{"id":"https://openalex.org/W3024771599","doi":"https://doi.org/10.1109/jbhi.2020.2993761","title":"PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data","display_name":"PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data","publication_year":2020,"publication_date":"2020-05-11","ids":{"openalex":"https://openalex.org/W3024771599","doi":"https://doi.org/10.1109/jbhi.2020.2993761","mag":"3024771599","pmid":"https://pubmed.ncbi.nlm.nih.gov/32396115"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2020.2993761","is_oa":true,"landing_page_url":"https://doi.org/10.1109/jbhi.2020.2993761","pdf_url":"https://ieeexplore.ieee.org/ielx7/6221020/9216186/09091025.pdf","source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ieeexplore.ieee.org/ielx7/6221020/9216186/09091025.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076460126","display_name":"Derek Reiman","orcid":"https://orcid.org/0000-0002-7955-3980"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Derek Reiman","raw_affiliation_strings":["Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086750542","display_name":"Ahmed A. Metwally","orcid":"https://orcid.org/0000-0002-0155-7412"},"institutions":[{"id":"https://openalex.org/I145487455","display_name":"Cairo University","ror":"https://ror.org/03q21mh05","country_code":"EG","type":"education","lineage":["https://openalex.org/I145487455"]},{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["EG","US"],"is_corresponding":false,"raw_author_name":"Ahmed A. Metwally","raw_affiliation_strings":["Department of Bioengineering and the Department of Computer Science, University of Illinois at Chicago, Chicago, IL, USA","Department of Systems and Biomedical Engineering, Faculty of Engineering, Cairo University, Giza, Egypt"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering and the Department of Computer Science, University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]},{"raw_affiliation_string":"Department of Systems and Biomedical Engineering, Faculty of Engineering, Cairo University, Giza, Egypt","institution_ids":["https://openalex.org/I145487455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007677073","display_name":"Jun Sun","orcid":"https://orcid.org/0000-0001-7465-3133"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Sun","raw_affiliation_strings":["Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025440962","display_name":"Yang Dai","orcid":"https://orcid.org/0000-0002-7638-849X"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Dai","raw_affiliation_strings":["Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076460126"],"corresponding_institution_ids":["https://openalex.org/I39422238"],"apc_list":null,"apc_paid":null,"fwci":4.3489,"has_fulltext":true,"cited_by_count":110,"citation_normalized_percentile":{"value":0.95538874,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"24","issue":"10","first_page":"2993","last_page":"3001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9984999895095825,"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":0.9984999895095825,"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":0.9977999925613403,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9728000164031982,"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/metagenomics","display_name":"Metagenomics","score":0.8050808906555176},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7079750299453735},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.692473828792572},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6526150703430176},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6340024471282959},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6244192123413086},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.5311583280563354},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4640018343925476},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4567983150482178},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.41960591077804565},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3897724449634552},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36829322576522827},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32908695936203003},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.10044345259666443},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09781220555305481},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09389698505401611},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07224369049072266}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8050808906555176},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7079750299453735},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.692473828792572},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6526150703430176},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6340024471282959},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6244192123413086},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.5311583280563354},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4640018343925476},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4567983150482178},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.41960591077804565},