{"id":"https://openalex.org/W2024845465","doi":"https://doi.org/10.1109/cec.2013.6557752","title":"Reverse engineering of kinetic reaction networks by means of Cartesian Genetic Programming and Particle Swarm Optimization","display_name":"Reverse engineering of kinetic reaction networks by means of Cartesian Genetic Programming and Particle Swarm Optimization","publication_year":2013,"publication_date":"2013-06-01","ids":{"openalex":"https://openalex.org/W2024845465","doi":"https://doi.org/10.1109/cec.2013.6557752","mag":"2024845465"},"language":"en","primary_location":{"id":"doi:10.1109/cec.2013.6557752","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2013.6557752","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE Congress on Evolutionary Computation","raw_type":"proceedings-article"},"type":"conference-paper","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/A5043650939","display_name":"Marco S. Nobile","orcid":"https://orcid.org/0000-0002-7692-7203"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco S. Nobile","raw_affiliation_strings":["Dipartimento di Informatica, Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano-Bicocca, Milano, Italy","Dipt. di Inf., Sist. e Comun., Univ. degli Studi di Milano-Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano-Bicocca, Milano, Italy","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"Dipt. di Inf., Sist. e Comun., Univ. degli Studi di Milano-Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072712347","display_name":"Daniela Besozzi","orcid":"https://orcid.org/0000-0001-5532-3059"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniela Besozzi","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 degli Studi di Milano, Milano, Italy","Dipt. di Inf., Univ. degli Studi di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 degli Studi di Milano, Milano, Italy","institution_ids":["https://openalex.org/I189158943"]},{"raw_affiliation_string":"Dipt. di Inf., Univ. degli Studi di Milano, Milan, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013723473","display_name":"Paolo Cazzaniga","orcid":"https://orcid.org/0000-0001-7780-0434"},"institutions":[{"id":"https://openalex.org/I11039511","display_name":"University of Bergamo","ror":"https://ror.org/02mbd5571","country_code":"IT","type":"education","lineage":["https://openalex.org/I11039511"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Cazzaniga","raw_affiliation_strings":["Dipartimento di Scienze Umane e Sociali, Universit\u00e0 degli Studi di Bergamo, Bergamo, Italy","Dipt. di Sci. Umane e Sociali, Univ. degli Studi di Bergamo, Bergamo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Scienze Umane e Sociali, Universit\u00e0 degli Studi di Bergamo, Bergamo, Italy","institution_ids":["https://openalex.org/I11039511"]},{"raw_affiliation_string":"Dipt. di Sci. Umane e Sociali, Univ. degli Studi di Bergamo, Bergamo, Italy","institution_ids":["https://openalex.org/I11039511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065568541","display_name":"Dario Pescini","orcid":"https://orcid.org/0000-0002-3090-4823"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Dario Pescini","raw_affiliation_strings":["Dipartimento di Statistica e Metodi Quantitativi, Universit\u00e0 degli Studi di Milano-Bicocca, Milano, Italy","Dipt. di Statistica e Metodi Quantitativi, Univ. degli Studi di Milano-Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Statistica e Metodi Quantitativi, Universit\u00e0 degli Studi di Milano-Bicocca, Milano, Italy","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"Dipt. di Statistica e Metodi Quantitativi, Univ. degli Studi di Milano-Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073163964","display_name":"Giancarlo Mauri","orcid":"https://orcid.org/0000-0003-3520-4022"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giancarlo Mauri","raw_affiliation_strings":["Dipartimento di Informatica, Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano-Bicocca, Milano, Italy","Dipt. di Inf., Sist. e Comun., Univ. degli Studi di Milano-Bicocca, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Sistemistica e Comunicazione, Universit\u00e0 degli Studi di Milano-Bicocca, Milano, Italy","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"Dipt. di Inf., Sist. e Comun., Univ. degli Studi di Milano-Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":12.3032,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.98694057,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1594","last_page":"1601"},"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9987000226974487,"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":0.9907000064849854,"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/particle-swarm-optimization","display_name":"Particle