{"id":"https://openalex.org/W4281385537","doi":"https://doi.org/10.1142/s0219720022500123","title":"Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network","display_name":"Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network","publication_year":2022,"publication_date":"2022-05-24","ids":{"openalex":"https://openalex.org/W4281385537","doi":"https://doi.org/10.1142/s0219720022500123","pmid":"https://pubmed.ncbi.nlm.nih.gov/35798684"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720022500123","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720022500123","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","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/A5083583971","display_name":"Nadia Tahiri","orcid":"https://orcid.org/0000-0002-1818-208X"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nadia Tahiri","raw_affiliation_strings":["Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada"],"raw_orcid":"https://orcid.org/0000-0002-1818-208X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087018456","display_name":"Andrey Veriga","orcid":null},"institutions":[{"id":"https://openalex.org/I178165815","display_name":"Astrakhan Tatischev State University","ror":"https://ror.org/04tf3kx07","country_code":"RU","type":"education","lineage":["https://openalex.org/I178165815"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrey Veriga","raw_affiliation_strings":["Center of Artificial Intelligence, Astrakhan State University, Astrakhan 414056, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Artificial Intelligence, Astrakhan State University, Astrakhan 414056, Russia","institution_ids":["https://openalex.org/I178165815"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063876203","display_name":"Aleksandr Koshkarov","orcid":"https://orcid.org/0000-0002-3630-2911"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Aleksandr Koshkarov","raw_affiliation_strings":["Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107233829","display_name":"B.V. Morozov","orcid":null},"institutions":[{"id":"https://openalex.org/I178165815","display_name":"Astrakhan Tatischev State University","ror":"https://ror.org/04tf3kx07","country_code":"RU","type":"education","lineage":["https://openalex.org/I178165815"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Boris Morozov","raw_affiliation_strings":["Department of Information Technology, Astrakhan State University, Astrakhan 414056, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, Astrakhan State University, Astrakhan 414056, Russia","institution_ids":["https://openalex.org/I178165815"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.1151,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.83017059,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"20","issue":"04","first_page":"2250012","last_page":"2250012"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"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":0.9871000051498413,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7598268389701843},{"id":"https://openalex.org/keywords/tree-rearrangement","display_name":"Tree rearrangement","score":0.628518283367157},{"id":"https://openalex.org/keywords/distance-matrices-in-phylogeny","display_name":"Distance matrices in phylogeny","score":0.6214948892593384},{"id":"https://openalex.org/keywords/distance-matrix","display_name":"Distance matrix","score":0.5540119409561157},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5347532033920288},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5293686389923096},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.516741931438446},{"id":"https://openalex.org/keywords/supertree","display_name":"Supertree","score":0.47263285517692566},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.4621921181678772},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.447933554649353},{"id":"https://openalex.org/keywords/invariant","display_name":"Invariant (physics)","score":0.43786129355430603},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.42389440536499023},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4209882318973541},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4207283556461334},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.37200289964675903},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.28242403268814087},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2758273482322693},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.17504945397377014},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07692262530326843}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7598268389701843},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.628518283367157},{"id":"https://openalex.org/C5349765","wikidata":"https://www.wikidata.org/wiki/Q5282866","display_name":"Distance matrices in phylogeny","level":2,"score":0.6214948892593384},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.5540119409561157},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5347532033920288},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5293686389923096},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.516741931438446},{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.47263285517692566},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.4621921181678772},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.447933554649353},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.43786129355430603},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.42389440536499023},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4209882318973541},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4207283556461334},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.37200289964675903},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.28242403268814087},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2758273482322693},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.17504945397377014},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07692262530326843},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0}],"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":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022761","descriptor_name":"Gene