{"id":"https://openalex.org/W4413393812","doi":"https://doi.org/10.23919/acc63710.2025.11108118","title":"Pareto-Optimal Interventions in Gene Regulatory Networks using Signal Temporal Logic","display_name":"Pareto-Optimal Interventions in Gene Regulatory Networks using Signal Temporal Logic","publication_year":2025,"publication_date":"2025-07-08","ids":{"openalex":"https://openalex.org/W4413393812","doi":"https://doi.org/10.23919/acc63710.2025.11108118","pmid":"https://pubmed.ncbi.nlm.nih.gov/41773284"},"language":"en","primary_location":{"id":"doi:10.23919/acc63710.2025.11108118","is_oa":false,"landing_page_url":"https://doi.org/10.23919/acc63710.2025.11108118","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 American Control Conference (ACC)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12950180/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101686503","display_name":"Seyed Hamid Hosseini","orcid":"https://orcid.org/0000-0002-4317-0216"},"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":"Seyed Hamid Hosseini","raw_affiliation_strings":["Northeastern University,Department of Electrical and Computer Engineering"],"affiliations":[{"raw_affiliation_string":"Northeastern University,Department of Electrical and Computer Engineering","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053550436","display_name":"Derya Aksaray","orcid":"https://orcid.org/0000-0003-4236-9116"},"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":"Derya Aksaray","raw_affiliation_strings":["Northeastern University,Department of Electrical and Computer Engineering"],"affiliations":[{"raw_affiliation_string":"Northeastern University,Department of Electrical and Computer Engineering","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"},"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,Department of Electrical and Computer Engineering"],"affiliations":[{"raw_affiliation_string":"Northeastern University,Department of Electrical and Computer Engineering","institution_ids":["https://openalex.org/I12912129"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101686503"],"corresponding_institution_ids":["https://openalex.org/I12912129"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20273012,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2025","issue":null,"first_page":"1379","last_page":"1386"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9955999851226807,"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":0.9955999851226807,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9805999994277954,"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/T10142","display_name":"Formal Methods in Verification","score":0.9545000195503235,"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/pareto-principle","display_name":"Pareto principle","score":0.6055150032043457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5651932954788208},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.5558053851127625},{"id":"https://openalex.org/keywords/psychological-intervention","display_name":"Psychological intervention","score":0.4588930606842041},{"id":"https://openalex.org/keywords/pareto-optimal","display_name":"Pareto optimal","score":0.44577693939208984},{"id":"https://openalex.org/keywords/temporal-logic","display_name":"Temporal logic","score":0.4369164705276489},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3746179938316345},{"id":"https://openalex.org/keywords/multi-objective-optimization","display_name":"Multi-objective optimization","score":0.26972144842147827},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2374001443386078},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.23470661044120789},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20349398255348206},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1847972571849823},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17280766367912292},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.14973148703575134}],"concepts":[{"id":"https://openalex.org/C137635306","wikidata":"https://www.wikidata.org/wiki/Q182667","display_name":"Pareto principle","level":2,"score":0.6055150032043457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5651932954788208},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.5558053851127625},{"id":"https://openalex.org/C27415008","wikidata":"https://www.wikidata.org/wiki/Q7256382","display_name":"Psychological intervention","level":2,"score":0.4588930606842041},{"id":"https://openalex.org/C2986314615","wikidata":"https://www.wikidata.org/wiki/Q36829","display_name":"Pareto optimal","level":3,"score":0.44577693939208984},{"id":"https://openalex.org/C25016198","wikidata":"https://www.wikidata.org/wiki/Q781833","display_name":"Temporal logic","level":2,"score":0.4369164705276489},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3746179938316345},{"id":"https://openalex.org/C68781425","wikidata":"https://www.wikidata.org/wiki/Q2052203","display_name":"Multi-objective