{"id":"https://openalex.org/W2165001851","doi":"https://doi.org/10.1093/bioinformatics/bth917","title":"Efficient approximations for learning phylogenetic HMM models from data","display_name":"Efficient approximations for learning phylogenetic HMM models from data","publication_year":2004,"publication_date":"2004-07-19","ids":{"openalex":"https://openalex.org/W2165001851","doi":"https://doi.org/10.1093/bioinformatics/bth917","mag":"2165001851","pmid":"https://pubmed.ncbi.nlm.nih.gov/15262795"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth917","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth917","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005113963","display_name":"Vladimir Jojic","orcid":null},"institutions":[{"id":"https://openalex.org/I1290206253","display_name":"Microsoft (United States)","ror":"https://ror.org/00d0nc645","country_code":"US","type":"company","lineage":["https://openalex.org/I1290206253"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vladimir Jojic","raw_affiliation_strings":["Microsoft Research, Redmond, WA 98052, USA. vjojic@psi.toronto.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microsoft Research, Redmond, WA 98052, USA. vjojic@psi.toronto.edu","institution_ids":["https://openalex.org/I1290206253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108373424","display_name":"Neboj\u0161a Joji\u0107","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nebojsa Jojic","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010587765","display_name":"Christopher Meek","orcid":"https://orcid.org/0000-0002-6744-0591"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chris Meek","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000414827","display_name":"Dan Geiger","orcid":"https://orcid.org/0000-0001-9988-0199"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dan Geiger","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061240989","display_name":"Adam Siepel","orcid":"https://orcid.org/0000-0002-3557-7219"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Adam Siepel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090849321","display_name":"David Haussler","orcid":"https://orcid.org/0000-0003-1533-4575"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David Haussler","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5016386034","display_name":"David Heckerman","orcid":"https://orcid.org/0000-0002-4274-6084"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"D. Heckerman","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8089,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.8436902,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"suppl_1","first_page":"i161","last_page":"i168"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6937000155448914,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6937000155448914,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.11990000307559967,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.023399999365210533,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6107208132743835},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5980868339538574},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5852439999580383},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5331194996833801},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5184156894683838},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3666417896747589},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19231748580932617},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10827317833900452},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06532883644104004}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6107208132743835},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5980868339538574},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5852439999580383},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5331194996833801},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5184156894683838},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3666417896747589},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19231748580932617},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10827317833900452},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06532883644104004}],"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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth917","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth917","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15262795","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15262795","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:repository.cshl.edu:31073","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.550000011920929}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1516111018","https://openalex.org/W1957469265","https://openalex.org/W1967131476","https://openalex.org/W1980452149","https://openalex.org/W1996387066","https://openalex.org/W1997945171","https://openalex.org/W2009570821","https://openalex.org/W2009596137","https://openalex.org/W2052576140","https://openalex.org/W2076634000","https://openalex.org/W2091851394","https://openalex.org/W2098678088","https://openalex.org/W2102424972","https://openalex.org/W2119632499","https://openalex.org/W2124608480","https://openalex.org/W2124790653","https://openalex.org/W2137188869","https://openalex.org/W2142664059","https://openalex.org/W2152512662","https://openalex.org/W2156521045","https://openalex.org/W2159080219","https://openalex.org/W2163941254","https://openalex.org/W2166444569","https://openalex.org/W2567948266"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W2033914206","https://openalex.org/W4283697347"],"abstract_inverted_index":{"MOTIVATION:":[0],"We":[1,63,90],"consider":[2,28,64],"models":[3,49,60,73],"useful":[4],"for":[5,67],"learning":[6],"an":[7,75],"evolutionary":[8],"or":[9],"phylogenetic":[10],"tree":[11],"from":[12,141],"data":[13,140],"consisting":[14],"of":[15,22,50,58,71,135],"DNA":[16],"sequences":[17],"corresponding":[18],"to":[19,104,117,139],"the":[20,23,41,46,56,69,94,107,122,129,142],"leaves":[21],"tree.":[24],"In":[25,109],"particular,":[26],"we":[27,39,111],"a":[29,113,155],"general":[30],"probabilistic":[31,48],"model":[32,43],"described":[33],"in":[34,78,120],"Siepel":[35,79],"and":[36,52,80,85,101],"Haussler":[37],"that":[38],"call":[40],"phylogenetic-HMM":[42,59],"which":[44,121],"generalizes":[45],"classical":[47],"Neyman":[51],"Felsenstein.":[53],"Unfortunately,":[54],"computing":[55,68],"likelihood":[57,70],"is":[61,125],"intractable.":[62],"several":[65,86],"approximations":[66],"such":[72],"including":[74],"approximation":[76,116,138],"introduced":[77],"Haussler,":[81],"loopy":[82],"belief":[83],"propagation":[84],"variational":[87,97,115],"methods.":[88],"RESULTS:":[89],"demonstrate":[91],"that,":[92],"unlike":[93],"other":[95],"approximations,":[96],"methods":[98],"are":[99,102],"accurate":[100],"guaranteed":[103],"lower":[105],"bound":[106],"likelihood.":[108],"addition,":[110],"identify":[112],"particular":[114],"be":[118],"best-one":[119],"posterior":[123],"distribution":[124],"variationally":[126],"approximated":[127],"using":[128],"classic":[130],"Neyman-Felsenstein":[131],"model.":[132],"The":[133],"application":[134],"our":[136],"best":[137],"cystic":[143],"fibrosis":[144],"transmembrane":[145],"conductance":[146],"regulator":[147],"gene":[148],"region":[149],"across":[150],"nine":[151],"eutherian":[152],"mammals":[153],"reveals":[154],"CpG":[156],"effect.":[157]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}