Related papers: Boolean Networks with Multi-Expressions and Parame…
Boolean equivalence allows Boolean networks with identical functionality to exhibit diverse graph structures. This gives more room for exploration in logic optimization, while also posing a challenge for tasks involving consistency between…
In this paper, we propose an approach for modeling and analysis of a number of phenomena of collective behavior. By collectives we mean multi-agent systems that transition from one state to another at discrete moments of time. The behavior…
This article is set in the field of regulation networks modeled by discrete dynamical systems. It focuses on Boolean automata networks. In such networks, there are many ways to update the states of every element. When this is done…
The information processing abilities of a multilayer neural network with a number of hidden units scaling as the input dimension are studied using statistical mechanics methods. The mapping from the input layer to the hidden units is…
We consider Boolean networks with interaction graphs partitioned into strongly connected components, which we call strong modules. This type of network decomposition has been considered in the literature, primarily from the perspective of…
Neural network design has utilized flexible nonlinear processes which can mimic biological systems, but has suffered from a lack of traceability in the resulting network. Graphical probabilistic models ground network design in probabilistic…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
We study a general set of models of social network evolution and dynamics. The models consist of both a dynamics on the network and evolution of the network. Links are formed preferentially between 'similar' nodes, where the similarity is…
The new concept of multilevel network is introduced in order to embody some topological properties of complex systems with structures in the mesoscale which are not completely captured by the classical models. This new model, which…
We formulate general rules for a coarse-graining of the dynamics, which we term `symbolic dynamics', of feedback networks with monotone interactions, such as most biological modules. Networks which are more complex than simple cyclic…
We evaluate the probability that a Boolean network returns to an attractor after perturbing h nodes. We find that the return probability as function of h can display a variety of different behaviours, which yields insights into the…
A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…
The study of neuronal morphology is important not only for its potential relationship with neuronal dynamics, but also as a means to classify diverse types of cells and compare than among species, organs, and conditions. In the present…
We describe systems using Kauffman and similar networks. They are directed funct ioning networks consisting of finite number of nodes with finite number of discr ete states evaluated in synchronous mode of discrete time. In this paper we…
Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question,…
To simplify the analysis of Boolean networks, a reduction in the number of components is often considered. A popular reduction method consists in eliminating components that are not autoregulated, using variable substitution. In this work,…
We consider a model for heterogeneous 'gene regulatory networks' that is a generalization of the model proposed by Chatterjee and Durrett (2011) as an "annealed approximation" of Kauffmann's (1969) random Boolean networks. In this model,…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
We prove that the fully asynchronous dynamics of a Boolean network $f:\{0,1\}^n\to\{0,1\}^n$ without negative loop can be simulated, in a very specific way, by a monotone Boolean network with $2n$ components. We then use this result to…
Genetic regulatory networks with adaptive responses are widely studied in biology. Usually, models consisting only of a few nodes have been considered. They present one input receptor for activation and one output node where the adaptive…