{"id":"https://openalex.org/W4206598221","doi":"https://doi.org/10.1109/bibm52615.2021.9669654","title":"Deep ensemble learning over the microbial phylogenetic tree (DeepEn-Phy)","display_name":"Deep ensemble learning over the microbial phylogenetic tree (DeepEn-Phy)","publication_year":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4206598221","doi":"https://doi.org/10.1109/bibm52615.2021.9669654","pmid":"https://pubmed.ncbi.nlm.nih.gov/36704639"},"language":"en","primary_location":{"id":"doi:10.1109/bibm52615.2021.9669654","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669654","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9875567","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031964723","display_name":"Wodan Ling","orcid":"https://orcid.org/0000-0001-7196-8543"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wodan Ling","raw_affiliation_strings":["Fred Hutchinson, Cancer Research Center, Seattle, USA","Fred Hutchinson Cancer Research Center, Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fred Hutchinson, Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Fred Hutchinson Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063098523","display_name":"Youran Qi","orcid":null},"institutions":[{"id":"https://openalex.org/I1311688040","display_name":"Amazon (United States)","ror":"https://ror.org/04mv4n011","country_code":"US","type":"company","lineage":["https://openalex.org/I1311688040"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Youran Qi","raw_affiliation_strings":["Amazon, Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Amazon, Seattle, USA","institution_ids":["https://openalex.org/I1311688040","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026919585","display_name":"Xing Hua","orcid":"https://orcid.org/0000-0002-8346-5887"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xing Hua","raw_affiliation_strings":["Fred Hutchinson, Cancer Research Center, Seattle, USA","Fred Hutchinson Cancer Research Center, Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fred Hutchinson, Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Fred Hutchinson Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000129649","display_name":"Michael C. Wu","orcid":"https://orcid.org/0000-0002-3357-6570"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael C. Wu","raw_affiliation_strings":["Fred Hutchinson, Cancer Research Center, Seattle, USA","Fred Hutchinson Cancer Research Center, Seattle, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fred Hutchinson, Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Fred Hutchinson Cancer Research Center, Seattle, USA","institution_ids":["https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.0402,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.74394786,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"2021","issue":null,"first_page":"470","last_page":"477"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9976999759674072,"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/T10066","display_name":"Gut microbiota and health","score":0.9976999759674072,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955999851226807,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9765999913215637,"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/phylogenetics","display_name":"Phylogenetics","score":0.715962290763855},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.637121856212616},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6052089929580688},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.600340723991394},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5577827095985413},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.5500867366790771},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5120804905891418},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5073005557060242},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.44357240200042725},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3861194849014282},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37071606516838074},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3558763265609741},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.27470678091049194},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09835949540138245},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.09723877906799316},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07690420746803284}],"concepts":[{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.715962290763855},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.637121856212616},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6052089929580688},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.600340723991394},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5577827095985413},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.5500867366790771},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5120804905891418},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5073005557060242},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.44357240200042725},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3861194849014282},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37071606516838074},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3558763265609741},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27470678091049194},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09835949540138245},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.09723877906799316},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07690420746803284}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm52615.2021.9669654","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669654","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:36704639","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36704639","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9875567","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9875567","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9875567","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9875567","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5611841272","display_name":null,"funder_award_id":"R01 HL155417","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6697275907","display_name":null,"funder_award_id":"R01 GM129512","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320314494","display_name":"Hope Foundation","ror":"https://ror.org/05wf1w785"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1501213224","https://openalex.org/W1522301498","https://openalex.org/W1988115241","https://openalex.org/W1988925586","https://openalex.org/W2041076979","https://openalex.org/W2071841602","https://openalex.org/W2072970694","https://openalex.org/W2099279254","https://openalex.org/W2102813808","https://openalex.org/W2135046866","https://openalex.org/W2136993578","https://openalex.org/W2159008215","https://openalex.org/W2163922914","https://openalex.org/W2345411160","https://openalex.org/W2401404581","https://openalex.org/W2463312000","https://openalex.org/W2510675082","https://openalex.org/W2647715950","https://openalex.org/W2883542968","https://openalex.org/W2887509155","https://openalex.org/W2963276645","https://openalex.org/W2975619549","https://openalex.org/W2977098467","https://openalex.org/W3024771599","https://openalex.org/W3096983624","https://openalex.org/W3132461044","https://openalex.org/W6631190155"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2949296710","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W1974895455"],"abstract_inverted_index":{"Successful":[0],"prediction":[1,41,113],"of":[2,28,76,86,138],"clinical":[3,23,59,108],"outcomes":[4],"facilitates":[5],"tailored":[6],"diagnosis":[7],"and":[8,51,106,119],"treatment.":[9],"The":[10,62],"microbiome":[11,99,140],"has":[12,36],"been":[13,37],"shown":[14],"to":[15,20,39,66,90,95,102,115],"be":[16],"an":[17,53],"important":[18],"biomarker":[19],"predict":[21,103],"host":[22,58],"outcomes.":[24,109],"Further,":[25],"the":[26,31,77,83,136],"incorporation":[27],"microbial":[29],"phylogeny,":[30,71],"evolutionary":[32],"relationship":[33],"among":[34],"microbes,":[35],"demonstrated":[38],"improve":[40],"accuracy.":[42],"We":[43,92],"propose":[44],"a":[45,96,126],"phylogeny-driven":[46],"deep":[47,120,131],"neural":[48,132],"network":[49,133],"(PhyNN)":[50],"develop":[52],"ensemble":[54],"method,":[55],"DeepEn-Phy,":[56],"for":[57,129],"outcome":[60],"prediction.":[61],"method":[63],"is":[64],"designed":[65],"optimally":[67],"extract":[68],"features":[69],"from":[70],"thereby":[72],"take":[73],"full":[74],"advantage":[75],"information":[78],"in":[79],"phylogeny":[80,87],"while":[81],"harnessing":[82],"core":[84],"principles":[85],"(in":[88],"contrast":[89],"taxonomy).":[91],"apply":[93],"DeepEn-Phy":[94,110,124],"real":[97],"large":[98],"data":[100],"set":[101],"both":[104],"categorical":[105],"continuous":[107],"demonstrates":[111],"superior":[112],"performance":[114],"existing":[116],"machine":[117],"learning":[118,121],"approaches.":[122],"Overall,":[123],"provides":[125],"new":[127],"strategy":[128],"designing":[130],"architectures":[134],"within":[135],"context":[137],"phylogeny-constrained":[139],"data.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}