arXiv subjects

Reinhard Laubenbacher

Publications and source records attributed to Reinhard Laubenbacher.

51 records · Page 3Linked to original sources

arXiv2008

Computer algebra in systems biology

Systems biology focuses on the study of entire biological systems rather than on their individual components. With the emergence of high-throughput data generation technologies for molecular biology and the development of advanced mathematical modeling techniques, this field promises to provide important new insights. At the same time, with the availability of increasingly powerful computers, computer algebra has developed into a useful tool for many applications. This article illustrates the use of computer algebra in systems biology by way of a well-known gene regulatory network, the Lac Operon in the bacterium E. coli.

cs.SC↗

arXiv2008

Inference of ecological interaction networks

The inference of the interactions between organisms in an ecosystem from observational data is an important problem in ecology. This paper presents a mathematical inference method, originally developed for the inference of biochemical networks in molecular biology, adapted for the inference of networks of ecological interactions. The method is applied to a network of invertebrate families (taxa) in a rice field.

q-bio.PE↗

arXiv2008

The Dynamics of Conjunctive and Disjunctive Boolean Networks

The relationship between the properties of a dynamical system and the structure of its defining equations has long been studied in many contexts. Here we study this problem for the class of conjunctive (resp. disjunctive) Boolean networks, that is, Boolean networks in which all Boolean functions are constructed with the AND (resp. OR) operator only. The main results of this paper describe network dynamics in terms of the structure of the network dependency graph (topology). For a given such network, all possible limit cycle lengths are computed and lower and upper bounds for the number of cycles of each length are given. In particular, the exact number of fixed points is obtained. The bounds are in terms of structural features of the dependency graph and its partially ordered set of strongly connected components. For networks with strongly connected dependency graph, the exact cycle structure is computed.

math.CO↗

arXiv2008

On the algebraic geometry of polynomial dynamical systems

This paper focuses on polynomial dynamical systems over finite fields. These systems appear in a variety of contexts, in computer science, engineering, and computational biology, for instance as models of intracellular biochemical networks. It is shown that several problems relating to their structure and dynamics, as well as control theory, can be formulated and solved in the language of algebraic geometry.

math.AG↗

arXiv2007

A mathematical formalism for agent-based modeling

Many complex systems can be modeled as multiagent systems in which the constituent entities (agents) interact with each other. The global dynamics of such a system is determined by the nature of the local interactions among the agents. Since it is difficult to formally analyze complex multiagent systems, they are often studied through computer simulations. While computer simulations can be very useful, results obtained through simulations do not formally validate the observed behavior. Thus, there is a need for a mathematical framework which one can use to represent multiagent systems and formally establish their properties. This work contains a brief exposition of some known mathematical frameworks that can model multiagent systems. The focus is on one such framework, namely that of finite dynamical systems. Both, deterministic and stochastic versions of this framework are discussed. The paper contains a sampling of the mathematical results from the literature to show how finite dynamical systems can be used to carry out a rigorous study of the properties of multiagent systems and it is shown how the framework can also serve as a universal model for computation.

cs.MA↗

arXiv2007

Design of experiments and biochemical network inference

Design of experiments is a branch of statistics that aims to identify efficient procedures for planning experiments in order to optimize knowledge discovery. Network inference is a subfield of systems biology devoted to the identification of biochemical networks from experimental data. Common to both areas of research is their focus on the maximization of information gathered from experimentation. The goal of this paper is to establish a connection between these two areas coming from the common use of polynomial models and techniques from computational algebra.

q-bio.MN↗

arXiv2007

The effect of negative feedback loops on the dynamics of Boolean networks

Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more regular behavior than those with more negative loops. To be precise, we study the relationship between the number of independent feedback loops and the number and length of the limit cycles in the phase space of dynamic Boolean networks. We show that, as the number of independent negative feedback loops increases, the number (length) of limit cycles tends to decrease (increase). These conclusions are consistent with the fact, for certain natural biological networks, that they on the one hand exhibit generally regular behavior and on the other hand show less negative feedback loops than randomized networks with the same numbers of nodes and connectivity.

