{"id":"https://openalex.org/W1576587727","doi":"https://doi.org/10.1137/140972081","title":"A Multilevel Adaptive Reaction-splitting Simulation Method for Stochastic Reaction Networks","display_name":"A Multilevel Adaptive Reaction-splitting Simulation Method for Stochastic Reaction Networks","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W1576587727","doi":"https://doi.org/10.1137/140972081","mag":"1576587727"},"language":"en","primary_location":{"id":"doi:10.1137/140972081","is_oa":false,"landing_page_url":"https://doi.org/10.1137/140972081","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Scientific Computing","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1406.1989","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112042007","display_name":"Alvaro Moraes","orcid":null},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Alvaro Moraes","raw_affiliation_strings":["King Abdullah University of Science & Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science & Technology","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004939553","display_name":"Ra\u00fal Tempone","orcid":"https://orcid.org/0000-0003-1967-4446"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Raul Tempone","raw_affiliation_strings":["King Abdullah University of Science & Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science & Technology","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059757671","display_name":"Pedro Vilanova","orcid":null},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Pedro Vilanova","raw_affiliation_strings":["King Abdullah University of Science & Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science & Technology","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":null,"apc_paid":null,"fwci":0.3206,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.65044009,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"38","issue":"4","first_page":"A2091","last_page":"A2117"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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/T13052","display_name":"Molecular Communication and Nanonetworks","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical 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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.949999988079071,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.6038765907287598},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.600038468837738},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.515910267829895},{"id":"https://openalex.org/keywords/partition","display_name":"Partition (number theory)","score":0.4834902882575989},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.469414085149765},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.43797117471694946},{"id":"https://openalex.org/keywords/stochastic-process","display_name":"Stochastic process","score":0.4301312267780304},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.42491668462753296},{"id":"https://openalex.org/keywords/stochastic-modelling","display_name":"Stochastic modelling","score":0.41724342107772827},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2718895673751831},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.0899718701839447}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6038765907287598},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.600038468837738},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.515910267829895},{"id":"https://openalex.org/C42812","wikidata":"https://www.wikidata.org/wiki/Q1082910","display_name":"Partition (number theory)","level":2,"score":0.4834902882575989},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.469414085149765},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.43797117471694946},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.4301312267780304},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.42491668462753296},{"id":"https://openalex.org/C127491075","wikidata":"https://www.wikidata.org/wiki/Q7617825","display_name":"Stochastic modelling","level":2,"score":0.41724342107772827},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2718895673751831},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0899718701839447},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1137/140972081","is_oa":false,"landing_page_url":"https://doi.org/10.1137/140972081","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Scientific Computing","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1406.1989","is_oa":true,"landing_page_url":"https://arxiv.org/abs/1406.1989","pdf_url":"https://arxiv.org/pdf/1406.1989","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:1576587727","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1406.1989","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:repository.kaust.edu.sa:10754/621915","is_oa":false,"landing_page_url":"http://hdl.handle.net/10754/621915","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"doi:10.48550/arxiv.1406.1989","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1406.1989","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1406.1989","is_oa":true,"landing_page_url":"https://arxiv.org/abs/1406.1989","pdf_url":"https://arxiv.org/pdf/1406.1989","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"score":0.8500000238418579,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1576587727.pdf","grobid_xml":"https://content.openalex.org/works/W1576587727.