{"id":"https://openalex.org/W2013655710","doi":"https://doi.org/10.1109/tevc.2015.2396199","title":"Gene Regulatory Network Evolution Through Augmenting Topologies","display_name":"Gene Regulatory Network Evolution Through Augmenting Topologies","publication_year":2015,"publication_date":"2015-01-23","ids":{"openalex":"https://openalex.org/W2013655710","doi":"https://doi.org/10.1109/tevc.2015.2396199","mag":"2013655710"},"language":"en","primary_location":{"id":"doi:10.1109/tevc.2015.2396199","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tevc.2015.2396199","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":"https://hal.science/hal-01332272","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011627812","display_name":"Sylvain Cussat\u2010Blanc","orcid":"https://orcid.org/0000-0003-1360-1932"},"institutions":[{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210160189","display_name":"Institut Polytechnique de Bordeaux","ror":"https://ror.org/054qv7y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210160189"]},{"id":"https://openalex.org/I3131550300","display_name":"Universit\u00e9 Toulouse-I-Capitole","ror":"https://ror.org/0443n9e75","country_code":"FR","type":"education","lineage":["https://openalex.org/I3131550300"]},{"id":"https://openalex.org/I4210119061","display_name":"Institut de Recherche en Informatique de Toulouse","ror":"https://ror.org/01rx4qw44","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I205747304","https://openalex.org/I205747304","https://openalex.org/I4210119061","https://openalex.org/I4387153255","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I4210152422","display_name":"Universit\u00e9 Toulouse - Jean Jaur\u00e8s","ror":"https://ror.org/04ezk3x31","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210152422","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sylvain Cussat-Blanc","raw_affiliation_strings":["University of Toulouse, Toulouse, France","UT Capitole - Universit\u00e9 Toulouse Capitole (2 rue du Doyen-Gabriel-Marty - 31042 Toulouse Cedex 9  - France)","IRIT-REVA - Real Expression Artificial Life (Institut de recherche en informatique de Toulouse - IRIT\r\n2 rue Charles Camichel \r\n31071 Toulouse Cedex 7 - France)"],"affiliations":[{"raw_affiliation_string":"University of Toulouse, Toulouse, France","institution_ids":["https://openalex.org/I17866349"]},{"raw_affiliation_string":"UT Capitole - Universit\u00e9 Toulouse Capitole (2 rue du Doyen-Gabriel-Marty - 31042 Toulouse Cedex 9  - France)","institution_ids":["https://openalex.org/I3131550300"]},{"raw_affiliation_string":"IRIT-REVA - Real Expression Artificial Life (Institut de recherche en informatique de Toulouse - IRIT\r\n2 rue Charles Camichel \r\n31071 Toulouse Cedex 7 - France)","institution_ids":["https://openalex.org/I4210152422","https://openalex.org/I134560555","https://openalex.org/I4210119061","https://openalex.org/I3131550300","https://openalex.org/I4210160189"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069859821","display_name":"Kyle Harrington","orcid":"https://orcid.org/0000-0002-7237-1973"},"institutions":[{"id":"https://openalex.org/I6902469","display_name":"Brandeis University","ror":"https://ror.org/05abbep66","country_code":"US","type":"education","lineage":["https://openalex.org/I6902469"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle Harrington","raw_affiliation_strings":["DEMO Laboratory, Brandeis University, Waltham, MA, USA","HMS - Harvard Medical School [Boston] (25 Shattuck Street Boston, MA 02115 - United States)"],"affiliations":[{"raw_affiliation_string":"DEMO Laboratory, Brandeis University, Waltham, MA, USA","institution_ids":["https://openalex.org/I6902469"]},{"raw_affiliation_string":"HMS - Harvard Medical School [Boston] (25 Shattuck Street Boston, MA 02115 - United States)","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065211438","display_name":"Jordan Pollack","orcid":"https://orcid.org/0009-0008-0819-3819"},"institutions":[{"id":"https://openalex.org/I6902469","display_name":"Brandeis University","ror":"https://ror.org/05abbep66","country_code":"US","type":"education","lineage":["https://openalex.org/I6902469"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jordan Pollack","raw_affiliation_strings":["DEMO Laboratory, Brandeis University, Waltham, MA, USA","Brandeis University (Brandeis University 415 South St. Waltham, MA 02453 - United States)"],"affiliations":[{"raw_affiliation_string":"DEMO Laboratory, Brandeis University, Waltham, MA, USA","institution_ids":["https://openalex.org/I6902469"]},{"raw_affiliation_string":"Brandeis University (Brandeis