534 research outputs found
The Number of Different Binary Functions Generated by NK-Kauffman Networks and the Emergence of Genetic Robustness
We determine the average number , of \textit{NK}-Kauffman
networks that give rise to the same binary function. We show that, for , there exists a connectivity critical value such that () for and
for . We find that is not a
constant, but scales very slowly with , as . The problem of genetic robustness emerges as a statistical property
of the ensemble of \textit{NK}-Kauffman networks and impose tight constraints
in the average number of epistatic interactions that the genotype-phenotype map
can have.Comment: 4 figures 18 page
The Number of Different Binary Functions Generated by NK-Kauffman Networks and the Emergence of Genetic Robustness
We determine the average number , of \textit{NK}-Kauffman
networks that give rise to the same binary function. We show that, for , there exists a connectivity critical value such that () for and
for . We find that is not a
constant, but scales very slowly with , as . The problem of genetic robustness emerges as a statistical property
of the ensemble of \textit{NK}-Kauffman networks and impose tight constraints
in the average number of epistatic interactions that the genotype-phenotype map
can have.Comment: 4 figures 18 page
A simulation-based method to evaluate the impact of product architecture on product evolvability
Products evolve over time via the continual redesigns of interdependent components. Product architecture, which is embodied in the structure of interactions among components, influences the ability for the product to be subsequently evolved. Despite extensive studies of change propagation via inter-component connections, little is known about the specific influences of product architecture on product evolvability. Related metrics and methods to assess the evolvability of products with given architectures are also under-developed. This paper proposes a simulation-based method to assess the isolated effect of product architecture on product evolvability by analyzing a design structure matrix. We define product evolvability as the ability of the product’s design to subsequently generate heritable performance-improving variations, and propose a quantitative measure for it. We demonstrate the proposed method by using it to investigate a wide spectrum of model-generated DSMs representing products with varied architectures, and show that modularity and inter-component influence cycles promote product evolvability. Our primary contribution is a repeatable method to assess and compare alternative product architectures for architecture selection or redesign for evolvability. A second contribution is the simulation-based evidence about the impacts of two particular product architectural patterns on product evolvability. Both contributions aim to aid in designing for evolvability.SUTD-MIT International Design Centre (IDC
Universality classes of interaction structures for NK fitness landscapes
Kauffman's NK-model is a paradigmatic example of a class of stochastic models
of genotypic fitness landscapes that aim to capture generic features of
epistatic interactions in multilocus systems. Genotypes are represented as
sequences of binary loci. The fitness assigned to a genotype is a sum of
contributions, each of which is a random function defined on a subset of loci. These subsets or neighborhoods determine the genetic interactions of
the model. Whereas earlier work on the NK model suggested that most of its
properties are robust with regard to the choice of neighborhoods, recent work
has revealed an important and sometimes counter-intuitive influence of the
interaction structure on the properties of NK fitness landscapes. Here we
review these developments and present new results concerning the number of
local fitness maxima and the statistics of selectively accessible (that is,
fitness-monotonic) mutational pathways. In particular, we develop a unified
framework for computing the exponential growth rate of the expected number of
local fitness maxima as a function of , and identify two different
universality classes of interaction structures that display different
asymptotics of this quantity for large . Moreover, we show that the
probability that the fitness landscape can be traversed along an accessible
path decreases exponentially in for a large class of interaction structures
that we characterize as locally bounded. Finally, we discuss the impact of the
NK interaction structures on the dynamics of evolution using adaptive walk
models.Comment: 61 pages, 9 figure
Emergence of robustness against noise: A structural phase transition in evolved models of gene regulatory networks
We investigate the evolution of Boolean networks subject to a selective
pressure which favors robustness against noise, as a model of evolved genetic
regulatory systems. By mapping the evolutionary process into a statistical
ensemble and minimizing its associated free energy, we find the structural
properties which emerge as the selective pressure is increased and identify a
phase transition from a random topology to a "segregated core" structure, where
a smaller and more densely connected subset of the nodes is responsible for
most of the regulation in the network. This segregated structure is very
similar qualitatively to what is found in gene regulatory networks, where only
a much smaller subset of genes --- those responsible for transcription factors
--- is responsible for global regulation. We obtain the full phase diagram of
the evolutionary process as a function of selective pressure and the average
number of inputs per node. We compare the theoretical predictions with Monte
Carlo simulations of evolved networks and with empirical data for Saccharomyces
cerevisiae and Escherichia coli.Comment: 12 pages, 10 figure
Criticality in conserved dynamical systems: Experimental observation vs. exact properties
Conserved dynamical systems are generally considered to be critical. We study
a class of critical routing models, equivalent to random maps, which can be
solved rigorously in the thermodynamic limit. The information flow is conserved
for these routing models and governed by cyclic attractors. We consider two
classes of information flow, Markovian routing without memory and vertex
routing involving a one-step routing memory. Investigating the respective cycle
length distributions for complete graphs we find log corrections to power-law
scaling for the mean cycle length, as a function of the number of vertices, and
a sub-polynomial growth for the overall number of cycles.
