{"id":"https://openalex.org/W2899545492","doi":"https://doi.org/10.1093/bioinformatics/bty908","title":"BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks","display_name":"BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks","publication_year":2018,"publication_date":"2018-11-04","ids":{"openalex":"https://openalex.org/W2899545492","doi":"https://doi.org/10.1093/bioinformatics/bty908","mag":"2899545492","pmid":"https://pubmed.ncbi.nlm.nih.gov/30395189"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty908","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty908","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044328870","display_name":"Ruiqing Zheng","orcid":"https://orcid.org/0000-0001-6372-6798"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruiqing Zheng","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032439086","display_name":"Xiang Chen","orcid":"https://orcid.org/0000-0002-6058-0049"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang Chen","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091157395","display_name":"Fang\u2010Xiang Wu","orcid":"https://orcid.org/0000-0002-4593-9332"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Fang-Xiang Wu","raw_affiliation_strings":["Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada","School of Information Science and Engineering, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]},{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101465265","display_name":"Yi Pan","orcid":"https://orcid.org/0000-0002-2766-3096"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yi Pan","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA, USA","School of Information Science and Engineering, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["School of Information Science and Engineering, Central South University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100719013"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.0675,"has_fulltext":false,"cited_by_count":86,"citation_normalized_percentile":{"value":0.92690639,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"11","first_page":"1893","last_page":"1900"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.964900016784668,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.964900016784668,"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":0.009399999864399433,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.009399999864399433,"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/computer-science","display_name":"Computer science","score":0.7632206678390503},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7114389538764954},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.689516544342041},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6647469401359558},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5635904669761658},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5466806888580322},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.466656893491745},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38604214787483215},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3556210398674011},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2713735103607178},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18164029717445374},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14483433961868286},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.09405097365379333}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7632206678390503},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7114389538764954},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.689516544342041},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6647469401359558},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5635904669761658},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5466806888580322},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.466656893491745},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38604214787483215},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3556210398674011},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2713735103607178},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18164029717445374},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14483433961868286},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.09405097365379333},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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}],"mesh":[{"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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty908","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty908","pdf_url":null,"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:30395189","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30395189","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5699999928474426}],"awards":[{"id":"https://openalex.org/G1729077721","display_name":null,"funder_award_id":"61732009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G358564744","display_name":null,"funder_award_id":"61420106009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4066238608","display_name":null,"funder_award_id":"B18059","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G8210156615","display_name":null,"funder_award_id":"61622213","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"},{"id":"https://openalex.org/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W605677922","https://openalex.org/W1480376833","https://openalex.org/W1971224531","https://openalex.org/W1984429906","https://openalex.org/W1990357088","https://openalex.org/W1990514789","https://openalex.org/W1993418188","https://openalex.org/W1993628165","https://openalex.org/W2002933157","https://openalex.org/W2003003919","https://openalex.org/W2027287962","https://openalex.org/W2029485495","https://openalex.org/W2076513103","https://openalex.org/W2078149659","https://openalex.org/W2098086436","https://openalex.org/W2106555403","https://openalex.org/W2109384743","https://openalex.org/W2111384508","https://openalex.org/W2112076978","https://openalex.org/W2114402708","https://openalex.org/W2121782762","https://openalex.org/W2122708083","https://openalex.org/W2126345910","https://openalex.org/W2126602684","https://openalex.org/W2141239733","https://openalex.org/W2142836135","https://openalex.org/W2145688713","https://openalex.org/W2149649623","https://openalex.org/W2160095931","https://openalex.org/W2161922735","https://openalex.org/W2163296115","https://openalex.org/W2165392091","https://openalex.org/W2227811471","https://openalex.org/W2232370058","https://openalex.org/W2295598076","https://openalex.org/W2303875941","https://openalex.org/W2337819340","https://openalex.org/W2615110909","https://openalex.org/W2911964244","https://openalex.org/W2920876032","https://openalex.org/W2947626232","https://openalex.org/W2950199998","https://openalex.org/W3099289621","https://openalex.org/W3102476541","https://openalex.org/W6670026339","https://openalex.org/W6759967005"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W2125652721","https://openalex.org/W1540371141","https://openalex.org/W2067869703","https://openalex.org/W2560421304","https://openalex.org/W2950199998","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"MOTIVATION:":[0],"Reconstructing":[1],"gene":[2,8,35,49],"regulatory":[3,97],"networks":[4],"(GRNs)":[5],"based":[6],"on":[7,135,147],"expression":[9,50],"profiles":[10],"is":[11,89,160],"still":[12],"an":[13],"enormous":[14],"challenge":[15],"in":[16,126],"systems":[17],"biology.":[18],"Random":[19],"forest-based":[20],"methods":[21,29,42],"have":[22],"been":[23],"proved":[24],"a":[25,79,90,103],"kind":[26],"of":[27,34,40,70,145,150,158],"efficient":[28],"to":[30,64,85,115,128],"evaluate":[31,116],"the":[32,38,66,117,130,142],"importance":[33],"regulations.":[36],"Nevertheless,":[37],"accuracy":[39,69],"traditional":[41],"can":[43],"be":[44],"further":[45],"improved.":[46],"With":[47],"time-series":[48],"data,":[51],"exploiting":[52],"inherent":[53],"time":[54,59,109],"information":[55,110],"and":[56,68,99,112,121,137],"high":[57],"order":[58],"lag":[60],"are":[61,123,168],"promising":[62],"strategies":[63],"improve":[65],"power":[67],"GRNs":[71],"inference.":[72],"RESULTS:":[73],"In":[74],"this":[75],"study,":[76],"we":[77],"propose":[78],"scalable,":[80],"flexible":[81],"approach":[82],"called":[83],"BiXGBoost":[84,88,107,127,146,159],"reconstruct":[86],"GRNs.":[87],"bidirectional-based":[91],"method":[92],"by":[93],"considering":[94],"both":[95],"candidate":[96],"genes":[98,101],"target":[100],"for":[102],"specific":[104],"gene.":[105],"Moreover,":[106],"utilizes":[108],"efficiently":[111],"integrates":[113],"XGBoost":[114],"feature":[118],"importance.":[119],"Randomization":[120],"regularization":[122],"also":[124],"applied":[125],"address":[129],"over-fitting":[131],"problem.":[132],"The":[133],"results":[134],"DREAM4":[136],"Escherichia":[138],"coli":[139],"datasets":[140],"show":[141],"good":[143],"performance":[144],"different":[148],"scale":[149],"networks.":[151],"AVAILABILITY":[152],"AND":[153],"IMPLEMENTATION:":[154],"Our":[155],"Python":[156],"implementation":[157],"available":[161,169],"at":[162,170],"https://github.com/zrq0123/BiXGBoost.":[163],"SUPPLEMENTARY":[164],"INFORMATION:":[165],"Supplementary":[166],"data":[167],"Bioinformatics":[171],"online.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
