2,074 research outputs found
Where are Bottlenecks in NK Fitness Landscapes?
Usually the offspring-parent fitness correlation is used to visualize and
analyze some caracteristics of fitness landscapes such as evolvability. In this
paper, we introduce a more general representation of this correlation, the
Fitness Cloud (FC). We use the bottleneck metaphor to emphasise fitness levels
in landscape that cause local search process to slow down. For a local search
heuristic such as hill-climbing or simulated annealing, FC allows to visualize
bottleneck and neutrality of landscapes. To confirm the relevance of the FC
representation we show where the bottlenecks are in the well-know NK fitness
landscape and also how to use neutrality information from the FC to combine
some neutral operator with local search heuristic
Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein
Can evolvability—the ability to produce adaptive heritable variation—itself evolve through adaptive Darwinian evolution? If so, then Darwinian evolution may help create the conditions that enable Darwinian evolution. Here I propose a framework that is suitable to address this question with available experimental data on adaptive landscapes. I introduce the notion of an evolvability-enhancing mutation, which increases the likelihood that subsequent mutations in an evolving organism, protein, or RNA molecule are adaptive. I search for such mutations in the experimentally characterized and combinatorially complete fitness landscapes of a protein and an RNA molecule. I find that such evolvability-enhancing mutations indeed exist. They constitute a small fraction of all mutations, which shift the distribution of fitness effects of subsequent mutations towards less deleterious mutations, and increase the incidence of beneficial mutations. Evolving populations which experience such mutations can evolve significantly higher fitness. The study of evolvability-enhancing mutations opens many avenues of investigation into the evolution of evolvability
Measuring the Evolvability Landscape to study Neutrality
This theoretical work defines the measure of autocorrelation of evolvability
in the context of neutral fitness landscape. This measure has been studied on
the classical MAX-SAT problem. This work highlight a new characteristic of
neutral fitness landscapes which allows to design new adapted metaheuristic
Scuba Search : when selection meets innovation
We proposed a new search heuristic using the scuba diving metaphor. This
approach is based on the concept of evolvability and tends to exploit
neutrality in fitness landscape. Despite the fact that natural evolution does
not directly select for evolvability, the basic idea behind the scuba search
heuristic is to explicitly push the evolvability to increase. The search
process switches between two phases: Conquest-of-the-Waters and
Invasion-of-the-Land. A comparative study of the new algorithm and standard
local search heuristics on the NKq-landscapes has shown advantage and limit of
the scuba search. To enlighten qualitative differences between neutral search
processes, the space is changed into a connected graph to visualize the
pathways that the search is likely to follow
ES Is More Than Just a Traditional Finite-Difference Approximator
An evolution strategy (ES) variant based on a simplification of a natural
evolution strategy recently attracted attention because it performs
surprisingly well in challenging deep reinforcement learning domains. It
searches for neural network parameters by generating perturbations to the
current set of parameters, checking their performance, and moving in the
aggregate direction of higher reward. Because it resembles a traditional
finite-difference approximation of the reward gradient, it can naturally be
confused with one. However, this ES optimizes for a different gradient than
just reward: It optimizes for the average reward of the entire population,
thereby seeking parameters that are robust to perturbation. This difference can
channel ES into distinct areas of the search space relative to gradient
descent, and also consequently to networks with distinct properties. This
unique robustness-seeking property, and its consequences for optimization, are
demonstrated in several domains. They include humanoid locomotion, where
networks from policy gradient-based reinforcement learning are significantly
less robust to parameter perturbation than ES-based policies solving the same
task. While the implications of such robustness and robustness-seeking remain
open to further study, this work's main contribution is to highlight such
differences and their potential importance
Origin of life in a digital microcosm
While all organisms on Earth descend from a common ancestor, there is no
consensus on whether the origin of this ancestral self-replicator was a one-off
event or whether it was only the final survivor of multiple origins. Here we
use the digital evolution system Avida to study the origin of self-replicating
computer programs. By using a computational system, we avoid many of the
uncertainties inherent in any biochemical system of self-replicators (while
running the risk of ignoring a fundamental aspect of biochemistry). We
generated the exhaustive set of minimal-genome self-replicators and analyzed
the network structure of this fitness landscape. We further examined the
evolvability of these self-replicators and found that the evolvability of a
self-replicator is dependent on its genomic architecture. We studied the
differential ability of replicators to take over the population when competed
against each other (akin to a primordial-soup model of biogenesis) and found
that the probability of a self-replicator out-competing the others is not
uniform. Instead, progenitor (most-recent common ancestor) genotypes are
clustered in a small region of the replicator space. Our results demonstrate
how computational systems can be used as test systems for hypotheses concerning
the origin of life.Comment: 20 pages, 7 figures. To appear in special issue of Philosophical
Transactions of the Royal Society A: Re-Conceptualizing the Origins of Life
from a Physical Sciences Perspectiv
On the Neutrality of Flowshop Scheduling Fitness Landscapes
Solving efficiently complex problems using metaheuristics, and in particular
local searches, requires incorporating knowledge about the problem to solve. In
this paper, the permutation flowshop problem is studied. It is well known that
in such problems, several solutions may have the same fitness value. As this
neutrality property is an important one, it should be taken into account during
the design of optimization methods. Then in the context of the permutation
flowshop, a deep landscape analysis focused on the neutrality property is
driven and propositions on the way to use this neutrality to guide efficiently
the search are given.Comment: Learning and Intelligent OptimizatioN Conference (LION 5), Rome :
Italy (2011
Critical properties of complex fitness landscapes
Evolutionary adaptation is the process that increases the fit of a population
to the fitness landscape it inhabits. As a consequence, evolutionary dynamics
is shaped, constrained, and channeled, by that fitness landscape. Much work has
been expended to understand the evolutionary dynamics of adapting populations,
but much less is known about the structure of the landscapes. Here, we study
the global and local structure of complex fitness landscapes of interacting
loci that describe protein folds or sets of interacting genes forming pathways
or modules. We find that in these landscapes, high peaks are more likely to be
found near other high peaks, corroborating Kauffman's "Massif Central"
hypothesis. We study the clusters of peaks as a function of the ruggedness of
the landscape and find that this clustering allows peaks to form interconnected
networks. These networks undergo a percolation phase transition as a function
of minimum peak height, which indicates that evolutionary trajectories that
take no more than two mutations to shift from peak to peak can span the entire
genetic space. These networks have implications for evolution in rugged
landscapes, allowing adaptation to proceed after a local fitness peak has been
ascended.Comment: 7 pages, 6 figures, requires alifex11.sty. To appear in Proceedings
of 12th International Conference on Artificial Lif
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