{"id":"https://openalex.org/W4317815301","doi":"https://doi.org/10.1109/wsc57314.2022.10015448","title":"GPU-Accelerated Simulation Ensembles of Stochastic Reaction Networks","display_name":"GPU-Accelerated Simulation Ensembles of Stochastic Reaction Networks","publication_year":2022,"publication_date":"2022-12-11","ids":{"openalex":"https://openalex.org/W4317815301","doi":"https://doi.org/10.1109/wsc57314.2022.10015448"},"language":"en","primary_location":{"id":"doi:10.1109/wsc57314.2022.10015448","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/wsc57314.2022.10015448","pdf_url":null,"source":{"id":"https://openalex.org/S4363607869","display_name":"2022 Winter Simulation Conference (WSC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 Winter Simulation Conference (WSC)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5029430276","display_name":"Till K\u00f6ster","orcid":"https://orcid.org/0000-0003-0869-381X"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Till Koster","raw_affiliation_strings":["Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059"],"affiliations":[{"raw_affiliation_string":"Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008933958","display_name":"Leon Herrmann","orcid":"https://orcid.org/0000-0002-9850-1203"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leon Herrmann","raw_affiliation_strings":["Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059"],"affiliations":[{"raw_affiliation_string":"Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042423448","display_name":"Philipp Andelfinger","orcid":"https://orcid.org/0000-0002-0211-7136"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Philipp Andelfinger","raw_affiliation_strings":["Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059"],"affiliations":[{"raw_affiliation_string":"Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063515034","display_name":"Adelinde M. Uhrmacher","orcid":"https://orcid.org/0000-0001-5256-4682"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Adelinde Uhrmacher","raw_affiliation_strings":["Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059"],"affiliations":[{"raw_affiliation_string":"Institute for Visual and Analytic Computing University of Rostock,Rostock,GERMANY,18059","institution_ids":["https://openalex.org/I4665924"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5029430276"],"corresponding_institution_ids":["https://openalex.org/I4665924"],"apc_list":null,"apc_paid":null,"fwci":0.8821,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.76265823,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"12","issue":null,"first_page":"2570","last_page":"2581"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9865000247955322,"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/T11321","display_name":"Error Correcting Code Techniques","score":0.9811999797821045,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/computer-science","display_name":"Computer science","score":0.872416079044342},{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.6923294067382812},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6064674854278564},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.5888766646385193},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5023396015167236},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.4767264425754547},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4714456796646118},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.44250500202178955},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.42548424005508423},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.41893669962882996},{"id":"https://openalex.org/keywords/execution-time","display_name":"Execution time","score":0.41862913966178894},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3943975269794464},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.345175564289093},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2312612235546112},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.2223900854587555},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.08931905031204224}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.872416079044342},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.6923294067382812},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6064674854278564},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.5888766646385193},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5023396015167236},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.4767264425754547},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4714456796646118},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.44250500202178955},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.42548424005508423},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.41893669962882996},{"id":"https://openalex.org/C2989134064","wikidata":"https://www.wikidata.org/wiki/Q288510","display_name":"Execution