{"id":"https://openalex.org/W4390692098","doi":"https://doi.org/10.1109/tcbb.2024.3352268","title":"Learning From an Artificial Neural Network in Phylogenetics","display_name":"Learning From an Artificial Neural Network in Phylogenetics","publication_year":2024,"publication_date":"2024-01-10","ids":{"openalex":"https://openalex.org/W4390692098","doi":"https://doi.org/10.1109/tcbb.2024.3352268","pmid":"https://pubmed.ncbi.nlm.nih.gov/38198267"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3352268","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3352268","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/4359833/10387771.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/4359833/10387771.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055260015","display_name":"Alina F. Leuchtenberger","orcid":"https://orcid.org/0000-0003-2566-4260"},"institutions":[{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I4210142901","display_name":"Vienna Biocenter","ror":"https://ror.org/04khwmr87","country_code":"AT","type":"other","lineage":["https://openalex.org/I4210142901"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Alina F. Leuchtenberger","raw_affiliation_strings":["Center for Integrative Bioinformatics Vienna, Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria","Center for Integrative Bioinformatics Vienna, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, Vienna, Austria","Medical University of Vienna, Center for Medical Biochemistry, Dr.-Bohr-Gasse 9, Vienna, Austria","Austria and the Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Center for Integrative Bioinformatics Vienna, Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I4210142901"]},{"raw_affiliation_string":"Center for Integrative Bioinformatics Vienna, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, Vienna, Austria","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I4210142901"]},{"raw_affiliation_string":"Medical University of Vienna, Center for Medical Biochemistry, Dr.-Bohr-Gasse 9, Vienna, Austria","institution_ids":["https://openalex.org/I76134821"]},{"raw_affiliation_string":"Austria and the Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I4210142901","https://openalex.org/I76134821"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085983122","display_name":"Arndt von Haeseler","orcid":"https://orcid.org/0000-0002-3366-4458"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Arndt von Haeseler","raw_affiliation_strings":["Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria","Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria","Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I76134821"]},{"raw_affiliation_string":"Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria","institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I76134821"]},{"raw_affiliation_string":"Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055260015"],"corresponding_institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I4210142901","https://openalex.org/I76134821"],"apc_list":null,"apc_paid":null,"fwci":0.4698,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61052735,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"21","issue":"2","first_page":"278","last_page":"288"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980999827384949,"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":0.9980999827384949,"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/T10385","display_name":"Plant Diversity and Evolution","score":0.992900013923645,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.9922000169754028,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6023537516593933},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5807198882102966},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5713172554969788},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.547960638999939},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5257133841514587},{"id":"https://openalex.org/keywords/simplicity","display_name":"Simplicity","score":0.42127931118011475},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.41680917143821716},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.40485161542892456},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34069037437438965},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.28384673595428467},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.16787511110305786},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16555055975914001},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.14733904600143433},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0892767608165741}],"concepts":[{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6023537516593933},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5807198882102966},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5713172554969788},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.547960638999939},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5257133841514587},{"id":"https://openalex.org/C2776372474","wikidata":"https://www.wikidata.org/wiki/Q508291","display_name":"Simplicity","level":2,"score":0.42127931118011475},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.41680917143821716},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.40485161542892456},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34069037437438965},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28384673595428467},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.16787511110305786},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16555055975914001},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.14733904600143433},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0892767608165741},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D010802","descriptor_name":"Phylogeny","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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3352268","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3352268","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/4359833/10387771.