Related papers: Complexity of limit-cycle problems in Boolean netw…
Boolean nets are Petri nets that permit at most one token per place. Research has approached this important subject in many ways which resulted in various different classes of boolean nets. But yet, they are only distinguished by the…
We propose new activity-dependent adaptive Boolean networks inspired by the cis-regulatory mechanism in gene regulatory networks. We analytically show that our model can be solved for stationary in-degree distribution for a wide class of…
The topological analysis of biological networks has been a prolific topic in network science during the last decade. A persistent problem with this approach is the inherent uncertainty and noisy nature of the data. One of the cases in which…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
We study experimentally the synchronization patterns in time-delayed directed Boolean networks of excitable systems. We observe a transition in the network dynamics when the refractory time of the individual systems is adjusted. When the…
The problem of reliability of the dynamics in biological regulatory networks is studied in the framework of a generalized Boolean network model with continuous timing and noise. Using well-known artificial genetic networks such as the…
In this paper, we analyze the complexity of functional programs written in the interaction-net computation model, an asynchronous, parallel and confluent model that generalizes linear-logic proof nets. Employing user-defined sized and…
Boolean networks have been successfully used in modelling gene regulatory networks. In this paper we propose a reduction method that reduces the complexity of a Boolean network but keeps dynamical properties and topological features and…
A Boolean network is a finite dynamical system, whose variables take values from a binary set. The value update rule for each variable is a Boolean function, depending on a selected subset of variables. Boolean networks have been widely…
There is an obvious need for improving the performance and accuracy of a Bayesian network as new data is observed. Because of errors in model construction and changes in the dynamics of the domains, we cannot afford to ignore the…
Many biological systems, such as metabolic pathways, exhibit bistability behavior: these biological systems exhibit two distinct stable states with switching between the two stable states controlled by certain conditions. Since…
Using a graph-theoretic approach, we derive a new sufficient condition for observability of a Boolean control network (BCN). Based on this condition, we describe two algorithms: the first selects a set of nodes so that observing this set…
A Boolean control network (BCN) is a discrete-time dynamical system whose variables take values from a binary set $\{0,1\}$. At each time step, each variable of the BCN updates its value simultaneously according to a Boolean function which…
Automata networks are a versatile model of finite discrete dynamical systems composed of interacting entities (the automata), able to embed any directed graph as a dynamics on its space of configurations (the set of vertices, representing…
We investigate the expressive power of neural networks from the point of view of descriptive complexity. We study neural networks that use floating-point numbers and piecewise polynomial activation functions from two perspectives: 1) the…
It is known that there are no more Lyndon words of length n than there are periodic necklaces of same length. This paper considers a similar problem where, additionally, the necklaces must be without some forbidden factors. This problem…
Among the fundamental questions in computer science is that of the impact of synchronism/asynchronism on computations, which has been addressed in various fields of the discipline: in programming, in networking, in concurrence theory, in…
The dynamics of Boolean networks (the N-K model) with scale-free topology are studied here. The existence of a phase transition governed by the value of the scale-free exponent of the network is shown analytically by analyzing the overlap…
In this article we study the minimum number $\kappa$ of additional automata that a Boolean automata network (BAN) associated with a given block-sequential update schedule needs in order to simulate a given BAN with a parallel update…
Boolean networks are a valuable class of discrete dynamical systems models, but they remain fundamentally limited by their inability to capture multi-way interactions in their components. To remedy this limitation, we propose a model of…