swarm optimization","score":0.7026145458221436},{"id":"https://openalex.org/keywords/reverse-engineering","display_name":"Reverse engineering","score":0.6884559392929077},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6805233359336853},{"id":"https://openalex.org/keywords/genetic-programming","display_name":"Genetic programming","score":0.6313978433609009},{"id":"https://openalex.org/keywords/parameterized-complexity","display_name":"Parameterized complexity","score":0.5552282333374023},{"id":"https://openalex.org/keywords/metaheuristic","display_name":"Metaheuristic","score":0.4792868494987488},{"id":"https://openalex.org/keywords/multi-swarm-optimization","display_name":"Multi-swarm optimization","score":0.47328609228134155},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47007519006729126},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.46534502506256104},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.46406230330467224},{"id":"https://openalex.org/keywords/cartesian-coordinate-system","display_name":"Cartesian coordinate system","score":0.45608943700790405},{"id":"https://openalex.org/keywords/evolutionary-computation","display_name":"Evolutionary computation","score":0.43192508816719055},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3763889670372009},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29952800273895264},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24175012111663818},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.21819868683815002},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.16919034719467163},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15131932497024536},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1109977662563324}],"concepts":[{"id":"https://openalex.org/C85617194","wikidata":"https://www.wikidata.org/wiki/Q2072794","display_name":"Particle swarm optimization","level":2,"score":0.7026145458221436},{"id":"https://openalex.org/C207850805","wikidata":"https://www.wikidata.org/wiki/Q269608","display_name":"Reverse engineering","level":2,"score":0.6884559392929077},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6805233359336853},{"id":"https://openalex.org/C110332635","wikidata":"https://www.wikidata.org/wiki/Q629498","display_name":"Genetic programming","level":2,"score":0.6313978433609009},{"id":"https://openalex.org/C165464430","wikidata":"https://www.wikidata.org/wiki/Q1570441","display_name":"Parameterized complexity","level":2,"score":0.5552282333374023},{"id":"https://openalex.org/C109718341","wikidata":"https://www.wikidata.org/wiki/Q1385229","display_name":"Metaheuristic","level":2,"score":0.4792868494987488},{"id":"https://openalex.org/C122357587","wikidata":"https://www.wikidata.org/wiki/Q6934508","display_name":"Multi-swarm optimization","level":3,"score":0.47328609228134155},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47007519006729126},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.46534502506256104},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.46406230330467224},{"id":"https://openalex.org/C16038011","wikidata":"https://www.wikidata.org/wiki/Q62912","display_name":"Cartesian coordinate system","level":2,"score":0.45608943700790405},{"id":"https://openalex.org/C105902424","wikidata":"https://www.wikidata.org/wiki/Q1197129","display_name":"Evolutionary computation","level":2,"score":0.43192508816719055},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3763889670372009},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29952800273895264},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24175012111663818},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.21819868683815002},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.16919034719467163},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15131932497024536},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1109977662563324},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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:10.1109/cec.2013.6557752","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cec.2013.6557752","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE Congress on Evolutionary Computation","raw_type":"proceedings-article"},{"id":"pmh:oai:aisberg.unibg.it:10446/29957","is_oa":false,"landing_page_url":"http://hdl.handle.net/10446/29957","pdf_url":null,"source":{"id":"https://openalex.org/S4377196347","display_name":"Aisberg (University of