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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:38198267","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38198267","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}],"best_oa_location":{"id":"doi:10.1109/tcbb.2024.3352268","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3352268","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/4359833/10387771.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.6200000047683716,"display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G1227914001","display_name":null,"funder_award_id":"DOC 32-B28","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G3313088681","display_name":null,"funder_award_id":"32-B28","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"},{"id":"https://openalex.org/G52688889","display_name":null,"funder_award_id":"FWF DOC 32-B28","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"}],"funders":[{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"},{"id":"https://openalex.org/F4320321691","display_name":"Universit\u00e4t Wien","ror":"https://ror.org/03prydq77"},{"id":"https://openalex.org/F4320323437","display_name":"Medizinische Universit\u00e4t Wien","ror":"https://ror.org/05n3x4p02"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390692098.pdf","grobid_xml":"https://content.openalex.org/works/W4390692098.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1966233419","https://openalex.org/W1971273325","https://openalex.org/W1991518077","https://openalex.org/W2013486172","https://openalex.org/W2064704042","https://openalex.org/W2105329815","https://openalex.org/W2111647009","https://openalex.org/W2139943756","https://openalex.org/W2141052558","https://openalex.org/W2148560957","https://openalex.org/W2480295938","https://openalex.org/W2516809705","https://openalex.org/W2614081736","https://openalex.org/W2973043487","https://openalex.org/W2996966823","https://openalex.org/W3041567587","https://openalex.org/W4220685469","https://openalex.org/W4233815609","https://openalex.org/W4234207117","https://openalex.org/W4247332402","https://openalex.org/W4283650386","https://openalex.org/W4386462191","https://openalex.org/W6804559366"],"related_works":["https://openalex.org/W2368019753","https://openalex.org/W2333930193","https://openalex.org/W2737356002","https://openalex.org/W2246241526","https://openalex.org/W4301122218","https://openalex.org/W2362218761","https://openalex.org/W2113708670","https://openalex.org/W2062354928","https://openalex.org/W2088120817","https://openalex.org/W2158340599"],"abstract_inverted_index":{"We":[0,128],"show":[1],"that":[2],"an":[3],"iterative":[4],"ansatz":[5],"of":[6,72,78,125],"deep":[7],"learning":[8],"and":[9,28,59,80,117],"human":[10],"intelligence":[11],"guided":[12],"simplification":[13,77],"may":[14],"lead":[15],"to":[16,64,90,131],"surprisingly":[17],"simple":[18],"solutions":[19],"for":[20,47],"a":[21,32],"difficult":[22],"problem":[23,34,46],"in":[24,35,69],"phylogenetics.":[25],"Distinguishing":[26],"Farris":[27,58],"Felsenstein":[29,60],"trees":[30],"is":[31,95,99],"longstanding":[33],"phylogenetic":[36],"tree":[37],"reconstruction.":[38],"The":[39],"Artificial":[40],"Neural":[41],"Network":[42],"F-zoneNN":[43,79],"solves":[44],"this":[45,107],"4-taxon":[48],"alignments":[49,124,135],"evolved":[50],"under":[51],"the":[52,76,85,110,132,144],"Jukes-Cantor":[53],"model.":[54],"It":[55],"distinguishes":[56],"between":[57],"trees,":[61],"but":[62],"owing":[63],"its":[65,70,105],"complexity,":[66],"lacks":[67],"transparency":[68],"mechanism":[71],"discernment.":[73],"Based":[74],"on":[75,114,121],"alignment":[81],"properties":[82],"we":[83],"constructed":[84],"function":[86,108],"FarFelDiscerner.":[87],"In":[88],"contrast":[89],"F-zoneNN,":[91],"FarFelDiscerner's":[92],"decision":[93],"process":[94],"understandable.":[96],"Moreover,":[97],"FarFelDiscerner":[98,130],"significantly":[100],"simpler":[101],"than":[102],"F-zoneNN.":[103],"Despite":[104],"simplicity":[106],"infers":[109],"tree-type":[111],"almost":[112],"perfectly":[113],"noise-free":[115],"data,":[116],"also":[118],"performs":[119],"well":[120],"simulated":[122],"noisy":[123],"finite":[126],"length.":[127],"applied":[129],"historical":[133],"Holometabola":[134],"where":[136],"it":[137],"places":[138],"Strepsiptera":[139],"with":[140,143],"beetles,":[141],"concordant":[142],"current":[145],"scientific":[146],"view.":[147]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