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W89812392","https://openalex.org/W1645305843","https://openalex.org/W1974631391","https://openalex.org/W1996641400","https://openalex.org/W2010934558","https://openalex.org/W2011432832","https://openalex.org/W2026245359","https://openalex.org/W2042321087","https://openalex.org/W2074401358","https://openalex.org/W2078734278","https://openalex.org/W2084924279","https://openalex.org/W2093122667","https://openalex.org/W2116620527","https://openalex.org/W2121777611","https://openalex.org/W2124924107","https://openalex.org/W2125744693","https://openalex.org/W2132302738","https://openalex.org/W2135734223","https://openalex.org/W2150800446","https://openalex.org/W2163715525","https://openalex.org/W2949349651","https://openalex.org/W2950303138","https://openalex.org/W2962834951","https://openalex.org/W3121345254"],"related_works":["https://openalex.org/W2804405002","https://openalex.org/W2914554257","https://openalex.org/W1680678217","https://openalex.org/W2076783137","https://openalex.org/W1654691188","https://openalex.org/W3134039335","https://openalex.org/W2141564166","https://openalex.org/W2112072995","https://openalex.org/W1590979129","https://openalex.org/W1589828999","https://openalex.org/W2097403647","https://openalex.org/W2628760336","https://openalex.org/W3108208380","https://openalex.org/W2949732416","https://openalex.org/W3023461260","https://openalex.org/W2945674393","https://openalex.org/W2972560617","https://openalex.org/W2944663555","https://openalex.org/W1809669710","https://openalex.org/W2953366998"],"abstract_inverted_index":{"In":[0],"this":[1,44],"work,":[2],"we":[3,46,61],"present":[4,195,219],"a":[5,49,57,63,83,86,93,131,147,161,166,175,185,190,196,215],"novel":[6,197],"multilevel":[7,133,246],"Monte":[8,134,247],"Carlo":[9,135,248],"method":[10,32,152,232],"for":[11,126],"kinetic":[12],"simulation":[13,122,242],"of":[14,54,56,74,89,141,143,178],"stochastic":[15,205,241],"reaction":[16,25,58,75],"networks":[17],"characterized":[18,80],"by":[19,81,209,250],"having":[20],"simultaneously":[21],"fast":[22,39],"and":[23,40,130,244,252],"slow":[24,41],"channels.":[26,42],"To":[27,43,137],"produce":[28],"efficient":[29],"simulations,":[30],"our":[31,151],"adaptively":[33,70],"classifies":[34],"the":[35,72,96,105,144,154,181,204,225,230,239,245],"reactions":[36],"channels":[37,76,101,113],"into":[38,77],"end,":[45],"first":[47],"introduce":[48],"state-dependent":[50],"quantity":[51],"named":[52],"level":[53,88],"activity":[55],"channel.":[59],"Then,":[60],"propose":[62],"low-cost":[64,198],"heuristic":[65],"that":[66,227],"allows":[67],"us":[68],"to":[69,158,238],"split":[71],"set":[73],"two":[78,220],"subsets":[79],"either":[82],"high":[84],"or":[85],"low":[87],"activity.":[90],"Based":[91],"on":[92,203,214],"time-splitting":[94],"technique,":[95],"increments":[97],"associated":[98,110],"with":[99,111,174,184,189,236],"high-activity":[100],"are":[102,114],"simulated":[103,115],"using":[104,116],"tau-leap":[106],"method,":[107,187],"while":[108],"those":[109],"low-activity":[112],"an":[117],"exact":[118],"method.":[119],"This":[120,170],"path":[121,128],"technique":[123,201],"is":[124,172],"amenable":[125],"coupled":[127],"generation":[129],"corresponding":[132],"algorithm.":[136],"estimate":[138],"expected":[139],"values":[140],"observables":[142],"system":[145],"at":[146],"prescribed":[148,162],"final":[149],"time,":[150],"bounds":[153],"global":[155],"computational":[156,176],"error":[157],"be":[159],"below":[160],"tolerance,":[163],"$TOL$,":[164],"within":[165],"given":[167],"confidence":[168],"level.":[169],"goal":[171],"achieved":[173],"complexity":[177],"order":[179],"$O(TOL^{-2})$,":[180],"same":[182],"as":[183],"pathwise-exact":[186],"but":[188],"smaller":[191],"constant.":[192],"We":[193,218],"also":[194],"control":[199],"variate":[200],"based":[202],"time":[206],"change":[207],"representation":[208],"Kurtz,":[210],"showing":[211],"its":[212],"performance":[213],"numerical":[216,221],"example.":[217],"examples":[222],"extracted":[223],"from":[224],"literature":[226],"show":[228],"how":[229],"reaction-splitting":[231],"obtains":[233],"substantial":[234],"gains":[235],"respect":[237],"standard":[240],"algorithm":[243],"approach":[249],"Anderson":[251],"Higham.":[253]},"counts_by_year":[{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2022-10-01T00:00:00"}