Transfer, Horizontal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720022500123","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720022500123","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":"pmid:35798684","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35798684","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5299999713897705,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334618","display_name":"Fonds de Recherche du Qu\u00e9bec - Sant\u00e9","ror":"https://ror.org/02eqrsj93"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1774207464","https://openalex.org/W1984017781","https://openalex.org/W2060425093","https://openalex.org/W2070620318","https://openalex.org/W2082711139","https://openalex.org/W2111211467","https://openalex.org/W2112620675","https://openalex.org/W2124808846","https://openalex.org/W2130921644","https://openalex.org/W2131944877","https://openalex.org/W2141052558","https://openalex.org/W2151062029","https://openalex.org/W2159579403","https://openalex.org/W2161444534","https://openalex.org/W2163949171","https://openalex.org/W2308528431","https://openalex.org/W2477464894","https://openalex.org/W2577202510","https://openalex.org/W2805555771","https://openalex.org/W2996962969","https://openalex.org/W3138967247","https://openalex.org/W4233815609"],"related_works":["https://openalex.org/W2001076853","https://openalex.org/W2769292036","https://openalex.org/W2963639031","https://openalex.org/W2151690408","https://openalex.org/W2145844324","https://openalex.org/W2890390314","https://openalex.org/W2765484734","https://openalex.org/W2052550780","https://openalex.org/W2111928042","https://openalex.org/W1003773566"],"abstract_inverted_index":{"The":[0,90,271,326,350,432],"evolutionary":[1,18,34,52,141,182,351,371,401,418],"histories":[2],"of":[3,7,36,58,79,87,100,106,113,120,187,194,215,249,251,259,277,284,295,308,310,353,363,403,434,463,497,502],"genes":[4,385],"are":[5,93,126,335,345],"susceptible":[6],"differing":[8],"greatly":[9],"from":[10,44,376],"each":[11,37,366,404],"other":[12],"which":[13,39,261,414,506],"could":[14],"be":[15,63,389,407,512],"explained":[16],"by":[17,391,409],"variations":[19],"in":[20,184,206,217,305,454,465,499],"horizontal":[21,393],"gene":[22,367,378,394,405],"transfers":[23],"or":[24,82,108,158,386,438,447],"biological":[25],"recombinations.":[26],"A":[27],"phylogenetic":[28,56,188,254,412],"tree":[29,47,95,241,423,437,446,489],"would":[30],"therefore":[31],"represent":[32,178],"the":[33,45,50,67,77,85,98,103,111,153,159,179,192,195,199,213,252,263,278,306,400,421,427,461,500,503],"history":[35,352,372,402],"gene,":[38],"may":[40,388,415],"present":[41,71,453],"different":[42,140,291,417],"patterns":[43,419],"species":[46,61,354,422],"that":[48,176,373,424],"defines":[49],"main":[51],"patterns.":[53,431],"In":[54,449],"addition,":[55],"trees":[57,75,101,114,123,173,255],"closely":[59],"related":[60],"should":[62],"merged,":[64],"thus":[65],"minimizing":[66],"topological":[68],"conflicts":[69],"they":[70],"and":[72,124,174,197,220,268,314,330,396,468,515],"obtaining":[73],"consensus":[74,94,172,436,445],"(in":[76,84],"case":[78,86],"homogeneous":[80],"data)":[81],"supertrees":[83,109,125,175,287],"heterogeneous":[88],"data).":[89],"traditional":[91,435],"approaches":[92,144],"inference":[96,307,440],"(if":[97,110],"set":[99,105,112,186],"contains":[102,115],"same":[104],"species)":[107],"different,":[116],"but":[117,280,292,358],"overlapping":[118,293],"sets":[119,258,294,362],"species).":[121],"Consensus":[122],"constructed":[127],"to":[128,139,148,361,379,486,511],"produce":[129],"unique":[130],"trees.":[131],"However,":[132],"these":[133],"methods":[134,441],"lose":[135],"precision":[136,193],"with":[137,290],"respect":[138],"variability.":[142],"Other":[143],"have":[145],"been":[146],"implemented":[147],"preserve":[149],"this":[150,450,508],"variability":[151],"using":[152,225,288,473],"[Formula:":[154,160],"see":[155,161],"text]-means":[156],"algorithm":[157],"text]-medoids":[162],"algorithm.":[163],"Using":[164],"a":[165,185,208,218,226,233,247,320,443,456,466,474,481,495],"new":[166,209,234,244,264,298,457,482,492,509],"method,":[167],"we":[168,452],"determine":[169],"all":[170],"possible":[171],"best":[177],"most":[180],"significant":[181],"models":[183],"trees,":[189,260,505],"thereby":[190],"increasing":[191],"results":[196],"decreasing":[198],"time":[200],"required.":[201],"Results:":[202],"This":[203,243,297,491],"paper":[204,272],"presents":[205],"detail":[207,455],"method":[210,458],"for":[211,239,256,426,459],"predicting":[212,460],"number":[214,248,462,496],"clusters":[216,250,464,498],"Robinson":[219,467],"Foulds":[221,469],"(RF)":[222,470],"distance":[223,471],"matrix":[224,472],"convolutional":[227,475],"neural":[228,476],"network":[229,477],"(CNN).":[230,478],"We":[231,479],"developed":[232,480],"CNN":[235,483],"approach":[236,265,484,510],"(called":[237],"CNNTrees)":[238],"multiple":[240,488],"classification.":[242,490],"strategy":[245,493],"returns":[246,494],"input":[253,504],"different-size":[257],"makes":[262],"more":[266,269,513,517],"stable":[267,514],"robust.":[270,518],"provides":[273],"an":[274,302],"in-depth":[275],"analysis":[276],"relevant,":[279],"very":[281],"difficult,":[282],"problem":[283],"constructing":[285],"alternative":[286],"phylogenies":[289],"taxa.":[296],"model":[299],"will":[300],"play":[301],"important":[303],"role":[304],"Trees":[309],"Life":[311],"(ToL).":[312],"Availability":[313],"implementation:":[315],"CNNTrees":[316],"is":[317,355,359,442],"available":[318,337,346],"through":[319],"web":[321],"server":[322],"at":[323,338],"https://tahirinadia.github.io/":[324],".":[325,340],"source":[327],"code,":[328],"data":[329,344],"information":[331],"about":[332],"installation":[333],"procedures":[334],"also":[336,516],"https://github.com/TahiriNadia/CNNTrees":[339],"Supplementary":[341,343],"information:":[342],"on":[347],"GitHub":[348],"platform.":[349],"not":[356],"unique,":[357],"specific":[360,392],"genes.":[364],"Indeed,":[365],"has":[368],"its":[369,410],"own":[370,411],"differs":[374],"considerably":[375],"one":[377],"another.":[380],"For":[381],"example,":[382],"some":[383],"individual":[384],"operons":[387],"affected":[390],"transfer":[395],"recombination":[397],"events.":[398],"Thus,":[399],"must":[406],"represented":[408],"tree,":[413],"exhibit":[416],"than":[420],"accounts":[425],"major":[428],"vertical":[429],"descent":[430],"result":[433],"supertree":[439],"single":[444],"supertree.":[448],"paper,":[451],"(CNNTrees)":[485],"construct":[487],"order":[501],"allows":[507]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
