{"id":"https://openalex.org/W3159742809","doi":"https://doi.org/10.1142/s0219720021500074","title":"Learning gene regulatory networks using gaussian process emulator and graphical LASSO","display_name":"Learning gene regulatory networks using gaussian process emulator and graphical LASSO","publication_year":2021,"publication_date":"2021-04-30","ids":{"openalex":"https://openalex.org/W3159742809","doi":"https://doi.org/10.1142/s0219720021500074","mag":"3159742809","pmid":"https://pubmed.ncbi.nlm.nih.gov/33930997"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720021500074","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720021500074","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5049456230","display_name":"H. Chatrabgoun","orcid":null},"institutions":[{"id":"https://openalex.org/I112312016","display_name":"Hamedan University of Medical Sciences","ror":"https://ror.org/02ekfbp48","country_code":"IR","type":"education","lineage":["https://openalex.org/I112312016"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"H. Chatrabgoun","raw_affiliation_strings":["Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran","institution_ids":["https://openalex.org/I112312016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053527206","display_name":"Ali Reza Soltanian","orcid":"https://orcid.org/0000-0002-7483-3502"},"institutions":[{"id":"https://openalex.org/I112312016","display_name":"Hamedan University of Medical Sciences","ror":"https://ror.org/02ekfbp48","country_code":"IR","type":"education","lineage":["https://openalex.org/I112312016"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"A. R. Soltanian","raw_affiliation_strings":["Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran","institution_ids":["https://openalex.org/I112312016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020895059","display_name":"Hossein Mahjub","orcid":"https://orcid.org/0000-0002-9375-3807"},"institutions":[{"id":"https://openalex.org/I112312016","display_name":"Hamedan University of Medical Sciences","ror":"https://ror.org/02ekfbp48","country_code":"IR","type":"education","lineage":["https://openalex.org/I112312016"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"H. Mahjub","raw_affiliation_strings":["Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran","institution_ids":["https://openalex.org/I112312016"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066501399","display_name":"Fatemeh Bahreini","orcid":"https://orcid.org/0000-0003-4444-1206"},"institutions":[{"id":"https://openalex.org/I112312016","display_name":"Hamedan University of Medical Sciences","ror":"https://ror.org/02ekfbp48","country_code":"IR","type":"education","lineage":["https://openalex.org/I112312016"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"F. Bahreini","raw_affiliation_strings":["Department of Molecular Medicine and Genetics, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine and Genetics, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran","institution_ids":["https://openalex.org/I112312016"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053527206"],"corresponding_institution_ids":["https://openalex.org/I112312016"],"apc_list":null,"apc_paid":null,"fwci":0.273,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.60918474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"19","issue":"03","first_page":"2150007","last_page":"2150007"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12814","display_name":"Gaussian Processes and Bayesian Inference","score":0.9958000183105469,"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"}},"topics":[{"id":"https://openalex.org/T12814","display_name":"Gaussian Processes and Bayesian Inference","score":0.9958000183105469,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9887999892234802,"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/T10848","display_name":"Advanced Multi-Objective Optimization Algorithms","score":0.9812999963760376,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/hyperparameter","display_name":"Hyperparameter","score":0.6569968461990356},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5693602561950684},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5465168952941895},{"id":"https://openalex.org/keywords/gaussian-process","display_name":"Gaussian process","score":0.5255217552185059},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5106423497200012},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5053303837776184},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5048738121986389},{"id":"https://openalex.org/keywords/multivariate-normal-distribution","display_name":"Multivariate normal distribution","score":0.4634217321872711},{"id":"https://openalex.org/keywords/lasso","display_name":"Lasso (programming language)","score":0.43664103746414185},{"id":"https://openalex.org/keywords/covariance-matrix","display_name":"Covariance matrix","score":0.42835694551467896},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3619997501373291},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3572659194469452},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.34864363074302673},{"id":"https://openalex.org/keywords/multivariate-statistics","display_name":"Multivariate statistics","score":0.2628170847892761}],"concepts":[{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.6569968461990356},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5693602561950684},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5465168952941895},{"id":"https://openalex.org/C61326573","wikidata":"https://www.wikidata.org/wiki/Q1496376","display_name":"Gaussian process","level":3,"score":0.5255217552185059},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5106423497200012},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5053303837776184},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5048738121986389},{"id":"https://openalex.org/C177384507","wikidata":"https://www.wikidata.org/wiki/Q1149000","display_name":"Multivariate