Approximate Reductions of Rational Dynamical Systems in CLUE

被引:1
作者
Jimenez-Pastor, Antonio [1 ]
Leguizamon-Robayo, Alexander [1 ]
Tschaikowski, Max [1 ]
Vandin, Andrea [2 ,3 ]
机构
[1] Aalborg Univ, Aalborg, Denmark
[2] St Anna Sch Adv Studies, Pisa, Italy
[3] DTU Tech Univ Denmark, Lyngby, Denmark
来源
COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY, CMSB 2024 | 2024年 / 14971卷
关键词
Approximate reduction; Dynamical systems; Constrained lumping; COMPLEXITY REDUCTION;
D O I
10.1007/978-3-031-71671-3_9
中图分类号
TP39 [计算机的应用];
学科分类号
081203 ; 0835 ;
摘要
In life sciences, deriving insights from dynamical systems can be challenging due to the large number of state variables involved. To address this, model reduction techniques can be used to project the system onto a lower-dimensional state space. CLUE is a tool that computes exact reductions for rational systems of ordinary differential equations. In this paper, we present an extension of CLUE to include approximate reductions which allow for larger aggregating power at the expense of a bounded error. Additionally, our extension includes new functionalities such as an interface to the model database ODEBase repository and simulation techniques for exploratory analyses.
引用
收藏
页码:108 / 116
页数:9
相关论文
共 34 条
[1]   Adaptive formal approximations of Markov chains [J].
Abate, Alessandro ;
Andriushchenko, Roman ;
Ceska, Milan ;
Kwiatkowska, Marta .
PERFORMANCE EVALUATION, 2021, 148
[2]   Complexity reduction preserving dynamical behavior of biochemical networks [J].
Apri, Mochamad ;
de Gee, Maarten ;
Molenaar, Jaap .
JOURNAL OF THEORETICAL BIOLOGY, 2012, 304 :16-26
[3]  
Bacci G, 2013, LECT NOTES COMPUT SC, V7795, P1, DOI 10.1007/978-3-642-36742-7_1
[4]   Tropical Abstraction of Biochemical Reaction Networks with Guarantees [J].
Beica, Andreea ;
Feret, Jerome ;
Petrov, Tatjana .
ELECTRONIC NOTES IN THEORETICAL COMPUTER SCIENCE, 2020, 350 :3-32
[5]   BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains [J].
Blinov, ML ;
Faeder, JR ;
Goldstein, B ;
Hlavacek, WS .
BIOINFORMATICS, 2004, 20 (17) :3289-3291
[6]  
Cardelli L., 2017, Syntactic Markovian bisimulation for chemical reaction networks
[7]   Exact maximal reduction of stochastic reaction networks by species lumping [J].
Cardelli, Luca ;
Perez-Verona, Isabel Cristina ;
Tribastone, Mirco ;
Tschaikowski, Max ;
Vandin, Andrea ;
Waizmann, Tabea .
BIOINFORMATICS, 2021, 37 (15) :2175-2182
[8]   From electric circuits to chemical networks [J].
Cardelli, Luca ;
Tribastone, Mirco ;
Tschaikowski, Max .
NATURAL COMPUTING, 2020, 19 (01) :237-248
[9]   ERODE: A Tool for the Evaluation and Reduction of Ordinary Differential Equations [J].
Cardelli, Luca ;
Tribastone, Mirco ;
Tschaikowski, Max ;
Vandin, Andrea .
TOOLS AND ALGORITHMS FOR THE CONSTRUCTION AND ANALYSIS OF SYSTEMS, TACAS 2017, PT II, 2017, 10206 :310-328
[10]   Maximal aggregation of polynomial dynamical systems [J].
Cardelli, Luca ;
Tribastone, Mirco ;
Tschaikowski, Max ;
Vandin, Andrea .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2017, 114 (38) :10029-10034