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 dep
th 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.
Toric posets are cyclic analogues of finite posets. They can be viewed combinatorially as equivalence classes of acyclic orientations generated by converting sources into sinks, or geometrically as chambers of toric graphic hyperplane arrangements. I
n this paper we study toric intervals, morphisms, and order ideals, and we provide a connection to cyclic reducibility and conjugacy in Coxeter groups.
Let G be a connected, loopless multigraph. The sandpile group of G is a finite abelian group associated to G whose order is equal to the number of spanning trees in G. Holroyd et al. used a dynamical process on graphs called rotor-routing to define a
simply transitive action of the sandpile group of G on its set of spanning trees. Their definition depends on two pieces of auxiliary data: a choice of a ribbon graph structure on G, and a choice of a root vertex. Chan, Church, and Grochow showed that if G is a planar ribbon graph, it has a canonical rotor-routing action associated to it, i.e., the rotor-routing action is actually independent of the choice of root vertex. It is well-known that the spanning trees of a planar graph G are in canonical bijection with those of its planar dual G*, and furthermore that the sandpile groups of G and G* are isomorphic. Thus, one can ask: are the two rotor-routing actions, of the sandpile group of G on its spanning trees, and of the sandpile group of G* on its spanning trees, compatible under plane duality? In this paper, we give an affirmative answer to this question, which had been conjectured by Baker.
We define toric partial orders, corresponding to regions of graphic toric hyperplane arrangements, just as ordinary partial orders correspond to regions of graphic hyperplane arrangements. Combinatorially, toric posets correspond to finite posets und
er the equivalence relation generated by converting minimal elements into maximal elements, or sources into sinks. We derive toric analogues for several features of ordinary partial orders, such as chains, antichains, transitivity, Hasse diagrams, linear extensions, and total orders.
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 o
f 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.
We say that a finite asynchronous cellular automaton (or more generally, any sequential dynamical system) is pi-independent if its set of periodic points are independent of the order that the local functions are applied. In this case, the local funct
ions permute the periodic points, and these permutations generate the dynamics group. We have previously shown that exactly 104 of the possible 256 cellular automaton rules are pi-independent. In this article, we classify the periodic states of these systems and describe their dynamics groups, which are quotients of Coxeter groups. The dynamics groups provide information about permissible dynamics as a function of update sequence and, as such, connect discrete dynamical systems, group theory, and algebraic combinatorics in a new and interesting way. We conclude with a discussion of numerous open problems and directions for future research.
