{"id":"https://openalex.org/W4311287631","doi":"https://doi.org/10.1093/bioinformatics/btac803","title":"HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs","display_name":"HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs","publication_year":2022,"publication_date":"2022-12-13","ids":{"openalex":"https://openalex.org/W4311287631","doi":"https://doi.org/10.1093/bioinformatics/btac803","pmid":"https://pubmed.ncbi.nlm.nih.gov/36511587"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac803","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac803","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac803/48763705/btac803.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac803/48763705/btac803.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061748348","display_name":"Marcus T. Moen","orcid":null},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Marcus T Moen","raw_affiliation_strings":["Department of Mathematics, University of Bergen , Bergen, Vestland, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Bergen , Bergen, Vestland, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016846029","display_name":"Iain G. Johnston","orcid":"https://orcid.org/0000-0001-8559-3519"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Iain G Johnston","raw_affiliation_strings":["CAMRIA Centre for Antimicrobial Resistance , Vestland, Norway","Computational Biology Unit, University of Bergen , Bergen, Vestland, Norway","Department of Mathematics, University of Bergen , Bergen, Vestland, Norway"],"raw_orcid":"https://orcid.org/0000-0001-8559-3519","affiliations":[{"raw_affiliation_string":"CAMRIA Centre for Antimicrobial Resistance , Vestland, Norway","institution_ids":[]},{"raw_affiliation_string":"Computational Biology Unit, University of Bergen , Bergen, Vestland, Norway","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Department of Mathematics, University of Bergen , Bergen, Vestland, Norway","institution_ids":["https://openalex.org/I4432739"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5016846029"],"corresponding_institution_ids":["https://openalex.org/I4432739"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7227,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.85116646,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2167000025510788,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2167000025510788,"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/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.13809999823570251,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.05550000071525574,"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/inference","display_name":"Inference","score":0.8299423456192017},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6792485117912292},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5213952660560608},{"id":"https://openalex.org/keywords/resampling","display_name":"Resampling","score":0.5114011168479919},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4807003140449524},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.4575265347957611},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4242042005062103},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.38730350136756897},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.3791493773460388}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.8299423456192017},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6792485117912292},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5213952660560608},{"id":"https://openalex.org/C150921843","wikidata":"https://www.wikidata.org/wiki/Q1170431","display_name":"Resampling","level":2,"score":0.5114011168479919},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4807003140449524},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.4575265347957611},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4242042005062103},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38730350136756897},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.3791493773460388}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac803","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac803","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac803/48763705/btac803.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:36511587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36511587","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:bora.uib.no:11250/3047679","is_oa":true,"landing_page_url":"https://hdl.handle.net/11250/3047679","pdf_url":"https://bora.uib.no/bora-xmlui/bitstream/11250/3047679/1/btac803.pdf","source":{"id":"https://openalex.org/S4306401716","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"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":"btac803","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9848056","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9848056","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/btac803","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac803","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac803/48763705/btac803.