{"id":"https://openalex.org/W4390075384","doi":"https://doi.org/10.1109/tcbb.2023.3345317","title":"BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction","display_name":"BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction","publication_year":2023,"publication_date":"2023-12-21","ids":{"openalex":"https://openalex.org/W4390075384","doi":"https://doi.org/10.1109/tcbb.2023.3345317","pmid":"https://pubmed.ncbi.nlm.nih.gov/38127613"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3345317","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3345317","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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/A5087247680","display_name":"Junchang Xin","orcid":"https://orcid.org/0000-0003-2077-8269"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junchang Xin","raw_affiliation_strings":["School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China","Key Laboratory of Big Data Management and Analytics (Liaoning Province), Northeastern University, Shenyang, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0003-2077-8269","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China","institution_ids":["https://openalex.org/I9224756"]},{"raw_affiliation_string":"Key Laboratory of Big Data Management and Analytics (Liaoning Province), Northeastern University, Shenyang, Liaoning, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103187987","display_name":"Mingcan Wang","orcid":"https://orcid.org/0000-0002-8386-4060"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingcan Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0002-8386-4060","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081033387","display_name":"Luxuan Qu","orcid":"https://orcid.org/0000-0001-8452-2743"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Luxuan Qu","raw_affiliation_strings":["School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0001-8452-2743","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Northeastern University, Shenyang, Liaoning, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Qi Chen","orcid":"https://orcid.org/0000-0002-1772-0499"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qi Chen","raw_affiliation_strings":["College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0002-1772-0499","affiliations":[{"raw_affiliation_string":"College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008779879","display_name":"Weiyiqi Wang","orcid":"https://orcid.org/0009-0004-0600-8828"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiyiqi Wang","raw_affiliation_strings":["College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, China"],"raw_orcid":"https://orcid.org/0009-0004-0600-8828","affiliations":[{"raw_affiliation_string":"College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103215657","display_name":"Zhiqiong Wang","orcid":"https://orcid.org/0000-0002-0095-0378"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiqiong Wang","raw_affiliation_strings":["College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, China"],"raw_orcid":"https://orcid.org/0000-0002-0095-0378","affiliations":[{"raw_affiliation_string":"College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, China","institution_ids":["https://openalex.org/I9224756"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I9224756"],"apc_list":null,"apc_paid":null,"fwci":1.0235,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.75011616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"21","issue":"1","first_page":"188","last_page":"199"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9955000281333923,"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":0.9955000281333923,"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/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.9926999807357788,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9890999794006348,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6461414694786072},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.6155149340629578},{"id":"https://openalex.org/keywords/dynamic-bayesian-network","display_name":"Dynamic Bayesian network","score":0.5900437235832214},{"id":"https://openalex.org/keywords/order","display_name":"Order (exchange)","score":0.5110756158828735},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48284584283828735},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4802180230617523},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4227331578731537},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4214057922363281},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.34140920639038086},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.325528085231781},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3030046224594116},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27726882696151733},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19180592894554138},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11086374521255493},{"id":"https://openalex.org/keywords/economics","display_name":"Economics","score":0.09506240487098694}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6461414694786072},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.6155149340629578},{"id":"https://openalex.org/C82142266","wikidata":"https://www.wikidata.org/wiki/Q3456604","display_name":"Dynamic Bayesian network","level":3,"score":0.5900437235832214},{"id":"https://openalex.org/C182306322","wikidata":"https://www.wikidata.org/wiki/Q1779371","display_name":"Order (exchange)","level":2,"score":0.5110756158828735},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48284584283828735},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4802180230617523},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4227331578731537},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4214057922363281},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.34140920639038086},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.325528085231781},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3030046224594116},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27726882696151733},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19180592894554138},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11086374521255493},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.09506240487098694},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"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":"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.2023.3345317","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3345317","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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:38127613","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38127613","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":[{"id":"https://metadata.un.org/sdg/17","score":0.44999998807907104,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G3479532904","display_name":null,"funder_award_id":"N2116016","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G4618686014","display_name":null,"funder_award_id":"62072089","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4817957346","display_name":null,"funder_award_id":"N2104001","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5475149831","display_name":null,"funder_award_id":"N2224001-10","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G7276962668","display_name":null,"funder_award_id":"N2019007","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1987757667","https://openalex.org/W2005495944","https://openalex.org/W2037069407","https://openalex.org/W2098086436","https://openalex.org/W2099900459","https://openalex.org/W2122708083","https://openalex.org/W2132512039","https://openalex.org/W2142390772","https://openalex.org/W2154293840","https://openalex.org/W2156426710","https://openalex.org/W2159941442","https://openalex.org/W2163296115","https://openalex.org/W2176372122","https://openalex.org/W2342019990","https://openalex.org/W2393503031","https://openalex.org/W2409401342","https://openalex.org/W2498761000","https://openalex.org/W2560486644","https://openalex.org/W2582743722","https://openalex.org/W2630377436","https://openalex.org/W2767976825","https://openalex.org/W2769550393","https://openalex.org/W2799451098","https://openalex.org/W2803928488","https://openalex.org/W2830996996","https://openalex.org/W2891115924","https://openalex.org/W2896693520","https://openalex.org/W2900341503","https://openalex.org/W2920876032","https://openalex.org/W2951850020","https://openalex.org/W2995360419","https://openalex.org/W2998917483","https://openalex.org/W3037958198","https://openalex.org/W3047945592","https://openalex.org/W3076814102","https://openalex.org/W3082974932","https://openalex.org/W3103217321","https://openalex.org/W3128925966","https://openalex.org/W3136903744","https://openalex.org/W3176710272","https://openalex.org/W3177750787","https://openalex.org/W3186348651","https://openalex.org/W3193795275","https://openalex.org/W3196689760","https://openalex.org/W3196837732","https://openalex.org/W3199213843","https://openalex.org/W3199285124","https://openalex.org/W3201667851","https://openalex.org/W4200553055","https://openalex.org/W4206804332","https://openalex.org/W4213213129","https://openalex.org/W4229028016","https://openalex.org/W4282932623","https://openalex.org/W4308552061","https://openalex.org/W4379117479","https://openalex.org/W4385618127","https://openalex.org/W4385695846","https://openalex.org/W4386821788","https://openalex.org/W4386965205","https://openalex.org/W6631593755","https://openalex.org/W6675294747","https://openalex.org/W6756083223","https://openalex.org/W6991263393"],"related_works":["https://openalex.org/W2544242547","https://openalex.org/W2119218276","https://openalex.org/W2369018153","https://openalex.org/W2530648058","https://openalex.org/W2386937658","https://openalex.org/W2124007391","https://openalex.org/W2578973671","https://openalex.org/W2349909726","https://openalex.org/W1965576512","https://openalex.org/W2215058820"],"abstract_inverted_index":{"Reconstructing":[0],"gene":[1],"regulatory":[2],"networks(GRNs)":[3],"is":[4,14,103,117,124],"an":[5,86],"increasingly":[6],"hot":[7],"topic":[8],"in":[9],"bioinformatics.":[10],"Dynamic":[11],"Bayesian":[12,161],"network(DBN)":[13],"a":[15,22,54,108],"stochastic":[16],"graph":[17],"model":[18,24,88,98,102],"commonly":[19],"used":[20],"as":[21,191],"vital":[23],"for":[25,114,169],"GRN":[26,44,115,170,195],"reconstruction.":[27,171],"But":[28],"probabilistic":[29],"characteristics":[30],"of":[31,37,77,81],"biological":[32],"networks":[33],"and":[34,46,61,75,99,135,152,165],"the":[35,78],"existence":[36],"data":[38],"noise":[39],"bring":[40],"great":[41],"challenges":[42],"to":[43,49,192],"reconstruction":[45,116,196],"always":[47],"lead":[48],"many":[50,159,166],"false":[51,181],"positive/negative":[52],"edges.${Score}_{Lasso}$is":[53],"hybrid":[55,109],"DBN":[56,60,92,111],"score":[57,112,122,142,163],"function":[58,113,123],"combining":[59],"linear":[62,96,132],"regression":[63,97,133],"with":[64,157],"good":[65],"performance.":[66,197],"Its":[67],"performance":[68],"is,":[69],"however,":[70],"limited":[71],"by":[72,126],"first-order":[73],"assumption":[74],"ignorance":[76],"initial":[79],"network":[80],"DBN.":[82],"In":[83],"this":[84],"article,":[85],"integrated":[87],"based":[89,129],"on":[90,106,130,139],"higher-order":[91,94,110],"model,":[93],"Lasso":[95,131],"Pearson":[100,136],"correlation":[101,137],"proposed.":[104],"Based":[105],"this,":[107],"proposed,":[118],"namely":[119],"BIC-LP.":[120],"BIC-LP":[121,176],"constructed":[125],"adding":[127],"terms":[128],"coefficients":[134,138],"classical":[140],"BIC":[141],"function.":[143],"Therefore,":[144],"it":[145],"could":[146],"capture":[147],"more":[148],"information":[149,154],"from":[150],"dataset":[151],"curb":[153],"loss,":[155],"compared":[156],"both":[158],"existing":[160],"family":[162],"functions":[164],"state-of-the-art":[167],"methods":[168],"Experimental":[172],"results":[173],"show":[174],"that":[175],"can":[177],"reasonably":[178],"eliminate":[179],"some":[180],"positive":[182,188],"edges":[183],"while":[184],"retaining":[185],"most":[186],"true":[187],"edges,":[189],"so":[190],"achieve":[193],"better":[194]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