University 415 South St. Waltham, MA 02453 - United States)","institution_ids":["https://openalex.org/I6902469"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011627812"],"corresponding_institution_ids":["https://openalex.org/I134560555","https://openalex.org/I17866349","https://openalex.org/I3131550300","https://openalex.org/I4210119061","https://openalex.org/I4210152422","https://openalex.org/I4210160189"],"apc_list":null,"apc_paid":null,"fwci":9.7921,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.97969884,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"6","first_page":"823","last_page":"837"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9997000098228455,"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/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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9833999872207642,"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/neuroevolution","display_name":"Neuroevolution","score":0.7470780611038208},{"id":"https://openalex.org/keywords/crossover","display_name":"Crossover","score":0.670130729675293},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.65328049659729},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.6467785835266113},{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.5797562003135681},{"id":"https://openalex.org/keywords/evolutionary-algorithm","display_name":"Evolutionary algorithm","score":0.5526700615882874},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5335144996643066},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.495632529258728},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.43789464235305786},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4160701036453247},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.30562931299209595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.104047030210495}],"concepts":[{"id":"https://openalex.org/C118070581","wikidata":"https://www.wikidata.org/wiki/Q2060528","display_name":"Neuroevolution","level":3,"score":0.7470780611038208},{"id":"https://openalex.org/C122507166","wikidata":"https://www.wikidata.org/wiki/Q628906","display_name":"Crossover","level":2,"score":0.670130729675293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.65328049659729},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.6467785835266113},{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.5797562003135681},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.5526700615882874},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5335144996643066},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.495632529258728},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.43789464235305786},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4160701036453247},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30562931299209595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.104047030210495},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":4,"locations":[{"id":"doi:10.1109/tevc.2015.2396199","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tevc.2015.2396199","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:publications.ut-capitole.fr:26564","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401335","display_name":"Toulouse 1 Capitole Publications (Universit\u00e9 Toulouse I Capitole)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I3131550300","host_organization_name":"Universit\u00e9 Toulouse-I-Capitole","host_organization_lineage":["https://openalex.org/I3131550300"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:HAL:hal-01332272v1","is_oa":true,"landing_page_url":"https://hal.science/hal-01332272","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Transactions on Evolutionary Computation, 2015, 19 (n\u00b0 6), pp.PP. 823-837. &#x27E8;10.1109/TEVC.2015.2396199&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:edoc.mdc-berlin.de:19281","is_oa":false,"landing_page_url":"http://edoc.mdc-berlin.de/19281/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"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"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-01332272v1","is_oa":true,"landing_page_url":"https://hal.science/hal-01332272","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Transactions on Evolutionary Computation, 2015, 19 (n\u00b0 6), pp.PP. 823-837. &#x27E8;10.1109/TEVC.2015.2396199&#x27E9;","raw_type":"Journal