{"id":"https://openalex.org/W4400957545","doi":"https://doi.org/10.1007/s11047-024-09989-y","title":"Reaction mining for reaction systems","display_name":"Reaction mining for reaction systems","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4400957545","doi":"https://doi.org/10.1007/s11047-024-09989-y"},"language":"en","primary_location":{"id":"doi:10.1007/s11047-024-09989-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-024-09989-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-024-09989-y.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s11047-024-09989-y.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066385212","display_name":"Artur M\u0119ski","orcid":"https://orcid.org/0000-0003-2917-8438"},"institutions":[{"id":"https://openalex.org/I4210087266","display_name":"Institute of Computer Science","ror":"https://ror.org/003fvp964","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210087266","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I4210159747","display_name":"Vector Oncology (United States)","ror":"https://ror.org/05mkxvs25","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159747"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL","US"],"is_corresponding":true,"raw_author_name":"Artur M\u0119ski","raw_affiliation_strings":["Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland","Vector GB Limited, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland","institution_ids":["https://openalex.org/I4210087266","https://openalex.org/I99542240"]},{"raw_affiliation_string":"Vector GB Limited, London, UK","institution_ids":["https://openalex.org/I4210159747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042490356","display_name":"Maciej Koutny","orcid":"https://orcid.org/0000-0003-4563-1378"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Maciej Koutny","raw_affiliation_strings":["School of Computing, Newcastle University, Newcastle upon Tyne, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Newcastle University, Newcastle upon Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036094384","display_name":"\u0141ukasz Mikulski","orcid":"https://orcid.org/0000-0002-6711-557X"},"institutions":[{"id":"https://openalex.org/I3019271933","display_name":"Nicolaus Copernicus University","ror":"https://ror.org/0102mm775","country_code":"PL","type":"education","lineage":["https://openalex.org/I3019271933"]},{"id":"https://openalex.org/I4210087266","display_name":"Institute of Computer Science","ror":"https://ror.org/003fvp964","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210087266","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"\u0141ukasz Mikulski","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, Nicolaus Copernicus University in Toru\u0144, Toru\u0144, Poland","Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, Nicolaus Copernicus University in Toru\u0144, Toru\u0144, Poland","institution_ids":["https://openalex.org/I3019271933"]},{"raw_affiliation_string":"Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland","institution_ids":["https://openalex.org/I4210087266","https://openalex.org/I99542240"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107808009","display_name":"Wojciech Penczek","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087266","display_name":"Institute of Computer Science","ror":"https://ror.org/003fvp964","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210087266","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Wojciech Penczek","raw_affiliation_strings":["Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland","institution_ids":["https://openalex.org/I4210087266","https://openalex.org/I99542240"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5066385212"],"corresponding_institution_ids":["https://openalex.org/I4210087266","https://openalex.org/I4210159747","https://openalex.org/I99542240"],"apc_list":{"value":2890,"currency":"USD","value_usd":2890},"apc_paid":{"value":2890,"currency":"USD","value_usd":2890},"fwci":0.4929,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.61236521,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"23","issue":"2","first_page":"323","last_page":"343"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9990000128746033,"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/T12029","display_name":"DNA and Biological Computing","score":0.9990000128746033,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9944000244140625,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.992900013923645,"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/computer-science","display_name":"Computer science","score":0.7701382637023926},{"id":"https://openalex.org/keywords/bespoke","display_name":"Bespoke","score":0.7557151913642883},{"id":"https://openalex.org/keywords/parametric-statistics","display_name":"Parametric statistics","score":0.5577634572982788},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5423665046691895},{"id":"https://openalex.org/keywords/theory-of-computation","display_name":"Theory of computation","score":0.5333808660507202},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5032493472099304},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.5010504722595215},{"id":"https://openalex.org/keywords/bounded-function","display_name":"Bounded