{"id":"https://openalex.org/W2902297217","doi":"https://doi.org/10.1109/tcbb.2018.2884459","title":"imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming","display_name":"imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming","publication_year":2018,"publication_date":"2018-11-30","ids":{"openalex":"https://openalex.org/W2902297217","doi":"https://doi.org/10.1109/tcbb.2018.2884459","mag":"2902297217","pmid":"https://pubmed.ncbi.nlm.nih.gov/30507538"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2884459","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2884459","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5071164294","display_name":"Niko Yasui","orcid":"https://orcid.org/0000-0002-1121-5870"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Niko Yasui","raw_affiliation_strings":["Department of Computing Science, University of Alberta, Canada"],"raw_orcid":"https://orcid.org/0000-0002-1121-5870","affiliations":[{"raw_affiliation_string":"Department of Computing Science, University of Alberta, Canada","institution_ids":["https://openalex.org/I154425047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018915189","display_name":"Chrysafis Vogiatzis","orcid":"https://orcid.org/0000-0003-0787-9380"},"institutions":[{"id":"https://openalex.org/I35777872","display_name":"North Carolina Agricultural and Technical State University","ror":"https://ror.org/02aze4h65","country_code":"US","type":"education","lineage":["https://openalex.org/I35777872"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chrysafis Vogiatzis","raw_affiliation_strings":["Department of Industrial and Systems Engineering, North Carolina A&#x0026;T State University, Greensboro, NC, USA"],"raw_orcid":"https://orcid.org/0000-0003-0787-9380","affiliations":[{"raw_affiliation_string":"Department of Industrial and Systems Engineering, North Carolina A&#x0026;T State University, Greensboro, NC, USA","institution_ids":["https://openalex.org/I35777872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079338715","display_name":"Ruriko Yoshida","orcid":"https://orcid.org/0000-0003-0995-2553"},"institutions":[{"id":"https://openalex.org/I35364215","display_name":"Naval Postgraduate School","ror":"https://ror.org/033yfkj90","country_code":"US","type":"education","lineage":["https://openalex.org/I1330347796","https://openalex.org/I3130687028","https://openalex.org/I35364215"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruriko Yoshida","raw_affiliation_strings":["Department of Operations Research, Naval Postgraduate School, Monterey, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-0995-2553","affiliations":[{"raw_affiliation_string":"Department of Operations Research, Naval Postgraduate School, Monterey, CA, USA","institution_ids":["https://openalex.org/I35364215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012922872","display_name":"Kenji Fukumizu","orcid":"https://orcid.org/0000-0002-3488-2625"},"institutions":[{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kenji Fukumizu","raw_affiliation_strings":["Institute of Statistical Mathematics, Graduate University of Advanced Studies, Tachikawa, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Statistical Mathematics, Graduate University of Advanced Studies, Tachikawa, Tokyo, Japan","institution_ids":["https://openalex.org/I4210134673"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1856,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.54743917,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"17","issue":"4","first_page":"1222","last_page":"1230"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10012","display_name":"Genetic diversity and population structure","score":0.9887999892234802,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.980400025844574,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.8175442218780518},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.7368836402893066},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6542458534240723},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.5916451215744019},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5739442706108093},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4917176067829132},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4892856776714325},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.44427067041397095},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.43187689781188965},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4273141026496887},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3393585681915283},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25953906774520874},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2582903802394867},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2579725980758667},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20977464318275452},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.15164339542388916},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09782388806343079}],"concepts":[{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.8175442218780518},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.7368836402893066},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6542458534240723},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.5916451215744019},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5739442706108093},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4917176067829132},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4892856776714325},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.44427067041397095},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.43187689781188965},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4273141026496887},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3393585681915283},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25953906774520874},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2582903802394867},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2579725980758667},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20977464318275452},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15164339542388916},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09782388806343079},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":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":"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":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2018.2884459","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2884459","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30507538","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30507538","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:calhoun.nps.edu:10945/64578","is_oa":false,"landing_page_url":"https://hdl.handle.net/10945/64578","pdf_url":null,"source":{"id":"https://openalex.org/S4306400952","display_name":"Calhoun: