scholarly journals Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations

2016 ◽  
Vol 283 (1836) ◽  
pp. 20160984 ◽  
Author(s):  
Héctor Cervera ◽  
Jasna Lalić ◽  
Santiago F. Elena
Keyword(s):  
Fitness Landscape ◽  
Rna Virus ◽  
Viral Evolution ◽  
Basin Of Attraction ◽  
Local Optimum ◽  
Historical Contingency ◽  
Recombination Rates ◽  
Local Optima ◽  
Adaptive Landscapes ◽  
Chance Events

Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an RNA virus move efficiently on a rugged landscape and scape from the basin of attraction of a local optimum. We have evolved a set of Tobacco etch virus genotypes located at increasing distances from a local adaptive optimum in a highly rugged fitness landscape, and we observed that few evolved lineages remained trapped in the local optimum, while many others explored distant regions of the landscape. Most of the diversification in fitness among the evolved lineages was explained by adaptation, while historical contingency and chance events contribution was less important. Our results demonstrate that the ruggedness of adaptive landscapes is not an impediment for RNA viruses to efficiently explore remote parts of it.

scholarly journals An Analysis of the Fitness Landscape of Travelling Salesman Problem

2016 ◽  
Vol 24 (2) ◽  
pp. 347-384 ◽  
Author(s):  
Mohammad-H. Tayarani-N. ◽  
Adam Prügel-Bennett
Keyword(s):  
Principal Component Analysis ◽  
Fitness Landscape ◽  
Travelling Salesman Problem ◽  
Principal Component ◽  
Component Analysis ◽  
Global Optimum ◽  
Local Optimum ◽  
Travelling Salesman ◽  
Local Optima ◽  
Expected Fitness

The fitness landscape of the travelling salesman problem is investigated for 11 different types of the problem. The types differ in how the distances between cities are generated. Many different properties of the landscape are studied. The properties chosen are all potentially relevant to choosing an appropriate search algorithm. The analysis includes a scaling study of the time to reach a local optimum, the number of local optima, the expected probability of reaching a local optimum as a function of its fitness, the expected fitness found by local search and the best fitness, the probability of reaching a global optimum, the distance between the local optima and the global optimum, the expected fitness as a function of the distance from an optimum, their basins of attraction and a principal component analysis of the local optima. The principal component analysis shows the correlation of the local optima in the component space. We show how the properties of the principal components of the local optima change from one problem type to another.

scholarly journals The rugged adaptive landscape of an emerging plant RNA virus

2014 ◽  
Author(s):  
Jasna Lalic ◽  
Santiago F. Elena
Keyword(s):  
Fitness Landscape ◽  
Rna Virus ◽  
Large Population ◽  
Emerging Infectious Diseases ◽  
Evolutionary Process ◽  
Adaptive Landscape ◽  
Evolutionary Potential ◽  
Recombination Rates ◽  
New Host ◽  
Population Sizes

RNA viruses are the main source of emerging infectious diseases owed to the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important parameter, which is usually neglected, is the topography of the fitness landscape, that is, how many fitness maxima exist and how well connected they are, which determines the number of accessible evolutionary pathways. To address this question, we have reconstructed the fitness landscape describing the adaptation of Tobacco etch potyvirus to its new host, Arabidopsis thaliana. Fitness was measured for most of the genotypes in the landscape, showing the existence of peaks and holes. We found prevailing epistatic effects between mutations, with cases of reciprocal sign epistasis being common at latter stages. Therefore, results suggest that the landscape was rugged and holey, with several local fitness peaks and a very limited number of potential neutral paths. The viral genotype fixed at the end of the evolutionary process was not on the global fitness optima but stuck into a suboptimal peak.

scholarly journals Tuning the course of evolution on the biophysical fitness landscape of an RNA virus

2016 ◽  
Author(s):  
Assaf Rotem ◽  
Adrian W.R. Serohijos ◽  
Connie B. Chang ◽  
Joshua T. Wolfe ◽  
Audrey E. Fischer ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Fitness Landscape ◽  
Rna Virus ◽  
Viral Evolution ◽  
Quantitative Description ◽  
Neutralizing Antibody ◽  
Viral Population ◽  
Evolutionary Pathway ◽  
Evolutionary Forces ◽  
Selection For

ABSTRACTPredicting viral evolution remains a major challenge with profound implications for public health. Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics device, the “Evolution Chip”, which propagates millions of independent viral sub-populations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs shape viral evolution.

