225 research outputs found
From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
Understanding how genotypes map onto phenotypes, fitness, and eventually
organisms is arguably the next major missing piece in a fully predictive theory
of evolution. We refer to this generally as the problem of the
genotype-phenotype map. Though we are still far from achieving a complete
picture of these relationships, our current understanding of simpler questions,
such as the structure induced in the space of genotypes by sequences mapped to
molecular structures, has revealed important facts that deeply affect the
dynamical description of evolutionary processes. Empirical evidence supporting
the fundamental relevance of features such as phenotypic bias is mounting as
well, while the synthesis of conceptual and experimental progress leads to
questioning current assumptions on the nature of evolutionary dynamics-cancer
progression models or synthetic biology approaches being notable examples. This
work delves into a critical and constructive attitude in our current knowledge
of how genotypes map onto molecular phenotypes and organismal functions, and
discusses theoretical and empirical avenues to broaden and improve this
comprehension. As a final goal, this community should aim at deriving an
updated picture of evolutionary processes soundly relying on the structural
properties of genotype spaces, as revealed by modern techniques of molecular
and functional analysis.Comment: 111 pages, 11 figures uses elsarticle latex clas
Online Diversity Control in Symbolic Regression via a Fast Hash-based Tree Similarity Measure
Diversity represents an important aspect of genetic programming, being
directly correlated with search performance. When considered at the genotype
level, diversity often requires expensive tree distance measures which have a
negative impact on the algorithm's runtime performance. In this work we
introduce a fast, hash-based tree distance measure to massively speed-up the
calculation of population diversity during the algorithmic run. We combine this
measure with the standard GA and the NSGA-II genetic algorithms to steer the
search towards higher diversity. We validate the approach on a collection of
benchmark problems for symbolic regression where our method consistently
outperforms the standard GA as well as NSGA-II configurations with different
secondary objectives.Comment: 8 pages, conference, submitted to congress on evolutionary
computatio
Evolvability and rate of evolution in evolutionary computation
Evolvability has emerged as a research topic in both natural and computational evolution. It is a notion put forward to investigate the fundamental mechanisms that enable a system to evolve. A number of hypotheses have been proposed in modern biological research based on the examination of various mechanisms in the biosphere for their contribution to evolvability. Therefore, it is intriguing to try to transfer new discoveries from Biology to and test them in Evolutionary Computation (EC) systems, so that computational models would be improved and a better understanding of general evolutional mechanisms is achieved. -- Rate of evolution comes in different flavors in natural and computational evolution. Specifically, we distinguish the rate of fitness progression from that of genetic substitutions. The former is a common concept in EC since the ability to explicitly quantify the fitness of an evolutionary individual is one of the most important differences between computational systems and natural systems. Within the biological research community, the definition of rate of evolution varies, depending on the objects being examined such as gene sequences, proteins, tissues, etc. For instance, molecular biologists tend to use the rate of genetic substitutions to quantify how fast evolution proceeds at the genetic level. This concept of rate of evolution focuses on the evolutionary dynamics underlying fitness development, due to the inability to mathematically define fitness in a natural system. In EC, the rate of genetic substitutions suggests an unconventional and potentially powerful method to measure the rate of evolution by accessing lower levels of evolutionary dynamics. -- Central to this thesis is our new definition of rate of evolution in EC. We transfer the method of measurement of the rate of genetic substitutions from molecular biology to EC. The implementation in a Genetic Programming (GP) system shows that such measurements can indeed be performed and reflect well how evolution proceeds. Below the level of fitness development it provides observables at the genetic level of a GP population during evolution. We apply this measurement method to investigate the effects of four major configuration parameters in EC, i.e., mutation rate, crossover rate, tournament selection size, and population size, and show that some insights can be gained into the effectiveness of these parameters with respect to evolution acceleration. Further, we observe that population size plays an important role in determining the rate of evolution. We formulate a new indicator based on this rate of evolution measurement to adjust population size dynamically during evolution. Such a strategy can stabilize the rate of genetic substitutions and effectively improve the performance of a GP system over fixed-size populations. This rate of evolution measure also provides an avenue to study evolvability, since it captures how the two sides of evolvability, i.e., variability and neutrality, interact and cooperate with each other during evolution. We show that evolvability can be better understood in the light of this interplay and how this can be used to generate adaptive phenotypic variation via harnessing random genetic variation. The rate of evolution measure and the adaptive population size scheme are further transferred to a Genetic Algorithm (GA) to solve a real world application problem - the wireless network planning problem. Computer simulation of such an application proves that the adaptive population size scheme is able to improve a GA's performance against conventional fixed population size algorithms
Evolvability-guided Optimization of Linear Deformation Setups for Evolutionary Design Optimization
Richter A. Evolvability-guided Optimization of Linear Deformation Setups for Evolutionary Design Optimization. Bielefeld: Universität Bielefeld; 2019.Andreas Richter gratefully acknowledges the financial support from Honda Research Institute Europe (HRI-EU).This thesis targets efficient solutions for optimal representation setups for evolutionary design optimization problems. The representation maps the abstract parameters of an optimizer to a meaningful variation of the design model, e.g., the shape of a car. Thereby, it determines the convergence speed to and the quality of the final result. Thus, engineers are eager to employ well-tuned representations to achieve high-quality design solutions. But, setting up optimal representations is a cumbersome process because the setup procedure requires detailed knowledge about the objective functions, e.g., a fluid dynamics simulation, and the parameters of the employed representation itself. Thus, we target efficient routines to set up representations automatically to support engineers from their tedious, partly manual work.
Inspired by the concept of evolvability, we present novel quality criteria for the evaluation of linear deformations commonly applied as representations. We define and analyze the criteria variability, regularity, and improvement potential which measure the expected quality and convergence speed of an evolutionary design optimization process based on the linear deformation setup. Moreover, we target the efficient optimization of deformation setups with respect to these three criteria. In dynamic design optimization scenarios a suitable compromise between exploration and exploitation is crucial for efficient solutions. We discuss the construction of optimal compromises for these dynamic scenarios with our criteria because they characterize exploration and exploitation.
As a result an engineer can initialize and adjust the deformation setup for improved convergence speed of a design process and for enhanced quality of the design solutions with our methods
Metabolite essentiality elucidates robustness of Escherichia coli metabolism
Complex biological systems are very robust to genetic and environmental
changes at all levels of organization. Many biological functions of Escherichia
coli metabolism can be sustained against single-gene or even multiple-gene
mutations by using redundant or alternative pathways. Thus, only a limited
number of genes have been identified to be lethal to the cell. In this regard,
the reaction-centric gene deletion study has a limitation in understanding the
metabolic robustness. Here, we report the use of flux-sum, which is the
summation of all incoming or outgoing fluxes around a particular metabolite
under pseudo-steady state conditions, as a good conserved property for
elucidating such robustness of E. coli from the metabolite point of view. The
functional behavior, as well as the structural and evolutionary properties of
metabolites essential to the cell survival, was investigated by means of a
constraints-based flux analysis under perturbed conditions. The essential
metabolites are capable of maintaining a steady flux-sum even against severe
perturbation by actively redistributing the relevant fluxes. Disrupting the
flux-sum maintenance was found to suppress cell growth. This approach of
analyzing metabolite essentiality provides insight into cellular robustness and
concomitant fragility, which can be used for several applications, including
the development of new drugs for treating pathogens.Comment: Supplements available at
http://stat.kaist.ac.kr/publication/2007/PJKim_pnas_supplement.pd
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