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3897724449634552},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36829322576522827},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32908695936203003},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.10044345259666443},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09781220555305481},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09389698505401611},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07224369049072266},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","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},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2020.2993761","is_oa":true,"landing_page_url":"https://doi.org/10.1109/jbhi.2020.2993761","pdf_url":"https://ieeexplore.ieee.org/ielx7/6221020/9216186/09091025.pdf","source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:32396115","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32396115","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1109/jbhi.2020.2993761","is_oa":true,"landing_page_url":"https://doi.org/10.1109/jbhi.2020.2993761","pdf_url":"https://ieeexplore.ieee.org/ielx7/6221020/9216186/09091025.pdf","source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3024771599.pdf","grobid_xml":"https://content.openalex.org/works/W3024771599.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W785854688","https://openalex.org/W1501213224","https://openalex.org/W1703384511","https://openalex.org/W1964027278","https://openalex.org/W1968893079","https://openalex.org/W1974088543","https://openalex.org/W1993784588","https://openalex.org/W2004549986","https://openalex.org/W2023615726","https://openalex.org/W2028582941","https://openalex.org/W2058029859","https://openalex.org/W2071841602","https://openalex.org/W2074405982","https://openalex.org/W2083176215","https://openalex.org/W2095705004","https://openalex.org/W2112796928","https://openalex.org/W2123059507","https://openalex.org/W2125826054","https://openalex.org/W2129690444","https://openalex.org/W2130725058","https://openalex.org/W2159675211","https://openalex.org/W2260815707","https://openalex.org/W2336376302","https://openalex.org/W2473355215","https://openalex.org/W2529534298","https://openalex.org/W2554225542","https://openalex.org/W2567872606","https://openalex.org/W2586959160","https://openalex.org/W2609405928","https://openalex.org/W2613043502","https://openalex.org/W2753944919","https://openalex.org/W2799722906","https://openalex.org/W2808466192","https://openalex.org/W2905357150","https://openalex.org/W2921789835","https://openalex.org/W2938740358","https://openalex.org/W2963776453","https://openalex.org/W2964321699","https://openalex.org/W6622746331","https://openalex.org/W6674330103","https://openalex.org/W6692546014","https://openalex.org/W6720006811","https://openalex.org/W6720224415"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W4388282505","https://openalex.org/W3198631238","https://openalex.org/W4372048956"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1,173],"of":[2,12,59,72,88,106,118,136,174,180,184],"the":[3,13,64,69,85,89,93,104,131,152,161,172,178,182],"host":[4,50,175],"phenotype":[5,51,176],"from":[6,151],"a":[7,33,60,76,145,166],"metagenomic":[8,77,100,116],"sample":[9],"and":[10,28,95,126,133,156],"identification":[11],"associated":[14],"microbial":[15,47,73,186],"markers":[16],"are":[17],"important":[18],"in":[19,46,75,99],"understanding":[20],"potential":[21],"host-microbiome":[22],"interactions":[23],"related":[24],"to":[25,83,110],"disease":[26],"initiation":[27],"progression.":[29],"We":[30,102],"introduce":[31],"PopPhy-CNN,":[32],"novel":[34,146],"convolutional":[35],"neural":[36],"network":[37],"(CNN)":[38],"learning":[39,169],"framework":[40,170],"that":[41],"effectively":[42],"exploits":[43],"phylogenetic":[44,65],"structure":[45],"taxa":[48,74],"for":[49,121,139,148,171],"prediction.":[52],"Our":[53],"approach":[54],"takes":[55],"an":[56],"input":[57],"format":[58],"2D":[61],"matrix":[62],"representing":[63],"tree":[66,94],"populated":[67],"with":[68,177],"relative":[70],"abundance":[71],"sample.":[78],"This":[79],"conversion":[80],"empowers":[81],"CNNs":[82],"explore":[84],"spatial":[86],"relationship":[87],"taxonomic":[90],"annotations":[91],"on":[92],"their":[96],"quantitative":[97],"characteristics":[98],"data.":[101],"show":[103,130],"competitiveness":[105],"our":[107,137],"model":[108,138],"compared":[109],"other":[111],"available":[112],"methods":[113],"using":[114],"nine":[115],"datasets":[117],"moderate":[119],"size":[120],"binary":[122],"classification.":[123,141],"With":[124],"synthetic":[125],"biological":[127],"datasets,":[128],"we":[129,143],"superior":[132],"robust":[134],"performance":[135,159],"multi-class":[140],"Furthermore,":[142],"design":[144],"scheme":[147],"feature":[149],"extraction":[150],"learned":[153],"CNN":[154],"models":[155],"demonstrate":[157],"improved":[158],"when":[160],"extracted":[162],"features.":[163],"PopPhy-CNN":[164],"is":[165],"practical":[167],"deep":[168],"ability":[179],"facilitating":[181],"retrieval":[183],"predictive":[185],"taxa.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":29},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
