{"id":"https://openalex.org/W2125636448","doi":"https://doi.org/10.1017/s1471068410000219","title":"Inference with constrained hidden Markov models in PRISM","display_name":"Inference with constrained hidden Markov models in PRISM","publication_year":2010,"publication_date":"2010-07-01","ids":{"openalex":"https://openalex.org/W2125636448","doi":"https://doi.org/10.1017/s1471068410000219","mag":"2125636448"},"language":"en","primary_location":{"id":"doi:10.1017/s1471068410000219","is_oa":false,"landing_page_url":"https://doi.org/10.1017/s1471068410000219","pdf_url":null,"source":{"id":"https://openalex.org/S59670734","display_name":"Theory and Practice of Logic Programming","issn_l":"1471-0684","issn":["1471-0684","1475-3081"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theory and Practice of Logic Programming","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1007.5421","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021255849","display_name":"Henning Christiansen","orcid":"https://orcid.org/0000-0003-4731-9927"},"institutions":[{"id":"https://openalex.org/I107707843","display_name":"Roskilde University","ror":"https://ror.org/014axpa37","country_code":"DK","type":"education","lineage":["https://openalex.org/I107707843"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"HENNING CHRISTIANSEN","raw_affiliation_strings":["Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#"],"affiliations":[{"raw_affiliation_string":"Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","institution_ids":["https://openalex.org/I107707843"]},{"raw_affiliation_string":"Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113443214","display_name":"Henri Theil","orcid":"https://orcid.org/0000-0002-8634-4781"},"institutions":[{"id":"https://openalex.org/I107707843","display_name":"Roskilde University","ror":"https://ror.org/014axpa37","country_code":"DK","type":"education","lineage":["https://openalex.org/I107707843"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"CHRISTIAN THEIL HAVE","raw_affiliation_strings":["Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#"],"affiliations":[{"raw_affiliation_string":"Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","institution_ids":["https://openalex.org/I107707843"]},{"raw_affiliation_string":"Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008089772","display_name":"Ole Torp Lassen","orcid":null},"institutions":[{"id":"https://openalex.org/I107707843","display_name":"Roskilde University","ror":"https://ror.org/014axpa37","country_code":"DK","type":"education","lineage":["https://openalex.org/I107707843"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"OLE TORP LASSEN","raw_affiliation_strings":["Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#"],"affiliations":[{"raw_affiliation_string":"Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","institution_ids":["https://openalex.org/I107707843"]},{"raw_affiliation_string":"Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014771093","display_name":"Matthieu Petit","orcid":"https://orcid.org/0000-0003-3267-9938"},"institutions":[{"id":"https://openalex.org/I107707843","display_name":"Roskilde University","ror":"https://ror.org/014axpa37","country_code":"DK","type":"education","lineage":["https://openalex.org/I107707843"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"MATTHIEU PETIT","raw_affiliation_strings":["Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#"],"affiliations":[{"raw_affiliation_string":"Research Group PLIS: Programming, Logic and Intelligent Systems, Department of Communication, Business and Information Technologies, Roskilde University, P.O.Box 260, DK-4000 Roskilde, Denmark (e-mail:","institution_ids":["https://openalex.org/I107707843"]},{"raw_affiliation_string":"Research group plis: programming, logic and intelligent systems, department of communication, business and information technologies, roskilde university, p.o.box 260, dk-4000 roskilde, denmark (e- ...#TAB#","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021255849"],"corresponding_institution_ids":["https://openalex.org/I107707843"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14480691,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":"4-6","first_page":"449","last_page":"464"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9991999864578247,"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"}},"topics":[{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9991999864578247,"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"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.998199999332428,"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"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9965999722480774,"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":0.824741542339325},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7363009452819824},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.6770423054695129},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6400070190429688},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.5719349384307861},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5291968584060669},{"id":"https://openalex.org/keywords/cardinality","display_name":"Cardinality (data modeling)","score":0.5281505584716797},{"id":"https://openalex.org/keywords/constraint-programming","display_name":"Constraint programming","score":0.4782915711402893},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47153860330581665},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4307529032230377},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4284258186817169},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37975794076919556},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2547258138656616},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2399316430091858},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.23132294416427612},{"id":"https://openalex.org/keywords/stochastic-programming","display_name":"Stochastic