{"id":"https://openalex.org/W4410000249","doi":"https://doi.org/10.1016/j.rico.2025.100570","title":"Bayesian topology inference of regulatory networks under partial observability","display_name":"Bayesian topology inference of regulatory networks under partial observability","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410000249","doi":"https://doi.org/10.1016/j.rico.2025.100570","pmid":"https://pubmed.ncbi.nlm.nih.gov/41867493"},"language":"en","primary_location":{"id":"doi:10.1016/j.rico.2025.100570","doi":"https://doi.org/10.1016/j.rico.2025.100570","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.rico.2025.100570","pdf_url":null,"source":{"id":"https://openalex.org/S4210182769","display_name":"Results in Control and Optimization","issn_l":"2666-7207","issn":["2666-7207"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Results in Control and Optimization","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.rico.2025.100570","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072786399","display_name":"Mohammad Alali","orcid":"https://orcid.org/0000-0002-5458-5273","observed_orcids":["https://orcid.org/0000-0002-5458-5273"]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mohammad Alali","raw_affiliation_strings":["Northeastern University, 360 Huntington Ave, Boston, MA, 02115, U.S"],"raw_orcid":"https://orcid.org/0000-0002-5458-5273","affiliations":[{"raw_affiliation_string":"Northeastern University, 360 Huntington Ave, Boston, MA, 02115, U.S","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017741575","display_name":"Mahdi Imani","orcid":"https://orcid.org/0000-0001-9570-9909","observed_orcids":["https://orcid.org/0000-0001-9570-9909"]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mahdi Imani","raw_affiliation_strings":["Northeastern University, 360 Huntington Ave, Boston, MA, 02115, U.S"],"raw_orcid":"https://orcid.org/0000-0001-9570-9909","affiliations":[{"raw_affiliation_string":"Northeastern University, 360 Huntington Ave, Boston, MA, 02115, U.S","institution_ids":["https://openalex.org/I12912129"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5072786399"],"corresponding_institution_ids":["https://openalex.org/I12912129"],"apc_list":{"value":1470,"currency":"USD","value_usd":1470},"apc_paid":{"value":1470,"currency":"USD","value_usd":1470},"fwci":0.2548,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.4262272,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":96},"biblio":{"volume":"19","issue":null,"first_page":"100570","last_page":"100570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T11236","display_name":"Control Systems and Identification","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.0,"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-inference","display_name":"gene regulatory network inference","score":0.8379999995231628},{"id":"https://openalex.org/keywords/network-topology-inference","display_name":"network topology inference","score":0.7950000166893005},{"id":"https://openalex.org/keywords/partial-observability","display_name":"partial observability","score":0.8009999990463257},{"id":"https://openalex.org/keywords/bayesian-optimization","display_name":"Bayesian optimization","score":0.9700000286102295},{"id":"https://openalex.org/keywords/gaussian-process-regression","display_name":"Gaussian process regression","score":0.9959999918937683},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.7429999709129333},{"id":"https://openalex.org/keywords/microbial-communities","display_name":"microbial communities","score":0.5120000243186951},{"id":"https://openalex.org/keywords/noisy-data","display_name":"noisy data","score":0.4729999899864197}],"concepts":[{"id":"https://openalex.org/C36299963","wikidata":"https://www.wikidata.org/wiki/Q1369844","display_name":"Observability","level":2,"score":0.9206664562225342},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.60675448179245},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5587671995162964},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.4772210717201233},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.47437626123428345},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.455870121717453},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.4363923966884613},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.38938871026039124},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33052629232406616},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.1675494909286499},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.06812912225723267}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1016/j.rico.2025.100570","doi":"https://doi.org/10.1016/j.rico.2025.100570","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.rico.2025.100570","pdf_url":null,"source":{"id":"https://openalex.org/S4210182769","display_name":"Results