{"id":"https://openalex.org/W2001887200","doi":"https://doi.org/10.1109/tevc.2014.2326863","title":"An Effective Method for Evolving Reaction Networks in Synthetic Biochemical Systems","display_name":"An Effective Method for Evolving Reaction Networks in Synthetic Biochemical Systems","publication_year":2015,"publication_date":"2015-01-23","ids":{"openalex":"https://openalex.org/W2001887200","doi":"https://doi.org/10.1109/tevc.2014.2326863","mag":"2001887200"},"language":"en","primary_location":{"id":"doi:10.1109/tevc.2014.2326863","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tevc.2014.2326863","pdf_url":null,"source":{"id":"https://openalex.org/S93787993","display_name":"IEEE Transactions on Evolutionary Computation","issn_l":"1089-778X","issn":["1089-778X","1941-0026"],"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 Transactions on Evolutionary Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068034920","display_name":"Huy Q. Dinh","orcid":"https://orcid.org/0000-0002-3307-1126"},"institutions":[{"id":"https://openalex.org/I4210145865","display_name":"IBM Research - Tokyo","ror":"https://ror.org/04915qk43","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210145865"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Huy Q. Dinh","raw_affiliation_strings":["IBA Laboratory, University of Tokyo, Tokyo, Japan","Department of Information and Communication Engineering, Graduate School of Information Science and TechnologyIBA Laboratory, University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBA Laboratory, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I4210145865"]},{"raw_affiliation_string":"Department of Information and Communication Engineering, Graduate School of Information Science and TechnologyIBA Laboratory, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002767684","display_name":"Nathana\u00ebl Aubert-Kato","orcid":"https://orcid.org/0000-0002-9100-1855"},"institutions":[{"id":"https://openalex.org/I127317711","display_name":"Tokyo University of Agriculture","ror":"https://ror.org/05crbcr45","country_code":"JP","type":"education","lineage":["https://openalex.org/I127317711"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Nathanael Aubert","raw_affiliation_strings":["HAGIYA Laboratory, University of Tokyo, Tokyo, Japan","Department of Computer Science, Graduate School of Information Science and TechnologyHAGIYA Laboratory, University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HAGIYA Laboratory, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I127317711"]},{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and TechnologyHAGIYA Laboratory, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008309887","display_name":"Nasimul Noman","orcid":"https://orcid.org/0000-0002-8566-0870"},"institutions":[{"id":"https://openalex.org/I78757542","display_name":"University of Newcastle Australia","ror":"https://ror.org/00eae9z71","country_code":"AU","type":"education","lineage":["https://openalex.org/I78757542"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Nasimul Noman","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, University of Newcastle, Callaghan, NSW, Australia","School of Electrical Engineering and Computer Science, University of Newcastle, Callaghan, NSW, Australia#N#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, University of Newcastle, Callaghan, NSW, Australia","institution_ids":["https://openalex.org/I78757542"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, University of Newcastle, Callaghan, NSW, Australia#N#","institution_ids":["https://openalex.org/I78757542"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078470183","display_name":"Teruo Fujii","orcid":"https://orcid.org/0000-0001-7529-6238"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Teruo Fujii","raw_affiliation_strings":["Center for International Research on Micromechatronics (CIRMM)/Institute of Industrial Science (IIS), University of Tokyo, Tokyo, Japan","[Center for International Research on Micromechatronics (CIRMM)/Institute of Industrial Science (IIS), University of Tokyo, Tokyo, Japan]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for International Research on Micromechatronics (CIRMM)/Institute of Industrial Science (IIS), University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"[Center for International Research on Micromechatronics (CIRMM)/Institute of Industrial Science (IIS), University of Tokyo, Tokyo, Japan]","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029632144","display_name":"Yannick Rondelez","orcid":"https://orcid.org/0000-0002-2565-476X"},"institutions":[{"id":"https://openalex.org/I4210088231","display_name":"Laboratory for Integrated Micro-Mechatronic