Related papers: Guiding the Self-organization of Random Boolean Ne…
The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…
Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…
In this paper we study finite dynamical systems with $n$ functions acting on the same set $X$, and probabilities assigned to these functions, that it is called Probabilistic Regulatory Gene Networks (PRN. his concept is the same or a…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
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…
A Relational Dependency Network (RDN) is a directed graphical model widely used for multi-relational data. These networks allow cyclic dependencies, necessary to represent relational autocorrelations. We describe an approach for learning…
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
Correct inference of genetic regulations inside a cell is one of the greatest challenges in post genomic era for the biologist and researchers. Several intelligent techniques and models were already proposed to identify the regulatory…
Reservoir computing provides a time and cost-efficient alternative to traditional learning methods.Critical regimes, known as the "edge of chaos," have been found to optimize computational performance in binary neural networks. However,…
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…
Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To…
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…
This paper proposes self-organization as a method to improve the efficiency and adaptability of bureaucracies and similar social systems. Bureaucracies are described as networks of agents, where the main design principle is to reduce local…
Boolean networks have been used in a variety of settings, as models for general complex systems as well as models of specific systems in diverse fields, such as biology, engineering, and computer science. Traditionally, their properties as…
We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We…
Many dynamical systems can be successfully analyzed by representing them as networks. Empirically measured networks and dynamic processes that take place in these situations show heterogeneous, non-Markovian, and intrinsically correlated…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
First, the topological structure of a transition system is studied. Then, two types of transition system (TS) representations of Boolean networks (BNs) and Boolean control networks (BCNs) are investigated. The first kind of representation…
It is an increasingly important problem to study conditions on the structure of a network that guarantee a given behavior for its underlying dynamical system. In this paper we report that a Boolean network may fall within the chaotic…