{"id":"https://openalex.org/W3011554441","doi":"https://doi.org/10.1093/bioinformatics/btaa164","title":"forgeNet: a graph deep neural network model using tree-based ensemble classifiers for feature graph construction","display_name":"forgeNet: a graph deep neural network model using tree-based ensemble classifiers for feature graph construction","publication_year":2020,"publication_date":"2020-03-09","ids":{"openalex":"https://openalex.org/W3011554441","doi":"https://doi.org/10.1093/bioinformatics/btaa164","mag":"3011554441","pmid":"https://pubmed.ncbi.nlm.nih.gov/32163118"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa164","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3507/33329382/btaa164.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3507/33329382/btaa164.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032281061","display_name":"Yunchuan Kong","orcid":null},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunchuan Kong","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics , Emory University, Atlanta, GA 30322, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics , Emory University, Atlanta, GA 30322, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016835023","display_name":"Tianwei Yu","orcid":"https://orcid.org/0000-0003-2502-1628"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tianwei Yu","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics , Emory University, Atlanta, GA 30322, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics , Emory University, Atlanta, GA 30322, USA","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5016835023"],"corresponding_institution_ids":["https://openalex.org/I150468666"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8714,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.8592932,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"36","issue":"11","first_page":"3507","last_page":"3515"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4650999903678894,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4650999903678894,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.07829999923706055,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.0478999987244606,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.762203574180603},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6182297468185425},{"id":"https://openalex.org/keywords/extractor","display_name":"Extractor","score":0.5866930484771729},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5806049704551697},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5607795715332031},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5589950084686279},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.5378005504608154},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5020577907562256},{"id":"https://openalex.org/keywords/feature-engineering","display_name":"Feature engineering","score":0.44615793228149414},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4079749882221222},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3449815511703491},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.13400709629058838}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.762203574180603},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6182297468185425},{"id":"https://openalex.org/C117978034","wikidata":"https://www.wikidata.org/wiki/Q5422192","display_name":"Extractor","level":2,"score":0.5866930484771729},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5806049704551697},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5607795715332031},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5589950084686279},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.5378005504608154},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5020577907562256},{"id":"https://openalex.org/C2778827112","wikidata":"https://www.wikidata.org/wiki/Q22245680","display_name":"Feature engineering","level":3,"score":0.44615793228149414},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4079749882221222},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3449815511703491},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.13400709629058838},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","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/C21880701","wikidata":"https://www.wikidata.org/wiki/Q2144042","display_name":"Process engineering","level":1,"score":0.0}],"mesh":[{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa164","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3507/33329382/btaa164.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32163118","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32163118","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7267822","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7267822","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa164","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3507/33329382/btaa164.