When observing experimentally a real-world dynamical system one normally
samples stochastically its phase space. The number and the length of the
attractors are then weighted by the size of their respective basins of
attraction. This situation is equivalent to `on the fly' generation of routing
tables for which we find power law scaling for the weighted average length of
attractors, for both conserved routing models. These results show that critical
dynamical systems are generically not scale-invariant, but may show power-law
scaling when sampled stochastically. It is hence important to distinguish
between intrinsic properties of a critical dynamical system and its behavior
that one would observe when randomly probing its phase space
The dynamics of correlated novelties
One new thing often leads to another. Such correlated novelties are a
familiar part of daily life. They are also thought to be fundamental to the
evolution of biological systems, human society, and technology. By opening new
possibilities, one novelty can pave the way for others in a process that
Kauffman has called "expanding the adjacent possible". The dynamics of
correlated novelties, however, have yet to be quantified empirically or modeled
mathematically. Here we propose a simple mathematical model that mimics the
process of exploring a physical, biological or conceptual space that enlarges
whenever a novelty occurs. The model, a generalization of Polya's urn, predicts
statistical laws for the rate at which novelties happen (analogous to Heaps'
law) and for the probability distribution on the space explored (analogous to
Zipf's law), as well as signatures of the hypothesized process by which one
novelty sets the stage for another. We test these predictions on four data sets
of human activity: the edit events of Wikipedia pages, the emergence of tags in
annotation systems, the sequence of words in texts, and listening to new songs
in online music catalogues. By quantifying the dynamics of correlated
novelties, our results provide a starting point for a deeper understanding of
the ever-expanding adjacent possible and its role in biological, linguistic,
cultural, and technological evolution
Statistical mechanics of complex networks
Complex networks describe a wide range of systems in nature and society, much
quoted examples including the cell, a network of chemicals linked by chemical
reactions, or the Internet, a network of routers and computers connected by
physical links. While traditionally these systems were modeled as random
graphs, it is increasingly recognized that the topology and evolution of real
networks is governed by robust organizing principles. Here we review the recent
advances in the field of complex networks, focusing on the statistical
mechanics of network topology and dynamics. After reviewing the empirical data
that motivated the recent interest in networks, we discuss the main models and
analytical tools, covering random graphs, small-world and scale-free networks,
as well as the interplay between topology and the network's robustness against
failures and attacks.Comment: 54 pages, submitted to Reviews of Modern Physic
Advances in Functional Decomposition: Theory and Applications
Functional decomposition aims at finding efficient representations for Boolean functions. It is used in many applications, including multi-level logic synthesis, formal verification, and testing.
This dissertation presents novel heuristic algorithms for functional decomposition. These algorithms take advantage of suitable representations of the Boolean functions in order to be efficient.
The first two algorithms compute simple-disjoint and disjoint-support decompositions. They are based on representing the target function by a Reduced Ordered Binary Decision Diagram (BDD). Unlike other BDD-based algorithms, the presented ones can deal with larger target functions and produce more decompositions without requiring expensive manipulations of the representation, particularly BDD reordering.
The third algorithm also finds disjoint-support decompositions, but it is based on a technique which integrates circuit graph analysis and BDD-based decomposition. The combination of the two approaches results in an algorithm which is more robust than a purely BDD-based one, and that improves both the quality of the results and the running time.
The fourth algorithm uses circuit graph analysis to obtain non-disjoint decompositions. We show that the problem of computing non-disjoint decompositions can be reduced to the problem of computing multiple-vertex dominators. We also prove that multiple-vertex dominators can be found in polynomial time. This result is important because there is no known polynomial time algorithm for computing all non-disjoint decompositions of a Boolean function.
The fifth algorithm provides an efficient means to decompose a function at the circuit graph level, by using information derived from a BDD representation. This is done without the expensive circuit re-synthesis normally associated with BDD-based decomposition approaches.
Finally we present two publications that resulted from the many detours we have taken along the winding path of our research
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