Systems","ror":"https://ror.org/0059vr703","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210088231","https://openalex.org/I4210095849","https://openalex.org/I74801974"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yannick Rondelez","raw_affiliation_strings":["Laboratory for Integrated Micromechanic Systems-National Scientific Research Center (LIMMS-CNRS), University of Tokyo, Tokyo, Japan","[Laboratory for Integrated Micromechanic Systems-National Scientific Research Center (LIMMS-CNRS), University of Tokyo, Tokyo, Japan]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Integrated Micromechanic Systems-National Scientific Research Center (LIMMS-CNRS), University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I4210088231","https://openalex.org/I74801974"]},{"raw_affiliation_string":"[Laboratory for Integrated Micromechanic Systems-National Scientific Research Center (LIMMS-CNRS), University of Tokyo, Tokyo, Japan]","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102742376","display_name":"Hitoshi Iba","orcid":"https://orcid.org/0000-0003-1607-1690"},"institutions":[{"id":"https://openalex.org/I4210145865","display_name":"IBM Research - Tokyo","ror":"https://ror.org/04915qk43","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210145865"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hitoshi Iba","raw_affiliation_strings":["IBA Laboratory, University of Tokyo, Tokyo, Japan","Department of Information and Communication Engineering, Graduate School of Information Science and TechnologyIBA Laboratory, University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBA Laboratory, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I4210145865"]},{"raw_affiliation_string":"Department of Information and Communication Engineering, Graduate School of Information Science and TechnologyIBA Laboratory, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.958,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.86032655,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"19","issue":"3","first_page":"374","last_page":"386"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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":0.9995999932289124,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9915000200271606,"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"}},{"id":"https://openalex.org/T12236","display_name":"Photoreceptor and optogenetics research","score":0.9884999990463257,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.766298234462738},{"id":"https://openalex.org/keywords/crossover","display_name":"Crossover","score":0.6970068216323853},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6740519404411316},{"id":"https://openalex.org/keywords/neuroevolution","display_name":"Neuroevolution","score":0.5957314372062683},{"id":"https://openalex.org/keywords/point","display_name":"Point (geometry)","score":0.45540887117385864},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4079291522502899},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.34432268142700195},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.34160417318344116},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32243573665618896},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.32100191712379456},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2165016531944275}],"concepts":[{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.766298234462738},{"id":"https://openalex.org/C122507166","wikidata":"https://www.wikidata.org/wiki/Q628906","display_name":"Crossover","level":2,"score":0.6970068216323853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6740519404411316},{"id":"https://openalex.org/C118070581","wikidata":"https://www.wikidata.org/wiki/Q2060528","display_name":"Neuroevolution","level":3,"score":0.5957314372062683},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.45540887117385864},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4079291522502899},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.34432268142700195},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.34160417318344116},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32243573665618896},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.32100191712379456},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2165016531944275},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/tevc.2014.2326863","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tevc.2014.2326863","pdf_url":null,"source":{"id":"https://openalex.org/S93787993","display_name":"IEEE Transactions on Evolutionary Computation","issn_l":"1089-778X","issn":["1089-778X","1941-0026"],"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 Transactions on Evolutionary