time","level":2,"score":0.41862913966178894},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3943975269794464},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.345175564289093},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2312612235546112},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.2223900854587555},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.08931905031204224},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/wsc57314.2022.10015448","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/wsc57314.2022.10015448","pdf_url":null,"source":{"id":"https://openalex.org/S4363607869","display_name":"2022 Winter Simulation Conference (WSC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 Winter Simulation Conference (WSC)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.6299999952316284,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G4218580009","display_name":null,"funder_award_id":"UH-66/13","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1490436385","https://openalex.org/W2042321087","https://openalex.org/W2044859335","https://openalex.org/W2072745964","https://openalex.org/W2078409452","https://openalex.org/W2078734278","https://openalex.org/W2084924279","https://openalex.org/W2091831308","https://openalex.org/W2093483582","https://openalex.org/W2095266728","https://openalex.org/W2100584922","https://openalex.org/W2101768141","https://openalex.org/W2105672886","https://openalex.org/W2111609443","https://openalex.org/W2129887243","https://openalex.org/W2148080122","https://openalex.org/W2155418451","https://openalex.org/W2163493106","https://openalex.org/W2167154952","https://openalex.org/W2345709169","https://openalex.org/W2572804059","https://openalex.org/W2614068870","https://openalex.org/W2792385328","https://openalex.org/W2810476603","https://openalex.org/W2914837232","https://openalex.org/W3034132595","https://openalex.org/W3206138075","https://openalex.org/W4251164127"],"related_works":["https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2149078538","https://openalex.org/W2080146221","https://openalex.org/W2370314112","https://openalex.org/W1912958759","https://openalex.org/W2792081825"],"abstract_inverted_index":{"Stochastic":[0],"Simulation":[1],"Algorithms":[2],"are":[3,29,136,174],"widely":[4],"used":[5,41],"for":[6,42,116,142,187],"simulating":[7],"reaction":[8],"networks":[9],"in":[10,58,67,75,96,151],"cellular":[11],"biology.":[12],"Due":[13],"to":[14,51,103,107,140,176,203],"the":[15,21,34,39,68,93,97,105,112,120,127,161,164,167],"stochastic":[16,88],"nature":[17],"of":[18,55,61,70,87,122,131,163,178],"models":[19,143,173,189],"and":[20,78],"large":[22,172],"parameter":[23],"spaces":[24],"involved,":[25],"many":[26],"simulation":[27,89],"runs":[28,56],"frequently":[30],"needed.":[31],"We":[32],"approach":[33],"computational":[35],"challenge":[36,121],"by":[37,44],"expanding":[38],"hardware":[40],"execution":[43,132,146],"massively":[45],"parallel":[46],"graphical":[47],"processing":[48],"units":[49],"(GPUs)":[50],"execute":[52],"these":[53],"ensembles":[54],"concurrently":[57],"a":[59,152,191,196],"form":[60,69],"coarse-grained":[62],"parallelization.":[63],"Such":[64],"computing":[65],"infrastructure":[66],"GPUs":[71,109],"is":[72,81,133],"readily":[73],"available":[74,115],"desktop":[76,193],"workstations":[77],"clusters":[79],"but":[80],"not":[82],"commonly":[83],"exploited":[84],"as":[85,201],"part":[86],"studies.":[90,118],"Building":[91],"on":[92,199],"existing":[94],"literature":[95],"field,":[98],"we":[99,149],"employ":[100],"state-of-the-art":[101],"algorithms":[102],"study":[104,154],"degree":[106],"which":[108,148],"can":[110],"augment":[111],"computation":[113],"resources":[114],"ensemble":[117],"Furthermore,":[119],"efficient":[123],"work":[124],"assignment":[125],"given":[126],"GPU's":[128],"synchronous":[129],"mode":[130],"explored.":[134],"There":[135],"several":[137],"algorithmic":[138],"tradeoffs":[139],"consider":[141],"with":[144],"different":[145,157],"characteristics,":[147],"investigate":[150],"performance":[153,168,200],"across":[155],"four":[156],"models.":[158],"To":[159],"explore":[160],"limitations":[162],"GPU-based":[165],"simulators,":[166],"characteristics":[169],"when":[170],"executing":[171],"compared":[175],"those":[177],"highly":[179],"optimized":[180],"CPU":[181,206],"simulators.":[182],"Our":[183],"results":[184],"indicate":[185],"that":[186],"some":[188],"adding":[190],"typical":[192],"GPU":[194],"has":[195],"similar":[197],"effect":[198],"up":[202],"40":[204],"added":[205],"cores.":[207]},"counts_by_year":[{"year":2024,"cited_by_count":2}],"updated_date":"2025-12-24T23:09:58.560324","created_date":"2025-10-10T00:00:00"}