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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/3","score":0.4099999964237213,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G6951923247","display_name":null,"funder_award_id":"805046","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7513016640","display_name":null,"funder_award_id":"TMS2020TMT11","funder_id":"https://openalex.org/F4320316417","funder_display_name":"Trond Mohn stiftelse"},{"id":"https://openalex.org/G7821318236","display_name":null,"funder_award_id":"TMS2021TMT09","funder_id":"https://openalex.org/F4320316417","funder_display_name":"Trond Mohn stiftelse"}],"funders":[{"id":"https://openalex.org/F4320316417","display_name":"Trond Mohn stiftelse","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4311287631.pdf","grobid_xml":"https://content.openalex.org/works/W4311287631.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1975407466","https://openalex.org/W1991874243","https://openalex.org/W2039577063","https://openalex.org/W2042220296","https://openalex.org/W2069196178","https://openalex.org/W2086699924","https://openalex.org/W2105594594","https://openalex.org/W2109077054","https://openalex.org/W2118207809","https://openalex.org/W2122082385","https://openalex.org/W2132886879","https://openalex.org/W2134871125","https://openalex.org/W2149958386","https://openalex.org/W2153938747","https://openalex.org/W2158619663","https://openalex.org/W2207661154","https://openalex.org/W2233432342","https://openalex.org/W2253465175","https://openalex.org/W2280923288","https://openalex.org/W2340974016","https://openalex.org/W2513118531","https://openalex.org/W2588969809","https://openalex.org/W2589408153","https://openalex.org/W2606156256","https://openalex.org/W2772124661","https://openalex.org/W2801141004","https://openalex.org/W2897562111","https://openalex.org/W2955648521","https://openalex.org/W2961700348","https://openalex.org/W2965390994","https://openalex.org/W2990080810","https://openalex.org/W3034877140","https://openalex.org/W3110394251","https://openalex.org/W3110657116","https://openalex.org/W3127809696","https://openalex.org/W4226155266","https://openalex.org/W4250847479","https://openalex.org/W4287086359","https://openalex.org/W6798519690"],"related_works":["https://openalex.org/W2753218748","https://openalex.org/W2774409638","https://openalex.org/W2789413038","https://openalex.org/W2889562828","https://openalex.org/W2953280030","https://openalex.org/W2952635455","https://openalex.org/W2104594922","https://openalex.org/W3002319139","https://openalex.org/W2589314268","https://openalex.org/W4300815303"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,66],"evolution":[2],"of":[3,14,23,35,63,73,83,165,177,184],"bacterial":[4],"drug":[5],"resistance":[6],"and":[7,16,19,88,139,195,198,207,216,218],"other":[8,17,178],"features":[9],"in":[10,204],"biology,":[11],"the":[12,31,52,81,175],"progression":[13],"cancer":[15],"diseases":[18],"a":[20,61,99,181],"wide":[21],"range":[22],"broader":[24],"questions":[25],"can":[26,110],"often":[27],"be":[28],"viewed":[29],"as":[30],"sequential":[32],"stochastic":[33],"acquisition":[34,176],"binary":[36],"traits":[37,57,166],"(e.g.":[38],"genetic":[39],"changes,":[40],"symptoms":[41],"or":[42,47,78,171],"characters).":[43],"Using":[44],"potentially":[45],"noisy":[46],"incomplete":[48],"data":[49,219,231],"to":[50,136,153,167,193],"learn":[51],"sequences":[53],"by":[54],"which":[55,75],"such":[56],"are":[58,232],"acquired":[59],"is":[60,68,223],"problem":[62,67],"general":[64,202],"interest.":[65],"complicated":[69],"for":[70,114,131,214,220],"large":[71],"numbers":[72],"traits,":[74,179],"may,":[76],"individually":[77],"synergistically,":[79],"influence":[80,173],"probability":[82],"further":[84],"acquisitions":[85],"both":[86],"positively":[87],"negatively.":[89],"Hypercubic":[90],"inference":[91,133,146,156,215],"approaches,":[92],"based":[93],"on":[94,98,174],"hidden":[95],"Markov":[96],"models":[97],"hypercubic":[100,132,155],"transition":[101],"network,":[102],"address":[103],"these":[104],"complications,":[105],"but":[106],"previous":[107,154],"Bayesian":[108],"instances":[109],"consume":[111],"substantial":[112],"time":[113],"converged":[115],"results,":[116],"limiting":[117],"their":[118],"practical":[119,150],"use.":[120],"RESULTS:":[121],"Here,":[122],"we":[123],"introduce":[124],"HyperHMM,":[125],"an":[126],"adapted":[127],"Baum-Welch":[128],"(expectation-maximization)":[129],"algorithm":[130],"with":[134],"resampling":[135],"quantify":[137],"uncertainty,":[138],"show":[140,159],"that":[141,160],"it":[142],"allows":[143,162],"orders-of-magnitude":[144],"faster":[145],"while":[147],"making":[148],"few":[149],"sacrifices":[151],"compared":[152],"approaches.":[157],"We":[158,189],"HyperHMM":[161],"any":[163],"combination":[164],"exert":[168],"arbitrary":[169],"positive":[170],"negative":[172],"relaxing":[180],"common":[182],"limitation":[183],"only":[185],"independent":[186],"trait":[187],"influences.":[188],"apply":[190],"this":[191],"approach":[192],"synthetic":[194],"biological":[196],"datasets":[197],"discuss":[199],"its":[200],"more":[201],"application":[203],"learning":[205],"evolutionary":[206],"progressive":[208],"pathways.":[209],"AVAILABILITY":[210],"AND":[211],"IMPLEMENTATION:":[212],"Code":[213],"visualization,":[217],"example":[221],"cases,":[222],"freely":[224],"available":[225,233],"at":[226,234],"https://github.com/StochasticBiology/hypercube-hmm.":[227],"SUPPLEMENTARY":[228],"INFORMATION:":[229],"Supplementary":[230],"Bioinformatics":[235],"online.":[236]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
