Search results for "fitness landscape"

Communities of Local Optima as Funnels in Fitness Landscapes

2016

We conduct an analysis of local optima networks extracted from fitness landscapes of the Kauffman NK model under iterated local search. Applying the Markov Cluster Algorithm for community detection to the local optima networks, we find that the landscapes consist of multiple clusters. This result complements recent findings in the literature that landscapes often decompose into multiple funnels, which increases their difficulty for iterated local search. Our results suggest that the number of clusters as well as the size of the cluster in which the global optimum is located are correlated to the search difficulty of landscapes. We conclude that clusters found by community detection in local…

Memetic Variation Local Search vs. Life-Time Learning in Electrical Impedance Tomography

2009

In this article, various metaheuristics for a numerical optimization problem with application to Electric Impedance Tomography are tested and compared. The experimental setup is composed of a real valued Genetic Algorithm, the Differential Evolution, a self adaptive Differential Evolution recently proposed in literature, and two novel Memetic Algorithms designed for the problem under study. The two proposed algorithms employ different algorithmic philosophies in the field of Memetic Computing. The first algorithm integrates a local search into the operations of the offspring generation, while the second algorithm applies a local search to individuals already generated in the spirit of life-…

The power of formalization and abstraction in evolutionary biologyThe Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces. (2006)…

2007

Differential Evolution with Fitness Diversity Self-adaptation

2009

This chapter proposes the integration of fitness diversity adaptation techniques within the parameter setting of Differential Evolution (DE). The scale factor and crossover rate are encoded within each genotype and self-adaptively updated during the evolution by means of a probabilistic criterion which takes into account the diversity properties of the entire population. The population size is also adaptively controlled by means of a novel technique based on a measurement of the fitness diversity. An extensive experimental setup has been implemented by including multivariate problems and hard to solve fitness landscapes. A comparison of the performance has been conducted by considering both…

Diffusion modeling of COVID-19 under lockdown

2021

Viral immune evasion by sequence variation is a significant barrier to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine design and coronavirus disease-2019 diffusion under lockdown are unpredictable with subsequent waves. Our group has developed a computational model rooted in physics to address this challenge, aiming to predict the fitness landscape of SARS-CoV-2 diffusion using a variant of the bidimensional Ising model (2DIMV) connected seasonally. The 2DIMV works in a closed system composed of limited interaction subjects and conditioned by only temperature changes. Markov chain Monte Carlo method shows that an increase in temperature implicates reduced virus diffusi…

RNA viruses as complex adaptive systems

2004

RNA viruses have high mutation rates and so their populations exist as dynamic and complex mutant distributions. It has been consistently observed that when challenged with a new environment, viral populations adapt following hyperbolic-like kinetics: adaptation is initially very rapid, but then slows down as fitness reaches an asymptotic value. These adaptive dynamics have been explained in terms of populations moving towards the top of peaks on rugged fitness landscapes. Fitness fluctuations of varying magnitude are observed during adaptation. Often the presence of fluctuations in the evolution of physical systems indicates some form of self-organization, or where many components of the s…

Super-fit and population size reduction in compact Differential Evolution

2011

Although Differential Evolution is an efficient and versatile optimizer, it has a wide margin of improvement. During the latest years much effort of computer scientists studying Differential Evolution has been oriented towards the improvement of the algorithmic paradigm by adding and modifying components. In particular, two modifications lead to important improvements to the original algorithmic performance. The first is the super-fit mechanism, that is the injection at the beginning of the optimization process of a solution previously improved by another algorithm. The second is the progressive reduction of the population size during the evolution of the population. Recently, the algorithm…

Nonlinearities in plant RNA virus fitness

2012

Una de las mayores amenazas tanto para la salud humana y animal, como para la agronomía es la emergencia de nuevas enfermedades infecciosas, la mayoría de las cuales están causadas por los virus de RNA. La emergencia viral es un problema complejo que consista en la adquisición de la variación genética, por mutación o recombinación, dentro de la población viral en el huésped reservorio la cual podría facilitar la capacidad de infectar de manera eficiente nuevos huéspedes. Los virus de RNA presentan a una evolucionabilidad extraordinaria por sus grandes tamaños poblacionales, cortos tiempos de generación y altas tasas de mutación y recombinación. Comprender los mecanismos evolutivos que podrí…