in Control and Optimization","issn_l":"2666-7207","issn":["2666-7207"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Results in Control and Optimization","raw_type":"journal-article"},{"id":"pmid:41867493","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41867493","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,"listed_in":[],"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":"Results in control and optimization","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13005241","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13005241/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13005241/pdf/nihms-2147583.pdf","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,"listed_in":[],"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":"Results Control Optim","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:2dd7181ce80940248c52c7e96151f1af","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/2dd7181ce80940248c52c7e96151f1af","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Results in Control and Optimization, Vol 19, Iss , Pp 100570- (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.rico.2025.100570","doi":"https://doi.org/10.1016/j.rico.2025.100570","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.rico.2025.100570","pdf_url":null,"source":{"id":"https://openalex.org/S4210182769","display_name":"Results in Control and Optimization","issn_l":"2666-7207","issn":["2666-7207"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Results in Control and Optimization","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2289997902","display_name":"III: Small: Statistical Inference through Data-Collection and Expert-Knowledge Incorporation","funder_award_id":"2311969","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3447059689","display_name":null,"funder_award_id":"R21 EB032480","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G4294695538","display_name":null,"funder_award_id":"W911NF2110299","funder_id":"https://openalex.org/F4320338507","funder_display_name":"Life Sciences Division, Army Research Office"},{"id":"https://openalex.org/G4874700971","display_name":null,"funder_award_id":"W911NF2110299","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"},{"id":"https://openalex.org/G5902281787","display_name":null,"funder_award_id":"W911NF2110299","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7878741421","display_name":null,"funder_award_id":"1R21EB032480-01","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320307904","display_name":"Oracle","ror":"https://ror.org/006c77m33"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"},{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"},{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"},{"id":"https://openalex.org/F4320338507","display_name":"Life Sciences Division, Army Research Office","ror":"https://ror.org/05aeehd63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W37038446","https://openalex.org/W51833465","https://openalex.org/W1501586228","https://openalex.org/W1510052597","https://openalex.org/W1600339875","https://openalex.org/W1978397363","https://openalex.org/W2003967703","https://openalex.org/W2009061689","https://openalex.org/W2047094503","https://openalex.org/W2058794142","https://openalex.org/W2078460342","https://openalex.org/W2098091224","https://openalex.org/W2101408219","https://openalex.org/W2113305236","https://openalex.org/W2126583902","https://openalex.org/W2130721915","https://openalex.org/W2132935366","https://openalex.org/W2145672247","https://openalex.org/W2192203593","https://openalex.org/W2527751063","https://openalex.org/W2586478664","https://openalex.org/W2592482446","https://openalex.org/W2593147488","https://openalex.org/W2796091538","https://openalex.org/W2802441085","https://openalex.org/W2805799371","https://openalex.org/W2891454102","https://openalex.org/W2976882512","https://openalex.org/W3082777162","https://openalex.org/W3103934441","https://openalex.org/W3106310405","https://openalex.org/W3198147676","https://openalex.org/W4206803396","https://openalex.org/W4211049957","https://openalex.org/W4214690320","https://openalex.org/W4233622718","https://openalex.org/W4238746485","https://openalex.org/W4253484285","https://openalex.org/W4312058912","https://openalex.org/W4