{"id":"https://openalex.org/W3111503053","doi":"https://doi.org/10.1109/access.2020.3043150","title":"Deep Neighbor Information Learning From Evolution Trees for Phylogenetic Likelihood Estimates","display_name":"Deep Neighbor Information Learning From Evolution Trees for Phylogenetic Likelihood Estimates","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3111503053","doi":"https://doi.org/10.1109/access.2020.3043150","mag":"3111503053"},"language":"en","primary_location":{"id":"doi:10.1109/access.2020.3043150","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3043150","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09285277.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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 Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09285277.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101935082","display_name":"Cheng Ling","orcid":"https://orcid.org/0000-0003-3827-849X"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Cheng Ling","raw_affiliation_strings":["Department of Computer Science and Technology, Beijing University of Chemical Technology, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Beijing University of Chemical Technology, Beijing, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005750337","display_name":"Wenhao Cheng","orcid":"https://orcid.org/0000-0002-5625-3811"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenhao Cheng","raw_affiliation_strings":["Department of Computer Science and Technology, Beijing University of Chemical Technology, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Beijing University of Chemical Technology, Beijing, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100425881","display_name":"Haoyu Zhang","orcid":"https://orcid.org/0000-0001-9260-0270"},"institutions":[{"id":"https://openalex.org/I31847773","display_name":"Zhejiang Ocean University","ror":"https://ror.org/03mys6533","country_code":"CN","type":"education","lineage":["https://openalex.org/I31847773"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoyu Zhang","raw_affiliation_strings":["School of Information Engineering, Zhejiang Ocean University, Zhoushan, China","School of Naval Architecture and Maritime, Zhejiang Ocean University, Zhoushan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhejiang Ocean University, Zhoushan, China","institution_ids":["https://openalex.org/I31847773"]},{"raw_affiliation_string":"School of Naval Architecture and Maritime, Zhejiang Ocean University, Zhoushan, China","institution_ids":["https://openalex.org/I31847773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030358048","display_name":"Hanhao Zhu","orcid":"https://orcid.org/0000-0003-2448-5412"},"institutions":[{"id":"https://openalex.org/I31847773","display_name":"Zhejiang Ocean University","ror":"https://ror.org/03mys6533","country_code":"CN","type":"education","lineage":["https://openalex.org/I31847773"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanhao Zhu","raw_affiliation_strings":["Institute of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China"],"affiliations":[{"raw_affiliation_string":"Institute of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China","institution_ids":["https://openalex.org/I31847773"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103878455","display_name":"Hua Zhang","orcid":"https://orcid.org/0000-0001-6143-402X"},"institutions":[{"id":"https://openalex.org/I31847773","display_name":"Zhejiang Ocean University","ror":"https://ror.org/03mys6533","country_code":"CN","type":"education","lineage":["https://openalex.org/I31847773"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Zhang","raw_affiliation_strings":["School of Information Engineering, Zhejiang Ocean University, Zhoushan, China","School of Naval Architecture and Maritime, Zhejiang Ocean University, Zhoushan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Zhejiang Ocean University, Zhoushan, China","institution_ids":["https://openalex.org/I31847773"]},{"raw_affiliation_string":"School of Naval Architecture and Maritime, Zhejiang Ocean University, Zhoushan, China","institution_ids":["https://openalex.org/I31847773"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5101935082"],"corresponding_institution_ids":["https://openalex.org/I75390827"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.3336,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.58349514,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"8","issue":null,"first_page":"220692","last_page":"220702"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9965000152587891,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9930999875068665,"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/computer-science","display_name":"Computer science","score":0.706411600112915},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6154781579971313},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5998241901397705},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5788109302520752},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5454677939414978},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.507337749004364},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.44877636432647705},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.43888431787490845},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.42377424240112305},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3251851797103882},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3213445544242859},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21241194009780884}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.706411600112915},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6154781579971313},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5998241901397705},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5788109302520752},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5454677939414978},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.507337749004364},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.44877636432647705},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.43888431787490845},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.42377424240112305},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3251851797103882},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3213445544242859},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21241194009780884},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2020.3043150","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3043150","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09285277.