Bergamo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11039511","host_organization_name":"University of Bergamo","host_organization_lineage":["https://openalex.org/I11039511"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:boa.unimib.it:10281/45574","is_oa":false,"landing_page_url":"http://hdl.handle.net/10281/45574","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"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":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1006858280","display_name":null,"funder_award_id":"CZ.1.07/2.3.00/20.0256","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G1900958124","display_name":"Software Components in Embedded Systems: Development and Verification","funder_award_id":"GAP202/11/0312","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W178214986","https://openalex.org/W1497256448","https://openalex.org/W1576660662","https://openalex.org/W1576818901","https://openalex.org/W1586724485","https://openalex.org/W1604789486","https://openalex.org/W1775913388","https://openalex.org/W1886596768","https://openalex.org/W1976811972","https://openalex.org/W1985911638","https://openalex.org/W1999902057","https://openalex.org/W2013156169","https://openalex.org/W2026440556","https://openalex.org/W2036259226","https://openalex.org/W2051959027","https://openalex.org/W2054300546","https://openalex.org/W2060579417","https://openalex.org/W2074304536","https://openalex.org/W2093410681","https://openalex.org/W2093470850","https://openalex.org/W2106142381","https://openalex.org/W2122950891","https://openalex.org/W2132018771","https://openalex.org/W2138148774","https://openalex.org/W2143955972","https://openalex.org/W2152195021","https://openalex.org/W2158777221","https://openalex.org/W2165603655","https://openalex.org/W2167154952","https://openalex.org/W2170484057","https://openalex.org/W2257802904","https://openalex.org/W2484971506","https://openalex.org/W6607236668","https://openalex.org/W6629610141","https://openalex.org/W6635095966","https://openalex.org/W6638085146","https://openalex.org/W6673698791","https://openalex.org/W6679652332"],"related_works":["https://openalex.org/W2363831530","https://openalex.org/W2363845219","https://openalex.org/W2381057835","https://openalex.org/W1789649838","https://openalex.org/W1780668307","https://openalex.org/W2091246427","https://openalex.org/W2029013302","https://openalex.org/W2559572301","https://openalex.org/W1589480767","https://openalex.org/W1523210215"],"abstract_inverted_index":{"The":[0],"modeling":[1],"of":[2,28,32,50,97,107,141,157],"biochemical":[3],"reaction":[4,75],"networks":[5,173],"is":[6,16,54,59,124,168],"a":[7,66,89,154],"fundamental":[8],"but":[9],"complex":[10],"task":[11],"in":[12,39,77,145],"Systems":[13],"Biology,":[14],"which":[15],"traditionally":[17],"performed":[18],"exploiting":[19],"human":[20],"expertise":[21],"and":[22,116],"the":[23,29,35,48,63,74,94,104,128,134,139,178],"available":[24],"experimental":[25,158],"data.":[26,180],"Because":[27],"general":[30],"lack":[31],"knowledge":[33],"on":[34,47,103],"molecular":[36],"mechanisms":[37],"occurring":[38],"living":[40],"cells,":[41],"an":[42],"intense":[43],"research":[44],"activity":[45],"focused":[46],"development":[49],"reverse":[51,95],"engineering":[52,96],"methodologies":[53],"currently":[55],"underway.":[56],"This":[57],"problem":[58],"further":[60],"complicated":[61],"by":[62],"fact":[64],"that":[65,165,174],"proper":[67],"parameterization":[68],"needs":[69],"to":[70,73,79,126,152,170],"be":[71],"associated":[72],"network,":[76],"order":[78],"investigate":[80],"its":[81],"dynamical":[82],"behavior.":[83],"In":[84,121],"this":[85],"work":[86],"we":[87,149],"propose":[88],"novel":[90],"computational":[91],"methodology":[92,144,167],"for":[93],"fully":[98],"parameterized":[99],"kinetic":[100,172],"networks,":[101],"based":[102],"combined":[105],"use":[106],"two":[108],"evolutionary":[109],"programming":[110],"techniques:":[111],"Cartesian":[112],"Genetic":[113],"Programming":[114],"(CGP)":[115],"Particle":[117],"Swarm":[118],"Optimization":[119],"(PSO).":[120],"particular,":[122],"CGP":[123],"used":[125],"infer":[127],"network":[129],"topology,":[130],"while":[131],"PSO":[132],"performs":[133],"parameter":[135],"estimation":[136],"task.":[137],"To":[138],"purpose":[140],"applying":[142],"our":[143,166],"routine":[146],"laboratory":[147],"environments,":[148],"designed":[150],"it":[151],"exploit":[153],"small":[155],"set":[156],"time":[159],"series":[160],"as":[161],"target.":[162],"We":[163],"show":[164],"able":[169],"reconstruct":[171],"perfectly":[175],"fit":[176],"with":[177],"target":[179]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}