Algorithmic reduction of biological networks with multiple time scales

DOI10.1007/S11786-021-00515-2zbMATH Open1484.13058arXiv2010.10129OpenAlexW3181504158MaRDI QIDQ2051597FDOQ2051597

Authors: Niclas Kruff, Christoph Lüders, Ovidiu Radulescu, Thomas Sturm, S Walcher 

Publication date: 24 November 2021

Published in: Mathematics in Computer Science (Search for Journal in Brave)

Abstract: We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks which comprise chemical reaction networks for cellular biochemistry, and compartmental models for pharmacology, epidemiology and ecology. Multiple time scales of a given network are obtained by scaling, based on tropical geometry. Our reduction is mathematically justified within a singular perturbation setting. The existence of invariant manifolds is subject to hyperbolicity conditions, for which we propose an algorithmic test based on Hurwitz criteria. We finally obtain a sequence of nested invariant manifolds and respective reduced systems on those manifolds. Our theoretical results are generally accompanied by rigorous algorithmic descriptions suitable for direct implementation based on existing off-the-shelf software systems, specifically symbolic computation libraries and Satisfiability Modulo Theories solvers. We present computational examples taken from the well-known BioModels database using our own prototypical implementations.

Full work available at URL: https://arxiv.org/abs/2010.10129

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zbMATH Keywords

dimension reductionmultiple time scalescompartmental modelinvariant setsingular perturbationtropical geometrychemical reaction networksymbolic computationsatisfiability modulo theoriespolynomial differential equationslogic computationreal algebraic computation

Mathematics Subject Classification ID

Symbolic computation and algebraic computation (68W30) Gröbner bases; other bases for ideals and modules (e.g., Janet and border bases) (13P10) Singular perturbations for ordinary differential equations (34E15) Invariant manifold theory for dynamical systems (37D10) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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Cited In (8)

• Parametric toricity of steady state varieties of reaction networks
• A skin microbiome model with AMP interactions and analysis of quasi-stability vs stability in population dynamics
• Reduction of Chemical Reaction Networks with Approximate Conservation Laws
• Qualitative dynamics of chemical reaction networks: an investigation using partial tropical equilibrations
• Reduction techniques for network validation in systems biology
• Dimensionality reduction of bistable biological systems
• LNetReduce: tool for reducing linear dynamic networks with separated timescales
• Complexity reduction preserving dynamical behavior of biochemical networks

Uses Software

• QEPCAD
• SymPy
• SMT-LIB
• REDLOG
• z3
• CVC4
• MathSAT5
• SMT-RAT
• BioModels
• PySMT

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