文章基本信息

标题：Forward and Backward Bisimulations for Chemical Reaction Networks
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作者：Luca Cardelli ; Mirco Tribastone ; Max Tschaikowski 等
期刊名称：LIPIcs : Leibniz International Proceedings in Informatics
电子版ISSN：1868-8969
出版年度：2015
卷号：42
页码：226-239
DOI：10.4230/LIPIcs.CONCUR.2015.226
出版社：Schloss Dagstuhl -- Leibniz-Zentrum fuer Informatik
摘要：We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class represents the exact sum of the concentrations of the species belonging to that class. Backward CRN bisimulation relates species that have identical solutions at all time points when starting from the same initial conditions. Both notions can be checked using only CRN syntactical information, i.e., by inspection of the set of reactions. We provide a unified algorithm that computes the coarsest refinement up to our bisimulations in polynomial time. Further, we give algorithms to compute quotient CRNs induced by a bisimulation. As an application, we find significant reductions in a number of models of biological processes from the literature. In two cases we allow the analysis of benchmark models which would be otherwise intractable due to their memory requirements.
关键词：Chemical reaction networks; ordinary differential equations; bisimulation; partition refinement