmh:oai:ir.lib.uth.gr:11615/79596","is_oa":false,"landing_page_url":"http://hdl.handle.net/11615/79596","pdf_url":null,"source":{"id":"https://openalex.org/S4306400243","display_name":"University of Thessaly Institutional Repository (University of Thessaly)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I145722265","host_organization_name":"University of Thessaly","host_organization_lineage":["https://openalex.org/I145722265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journalArticle"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.6600000262260437}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320286","display_name":"University College London","ror":"https://ror.org/02jx3x895"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1605593725","https://openalex.org/W1939505221","https://openalex.org/W1999761245","https://openalex.org/W2005120335","https://openalex.org/W2006201402","https://openalex.org/W2010266346","https://openalex.org/W2026480276","https://openalex.org/W2034962735","https://openalex.org/W2077837709","https://openalex.org/W2078512978","https://openalex.org/W2078889580","https://openalex.org/W2080382112","https://openalex.org/W2094512392","https://openalex.org/W2105199251","https://openalex.org/W2109553965","https://openalex.org/W2117325244","https://openalex.org/W2123186393","https://openalex.org/W2125838338","https://openalex.org/W2146971959","https://openalex.org/W2147596629","https://openalex.org/W2147905080","https://openalex.org/W2158623906","https://openalex.org/W2160355390","https://openalex.org/W2164751980","https://openalex.org/W2165363237","https://openalex.org/W2166187656","https://openalex.org/W2510407459","https://openalex.org/W2611927968","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W1510894296","https://openalex.org/W2134386692","https://openalex.org/W2082284720","https://openalex.org/W2084326697","https://openalex.org/W2194396582","https://openalex.org/W2027903142","https://openalex.org/W2116722627","https://openalex.org/W2354322608","https://openalex.org/W2379938888","https://openalex.org/W2804608325"],"abstract_inverted_index":{"Hidden":[0],"Markov":[1],"Models":[2],"(HMMs)":[3],"are":[4,191,220],"probabilistic":[5],"models":[6],"widely":[7],"used":[8],"in":[9,58,65,89,121,163],"computational":[10],"molecular":[11],"biology.":[12],"However,":[13],"the":[14,23,29,44,47,59,70,75,86,91,101,116,119,122,130,142,146,154,193,199,212],"Markovian":[15],"assumption":[16],"regarding":[17],"transition":[18],"probabilities":[19],"which":[20,90,124,211],"dictates":[21],"that":[22],"observed":[24,93,109],"symbol":[25,94],"depends":[26,98],"only":[27],"on":[28,69,74,100,105],"current":[30,92,102],"state":[31,103],"may":[32,203],"not":[33],"be":[34],"sufficient":[35],"for":[36,145,210],"some":[37],"biological":[38,168],"problems.":[39],"In":[40],"order":[41,49],"to":[42,61,226],"overcome":[43],"limitations":[45],"of":[46,53,85,108,115,150,156,166,176,181],"first":[48],"HMM,":[50],"a":[51,82,106,164],"number":[52,165],"extensions":[54],"have":[55],"been":[56],"proposed":[57],"literature":[60],"incorporate":[62],"past":[63],"information":[64],"HMMs":[66],"conditioning":[67],"either":[68],"hidden":[71],"states,":[72],"or":[73,77],"observations,":[76],"both.":[78],"Here,":[79],"we":[80],"implement":[81],"simple":[83],"extension":[84],"standard":[87],"HMM":[88],"(amino":[95],"acid":[96],"residue)":[97],"both":[99],"and":[104,148,160,179,198,218],"series":[107],"previous":[110],"symbols.":[111],"The":[112,184,208],"major":[113],"advantage":[114],"method":[117],"is":[118,125],"simplicity":[120],"implementation,":[123],"achieved":[126],"by":[127,172,196],"properly":[128],"transforming":[129],"observation":[131],"sequence,":[132],"using":[133,205],"an":[134],"extended":[135],"alphabet.":[136],"Thus,":[137],"it":[138],"can":[139],"utilize":[140],"all":[141],"available":[143,221],"algorithms":[144],"training":[147],"decoding":[149],"HMMs.":[151],"We":[152],"investigated":[153],"use":[155],"several":[157],"encoding":[158],"schemes":[159],"performed":[161],"tests":[162],"important":[167],"problems":[169],"previously":[170],"studied":[171],"our":[173],"team":[174],"(prediction":[175],"transmembrane":[177],"proteins":[178],"prediction":[180,201],"signal":[182],"peptides).":[183],"evaluation":[185],"shows":[186],"that,":[187],"when":[188],"enough":[189],"data":[190],"available,":[192],"performance":[194],"increased":[195],"1.8%\u20138.2%":[197],"existing":[200],"methods":[202],"improve":[204],"this":[206],"approach.":[207],"methods,":[209],"improvement":[213],"was":[214],"significant":[215],"(PRED-TMBB2,":[216],"PRED-TAT":[217],"HMM-TM),":[219],"as":[222],"web-servers":[223],"freely":[224],"accessible":[225],"academic":[227],"users":[228],"at":[229],"www.compgen.org/tools/":[230],".":[231]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2018-08-22T00:00:00"}