Reverse-engineering of polynomial dynamical systems

DOI10.1016/J.AAM.2006.08.004zbMATH Open1129.93026arXivq-bio/0605032OpenAlexW2026726507MaRDI QIDQ2467344FDOQ2467344

Mike Stillman, Reinhard Laubenbacher, Brandilyn Stigler, Abdul Salam Jarrah

Publication date: 21 January 2008

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

Abstract: Multivariate polynomial dynamical systems over finite fields have been studied in several contexts, including engineering and mathematical biology. An important problem is to construct models of such systems from a partial specification of dynamic properties, e.g., from a collection of state transition measurements. Here, we consider static models, which are directed graphs that represent the causal relationships between system variables, so-called wiring diagrams. This paper contains an algorithm which computes all possible minimal wiring diagrams for a given set of state transition measurements. The paper also contains several statistical measures for model selection. The algorithm uses primary decomposition of monomial ideals as the principal tool. An application to the reverse-engineering of a gene regulatory network is included. The algorithm and the statistical measures are implemented in Macaulay2 and are available from the authors.

Full work available at URL: https://arxiv.org/abs/q-bio/0605032

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zbMATH Keywords

decompositionfinite fieldmonomial idealgene regulatory networkfinite dynamical systemreverse-engineering

Mathematics Subject Classification ID

Neural networks for/in biological studies, artificial life and related topics (92B20) Gröbner bases; other bases for ideals and modules (e.g., Janet and border bases) (13P10) Multivariable systems, multidimensional control systems (93C35)

Cites Work

• Logical identification of all steady states: The concept of feedback loop characteristic states
• A computational algebra approach to the reverse engineering of gene regulatory networks
• Linear analysis of switching nets
• The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in \textit{Drosophila melanogaster}
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• Computing irredundant irreducible decompositions of large scale monomial ideals
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• Assessing cellular automata based models using partial differential equations
• Algebraic dependency models of protein signal transduction networks from time-series data

Cited In (23)

• The Minimal Hitting Set Generation Problem: Algorithms and Computation
• Geometric characterization of data sets with unique reduced Gröbner bases
• Probability estimates for reachability of linear systems defined over finite fields
• Why did the shape of your network change? (On detecting network anomalies via non-local curvatures)
• Reversibility in polynomial systems of ODE's
• A Unified Approach to Reverse Engineering and Data Selection for Unique Network Identification
• Computing Linear Extensions for Polynomial Posets Subject to Algebraic Constraints
• Identification and stabilization of faulty Boolean control networks
• Algebraic network reconstruction of discrete dynamical systems
• Forecasting polynomial dynamics
• Parameter estimation for Boolean models of biological networks
• Noise-tolerant algebraic method for reconstruction of nonlinear dynamical systems
• Title not available (Why is that?)
• On the dynamics of endomorphisms of finite groups
• Primary decomposition of squarefree pseudomonomial ideals
• Polynomial Equations over Finite, Discrete-Time Dynamical Systems
• Inferring biologically relevant models: nested canalyzing functions
• Neural codes and the factor complex
• Reduction of Boolean network models
• The neural ring: an algebraic tool for analyzing the intrinsic structure of neural codes
• Analytical approach for simplifying dynamical systems of polynomial type.
• Quantifier Elimination over Finite Fields Using Gröbner Bases
• Algebraic Models and Their Use in Systems Biology

Uses Software

• Macaulay2

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