q-bio.QM↗

arXiv2007

Nested Canalyzing, unate cascade, and polynomial functions

This paper focuses on the study of certain classes of Boolean functions that have appeared in several different contexts. Nested canalyzing functions have been studied recently in the context of Boolean network models of gene regulatory networks. In the same context, polynomial functions over finite fields have been used to develop network inference methods for gene regulatory networks. Finally, unate cascade functions have been studied in the design of logic circuits and binary decision diagrams. This paper shows that the class of nested canalyzing functions is equal to that of unate cascade functions. Furthermore, it provides a description of nested canalyzing functions as a certain type of Boolean polynomial function. Using the polynomial framework one can show that the class of nested canalyzing functions, or, equivalently, the class of unate cascade functions, forms an algebraic variety which makes their analysis amenable to the use of techniques from algebraic geometry and computational algebra. As a corollary of the functional equivalence derived here, a formula in the literature for the number of unate cascade functions provides such a formula for the number of nested canalyzing functions.

q-bio.QM↗

arXiv2006

Reverse-engineering of polynomial dynamical systems

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.

q-bio.QM↗

arXiv2004

Boolean Monomial Dynamical Systems

An important problem in the theory of finite dynamical systems is to link the structure of a system with its dynamics. This paper contains such a link for a family of nonlinear systems over the field with two elements. For systems that can be described by monomials (including Boolean AND systems), one can obtain information about the limit cycle structure from the structure of the monomials. In particular, the paper contains a sufficient condition for a monomial system to have only fixed points as limit cycles. This condition depends on the cycle structure of the dependency graph of the system and can be verified in polynomial time.

math.CO↗

arXiv2003

A Computational Algebra Approach to the Reverse Engineering of Gene Regulatory Networks

This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The simplest examples of such models are Boolean networks, in which variables have only two possible states. The use of a larger number of possible states allows a finer discretization of experimental data and more than one possible mode of action for the variables, depending on threshold values. Furthermore, with a suitable choice of state set, one can employ powerful tools from computational algebra, that underlie the reverse-engineering algorithm, avoiding costly enumeration strategies. To perform well, the algorithm requires wildtype together with perturbation time courses. This makes it suitable for small to meso-scale networks rather than networks on a genome-wide scale. The complexity of the algorithm is quadratic in the number of variables and cubic in the number of time points. The algorithm is validated on a recently published Boolean network model of segment polarity development in Drosophila melanogaster.

q-bio.QM↗

arXiv2003

Generic Cohen-Macaulay monomial ideals

Given a simplicial complex, it is easy to construct a generic deformation of its Stanley-Reisner ideal. The main question under investigation in this paper is how to characterize the simplicial complexes such that their Stanley-Reisner ideals have Cohen-Macaulay generic deformations. Algorithms are presented to construct such deformations for matroid complexes, shifted complexes, and tree complexes.

math.AC↗

arXiv2001

The Center Variety of Polynomial Differential Systems

We investigate the symmetry component of the center variety of polynomial differential systems, corresponding to systems with an axis of symmetry in the real plane. We give a general algorithm to find this irreducible subvariety and compute its dimension. We show that our methods provide a simple way to compute the radical of the ideal generated by the focus quantities and, therefore, to estimate the cyclicity of a center in the case when the ideal is radical. In particular, we use our methods to get a simple proof of the famous Bautin theorem on the cyclicity of the quadratic system.

math.DS↗

arXiv2001

Classification of Finite Dynamical Systems

This paper is motivated by the theory of sequential dynamical systems, developed as a basis for a mathematical theory of computer simulation. It contains a classification of finite dynamical systems on binary strings, which are obtained by composing functions defined on the coordinates. The classification is in terms of the dependency relations among the coordinate functions. It suggests a natural notion of the linearization of a system. Furthermore, it contains a sharp upper bound on the number of systems in terms of the dependencies among the coordinate functions. This upper bound generalizes an upper bound for sequential dynamical systems.

math.DS↗

arXiv2001

Generic ideals and Moreno-Soc{\'ı}as conjecture

Let $f_1, ..., f_n$ be homogeneous polynomials generating a generic ideal $I$ in the ring of polynomials in $n$ variables over an infinite field. Moreno-Socías conjectured that for the graded reverse lexicographic term ordering, the initial ideal ${\rm in}(I)$ is a weakly reverse lexicographic ideal. This paper contains a new proof of Moreno-Soc{\'ı}as' conjecture for the case $n=2$.

math.AC↗