normal distribution","level":3,"score":0.4634217321872711},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.43664103746414185},{"id":"https://openalex.org/C185142706","wikidata":"https://www.wikidata.org/wiki/Q1134404","display_name":"Covariance matrix","level":2,"score":0.42835694551467896},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3619997501373291},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3572659194469452},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.34864363074302673},{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.2628170847892761},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine 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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","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:10.1142/s0219720021500074","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720021500074","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:33930997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33930997","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1494413412","https://openalex.org/W1503398984","https://openalex.org/W1827378692","https://openalex.org/W1982510939","https://openalex.org/W1993418188","https://openalex.org/W2004185360","https://openalex.org/W2005495944","https://openalex.org/W2008737153","https://openalex.org/W2010824638","https://openalex.org/W2018747370","https://openalex.org/W2024318675","https://openalex.org/W2056636001","https://openalex.org/W2060780143","https://openalex.org/W2062125287","https://openalex.org/W2074360197","https://openalex.org/W2081746825","https://openalex.org/W2084847607","https://openalex.org/W2094239847","https://openalex.org/W2117007075","https://openalex.org/W2118308505","https://openalex.org/W2121551152","https://openalex.org/W2132555912","https://openalex.org/W2148289138","https://openalex.org/W2156066129","https://openalex.org/W2272700822","https://openalex.org/W2334035995","https://openalex.org/W2484695609","https://openalex.org/W2760174268","https://openalex.org/W2772709428","https://openalex.org/W2953207088","https://openalex.org/W3018406264","https://openalex.org/W3098745759","https://openalex.org/W3105776335","https://openalex.org/W3144619878","https://openalex.org/W4211049957","https://openalex.org/W4230674625","https://openalex.org/W4299515571","https://openalex.org/W4388323202"],"related_works":["https://openalex.org/W2141609920","https://openalex.org/W4286748465","https://openalex.org/W3118984993","https://openalex.org/W2144336328","https://openalex.org/W3196933554","https://openalex.org/W4294619368","https://openalex.org/W4380558509","https://openalex.org/W3134381438","https://openalex.org/W2801379595","https://openalex.org/W1555936174"],"abstract_inverted_index":{"Large":[0],"amounts":[1],"of":[2,24,35,39,56,111,141,192,213,227,236,246],"research":[3,215],"efforts":[4],"have":[5,250],"been":[6],"focused":[7],"on":[8,15],"learning":[9,104],"gene":[10,16,37],"regulatory":[11],"networks":[12,47],"(GRNs)":[13],"based":[14],"expression":[17],"data":[18],"to":[19,121,135,164,205,207,218],"understand":[20],"the":[21,29,32,36,53,57,61,72,133,137,154,159,166,170,190,195,234,241,244,247,256],"functional":[22],"basis":[23],"a":[25,42,109,251],"living":[26],"organism.":[27],"Under":[28],"assumption":[30,235],"that":[31],"joint":[33],"distribution":[34,259],"expressions":[38],"interest":[40],"is":[41,95],"multivariate":[43,237,257],"normal":[44,238],"distribution,":[45,239],"such":[46],"can":[48,118,187],"be":[49,119],"constructed":[50],"by":[51,77,125],"assessing":[52],"nonzero":[54],"elements":[55],"inverse":[58],"covariance":[59],"matrix,":[60],"so-called":[62],"precision":[63,146,196,202],"matrix":[64,147,203],"or":[65],"concentration":[66],"matrix.":[67,197],"This":[68],"may":[69],"not":[70],"reflect":[71],"true":[73],"connectivity":[74],"between":[75],"genes":[76],"considering":[78],"just":[79],"pairwise":[80],"linear":[81],"correlations.":[82],"To":[83],"relax":[84],"this":[85,151],"limitative":[86],"constraint,":[87],"we":[88,157,176,186,199],"employ":[89],"Gaussian":[90,258],"process":[91],"(GP)":[92],"model":[93],"which":[94,117],"well":[96],"known":[97,113],"as":[98,114],"computationally":[99],"efficient":[100],"non-parametric":[101],"Bayesian":[102],"machine":[103],"technique.":[105,182],"GPs":[106],"are":[107,216],"among":[108],"class":[110],"methods":[112],"kernel":[115,163,178],"machines":[116],"used":[120,217],"approximate":[122],"complex":[123],"problems":[124],"tuning":[126],"their":[127],"hyperparameters.":[128],"In":[129,150],"fact,":[130],"GP":[131,160],"creates":[132],"ability":[134],"use":[136,245],"capacity":[138],"and":[139,148,174,240],"potential":[140],"different":[142,225],"kernels":[143,248],"in":[144,153,194],"constructing":[145],"GRNs.":[149],"paper,":[152],"first":[155],"step,":[156],"choose":[158],"with":[161,221],"appropriate":[162],"learn":[165],"considered":[167],"GRNs":[168,220],"from":[169],"observed":[171],"genetic":[172],"data,":[173],"then":[175],"estimate":[177],"hyperparameters":[179],"using":[180,233],"rule-of-thumb":[181],"Using":[183],"these":[184],"hyperparameters,":[185],"also":[188],"control":[189],"degree":[191],"sparseness":[193],"Then":[198],"obtain":[200],"kernel-based":[201,209],"similar":[204],"GLASSO":[206],"construct":[208,219],"GRN.":[210],"The":[211],"findings":[212],"our":[214],"high":[222],"performance,":[223],"for":[224],"species":[226],"Drosophila":[228],"fly":[229],"rather":[230],"than":[231,255],"simply":[232],"GPs,":[242],"despite":[243],"capacity,":[249],"much":[252],"better":[253],"performance":[254],"assumption.":[260]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}