Stratification and enumeration of Boolean functions by canalizing depth

Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The canalizing depth of a function describes how many canalizing variables can be recursively picked off, until a non-canalizing function remains. In this paper, we show how every Boolean function has a unique algebraic form involving extended monomial layers and a well-defined core polynomial. This generalizes recent work on the algebraic structure of nested canalizing functions, and it yields a stratification of all Boolean functions by their canalizing depth. As a result, we obtain closed formulas for the number of n-variable Boolean functions with depth k, which simultaneously generalizes enumeration formulas for canalizing, and nested canalizing functions

On Enumeration of Conjugacy Classes of Coxeter Elements

In this paper we study the equivalence relation on the set of acyclic orientations of a graph Y that arises through source-to-sink conversions. This source-to-sink conversion encodes, e.g. conjugation of Coxeter elements of a Coxeter group. We give a direct proof of a recursion for the number of equivalence classes of this relation for an arbitrary graph Y using edge deletion and edge contraction of non-bridge edges. We conclude by showing how this result may also be obtained through an evaluation of the Tutte polynomial as T(Y,1,0), and we provide bijections to two other classes of acyclic orientations that are known to be counted in the same way. A transversal of the set of equivalence classes is given.Comment: Added a few results about connections to the Tutte polynomia

Equivalences on Acyclic Orientations

The cyclic and dihedral groups can be made to act on the set Acyc(Y) of acyclic orientations of an undirected graph Y, and this gives rise to the equivalence relations ~kappa and ~delta, respectively. These two actions and their corresponding equivalence classes are closely related to combinatorial problems arising in the context of Coxeter groups, sequential dynamical systems, the chip-firing game, and representations of quivers. In this paper we construct the graphs C(Y) and D(Y) with vertex sets Acyc(Y) and whose connected components encode the equivalence classes. The number of connected components of these graphs are denoted kappa(Y) and delta(Y), respectively. We characterize the structure of C(Y) and D(Y), show how delta(Y) can be derived from kappa(Y), and give enumeration results for kappa(Y). Moreover, we show how to associate a poset structure to each kappa-equivalence class, and we characterize these posets. This allows us to create a bijection from Acyc(Y)/~kappa to the union of Acyc(Y')/~kappa and Acyc(Y'')/~kappa, Y' and Y'' denote edge deletion and edge contraction for a cycle-edge in Y, respectively, which in turn shows that kappa(Y) may be obtained by an evaluation of the Tutte polynomial at (1,0).Comment: The original paper was extended, reorganized, and split into two papers (see also arXiv:0802.4412

Cycle Equivalence of Graph Dynamical Systems

Graph dynamical systems (GDSs) can be used to describe a wide range of distributed, nonlinear phenomena. In this paper we characterize cycle equivalence of a class of finite GDSs called sequential dynamical systems SDSs. In general, two finite GDSs are cycle equivalent if their periodic orbits are isomorphic as directed graphs. Sequential dynamical systems may be thought of as generalized cellular automata, and use an update order to construct the dynamical system map. The main result of this paper is a characterization of cycle equivalence in terms of shifts and reflections of the SDS update order. We construct two graphs C(Y) and D(Y) whose components describe update orders that give rise to cycle equivalent SDSs. The number of components in C(Y) and D(Y) is an upper bound for the number of cycle equivalence classes one can obtain, and we enumerate these quantities through a recursion relation for several graph classes. The components of these graphs encode dynamical neutrality, the component sizes represent periodic orbit structural stability, and the number of components can be viewed as a system complexity measure

Coxeter Groups and Asynchronous Cellular Automata

The dynamics group of an asynchronous cellular automaton (ACA) relates properties of its long term dynamics to the structure of Coxeter groups. The key mathematical feature connecting these diverse fields is involutions. Group-theoretic results in the latter domain may lead to insight about the dynamics in the former, and vice-versa. In this article, we highlight some central themes and common structures, and discuss novel approaches to some open and open-ended problems. We introduce the state automaton of an ACA, and show how the root automaton of a Coxeter group is essentially part of the state automaton of a related ACA.Comment: 10 pages, 4 figure

Nested canalyzing depth and network stability

We introduce the nested canalyzing depth of a function, which measures the extent to which it retains a nested canalyzing structure. We characterize the structure of functions with a given depth and compute the expected activities and sensitivities of the variables. This analysis quantifies how canalyzation leads to higher stability in Boolean networks. It generalizes the notion of nested canalyzing functions (NCFs), which are precisely the functions with maximum depth. NCFs have been proposed as gene regulatory network models, but their structure is frequently too restrictive and they are extremely sparse. We find that functions become decreasingly sensitive to input perturbations as the canalyzing depth increases, but exhibit rapidly diminishing returns in stability. Additionally, we show that as depth increases, the dynamics of networks using these functions quickly approach the critical regime, suggesting that real networks exhibit some degree of canalyzing depth, and that NCFs are not significantly better than functions of sufficient depth for many applications of the modeling and reverse engineering of biological networks.Comment: 13 pages, 2 figure

A Novel Proof of the Heine-Borel Theorem

Every beginning real analysis student learns the classic Heine-Borel theorem, that the interval [0,1] is compact. In this article, we present a proof of this result that doesn't involve the standard techniques such as constructing a sequence and appealing to the completeness of the reals. We put a metric on the space of infinite binary sequences and prove that compactness of this space follows from a simple combinatorial lemma. The Heine-Borel theorem is an immediate corollary

Braids and Juggling Patterns

There are several ways to describe juggling patterns mathematically using combinatorics and algebra. In my thesis I use these ideas to build a new system using braid groups. A new kind of graph arises that helps describe all braids that can be juggled