{"id":"https://openalex.org/W3097009024","doi":"https://doi.org/10.1109/tcbb.2020.3034861","title":"Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data","display_name":"Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data","publication_year":2020,"publication_date":"2020-10-29","ids":{"openalex":"https://openalex.org/W3097009024","doi":"https://doi.org/10.1109/tcbb.2020.3034861","mag":"3097009024","pmid":"https://pubmed.ncbi.nlm.nih.gov/33119511"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3034861","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3034861","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5014843434","display_name":"Omid Abbaszadeh","orcid":"https://orcid.org/0000-0002-8923-940X"},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Omid Abbaszadeh","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Zanajan, Zanjan, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Zanajan, Zanjan, Iran","institution_ids":["https://openalex.org/I99861883"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061289292","display_name":"Ali Azarpeyvand","orcid":"https://orcid.org/0000-0002-4166-7528"},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Ali Azarpeyvand","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Zanajan, Zanjan, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Zanajan, Zanjan, Iran","institution_ids":["https://openalex.org/I99861883"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041675442","display_name":"Alireza Khanteymoori","orcid":"https://orcid.org/0000-0001-6811-9196"},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Alireza Khanteymoori","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Zanajan, Zanjan, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Zanajan, Zanjan, Iran","institution_ids":["https://openalex.org/I99861883"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060243943","display_name":"Abbas Bahari","orcid":"https://orcid.org/0000-0003-1913-4837"},"institutions":[{"id":"https://openalex.org/I99861883","display_name":"University of Zanjan","ror":"https://ror.org/05e34ej29","country_code":"IR","type":"education","lineage":["https://openalex.org/I99861883"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Abbas Bahari","raw_affiliation_strings":["Research Institute of Modern Biological Techniques, University of Zanjan, Zanjan, Iran"],"affiliations":[{"raw_affiliation_string":"Research Institute of Modern Biological Techniques, University of Zanjan, Zanjan, Iran","institution_ids":["https://openalex.org/I99861883"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014843434"],"corresponding_institution_ids":["https://openalex.org/I99861883"],"apc_list":null,"apc_paid":null,"fwci":0.1669,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.51102274,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"1545","last_page":"1557"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9991999864578247,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9959999918937683,"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":0.6819131374359131},{"id":"https://openalex.org/keywords/graphical-model","display_name":"Graphical model","score":0.6413791179656982},{"id":"https://openalex.org/keywords/covariance","display_name":"Covariance","score":0.5872467756271362},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.5615324974060059},{"id":"https://openalex.org/keywords/covariance-matrix","display_name":"Covariance matrix","score":0.518858790397644},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5181785821914673},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5091819167137146},{"id":"https://openalex.org/keywords/estimation-of-covariance-matrices","display_name":"Estimation of covariance matrices","score":0.4721301198005676},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.45719826221466064},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45524758100509644},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38872021436691284},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.336097776889801},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1987466812133789},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12150585651397705}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6819131374359131},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.6413791179656982},{"id":"https://openalex.org/C178650346","wikidata":"https://www.wikidata.org/wiki/Q201984","display_name":"Covariance","level":2,"score":0.5872467756271362},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.5615324974060059},{"id":"https://openalex.org/C185142706","wikidata":"https://www.wikidata.org/wiki/Q1134404","display_name":"Covariance matrix","level":2,"score":0.518858790397644},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5181785821914673},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5091819167137146},{"id":"https://openalex.org/C180877172","wikidata":"https://www.wikidata.org/wiki/Q5401390","display_name":"Estimation of covariance