13,240 research outputs found
Boolean Dynamics with Random Couplings
This paper reviews a class of generic dissipative dynamical systems called
N-K models. In these models, the dynamics of N elements, defined as Boolean
variables, develop step by step, clocked by a discrete time variable. Each of
the N Boolean elements at a given time is given a value which depends upon K
elements in the previous time step.
We review the work of many authors on the behavior of the models, looking
particularly at the structure and lengths of their cycles, the sizes of their
basins of attraction, and the flow of information through the systems. In the
limit of infinite N, there is a phase transition between a chaotic and an
ordered phase, with a critical phase in between.
We argue that the behavior of this system depends significantly on the
topology of the network connections. If the elements are placed upon a lattice
with dimension d, the system shows correlations related to the standard
percolation or directed percolation phase transition on such a lattice. On the
other hand, a very different behavior is seen in the Kauffman net in which all
spins are equally likely to be coupled to a given spin. In this situation,
coupling loops are mostly suppressed, and the behavior of the system is much
more like that of a mean field theory.
We also describe possible applications of the models to, for example, genetic
networks, cell differentiation, evolution, democracy in social systems and
neural networks.Comment: 69 pages, 16 figures, Submitted to Springer Applied Mathematical
Sciences Serie
Relative Stability of Network States in Boolean Network Models of Gene Regulation in Development
Progress in cell type reprogramming has revived the interest in Waddington's
concept of the epigenetic landscape. Recently researchers developed the
quasi-potential theory to represent the Waddington's landscape. The
Quasi-potential U(x), derived from interactions in the gene regulatory network
(GRN) of a cell, quantifies the relative stability of network states, which
determine the effort required for state transitions in a multi-stable dynamical
system. However, quasi-potential landscapes, originally developed for
continuous systems, are not suitable for discrete-valued networks which are
important tools to study complex systems. In this paper, we provide a framework
to quantify the landscape for discrete Boolean networks (BNs). We apply our
framework to study pancreas cell differentiation where an ensemble of BN models
is considered based on the structure of a minimal GRN for pancreas development.
We impose biologically motivated structural constraints (corresponding to
specific type of Boolean functions) and dynamical constraints (corresponding to
stable attractor states) to limit the space of BN models for pancreas
development. In addition, we enforce a novel functional constraint
corresponding to the relative ordering of attractor states in BN models to
restrict the space of BN models to the biological relevant class. We find that
BNs with canalyzing/sign-compatible Boolean functions best capture the dynamics
of pancreas cell differentiation. This framework can also determine the genes'
influence on cell state transitions, and thus can facilitate the rational
design of cell reprogramming protocols.Comment: 24 pages, 6 figures, 1 tabl
Boolean networks with robust and reliable trajectories
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 probability that the dynamics return to the reliable trajectory after a
perturbation of the state of a single node. In order to achieve high
robustness, we navigate through the space of possible update functions by using
an evolutionary algorithm. We constrain the networks to having the minimum
number of connections required to obtain the reliable trajectory. Surprisingly,
we find that robustness always reaches values close to 100 percent during the
evolutionary optimization process. The set of update functions can be evolved
such that it differs only slightly from that of networks that were not
optimized with respect to robustness. The state space of the optimized networks
is dominated by the basin of attraction of the reliable trajectory.Comment: 12 pages, 9 figure
Numerical and Theoretical Studies of Noise Effects in the Kauffman Model
In this work we analyze the stochastic dynamics of the Kauffman model
evolving under the influence of noise. By considering the average crossing time
between two distinct trajectories, we show that different Kauffman models
exhibit a similar kind of behavior, even when the structure of their basins of
attraction is quite different. This can be considered as a robust property of
these models. We present numerical results for the full range of noise level
and obtain approximate analytic expressions for the above crossing time as a
function of the noise in the limit cases of small and large noise levels.Comment: 24 pages, 9 figures, Submitted to the Journal of Statistical Physic
Stochastic neural network models for gene regulatory networks
