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

binomial idealchemical reaction networkspolynomial systems in biologysteady states

Mathematics Subject Classification ID

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

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.

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• Testing binomiality of chemical reaction networks using comprehensive Gröbner systems
• Finding binomials in polynomial ideals
• Efficiently and effectively recognizing toricity of steady state varieties
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Cites work

• A new efficient algorithm for computing Gröbner bases (F₄)
• A Singular Introduction to Commutative Algebra
• Binomial ideals
• Chemical reaction systems with toric steady states
• Decompositions of commutative monoid congruences and binomial ideals.
• Graph-theoretic criteria for injectivity and unique equilibria in general chemical reaction systems
• scientific article; zbMATH DE number 704831 (Why is no real title available?)
• scientific article; zbMATH DE number 5047784 (Why is no real title available?)
• scientific article; zbMATH DE number 967945 (Why is no real title available?)
• MAPK's networks and their capacity for multistationarity due to toric steady states
• Multiple Equilibria in Complex Chemical Reaction Networks: II. The Species-Reaction Graph
• Multiple Equilibria in Complex Chemical Reaction Networks: Semiopen Mass Action Systems
• Multistationarity in mass action networks with applications to ERK activation
• Positive margins and primary decomposition
• Power-law kinetics and determinant criteria for the preclusion of multistationarity in networks of interacting species
• Simplifying the Jacobian criterion for precluding multistationarity in chemical reaction networks
• Translated chemical reaction networks

Cited in

(11)

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

Describes a project that uses

Uses Software

• Binomials.m2
• SINGULAR
• Macaulay2

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