Computation","raw_type":"journal-article"},{"id":"pmh:oai:figshare.com:article/29008172","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Journal contribution"},{"id":"pmh:uon:28084","is_oa":false,"landing_page_url":"http://hdl.handle.net/1959.13/1338714","pdf_url":null,"source":{"id":"https://openalex.org/S4306401391","display_name":"NOVA (University of Newcastle, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78757542","host_organization_name":"University of Newcastle Australia","host_organization_lineage":["https://openalex.org/I78757542"],"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":"journal article"}],"best_oa_location":{"id":"pmh:oai:figshare.com:article/29008172","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Journal contribution"},"sustainable_development_goals":[{"score":0.41999998688697815,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W41687329","https://openalex.org/W1595159159","https://openalex.org/W1595498733","https://openalex.org/W1645305843","https://openalex.org/W1695722131","https://openalex.org/W1964850787","https://openalex.org/W1964928696","https://openalex.org/W1978043574","https://openalex.org/W1985032743","https://openalex.org/W1986292487","https://openalex.org/W1986482900","https://openalex.org/W1993546274","https://openalex.org/W1996197315","https://openalex.org/W2000804241","https://openalex.org/W2002189052","https://openalex.org/W2003350518","https://openalex.org/W2006672618","https://openalex.org/W2008449595","https://openalex.org/W2008626444","https://openalex.org/W2013533966","https://openalex.org/W2017862866","https://openalex.org/W2019998456","https://openalex.org/W2022891974","https://openalex.org/W2030945597","https://openalex.org/W2038679774","https://openalex.org/W2046355391","https://openalex.org/W2049311792","https://openalex.org/W2055605610","https://openalex.org/W2058132311","https://openalex.org/W2058221907","https://openalex.org/W2075031385","https://openalex.org/W2077480167","https://openalex.org/W2080074374","https://openalex.org/W2099915788","https://openalex.org/W2108903561","https://openalex.org/W2111818118","https://openalex.org/W2111935653","https://openalex.org/W2113371890","https://openalex.org/W2127641960","https://openalex.org/W2132366653","https://openalex.org/W2144588155","https://openalex.org/W2146879413","https://openalex.org/W2150249752","https://openalex.org/W2155921792","https://openalex.org/W2157857537","https://openalex.org/W2166513470","https://openalex.org/W2169436912","https://openalex.org/W2186876778","https://openalex.org/W2324786322","https://openalex.org/W2326053725","https://openalex.org/W4285719527","https://openalex.org/W6637411551","https://openalex.org/W6676794193"],"related_works":["https://openalex.org/W2168909409","https://openalex.org/W2144357723","https://openalex.org/W2950402165","https://openalex.org/W2114981325","https://openalex.org/W4302038648","https://openalex.org/W2099397840","https://openalex.org/W2249125133","https://openalex.org/W2857150653","https://openalex.org/W2111935653","https://openalex.org/W3102731759"],"abstract_inverted_index":{"In":[0],"this":[1,80],"paper,":[2],"we":[3],"introduce":[4],"our":[5],"approach":[6],"for":[7,129],"evolving":[8,83],"reaction":[9,44],"networks.":[10],"It":[11,49],"is":[12,110],"an":[13],"efficient":[14],"derivative":[15],"of":[16,19,27,38,46,74,133],"the":[17,25,36,60,63,75,107,130],"neuroevolution":[18],"augmenting":[20],"topologies":[21],"algorithm":[22],"directed":[23],"at":[24],"evolution":[26],"biochemical":[28,76,85],"systems":[29],"or":[30],"molecular":[31,90,134],"programs.":[32,135],"Our":[33,102],"method":[34],"addresses":[35],"problem":[37],"meaningful":[39],"crossovers":[40],"between":[41],"two":[42],"chemical":[43],"networks":[45,96],"different":[47],"topologies.":[48],"also":[50],"builds":[51],"on":[52],"features":[53],"such":[54],"as":[55],"speciation":[56],"to":[57,62,87],"speed":[58],"up":[59],"search,":[61],"point":[64],"where":[65],"it":[66],"can":[67,126],"deal":[68],"with":[69],"complete,":[70],"realistic":[71],"mathematical":[72],"models":[73],"processes.":[77],"We":[78],"demonstrate":[79],"framework":[81],"by":[82,115],"credible":[84],"answers":[86],"challenging":[88],"autonomous":[89],"problems:":[91],"in":[92,124],"vitro":[93],"batch":[94],"oscillatory":[95],"that":[97,106],"match":[98],"specific":[99],"oscillation":[100],"shapes.":[101],"experimental":[103],"results":[104],"suggest":[105],"search":[108],"space":[109],"efficiently":[111],"covered":[112],"and":[113,118],"that,":[114],"using":[116],"crossover":[117],"preserving":[119],"topological":[120],"innovations,":[121],"significant":[122],"improvements":[123],"performance":[125],"be":[127],"obtained":[128],"automatic":[131],"design":[132]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