optimization","level":2,"score":0.26972144842147827},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2374001443386078},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.23470661044120789},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20349398255348206},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1847972571849823},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17280766367912292},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.14973148703575134},{"id":"https://openalex.org/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.23919/acc63710.2025.11108118","is_oa":false,"landing_page_url":"https://doi.org/10.23919/acc63710.2025.11108118","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 American Control Conference (ACC)","raw_type":"proceedings-article"},{"id":"pmid:41773284","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41773284","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":"Proceedings of the ... American Control Conference. American Control Conference","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12950180","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12950180/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc Am Control Conf","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12950180","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12950180/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc Am Control Conf","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W189973795","https://openalex.org/W1533557569","https://openalex.org/W1547304883","https://openalex.org/W2049399166","https://openalex.org/W2130721915","https://openalex.org/W2159638256","https://openalex.org/W2160904474","https://openalex.org/W2796091538","https://openalex.org/W2982380908","https://openalex.org/W3066334675","https://openalex.org/W3141998036","https://openalex.org/W3148828413","https://openalex.org/W3216493670","https://openalex.org/W4280607022","https://openalex.org/W4295850088","https://openalex.org/W4313482696","https://openalex.org/W4383032290","https://openalex.org/W4391164360","https://openalex.org/W4392563562","https://openalex.org/W4392646696","https://openalex.org/W4393404779","https://openalex.org/W4396999865","https://openalex.org/W4402436959","https://openalex.org/W4402641466","https://openalex.org/W4403534516","https://openalex.org/W4405303508","https://openalex.org/W4407411658"],"related_works":["https://openalex.org/W1963790170","https://openalex.org/W2073298047","https://openalex.org/W2033790662","https://openalex.org/W2586328217","https://openalex.org/W2049264236","https://openalex.org/W317165722","https://openalex.org/W2728870795","https://openalex.org/W312725187","https://openalex.org/W1999828099","https://openalex.org/W2078568741"],"abstract_inverted_index":{"This":[0],"paper":[1,71],"presents":[2],"a":[3,84,115,123],"framework":[4],"for":[5,48],"identifying":[6],"Pareto-optimal":[7,116],"intervention":[8,38,57,81,146],"policies":[9],"in":[10,22,43,141],"Gene":[11],"Regulatory":[12],"Networks":[13],"(GRNs),":[14],"addressing":[15],"both":[16],"the":[17,65,80,136],"complexity":[18],"and":[19,31,59,78,108,144],"uncertainty":[20],"inherent":[21],"biological":[23],"systems.":[24],"Existing":[25],"methods,":[26],"such":[27],"as":[28,83],"dynamic":[29],"programming":[30],"reinforcement":[32],"learning,":[33],"focus":[34],"primarily":[35],"on":[36,100],"average":[37],"performance.":[39,147],"However,":[40],"practical":[41],"interventions":[42],"systems":[44],"biology":[45],"must":[46],"account":[47],"multiple":[49],"competing":[50],"objectives,":[51],"including":[52],"worst-case":[53],"performance,":[54],"response":[55],"time,":[56],"frequency,":[58],"long-term":[60],"system":[61],"stability.":[62],"To":[63],"model":[64],"stochastic":[66],"dynamics":[67],"of":[68,104,118,126,138],"GRNs,":[69],"this":[70],"employs":[72],"Boolean":[73],"networks":[74],"with":[75,122],"perturbations":[76],"(BNp)":[77],"formulates":[79],"problem":[82],"constrained":[85],"multi-objective":[86],"optimization":[87],"task.":[88],"Signal":[89],"Temporal":[90],"Logic":[91],"(STL)":[92],"is":[93],"leveraged":[94],"to":[95,129],"evaluate":[96],"policies,":[97,119],"particularly":[98],"focusing":[99],"maximizing":[101],"intervals":[102],"free":[103],"therapeutic":[105],"side":[106],"effects":[107],"minimizing":[109],"repeated":[110],"interventions.":[111],"Our":[112],"method":[113],"generates":[114],"set":[117],"providing":[120],"biologists":[121],"flexible":[124],"range":[125],"solutions":[127],"tailored":[128],"specific":[130],"experimental":[131],"needs.":[132],"Numerical":[133],"experiments":[134],"demonstrate":[135],"effectiveness":[137],"our":[139],"approach":[140],"achieving":[142],"robust":[143],"efficient":[145]},"counts_by_year":[],"updated_date":"2026-03-05T09:29:38.588285","created_date":"2025-10-10T00:00:00"}