matrices","level":3,"score":0.4721301198005676},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.45719826221466064},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45524758100509644},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38872021436691284},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.336097776889801},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1987466812133789},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12150585651397705},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.3034861","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3034861","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33119511","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33119511","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4000000059604645}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1520434148","https://openalex.org/W1549823682","https://openalex.org/W1584444527","https://openalex.org/W1598266570","https://openalex.org/W1706044825","https://openalex.org/W1851422093","https://openalex.org/W1966716734","https://openalex.org/W1968634476","https://openalex.org/W1971672021","https://openalex.org/W1990512452","https://openalex.org/W2026584719","https://openalex.org/W2032783896","https://openalex.org/W2034028219","https://openalex.org/W2044525257","https://openalex.org/W2049131636","https://openalex.org/W2062125287","https://openalex.org/W2076513103","https://openalex.org/W2081746825","https://openalex.org/W2084029198","https://openalex.org/W2097953983","https://openalex.org/W2099900459","https://openalex.org/W2105760337","https://openalex.org/W2105924489","https://openalex.org/W2106555403","https://openalex.org/W2108153777","https://openalex.org/W2109384743","https://openalex.org/W2119412782","https://openalex.org/W2123270810","https://openalex.org/W2124985265","https://openalex.org/W2125910575","https://openalex.org/W2128517432","https://openalex.org/W2132555912","https://openalex.org/W2151128232","https://openalex.org/W2152401289","https://openalex.org/W2152941516","https://openalex.org/W2163296115","https://openalex.org/W2163480486","https://openalex.org/W2164278908","https://openalex.org/W2175677210","https://openalex.org/W2277973662","https://openalex.org/W2293018703","https://openalex.org/W2327972292","https://openalex.org/W2402595598","https://openalex.org/W2586275266","https://openalex.org/W2588199737","https://openalex.org/W2607356028","https://openalex.org/W2611370172","https://openalex.org/W2735521500","https://openalex.org/W2791698794","https://openalex.org/W2805920247","https://openalex.org/W2850647469","https://openalex.org/W2890301877","https://openalex.org/W2913354234","https://openalex.org/W2916479752","https://openalex.org/W2950434449","https://openalex.org/W3026277942","https://openalex.org/W4213251304","https://openalex.org/W4294216483","https://openalex.org/W4388323202","https://openalex.org/W6631593755","https://openalex.org/W6637535267","https://openalex.org/W6682227116","https://openalex.org/W6777603554"],"related_works":["https://openalex.org/W3183113072","https://openalex.org/W2126934800","https://openalex.org/W2187019487","https://openalex.org/W1715419791","https://openalex.org/W643788828","https://openalex.org/W2158940596","https://openalex.org/W2126916073","https://openalex.org/W4200510307","https://openalex.org/W2886934452","https://openalex.org/W2024369332"],"abstract_inverted_index":{"Previous":[0],"efforts":[1],"in":[2,32,59,95,115,122,147],"gene":[3,49],"network":[4,33,50],"reconstruction":[5,34],"have":[6],"mainly":[7],"focused":[8],"on":[9,130,162],"data-driven":[10],"modeling,":[11],"with":[12,54],"little":[13],"attention":[14],"paid":[15],"to":[16,101,138],"knowledge-based":[17],"approaches.":[18],"Leveraging":[19],"prior":[20,57,113],"knowledge,":[21],"however,":[22],"is":[23,93],"a":[24,48,82],"promising":[25],"paradigm":[26],"that":[27],"has":[28],"been":[29],"gaining":[30],"momentum":[31],"and":[35,55,62,132,152,181],"computational":[36],"biology":[37],"research":[38,80],"communities.":[39],"This":[40,107],"paper":[41],"proposes":[42],"two":[43],"new":[44],"algorithms":[45,143],"for":[46],"reconstructing":[47],"from":[51,68,174],"expression":[52],"profiles":[53],"without":[56],"knowledge":[58,114],"small":[60],"sample":[61],"high-dimensional":[63],"settings.":[64],"First,":[65],"using":[66],"tools":[67],"the":[69,74,78,86,96,103,110,116,123,141,156,163,175],"statistical":[70],"estimation":[71],"theory,":[72],"particularly":[73],"empirical":[75],"Bayesian":[76],"approach,":[77],"current":[79],"estimates":[81],"covariance":[83,91,117],"matrix":[84,92],"via":[85],"shrinkage":[87],"method.":[88],"Second,":[89],"estimated":[90],"employed":[94],"penalized":[97],"normal":[98],"likelihood":[99],"method":[100,161],"select":[102],"Gaussian":[104,124],"graphical":[105,125],"model.":[106],"formulation":[108],"allows":[109],"application":[111],"of":[112,149,166],"estimation,":[118],"as":[119,121],"well":[120],"model":[126],"selection.":[127],"Experimental":[128],"results":[129,146],"simulated":[131],"real":[133],"datasets":[134],"show":[135],"that,":[136],"compared":[137],"state-of-the-art":[139],"methods,":[140],"proposed":[142],"achieve":[144],"better":[145],"terms":[148],"both":[150],"PR":[151],"ROC":[153],"curves.":[154],"Finally,":[155],"present":[157],"work":[158],"applies":[159],"its":[160],"RNA-seq":[164],"data":[165,183],"human":[167],"gastric":[168],"atrophy":[169],"patients,":[170],"which":[171],"was":[172],"obtained":[173],"EMBL-EBI":[176],"database.":[177],"The":[178],"source":[179],"codes":[180],"relevant":[182],"can":[184],"be":[185],"downloaded":[186],"from:":[187],"https://github.com/AbbaszadehO/DKGN.":[188]},"counts_by_year":[{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}