The Influence of Canalization on the Robustness of Boolean Networks

Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed by $k$-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept to $c$-sensitivity and provides formulas for the activities and $c$-sensitivity of general $k$-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of the $c$-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally efficient way to obtain Derrida values of Boolean networks, deterministic or stochastic, that does not involve simulation.Comment: 16 pages, 2 figures, 3 table

State Concentration Exponent as a Measure of Quickness in Kauffman-type Networks

We study the dynamics of randomly connected networks composed of binary Boolean elements and those composed of binary majority vote elements. We elucidate their differences in both sparsely and densely connected cases. The quickness of large network dynamics is usually quantified by the length of transient paths, an analytically intractable measure. For discrete-time dynamics of networks of binary elements, we address this dilemma with an alternative unified framework by using a concept termed state concentration, defined as the exponent of the average number of t-step ancestors in state transition graphs. The state transition graph is defined by nodes corresponding to network states and directed links corresponding to transitions. Using this exponent, we interrogate the dynamics of random Boolean and majority vote networks. We find that extremely sparse Boolean networks and majority vote networks with arbitrary density achieve quickness, owing in part to long-tailed in-degree distributions. As a corollary, only relatively dense majority vote networks can achieve both quickness and robustness.Comment: 6 figure

Discrete time piecewise affine models of genetic regulatory networks

We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables represent gene expression levels. When compared to other models of regulatory networks, these models have an additional parameter which is identified as quantifying interaction delays. In spite of their simplicity, their dynamics presents a rich variety of behaviours. This phenomenology is not limited to piecewise affine model but extends to smooth nonlinear discrete time models of regulatory networks. In a first step, our analysis concerns general properties of networks on arbitrary graphs (characterisation of the attractor, symbolic dynamics, Lyapunov stability, structural stability, symmetries, etc). In a second step, focus is made on simple circuits for which the attractor and its changes with parameters are described. In the negative circuit of 2 genes, a thorough study is presented which concern stable (quasi-)periodic oscillations governed by rotations on the unit circle -- with a rotation number depending continuously and monotonically on threshold parameters. These regular oscillations exist in negative circuits with arbitrary number of genes where they are most likely to be observed in genetic systems with non-negligible delay effects.Comment: 34 page

Complexity and Information: Measuring Emergence, Self-organization, and Homeostasis at Multiple Scales

Concepts used in the scientific study of complex systems have become so widespread that their use and abuse has led to ambiguity and confusion in their meaning. In this paper we use information theory to provide abstract and concise measures of complexity, emergence, self-organization, and homeostasis. The purpose is to clarify the meaning of these concepts with the aid of the proposed formal measures. In a simplified version of the measures (focusing on the information produced by a system), emergence becomes the opposite of self-organization, while complexity represents their balance. Homeostasis can be seen as a measure of the stability of the system. We use computational experiments on random Boolean networks and elementary cellular automata to illustrate our measures at multiple scales.Comment: 42 pages, 11 figures, 2 table

Complex Networks

Introduction to the Special Issue on Complex Networks, Artificial Life journal.Comment: 7 pages, in pres