Related papers: Finding the fixed points of a Boolean network from…
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,…
In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows to prune simple logical cascades and under-determined variables, returning thereby…
To each Boolean function F from {0,1}^n to itself and each point x in {0,1}^n, we associate the signed directed graph G_F(x) of order n that contains a positive (resp. negative) arc from j to i if the partial derivative of f_i with respect…
Despite the large quantity of information available, thorough researches in various biological databases are still needed in order to reconstruct and understand the steps that lead to known or new phenomena. By using protein-protein…
This paper investigates the stabilization of probabilistic Boolean networks (PBNs) via a novel pinning control strategy based on network structure. In a PBN, the evolution equation of each gene switches among a collection of candidate…
In this paper we study the dynamical behavior of Boolean networks with firing memory, namely Boolean networks whose vertices are updated synchronously depending on their proper Boolean local transition functions so that each vertex remains…
The biologist Ren\'e Thomas conjectured, twenty years ago, that the presence of a negative feedback circuit in the interaction graph of a dynamical system is a necessary condition for this system to produce sustained oscillations. In this…
Boolean Networks (BNs) serve as a fundamental modeling framework for capturing complex dynamical systems across various domains, including systems biology, computational logic, and artificial intelligence. A crucial property of BNs is the…
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…
We analyse a model of fixed in-degree Random Boolean Networks in which the fraction of input-receiving nodes is controlled by a parameter gamma. We investigate analytically and numerically the dynamics of graphs under a parallel XOR…
A Boolean network is a mapping $f :\{0,1\}^n \to \{0,1\}^n$, which can be used to model networks of $n$ interacting entities, each having a local Boolean state that evolves over time according to a deterministic function of the current…
Recurrent neural networks are widely used in speech and language processing. Due to dependency on the past, standard algorithms for training these models, such as back-propagation through time (BPTT), cannot be efficiently parallelised.…
Boolean networks have been the object of much attention, especially since S. Kauffman proposed them in the 1960's as models for gene regulatory networks. These systems are characterized by being defined on a Boolean state space and by…
A Boolean network (BN) with $n$ components is a discrete dynamical system described by the successive iterations of a function $f:\{0,1\}^n\to\{0,1\}^n$. In most applications, the main parameter is the interaction graph of $f$: the digraph…
Boolean networks (BNs) are discrete dynamical systems with applications to the modeling of cellular behaviors. In this paper, we demonstrate how the software BoNesis can be employed to exhaustively identify combinations of perturbations…
A Boolean network is a discrete dynamical system operating on vectors of Boolean variables. The action of a Boolean network can be conveniently expressed as a system of Boolean update functions, computing the new values for each component…
We study Boolean networks which are simple spatial models of the highly conserved Delta-Notch system. The models assume the inhibition of Delta in each cell by Notch in the same cell, and the activation of Notch in presence of Delta in…
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,…
Networked discrete dynamical systems are often used to model the spread of contagions and decision-making by agents in coordination games. Fixed points of such dynamical systems represent configurations to which the system converges. In the…
We study fixed points of cellular automata with $N$ sites on random sparse graphs. In the large $N$ limit such models are known to exhibit phase transitions, from a ``frozen'' phase, where at most a finite number of sites fluctuate at long…