The Naval Postgraduate School Institutional Archive (Naval Postgraduate School)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35364215","host_organization_name":"Naval Postgraduate School","host_organization_lineage":["https://openalex.org/I35364215"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2250548416","display_name":null,"funder_award_id":"1355466","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2570991460","display_name":null,"funder_award_id":"1622369","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"},{"id":"https://openalex.org/G333593389","display_name":null,"funder_award_id":"JSPS KAKENHI 26280009","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310587","display_name":"North Carolina Agricultural and Technical State University","ror":"https://ror.org/02aze4h65"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320337380","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1966972227","https://openalex.org/W2005129098","https://openalex.org/W2016488737","https://openalex.org/W2032016329","https://openalex.org/W2032279931","https://openalex.org/W2037654474","https://openalex.org/W2042696830","https://openalex.org/W2060425093","https://openalex.org/W2063023900","https://openalex.org/W2092493619","https://openalex.org/W2097706568","https://openalex.org/W2101457141","https://openalex.org/W2102230945","https://openalex.org/W2103412835","https://openalex.org/W2107608009","https://openalex.org/W2125070329","https://openalex.org/W2129682166","https://openalex.org/W2129696562","https://openalex.org/W2131487439","https://openalex.org/W2136353610","https://openalex.org/W2139086629","https://openalex.org/W2139736670","https://openalex.org/W2140099453","https://openalex.org/W2145608399","https://openalex.org/W2145754476","https://openalex.org/W2147432522","https://openalex.org/W2151409320","https://openalex.org/W2151690408","https://openalex.org/W2152341912","https://openalex.org/W2152933358","https://openalex.org/W2155998147","https://openalex.org/W2156524622","https://openalex.org/W2160971996","https://openalex.org/W2163924163","https://openalex.org/W2166029961","https://openalex.org/W2176633348","https://openalex.org/W2195393701","https://openalex.org/W2229908198","https://openalex.org/W2272332482","https://openalex.org/W2594416172","https://openalex.org/W2611511275","https://openalex.org/W2798084948","https://openalex.org/W2963076108","https://openalex.org/W4210681352","https://openalex.org/W4230603454","https://openalex.org/W4231338500","https://openalex.org/W4388212639","https://openalex.org/W6658336452","https://openalex.org/W6674647444","https://openalex.org/W6685653908","https://openalex.org/W6689475862","https://openalex.org/W6693930347","https://openalex.org/W6737611581","https://openalex.org/W6765858115"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W2055961818","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W4254268221"],"abstract_inverted_index":{"Advances":[0],"in":[1,80,164,198,207,258,265,288,298],"modern":[2],"genomics":[3],"have":[4],"allowed":[5],"researchers":[6],"to":[7,72,118,157],"apply":[8],"phylogenetic":[9],"analyses":[10],"on":[11,133],"a":[12,30,44,53,64,141,165,171,180,189],"genome-wide":[13],"scale.":[14],"While":[15],"large":[16,54],"volumes":[17],"of":[18,47,56,63,144,167,191,238,295],"genomic":[19],"data":[20,27,81,107,124],"can":[21,95,186,309],"be":[22,310],"generated":[23],"cheaply":[24],"and":[25,32,50,85,129,151,221,231,234,254,268,276,306],"quickly,":[26],"missingness":[28],"is":[29,40,104,108,117,137],"non-trivial":[31],"somewhat":[33],"expected":[34],"problem.":[35],"Since":[36],"the":[37,60,111,126,131,159,203,213,217,236,239,243,272,289,296],"available":[38,139],"information":[39,83,136,264],"often":[41],"incomplete":[42,263],"for":[43],"given":[45],"set":[46,166,190],"genetic":[48,66],"loci":[49],"individual":[51],"organisms,":[52],"proportion":[55],"trees":[57,169,193,215,261],"that":[58,185],"depict":[59],"evolutionary":[61],"history":[62],"single":[65],"locus,":[67],"called":[68],"gene":[69,86,92,98,100,112,127,168,192,209,214,260,300],"trees,":[70,93,128],"fail":[71],"contain":[73],"all":[74,120],"individuals.":[75],"Data":[76],"incompleteness":[77],"causes":[78],"difficulties":[79],"collection,":[82],"extraction,":[84],"tree":[87,301],"inference.":[88],"Furthermore,":[89],"identifying":[90],"outlying":[91],"which":[94],"represent":[96],"horizontal":[97],"transfers,":[99],"duplications,":[101],"or":[102],"hybridizations,":[103],"difficult":[105],"when":[106],"missing":[109,123,160,197,204,244],"from":[110,125],"trees.":[113],"The":[114],"typical":[115],"approach":[116,156],"remove":[119],"individuals":[121,134,297],"with":[122,194,226,262],"focus":[130],"analysis":[132],"whose":[135],"fully":[138],"-":[140],"huge":[142],"loss":[143],"information.":[145],"In":[146,271],"this":[147],"work,":[148],"we":[149,246],"propose":[150],"design":[152],"an":[153],"optimization-based":[154],"imputation":[155,279],"infer":[158],"distances":[161,206],"between":[162],"leaves":[163,195],"via":[170],"mixed":[172],"integer":[173],"non-linear":[174,251],"programming":[175,252],"model.":[176],"We":[177],"also":[178],"present":[179],"new":[181],"research":[182],"pipeline,":[183],"imPhy,":[184],"(i)":[187],"simulate":[188],"randomly":[196],"each":[199,208,299],"tree,":[200,210],"(ii)":[201],"impute":[202,242],"pairwise":[205],"(iii)":[211],"reconstruct":[212],"using":[216],"Neighbor":[218],"Joining":[219],"(NJ)":[220],"Unweighted":[222],"Pair":[223],"Group":[224],"Method":[225],"Arithmetic":[227],"Mean":[228],"(UPGMA)":[229],"methods,":[230],"(iv)":[232],"analyze":[233],"report":[235],"efficiency":[237],"reconstruction.":[240],"To":[241],"leaves,":[245],"employ":[247],"our":[248,278],"newly":[249],"proposed":[250],"framework,":[253],"demonstrate":[255],"its":[256],"capability":[257],"reconstructing":[259],"both":[266],"simulated":[267],"empirical":[269,273],"datasets.":[270],"datasets":[274],"apicomplexa":[275],"lungfish,":[277],"has":[280],"very":[281],"small":[282],"normalized":[283],"mean":[284],"square":[285],"errors,":[286],"even":[287],"extreme":[290],"case":[291],"where":[292],"50":[293],"percent":[294],"are":[302],"missing.":[303],"Data,":[304],"software,":[305],"user":[307],"manuals":[308],"found":[311],"at":[312],"https://github.com/yasuiniko/imPhy.":[313]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