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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 Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:b52c70d4c6e1462bbbb35a318d49877d","is_oa":true,"landing_page_url":"https://doaj.org/article/b52c70d4c6e1462bbbb35a318d49877d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 8, Pp 220692-220702 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2020.3043150","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3043150","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09285277.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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 Access","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2971566304","display_name":null,"funder_award_id":"61602026","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4667037360","display_name":null,"funder_award_id":"202060","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3111503053.pdf","grobid_xml":"https://content.openalex.org/works/W3111503053.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W191821314","https://openalex.org/W1663973292","https://openalex.org/W1911863642","https://openalex.org/W1966363110","https://openalex.org/W1985372952","https://openalex.org/W1985887223","https://openalex.org/W1995141949","https://openalex.org/W2004212407","https://openalex.org/W2005571584","https://openalex.org/W2009068374","https://openalex.org/W2009086942","https://openalex.org/W2036628186","https://openalex.org/W2072329064","https://openalex.org/W2079292425","https://openalex.org/W2101464940","https://openalex.org/W2102424972","https://openalex.org/W2103513093","https://openalex.org/W2108034499","https://openalex.org/W2110369783","https://openalex.org/W2114508120","https://openalex.org/W2119632499","https://openalex.org/W2120663060","https://openalex.org/W2123758939","https://openalex.org/W2123906840","https://openalex.org/W2125359798","https://openalex.org/W2129690060","https://openalex.org/W2141052558","https://openalex.org/W2141761963","https://openalex.org/W2146396346","https://openalex.org/W2150783480","https://openalex.org/W2151464048","https://openalex.org/W2152303410","https://openalex.org/W2156219515","https://openalex.org/W2157755551","https://openalex.org/W2159816280","https://openalex.org/W2161444534","https://openalex.org/W2168432681","https://openalex.org/W2169277778","https://openalex.org/W2240556276","https://openalex.org/W2375303405","https://openalex.org/W2564124613","https://openalex.org/W2612166593","https://openalex.org/W2740556548","https://openalex.org/W2783041286","https://openalex.org/W2884258548","https://openalex.org/W2908324956","https://openalex.org/W2918410041","https://openalex.org/W2944497784","https://openalex.org/W2969547916","https://openalex.org/W2991385399","https://openalex.org/W3031527830","https://openalex.org/W4235200155","https://openalex.org/W6648804044","https://openalex.org/W6762515864"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2097707447","https://openalex.org/W2362218761","https://openalex.org/W2113708670","https://openalex.org/W2062354928","https://openalex.org/W2088120817","https://openalex.org/W2158340599"],"abstract_inverted_index":{"Likelihood":[0,35],"probability":[1],"based":[2,78],"phylogenetic":[3,50,227,237],"analysis":[4,51,168,201,238],"approaches":[5],"have":[6],"contributed":[7],"to":[8,28,117,133,161,178,194,223],"impressive":[9],"advances":[10],"in":[11,225,233,244,258],"minimizing":[12],"the":[13,17,29,42,64,89,96,120,124,131,137,141,147,167,180,190,200,234],"variance":[14],"of":[15,33,44,57,66,99,115,123,126,149,153,169,187,192,202,215,217,236,250],"estimating":[16],"evolutionary":[18,218],"parameters.":[19],"However,":[20],"their":[21],"actual":[22],"applications":[23],"are":[24],"greatly":[25,62],"limited":[26],"due":[27],"very":[30,176],"time-consuming":[31],"calculations":[32,122,148],"Conditional":[34],"Probabilities":[36],"(CLPs).":[37],"Accurately":[38],"and":[39,80,108,220,247],"quickly":[40],"obtaining":[41],"likelihoods":[43],"massive":[45],"tree":[46,127],"samples":[47],"can":[48,163,196],"facilitate":[49],"process.":[52],"Inspired":[53],"by":[54,136],"recent":[55],"advance":[56],"machine":[58,241],"learning":[59,79,242],"techniques":[60],"that":[61],"improve":[63],"performance":[65,154],"many":[67],"related":[68],"prediction":[69,81,112,135,249],"tasks,":[70],"this":[71],"study":[72,231],"proposes":[73],"a":[74,110,134,212,240],"Random":[75],"Forest":[76],"(RF)":[77],"approach,":[82],"called":[83],"NeoPLE.":[84],"The":[85],"approach":[86,243],"initially":[87],"learns":[88],"deep":[90],"neighbor":[91],"information":[92,104],"between":[93],"nodes":[94],"from":[95,105,159],"topology":[97],"representations":[98],"evolution":[100,251],"trees,":[101,107,252],"integrates":[102],"likelihood":[103,142,248],"these":[106],"trains":[109],"non-linear":[111],"model.":[113],"Instead":[114],"having":[116,183],"depend":[118],"on":[119,166,199],"recursive":[121],"CLPs":[125],"nodes,":[128],"NeoPLE":[129,174,208],"transfers":[130],"process":[132],"trained":[138],"model,":[139],"thus":[140],"estimates":[143],"become":[144],"irrelevant":[145],"with":[146],"CLPs.":[150],"In":[151,206],"terms":[152],"improvement,":[155],"speedup":[156],"factors":[157],"ranging":[158],"2.1":[160],"3.5X":[162],"be":[164,197],"achieved":[165,198],"realistic":[170],"data":[171,181,204],"sets.":[172,205],"Moreover,":[173],"is":[175,209,221],"suitable":[177],"handle":[179],"sets":[182],"relatively":[184],"large":[185],"number":[186],"alignment":[188],"sites,":[189],"factor":[191],"up":[193],"27.5X":[195],"simulated":[203],"addition,":[207],"robust":[210],"against":[211],"wide":[213],"range":[214],"choices":[216],"models":[219],"ready":[222],"integrate":[224],"more":[226],"inference":[228],"tools.":[229],"This":[230],"fills":[232],"gaps":[235],"using":[239],"feature":[245],"representation":[246],"which":[253],"has":[254],"not":[255],"been":[256],"reported":[257],"literatures.":[259]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