articles"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6737408592","display_name":null,"funder_award_id":"0757452","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W50076749","https://openalex.org/W104630046","https://openalex.org/W106550765","https://openalex.org/W182904178","https://openalex.org/W614012683","https://openalex.org/W986840029","https://openalex.org/W1489863191","https://openalex.org/W1497256448","https://openalex.org/W1517016597","https://openalex.org/W1541501294","https://openalex.org/W1557212434","https://openalex.org/W1571206353","https://openalex.org/W1580267071","https://openalex.org/W1585335425","https://openalex.org/W1587294773","https://openalex.org/W1593148604","https://openalex.org/W1598117745","https://openalex.org/W1784796383","https://openalex.org/W1814244002","https://openalex.org/W1884068937","https://openalex.org/W1971224531","https://openalex.org/W1985912235","https://openalex.org/W2012059925","https://openalex.org/W2017106121","https://openalex.org/W2022818567","https://openalex.org/W2041499406","https://openalex.org/W2041905891","https://openalex.org/W2056188428","https://openalex.org/W2072265663","https://openalex.org/W2081969633","https://openalex.org/W2097571405","https://openalex.org/W2097706568","https://openalex.org/W2098655706","https://openalex.org/W2099233884","https://openalex.org/W2099233925","https://openalex.org/W2110607490","https://openalex.org/W2111276186","https://openalex.org/W2111935653","https://openalex.org/W2122689321","https://openalex.org/W2126926002","https://openalex.org/W2127218421","https://openalex.org/W2135356257","https://openalex.org/W2136605310","https://openalex.org/W2138784882","https://openalex.org/W2140685838","https://openalex.org/W2145403262","https://openalex.org/W2153684665","https://openalex.org/W2160485199","https://openalex.org/W2165944157","https://openalex.org/W2405288126","https://openalex.org/W2406691808","https://openalex.org/W2695777493","https://openalex.org/W3149025087","https://openalex.org/W4241088457","https://openalex.org/W6601962754","https://openalex.org/W6604250625","https://openalex.org/W6625852047","https://openalex.org/W6634749613","https://openalex.org/W6634952865","https://openalex.org/W6638395436","https://openalex.org/W6674647444","https://openalex.org/W6674929363","https://openalex.org/W6678845729","https://openalex.org/W6678914141","https://openalex.org/W6684157047","https://openalex.org/W6713757964","https://openalex.org/W6714075783"],"related_works":["https://openalex.org/W2168909409","https://openalex.org/W2144357723","https://openalex.org/W2950402165","https://openalex.org/W1606499289","https://openalex.org/W1985939653","https://openalex.org/W2741252017","https://openalex.org/W2911578165","https://openalex.org/W2626282817","https://openalex.org/W3102731759","https://openalex.org/W4385483662"],"abstract_inverted_index":{"Artificial":[0],"gene":[1,115],"regulatory":[2],"networks":[3,98],"(GRNs)":[4],"are":[5,56],"biologically":[6],"inspired":[7,85],"dynamical":[8],"systems":[9],"used":[10,76],"to":[11,23,41,74,136,141],"control":[12],"various":[13],"kinds":[14],"of":[15,53,81,90,127],"agents,":[16],"from":[17,148],"the":[18,43,50,87,125,154],"cells":[19],"in":[20,39,95],"developmental":[21],"models":[22],"embodied":[24],"robot":[25],"swarms.":[26],"Most":[27],"recent":[28],"work":[29],"uses":[30],"a":[31,46,66,106,110,137],"genetic":[32,72],"algorithm":[33,62,130,156],"(GA)":[34],"or":[35],"an":[36,61],"evolution":[37],"strategy":[38],"order":[40],"optimize":[42],"network":[44,67],"for":[45,77],"specific":[47,107],"task.":[48],"However,":[49],"empirical":[51],"performances":[52],"these":[54],"algorithms":[55],"unsatisfactory.":[57],"This":[58,83],"paper":[59],"presents":[60],"that":[63],"primarily":[64],"exploits":[65],"distance":[68],"metric,":[69],"which":[70],"allows":[71],"similarity":[73],"be":[75],"speciation":[78,118],"and":[79,99,117,140],"variation":[80],"GRNs.":[82],"algorithm,":[84],"by":[86,131],"successful":[88],"neuroevolution":[89],"augmenting":[91],"topologies":[92],"algorithm's":[93],"use":[94],"evolving":[96],"neural":[97],"compositional":[100],"pattern-producing":[101],"networks,":[102],"is":[103],"based":[104,113,119],"on":[105,114,144,158],"initialization":[108],"method,":[109],"crossover":[111],"operator":[112],"alignment,":[116],"upon":[120],"GRN":[121],"structures.":[122],"We":[123],"demonstrate":[124],"effectiveness":[126],"this":[128],"new":[129],"comparing":[132],"our":[133],"approach":[134],"both":[135],"standard":[138],"GA":[139],"evolutionary":[142],"programming":[143],"four":[145],"different":[146],"experiments":[147],"three":[149],"distinct":[150],"problem":[151],"domains,":[152],"where":[153],"proposed":[155],"excels":[157],"all":[159],"experiments.":[160]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