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5899999737739563,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G3964006637","display_name":null,"funder_award_id":"R01GM124061","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7211878532","display_name":null,"funder_award_id":"R01 GM124061","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W277755990","https://openalex.org/W600208884","https://openalex.org/W1484040084","https://openalex.org/W1484418241","https://openalex.org/W1987776395","https://openalex.org/W1990067807","https://openalex.org/W2008620264","https://openalex.org/W2024311320","https://openalex.org/W2025944550","https://openalex.org/W2031218556","https://openalex.org/W2060742428","https://openalex.org/W2061771504","https://openalex.org/W2066430720","https://openalex.org/W2070493638","https://openalex.org/W2071913912","https://openalex.org/W2072202257","https://openalex.org/W2081113032","https://openalex.org/W2096283457","https://openalex.org/W2096863518","https://openalex.org/W2101234009","https://openalex.org/W2117193174","https://openalex.org/W2128689695","https://openalex.org/W2130319566","https://openalex.org/W2135046866","https://openalex.org/W2138255346","https://openalex.org/W2140883620","https://openalex.org/W2153601733","https://openalex.org/W2160514535","https://openalex.org/W2415153693","https://openalex.org/W2483206378","https://openalex.org/W2488345387","https://openalex.org/W2557283755","https://openalex.org/W2564080831","https://openalex.org/W2589411605","https://openalex.org/W2593086047","https://openalex.org/W2738689405","https://openalex.org/W2784146930","https://openalex.org/W2791929441","https://openalex.org/W2800103855","https://openalex.org/W2801467013","https://openalex.org/W2895653425","https://openalex.org/W2911964244","https://openalex.org/W2912934387","https://openalex.org/W2921066798","https://openalex.org/W2951055789","https://openalex.org/W2955675297","https://openalex.org/W2964304355","https://openalex.org/W3000945797","https://openalex.org/W3106134091","https://openalex.org/W4212883601","https://openalex.org/W6675354045","https://openalex.org/W6741293133"],"related_works":["https://openalex.org/W3082848404","https://openalex.org/W1979583797","https://openalex.org/W2016864125","https://openalex.org/W2372254676","https://openalex.org/W4375867731","https://openalex.org/W2080135837","https://openalex.org/W2793679056","https://openalex.org/W3145050838","https://openalex.org/W4360615883","https://openalex.org/W3034267371"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1],"unique":[2],"challenge":[3],"in":[4,134],"predictive":[5],"model":[6,99,155],"building":[7],"for":[8,31,141,180],"omics":[9,181],"data":[10,197],"has":[11,59],"been":[12,60],"the":[13,20,47,52,78,117,128,148,153,169],"small":[14],"number":[15],"of":[16,23,77],"samples":[17],"(n)":[18],"versus":[19],"large":[21],"amount":[22],"features":[24],"(p).":[25],"This":[26],"'n\u226ap'":[27],"property":[28],"brings":[29],"difficulties":[30],"disease":[32],"outcome":[33],"classification":[34,85,98,165],"using":[35],"deep":[36,54,110,177],"learning":[37,40,178],"techniques.":[38],"Sparse":[39],"by":[41],"incorporating":[42],"known":[43],"functional":[44],"relationships":[45],"between":[46],"biological":[48],"units,":[49],"such":[50,67],"as":[51],"graph-embedded":[53,109],"feedforward":[55,111],"network":[56,112],"(GEDFN)":[57],"model,":[58,114],"a":[61,96,107,121,135,142,172],"solution":[62],"to":[63,115,175],"this":[64,92],"issue.":[65],"However,":[66],"methods":[68],"require":[69],"an":[70],"existing":[71],"feature":[72,79,87,123,129],"graph,":[73],"and":[74,86,94,138,159],"potential":[75],"mis-specification":[76],"graph":[80,124,130],"can":[81,131],"be":[82,132],"harmful":[83],"on":[84,102],"selection.":[88],"RESULTS:":[89],"To":[90,146],"address":[91],"limitation":[93],"develop":[95],"robust":[97],"without":[100],"relying":[101],"external":[103],"knowledge,":[104],"we":[105,151],"propose":[106],"forest":[108,122],"(forgeNet)":[113],"integrate":[116],"GEDFN":[118],"architecture":[119],"with":[120,156],"extractor,":[125],"so":[126],"that":[127,168],"learned":[133],"supervised":[136],"manner":[137],"specifically":[139],"constructed":[140],"given":[143],"prediction":[144],"task.":[145],"validate":[147],"method's":[149],"capability,":[150],"experimented":[152],"forgeNet":[154],"both":[157],"synthetic":[158],"real":[160],"datasets.":[161],"The":[162,186],"resulting":[163],"high":[164],"accuracy":[166],"suggests":[167],"method":[170,187],"is":[171,188],"valuable":[173],"addition":[174],"sparse":[176],"models":[179],"data.":[182],"AVAILABILITY":[183],"AND":[184],"IMPLEMENTATION:":[185],"available":[189,199],"at":[190,200],"https://github.com/yunchuankong/forgeNet.":[191],"CONTACT:":[192],"tianwei.yu@emory.edu.":[193],"SUPPLEMENTARY":[194],"INFORMATION:":[195],"Supplementary":[196],"are":[198],"Bioinformatics":[201],"online.":[202]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
