{"id":"https://openalex.org/W4404186384","doi":"https://doi.org/10.1186/s12859-024-05966-5","title":"Abstraction-based segmental simulation of reaction networks using adaptive memoization","display_name":"Abstraction-based segmental simulation of reaction networks using adaptive memoization","publication_year":2024,"publication_date":"2024-11-08","ids":{"openalex":"https://openalex.org/W4404186384","doi":"https://doi.org/10.1186/s12859-024-05966-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/39516723"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05966-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05966-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05966-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05966-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005656023","display_name":"Martin Helfrich","orcid":"https://orcid.org/0000-0002-3191-8098"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Martin Helfrich","raw_affiliation_strings":["Department of Computer Science, Technical University of Munich, Garching\u00a0b., Munich, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Technical University of Munich, Garching\u00a0b., Munich, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047861254","display_name":"Roman Andriushchenko","orcid":"https://orcid.org/0000-0002-1286-934X"},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Roman Andriushchenko","raw_affiliation_strings":["Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001379903","display_name":"Milan \u010ce\u0161ka","orcid":"https://orcid.org/0000-0002-0300-9727"},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Milan \u010ce\u0161ka","raw_affiliation_strings":["Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic. ceskam@fit.vutbr.cz","Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic. ceskam@fit.vutbr.cz","institution_ids":["https://openalex.org/I60587646"]},{"raw_affiliation_string":"Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074485601","display_name":"Jan K\u0159et\u00ednsk\u00fd","orcid":"https://orcid.org/0000-0002-8122-2881"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["CZ","DE"],"is_corresponding":false,"raw_author_name":"Jan K\u0159et\u00ednsk\u00fd","raw_affiliation_strings":["Department of Computer Science, Technical University of Munich, Garching\u00a0b., Munich, Germany","Faculty of Informatics, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Technical University of Munich, Garching\u00a0b., Munich, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Faculty of Informatics, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052435131","display_name":"\u0160tefan Marti\u010dek","orcid":"https://orcid.org/0000-0003-4498-7436"},"institutions":[{"id":"https://openalex.org/I60587646","display_name":"Brno University of Technology","ror":"https://ror.org/03613d656","country_code":"CZ","type":"education","lineage":["https://openalex.org/I60587646"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"\u0160tefan Marti\u010dek","raw_affiliation_strings":["Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic","institution_ids":["https://openalex.org/I60587646"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061586199","display_name":"David \u0160afr\u00e1nek","orcid":"https://orcid.org/0000-0002-0713-2431"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"David \u0160afr\u00e1nek","raw_affiliation_strings":["Faculty of Informatics, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Faculty of Informatics, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5005656023"],"corresponding_institution_ids":["https://openalex.org/I62916508"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17795434,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"25","issue":"1","first_page":"350","last_page":"350"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9909999966621399,"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":0.9574000239372253,"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/memoization","display_name":"Memoization","score":0.8075543642044067},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7457171678543091},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.7300972938537598},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3868195414543152},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.33253243565559387}],"concepts":[{"id":"https://openalex.org/C79516417","wikidata":"https://www.wikidata.org/wiki/Q1376168","display_name":"Memoization","level":4,"score":0.8075543642044067},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7457171678543091},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.7300972938537598},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3868195414543152},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.33253243565559387},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C42560504","wikidata":"https://www.wikidata.org/wiki/Q15419395","display_name":"Top-down parsing","level":3,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05966-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05966-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05966-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39516723","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39516723","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11549863","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11549863","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11549863/pdf/12859_2024_Article_5966.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:9c5f251963bf4bff8d0f2c71e710a3f9","is_oa":true,"landing_page_url":"https://doaj.org/article/9c5f251963bf4bff8d0f2c71e710a3f9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-24 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05966-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05966-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05966-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6899999976158142}],"awards":[{"id":"https://openalex.org/G1633333669","display_name":null,"funder_award_id":"427755713","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3161690021","display_name":null,"funder_award_id":"GJ20-02328Y","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8220384988","display_name":null,"funder_award_id":"internal project FIT-S-23-8151,","funder_id":"https://openalex.org/F4320336543","funder_display_name":"Fakulta Informa\u010dn\u00edch Technologi\u00ed, Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Brn\u011b"},{"id":"https://openalex.org/G8330397625","display_name":null,"funder_award_id":"Funding","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8404958574","display_name":null,"funder_award_id":"378803395","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"},{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"},{"id":"https://openalex.org/F4320326548","display_name":"Masarykova Univerzita","ror":"https://ror.org/02j46qs45"},{"id":"https://openalex.org/F4320336543","display_name":"Fakulta Informa\u010dn\u00edch Technologi\u00ed, Vysok\u00e9 U\u010den\u00ed Technick\u00e9 v Brn\u011b","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404186384.pdf","grobid_xml":"https://content.openalex.org/works/W4404186384.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1902630711","https://openalex.org/W1973890190","https://openalex.org/W1974817122","https://openalex.org/W1988123909","https://openalex.org/W2000804241","https://openalex.org/W2011432832","https://openalex.org/W2018670096","https://openalex.org/W2019768978","https://openalex.org/W2034375827","https://openalex.org/W2044859335","https://openalex.org/W2046451925","https://openalex.org/W2050114113","https://openalex.org/W2066594542","https://openalex.org/W2072077152","https://openalex.org/W2085061065","https://openalex.org/W2090248212","https://openalex.org/W2101768141","https://openalex.org/W2102653059","https://openalex.org/W2116620527","https://openalex.org/W2121061285","https://openalex.org/W2124391925","https://openalex.org/W2127660420","https://openalex.org/W2127740987","https://openalex.org/W2131176356","https://openalex.org/W2133035852","https://openalex.org/W2137904930","https://openalex.org/W2152803686","https://openalex.org/W2155418451","https://openalex.org/W2162556737","https://openalex.org/W2165240751","https://openalex.org/W2167718560","https://openalex.org/W2171280873","https://openalex.org/W2265281604","https://openalex.org/W2905223430","https://openalex.org/W2963834876","https://openalex.org/W3043024808","https://openalex.org/W3099488856","https://openalex.org/W3155953569","https://openalex.org/W3190689743","https://openalex.org/W3190842559","https://openalex.org/W3202931079","https://openalex.org/W3208745067","https://openalex.org/W3216366002","https://openalex.org/W4292227698","https://openalex.org/W4293565763","https://openalex.org/W4311625853","https://openalex.org/W4386380088"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2966056201","https://openalex.org/W2182406401","https://openalex.org/W4233991731","https://openalex.org/W2772415251","https://openalex.org/W2971785569","https://openalex.org/W2610985003","https://openalex.org/W2583648466"],"abstract_inverted_index":{"We":[0],"demonstrate":[1],"that":[2],"in":[3],"combination":[4],"with":[5],"a":[6],"novel":[7],"fully":[8],"automatic":[9],"and":[10,24],"adaptive":[11],"hybrid":[12],"simulation":[13],"scheme,":[14],"we":[15],"can":[16],"speed":[17],"up":[18],"the":[19,27],"generation":[20],"of":[21,30],"trajectories":[22],"significantly":[23],"correctly":[25],"predict":[26],"transient":[28],"behavior":[29],"complex":[31],"stochastic":[32],"systems.":[33]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