programming","score":0.1463959813117981}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.824741542339325},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7363009452819824},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.6770423054695129},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6400070190429688},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.5719349384307861},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5291968584060669},{"id":"https://openalex.org/C87117476","wikidata":"https://www.wikidata.org/wiki/Q362383","display_name":"Cardinality (data modeling)","level":2,"score":0.5281505584716797},{"id":"https://openalex.org/C173404611","wikidata":"https://www.wikidata.org/wiki/Q528588","display_name":"Constraint programming","level":3,"score":0.4782915711402893},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47153860330581665},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4307529032230377},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4284258186817169},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37975794076919556},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2547258138656616},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2399316430091858},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.23132294416427612},{"id":"https://openalex.org/C137631369","wikidata":"https://www.wikidata.org/wiki/Q7617831","display_name":"Stochastic programming","level":2,"score":0.1463959813117981},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1017/s1471068410000219","is_oa":false,"landing_page_url":"https://doi.org/10.1017/s1471068410000219","pdf_url":null,"source":{"id":"https://openalex.org/S59670734","display_name":"Theory and Practice of Logic Programming","issn_l":"1471-0684","issn":["1471-0684","1475-3081"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theory and Practice of Logic Programming","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1007.5421","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1007.5421","pdf_url":"https://arxiv.org/pdf/1007.5421","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"mag:2125636448","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1007.5421.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:pure.atira.dk:publications/5f69fc80-8d91-11df-954c-000ea68e967b","is_oa":false,"landing_page_url":"https://forskning.ruc.dk/da/publications/5f69fc80-8d91-11df-954c-000ea68e967b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401457","display_name":"RUCforsk (Roskilde University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I107707843","host_organization_name":"Roskilde University","host_organization_lineage":["https://openalex.org/I107707843"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Christiansen, H, Have, C T, Lassen, O T & Petit, M 2010, 'Inference with constrained hidden Markov models in PRISM', Theory and Practice of Logic Programming, vol. 10, no. 4-6, pp. 449-464. https://doi.org/10.1017/S1471068410000219","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.48550/arxiv.1007.5421","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1007.5421","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1007.5421","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1007.5421","pdf_url":"https://arxiv.org/pdf/1007.5421","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320335354","display_name":"Strategic Research Council","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125636448.pdf","grobid_xml":"https://content.openalex.org/works/W2125636448.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W173113430","https://openalex.org/W1518458436","https://openalex.org/W1543028224","https://openalex.org/W1836031362","https://openalex.org/W1991133427","https://openalex.org/W2004059413","https://openalex.org/W2011617423","https://openalex.org/W2100145144","https://openalex.org/W2118656391","https://openalex.org/W2125838338","https://openalex.org/W2141732516","https://openalex.org/W2177977456","https://openalex.org/W2283350629","https://openalex.org/W2890040444","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2522597118","https://openalex.org/W2248934801","https://openalex.org/W2622364826","https://openalex.org/W2988290054","https://openalex.org/W3101787353","https://openalex.org/W3005679805","https://openalex.org/W2041345209","https://openalex.org/W2949995692","https://openalex.org/W3112885990","https://openalex.org/W1573172661","https://openalex.org/W2903958360","https://openalex.org/W1625318532","https://openalex.org/W3183062813","https://openalex.org/W2962919508","https://openalex.org/W2171016142","https://openalex.org/W2735743125","https://openalex.org/W3038379741","https://openalex.org/W3014266848","https://openalex.org/W304228415","https://openalex.org/W1753658588"],"abstract_inverted_index":{"Abstract":[0],"A":[1],"Hidden":[2],"Markov":[3],"Model":[4],"(HMM)":[5],"is":[6,12],"a":[7,69],"common":[8],"statistical":[9],"model":[10],"which":[11],"widely":[13],"used":[14],"for":[15,43,72],"analysis":[16],"of":[17,58,99],"biological":[18],"sequence":[19],"data":[20],"and":[21,38,62,77,85],"other":[22],"sequential":[23],"phenomena.":[24],"In":[25],"the":[26,95],"present":[27,39,68],"paper":[28],"we":[29],"show":[30,78],"how":[31,79],"HMMs":[32,47,74],"can":[33],"be":[34],"extended":[35],"with":[36,48,75],"side-constraints":[37,49,76],"constraint":[40],"solving":[41],"techniques":[42],"efficient":[44],"inference.":[45,66],"Defining":[46],"in":[50,56],"Constraint":[51],"Logic":[52],"Programming":[53],"has":[54],"advantages":[55],"terms":[57],"more":[59],"compact":[60],"expression":[61],"pruning":[63],"opportunities":[64],"during":[65],"We":[67,89],"PRISM-based":[70],"framework":[71],"extending":[73],"well-known":[80],"constraints":[81],"such":[82],"as":[83],"cardinality":[84],"all_different":[86],"are":[87],"integrated.":[88],"experimentally":[90],"validate":[91],"our":[92],"approach":[93],"on":[94],"biologically":[96],"motivated":[97],"problem":[98],"global":[100],"pairwise":[101],"alignment.":[102]},"counts_by_year":[],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}