Recent advances in gene-expression profiling technologies provide large amounts of gene expression data. This raises the possibility for a functional understanding of genome dynamics by means of mathematical modelling. As gene expression involves intrinsic noise, stochastic models are essential for better descriptions of gene regulatory networks. However, stochastic modelling for large scale gene expression data sets is still in the very early developmental stage. In this paper we present some stochastic models by introducing stochastic processes into neural network models that can describe intermediate regulation for large scale gene networks. Poisson random variables are used to represent chance events in the processes of synthesis and degradation. For expression data with normalized concentrations, exponential or normal random variables are used to realize fluctuations. Using a network with three genes, we show how to use stochastic simulations for studying robustness and stability properties of gene expression patterns under the influence of noise, and how to use stochastic models to predict statistical distributions of expression levels in population of cells. The discussion suggest that stochastic neural network models can give better description of gene regulatory networks and provide criteria for measuring the reasonableness o mathematical models
Scaling in a general class of critical random Boolean networks
We derive analytically the scaling behavior in the thermodynamic limit of the
number of nonfrozen and relevant nodes in the most general class of critical
Kauffman networks for any number of inputs per node, and for any choice of the
probability distribution for the Boolean functions. By defining and analyzing a
stochastic process that determines the frozen core we can prove that the mean
number of nonfrozen nodes in any critical network with more than one input per
node scales with the network size as , with only
nonfrozen nodes having two nonfrozen inputs and the number of nonfrozen nodes
with more than two inputs being finite in the thermodynamic limit. Using these
results we can conclude that the mean number of relevant nodes increases for
large as , with only a finite number of relevant nodes having two
relevant inputs, and a vanishing fraction of nodes having more than three of
them. It follows that all relevant components apart from a finite number are
simple loops, and that the mean number and length of attractors increases
faster than any power law with network size.Comment: 11 page
Topology of biological networks and reliability of information processing
Biological systems rely on robust internal information processing: Survival
depends on highly reproducible dynamics of regulatory processes. Biological
information processing elements, however, are intrinsically noisy (genetic
switches, neurons, etc.). Such noise poses severe stability problems to system
behavior as it tends to desynchronize system dynamics (e.g. via fluctuating
response or transmission time of the elements). Synchronicity in parallel
information processing is not readily sustained in the absence of a central
clock. Here we analyze the influence of topology on synchronicity in networks
of autonomous noisy elements. In numerical and analytical studies we find a
clear distinction between non-reliable and reliable dynamical attractors,
depending on the topology of the circuit. In the reliable cases, synchronicity
is sustained, while in the unreliable scenario, fluctuating responses of single
elements can gradually desynchronize the system, leading to non-reproducible
behavior. We find that the fraction of reliable dynamical attractors strongly
correlates with the underlying circuitry. Our model suggests that the observed
motif structure of biological signaling networks is shaped by the biological
requirement for reproducibility of attractors.Comment: 7 pages, 7 figure
A characterization of the Edge of Criticality in Binary Echo State Networks
Echo State Networks (ESNs) are simplified recurrent neural network models
composed of a reservoir and a linear, trainable readout layer. The reservoir is
tunable by some hyper-parameters that control the network behaviour. ESNs are
known to be effective in solving tasks when configured on a region in
(hyper-)parameter space called \emph{Edge of Criticality} (EoC), where the
system is maximally sensitive to perturbations hence affecting its behaviour.
In this paper, we propose binary ESNs, which are architecturally equivalent to
standard ESNs but consider binary activation functions and binary recurrent
weights. For these networks, we derive a closed-form expression for the EoC in
the autonomous case and perform simulations in order to assess their behavior
in the case of noisy neurons and in the presence of a signal. We propose a
theoretical explanation for the fact that the variance of the input plays a
major role in characterizing the EoC
Mutual information in random Boolean models of regulatory networks
The amount of mutual information contained in time series of two elements
gives a measure of how well their activities are coordinated. In a large,
complex network of interacting elements, such as a genetic regulatory network
within a cell, the average of the mutual information over all pairs is a
global measure of how well the system can coordinate its internal dynamics. We
study this average pairwise mutual information in random Boolean networks
(RBNs) as a function of the distribution of Boolean rules implemented at each
element, assuming that the links in the network are randomly placed. Efficient
numerical methods for calculating show that as the number of network nodes
N approaches infinity, the quantity N exhibits a discontinuity at parameter
values corresponding to critical RBNs. For finite systems it peaks near the
critical value, but slightly in the disordered regime for typical parameter
variations. The source of high values of N is the indirect correlations
between pairs of elements from different long chains with a common starting
point. The contribution from pairs that are directly linked approaches zero for
critical networks and peaks deep in the disordered regime.Comment: 11 pages, 6 figures; Minor revisions for clarity and figure format,
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