function","score":0.42648908495903015},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3196161985397339},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13389888405799866}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7701382637023926},{"id":"https://openalex.org/C44210515","wikidata":"https://www.wikidata.org/wiki/Q16968978","display_name":"Bespoke","level":2,"score":0.7557151913642883},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.5577634572982788},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5423665046691895},{"id":"https://openalex.org/C24858836","wikidata":"https://www.wikidata.org/wiki/Q844718","display_name":"Theory of computation","level":2,"score":0.5333808660507202},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5032493472099304},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.5010504722595215},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.42648908495903015},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3196161985397339},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13389888405799866},{"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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s11047-024-09989-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-024-09989-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-024-09989-y.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s11047-024-09989-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-024-09989-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-024-09989-y.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4400957545.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W135965196","https://openalex.org/W588789200","https://openalex.org/W595285250","https://openalex.org/W1480909796","https://openalex.org/W1572136279","https://openalex.org/W1576702025","https://openalex.org/W1787074469","https://openalex.org/W1972648361","https://openalex.org/W1983695368","https://openalex.org/W1984586189","https://openalex.org/W1992112582","https://openalex.org/W1995984957","https://openalex.org/W1999103908","https://openalex.org/W2003063390","https://openalex.org/W2009237435","https://openalex.org/W2017288340","https://openalex.org/W2019624322","https://openalex.org/W2023752208","https://openalex.org/W2025782239","https://openalex.org/W2031369606","https://openalex.org/W2036546758","https://openalex.org/W2114365801","https://openalex.org/W2132434714","https://openalex.org/W2146183673","https://openalex.org/W2148456801","https://openalex.org/W2155953212","https://openalex.org/W2215907076","https://openalex.org/W2294464936","https://openalex.org/W2318543175","https://openalex.org/W2336875695","https://openalex.org/W2478000639","https://openalex.org/W2494337022","https://openalex.org/W2570743269","https://openalex.org/W2588843024","https://openalex.org/W2742475082","https://openalex.org/W2805607193","https://openalex.org/W2922484450","https://openalex.org/W2962680084","https://openalex.org/W3110404123","https://openalex.org/W4249885861","https://openalex.org/W4385216613"],"related_works":["https://openalex.org/W2181465263","https://openalex.org/W3093969907","https://openalex.org/W3202725889","https://openalex.org/W2232750048","https://openalex.org/W2212726445","https://openalex.org/W4244794230","https://openalex.org/W4389712339","https://openalex.org/W2806540758","https://openalex.org/W2494533090","https://openalex.org/W3082526343"],"abstract_inverted_index":{"Abstract":[0],"Reaction":[1],"systems":[2,36,130,178],"are":[3],"a":[4,20,69,80,91,143,152,161,166,184],"formal":[5],"model":[6,190],"for":[7,22,192],"computational":[8],"processing":[9],"in":[10,37,122,150,160,179],"which":[11,38],"reactions":[12,46],"operate":[13,47],"on":[14,48,188,200],"sets":[15,52],"of":[16,27,53,65,83,105,110,136,175,208],"entities":[17,39],"(molecules)":[18],"providing":[19],"framework":[21,57],"dealing":[23],"with":[24,34,62,94,131],"qualitative":[25],"aspects":[26,64],"biochemical":[28],"systems.":[29],"This":[30],"paper":[31,126,171],"is":[32,142],"concerned":[33],"reaction":[35,66,92,129,157,177],"can":[40],"have":[41],"discrete":[42,95],"concentrations,":[43],"and":[44,68,78,102,182],"so":[45],"multisets":[49],"rather":[50],"than":[51],"entities.":[54],"The":[55,139],"resulting":[56,156],"allows":[58,74],"one":[59,75],"to":[60,76],"deal":[61],"quantitative":[63],"systems,":[67],"bespoke":[70],"linear-time":[71],"temporal":[72,168],"logic":[73,169],"express":[77],"verify":[79],"wide":[81],"range":[82],"key":[84],"behavioural":[85],"system":[86,93,158],"properties.":[87],"In":[88],"practical":[89],"applications,":[90],"concentrations":[96],"may":[97],"only":[98],"be":[99],"partially":[100],"specified,":[101],"the":[103,111,124,148,155,194,201,206,209],"possibility":[104],"an":[106,115,173],"effective":[107],"automated":[108],"calculation":[109],"missing":[112],"details":[113],"provides":[114,172],"attractive":[116],"design":[117],"approach.":[118],"With":[119],"this":[120],"idea":[121],"mind,":[123],"current":[125],"discusses":[127],"parametric":[128,176],"parameters":[132,149],"representing":[133],"unknown":[134],"parts":[135],"hypothetical":[137],"reactions.":[138],"main":[140],"result":[141],"method":[144],"aimed":[145],"at":[146],"replacing":[147],"such":[151],"way":[153],"that":[154],"operating":[159],"specified":[162],"external":[163],"environment":[164],"satisfies":[165],"given":[167],"formula.This":[170],"encoding":[174],"smt":[180],",":[181],"outlines":[183],"synthesis":[185,195,211],"procedure":[186],"based":[187],"bounded":[189],"checking":[191],"solving":[193],"problem.":[196],"It":[197],"also":[198],"reports":[199],"initial":[202],"experimental":[203],"results":[204],"demonstrating":[205],"feasibility":[207],"novel":[210],"method.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}