313482696","https://openalex.org/W4366464224","https://openalex.org/W4366498340","https://openalex.org/W4383218499","https://openalex.org/W4390684261","https://openalex.org/W4391126196","https://openalex.org/W4391164360","https://openalex.org/W4391172914","https://openalex.org/W4391598097","https://openalex.org/W4391733770","https://openalex.org/W4392563562","https://openalex.org/W4393404779","https://openalex.org/W4394570041","https://openalex.org/W4395039471","https://openalex.org/W4396999865","https://openalex.org/W4399041751","https://openalex.org/W4399100951","https://openalex.org/W4406764503","https://openalex.org/W6682642761","https://openalex.org/W6757033530","https://openalex.org/W6776994607","https://openalex.org/W6800644531","https://openalex.org/W6854087403","https://openalex.org/W6855550351","https://openalex.org/W6855715117","https://openalex.org/W6860332231","https://openalex.org/W6861032269","https://openalex.org/W6863187311","https://openalex.org/W6864143783","https://openalex.org/W6866642195","https://openalex.org/W6872379462","https://openalex.org/W6876324592","https://openalex.org/W6877048524","https://openalex.org/W6877509859"],"related_works":["https://openalex.org/W2372267530","https://openalex.org/W2969189870","https://openalex.org/W3015855446","https://openalex.org/W2965643117","https://openalex.org/W4303857162","https://openalex.org/W2407375987","https://openalex.org/W3049691116","https://openalex.org/W2505726097","https://openalex.org/W2950975704","https://openalex.org/W2010643158"],"abstract_inverted_index":{"Biological":[0],"systems,":[1],"such":[2,83],"as":[3,141,155],"microbial":[4,43,50],"communities":[5,51],"in":[6,13,35],"metagenomics":[7],"and":[8,45,59,95,108,116,134,169,199,208,234],"gene":[9,41],"regulatory":[10,138],"networks":[11,84,139],"(GRNs)":[12],"genomics,":[14],"are":[15],"composed":[16],"of":[17,21,69,82,98,137,185],"a":[18,32,127,170],"vast":[19],"number":[20],"interacting":[22,71],"components":[23],"observed":[24,62,73],"through":[25,63],"inherently":[26],"noisy":[27],"data.":[28],"These":[29],"systems":[30,145],"play":[31],"critical":[33],"role":[34],"understanding":[36],"fundamental":[37],"biological":[38,118],"processes,":[39],"including":[40],"regulation,":[42],"interactions,":[44],"cellular":[46],"dynamics.":[47],"For":[48,212],"example,":[49],"involve":[52],"complex":[53,117],"interactions":[54],"between":[55],"microbes,":[56],"bacteria,":[57],"genes,":[58],"small":[60],"molecules":[61],"omics":[64],"data,":[65],"while":[66],"GRNs":[67],"consist":[68],"numerous":[70],"genes":[72],"via":[74],"various":[75],"gene-expression":[76],"technologies.":[77],"However,":[78],"reconstructing":[79],"the":[80,96,150,176,182,189,213,225],"topology":[81,129,196,227],"poses":[85],"significant":[86],"challenges":[87],"due":[88],"to":[89,174],"their":[90],"large":[91,115],"scale,":[92],"high":[93],"dimensionality,":[94],"presence":[97],"noise.":[99],"Existing":[100],"inference":[101,136],"techniques":[102],"often":[103],"struggle":[104],"with":[105,161,197,206,218,231],"scalability,":[106],"interpretability,":[107],"overfitting,":[109],"making":[110],"them":[111],"unsuitable":[112],"for":[113,132,159],"analyzing":[114],"systems.":[119],"To":[120],"overcome":[121],"these":[122],"challenges,":[123],"this":[124],"paper":[125],"proposes":[126],"Bayesian":[128,162],"optimization":[130],"framework":[131],"efficient":[133],"scalable":[135],"modeled":[140],"partially-observed":[142],"Boolean":[143,151],"dynamical":[144],"(POBDS).":[146],"The":[147],"method":[148,193,223],"combines":[149],"Kalman":[152],"Filter":[153],"(BKF)":[154],"an":[156],"optimal":[157],"estimator":[158],"POBDS,":[160],"optimization,":[163],"which":[164],"employs":[165],"Gaussian":[166],"Process":[167],"regression":[168],"topology-inspired":[171],"kernel":[172],"function":[173],"model":[175],"log-likelihood":[177,205],"function.":[178],"Numerical":[179],"experiments":[180],"demonstrate":[181],"superior":[183],"performance":[184],"our":[186,192],"framework.":[187],"In":[188],"p53-MDM2":[190],"network,":[191],"accurately":[194],"infers":[195],"8":[198],"16":[200],"unknown":[201,220],"regulations,":[202,221],"achieving":[203],"higher":[204],"100":[207],"200":[209],"evaluations,":[210],"respectively.":[211],"mammalian":[214],"cell":[215],"cycle":[216],"network":[217],"10":[219],"proposed":[222],"identifies":[224],"correct":[226],"among":[228],"59,049":[229],"possibilities":[230],"lower":[232],"error":[233],"faster":[235],"convergence.":[236]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2025-10-10T00:00:00"}