Detecting binomiality

DOI10.1016/J.AAM.2015.08.004MaRDI QIDQ745070zbMATH OpenOpenAlexFDO

Authors Carsten Conradi, Thomas Kahle

Publication date 13 October 2015

Published in Advances in Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1502.04893

zbMATH Keywords

chemical reaction networkssteady statesbinomial idealpolynomial systems in biology

Mathematics Subject Classification ID

Dynamical systems in biology (37N25) Systems biology, networks (92C42) Gröbner bases; other bases for ideals and modules (e.g., Janet and border bases) (13P10) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25) Solving polynomial systems; resultants (13P15)

Abstract: Binomial ideals are special polynomial ideals with many algorithmically and theoretically nice properties. We discuss the problem of deciding if a given polynomial ideal is binomial. While the methods are general, our main motivation and source of examples is the simplification of steady state equations of chemical reaction networks. For homogeneous ideals we give an efficient, Gr"obner-free algorithm for binomiality detection, based on linear algebra only. On inhomogeneous input the algorithm can only give a sufficient condition for binomiality. As a remedy we construct a heuristic toolbox that can lead to simplifications even if the given ideal is not binomial.

Recommendations

• Testing binomiality of chemical reaction networks using comprehensive Gröbner systems
• Finding binomials in polynomial ideals
• Efficiently and effectively recognizing toricity of steady state varieties
• A divide and conquer method to compute binomial ideals
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Cited in

(10)

• Gröbner bases of reaction networks with intermediate species
• Parametric toricity of steady state varieties of reaction networks
• Testing binomiality of chemical reaction networks using comprehensive Gröbner systems
• Multistationarity questions in reduced versus extended biochemical networks
• Efficiently and effectively recognizing toricity of steady state varieties
• Finding binomials in polynomial ideals
• Families of toric chemical reaction networks
• Parity binomial edge ideals
• Binomiality testing and computing sparse polynomials via witness sets
• A world of binomials

Describes a project that uses

Uses Software

• Binomials.m2
• SINGULAR
• Macaulay2

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