Advanced Fitness Landscape Analysis and the Performance of Memetic Algorithms

2004 ◽  
Vol 12 (3) ◽  
pp. 303-325 ◽  
Author(s):  
Peter Merz
Keyword(s):  
Local Search ◽  
Fitness Landscape ◽  
Memetic Algorithms ◽  
Fitness Landscapes ◽  
Local Optimum ◽  
Local Optima ◽  
Statistical Measures ◽  
Efficiency And Effectiveness ◽  
Meta Search ◽  
Basins Of Attractions

Memetic algorithms (MAs) have demonstrated very effective in combinatorial optimization. This paper offers explanations as to why this is so by investigating the performance of MAs in terms of efficiency and effectiveness. A special class of MAs is used to discuss efficiency and effectiveness for local search and evolutionary meta-search. It is shown that the efficiency of MAs can be increased drastically with the use of domain knowledge. However, effectiveness highly depends on the structure of the problem. As is well-known, identifying this structure is made easier with the notion of fitness landscapes: the local properties of the fitness landscape strongly influence the effectiveness of the local search while the global properties strongly influence the effectiveness of the evolutionary meta-search. This paper also introduces new techniques for analyzing the fitness landscapes of combinatorial problems; these techniques focus on the investigation of random walks in the fitness landscape starting at locally optimal solutions as well as on the escape from the basins of attractions of current local optima. It is shown for NK-landscapes and landscapes of the unconstrained binary quadratic programming problem (BQP) that a random walk to another local optimum can be used to explain the efficiency of recombination in comparison to mutation. Moreover, the paper shows that other aspects like the size of the basins of attractions of local optima are important for the efficiency of MAs and a local search escape analysis is proposed. These simple analysis techniques have several advantages over previously proposed statistical measures and provide valuable insight into the behaviour of MAs on different kinds of landscapes.

scholarly journals Sales Growth Rate Forecasting Using Improved PSO and SVM

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Xibin Wang ◽  
Junhao Wen ◽  
Shafiq Alam ◽  
Xiang Gao ◽  
Zhuo Jiang ◽  
...  
Keyword(s):  
Growth Rate ◽  
Decisive Role ◽  
Convergence Speed ◽  
Classification Model ◽  
Support Vector ◽  
Local Optimum ◽  
Sales Growth ◽  
Local Optima ◽  
Proposed Model ◽  
Forecasting Performance

Accurate forecast of the sales growth rate plays a decisive role in determining the amount of advertising investment. In this study, we present a preclassification and later regression based method optimized by improved particle swarm optimization (IPSO) for sales growth rate forecasting. We use support vector machine (SVM) as a classification model. The nonlinear relationship in sales growth rate forecasting is efficiently represented by SVM, while IPSO is optimizing the training parameters of SVM. IPSO addresses issues of traditional PSO, such as relapsing into local optimum, slow convergence speed, and low convergence precision in the later evolution. We performed two experiments; firstly, three classic benchmark functions are used to verify the validity of the IPSO algorithm against PSO. Having shown IPSO outperform PSO in convergence speed, precision, and escaping local optima, in our second experiment, we apply IPSO to the proposed model. The sales growth rate forecasting cases are used to testify the forecasting performance of proposed model. According to the requirements and industry knowledge, the sample data was first classified to obtain types of the test samples. Next, the values of the test samples were forecast using the SVM regression algorithm. The experimental results demonstrate that the proposed model has good forecasting performance.

scholarly journals A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 104
Author(s):  
Adam A. Capoferri ◽  
Wei Shao ◽  
Jon Spindler ◽  
John M. Coffin ◽  
Jason W. Rausch ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Rna Virus ◽  
Viral Evolution ◽  
The United States ◽  
Virus Spread ◽  
Immune Pressure ◽  
Viral Genetic Diversity ◽  
Genetic Sampling ◽  
The U.S

COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced immune pressure and prior infections might be expected to influence viral evolution. Accordingly, we conducted a study to characterize the spread of SARS-CoV-2 in the U.S. pre-vaccination, investigate the depth and uniformity of genetic surveillance during this period, and measure and otherwise characterize changing viral genetic diversity, including by comparison with more recently emergent variants of concern (VOCs). In 2020, SARS-CoV-2 spread across the U.S. in three phases distinguishable by peaks in the numbers of infections and shifting geographical distributions. Virus was genetically sampled during this period at an overall rate of ~1.2%, though there was a substantial mismatch between case rates and genetic sampling nationwide. Viral genetic diversity tripled over this period but remained low in comparison to other widespread RNA virus pathogens, and although 54 amino acid changes were detected at frequencies exceeding 5%, linkage among them was not observed. Based on our collective observations, our analysis supports a targeted strategy for worldwide genetic surveillance as perhaps the most sensitive and efficient means of detecting new VOCs.

Local Best Particle Swarm Optimization Using Crown Jewel Defense Strategy

2018 ◽  
pp. 27-52 ◽  
Author(s):  
Jiarui Zhou ◽  
Junshan Yang ◽  
Ling Lin ◽  
Zexuan Zhu ◽  
Zhen Ji
Keyword(s):  
Particle Swarm Optimization ◽  
High Efficiency ◽  
Particle Swarm ◽  
Global Optimum ◽  
Population Diversity ◽  
Local Optimum ◽  
Swarm Optimization ◽  
Local Optima ◽  
Von Neumann ◽  
Swarm Intelligence Algorithm

Particle swarm optimization (PSO) is a swarm intelligence algorithm well known for its simplicity and high efficiency on various problems. Conventional PSO suffers from premature convergence due to the rapid convergence speed and lack of population diversity. It is easy to get trapped in local optima. For this reason, improvements are made to detect stagnation during the optimization and reactivate the swarm to search towards the global optimum. This chapter imposes the reflecting bound-handling scheme and von Neumann topology on PSO to increase the population diversity. A novel crown jewel defense (CJD) strategy is introduced to restart the swarm when it is trapped in a local optimum region. The resultant algorithm named LCJDPSO-rfl is tested on a group of unimodal and multimodal benchmark functions with rotation and shifting. Experimental results suggest that the LCJDPSO-rfl outperforms state-of-the-art PSO variants on most of the functions.

scholarly journals The topology of evolutionary novelty and innovation in macroevolution

2017 ◽  
Vol 372 (1735) ◽  
pp. 20160422 ◽  
Author(s):  
Douglas H. Erwin
Keyword(s):  
Evolutionary Theory ◽  
Fitness Landscape ◽  
Conceptual Metaphor ◽  
Functional Trait ◽  
Evolutionary Change ◽  
Evolutionary Novelty ◽  
Adaptive Landscapes ◽  
George Gaylord Simpson

Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arising by accessing previously inaccessible or difficult to reach regions of a space. Here I discuss the nature of evolutionary novelty and innovation within the context of evolutionary spaces, and argue that the primacy of search as a conceptual metaphor ignores the generation of new spaces as well as other changes that have played important evolutionary roles. This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’.

Biophysical determinants of mutational robustness in a viral molecular fitness landscape

2017 ◽  
Author(s):  
Manasi A. Pethe ◽  
Aliza B. Rubenstein ◽  
Dmitri Zorine ◽  
Sagar D. Khare
Keyword(s):  
Fitness Landscape ◽  
Rna Virus ◽  
Fitness Landscapes ◽  
Viral Fitness ◽  
Mutational Robustness ◽  
Hcv Protease ◽  
Viral Polyprotein ◽  
Biophysical Interactions ◽  
Proteins And Peptides

Biophysical interactions between proteins and peptides are key determinants of genotype-fitness landscapes, but an understanding of how molecular structure and residue-level energetics at protein-peptide interfaces shape functional landscapes remains elusive. Combining information from yeast-based library screening, next-generation sequencing and structure-based modeling, we report comprehensive sequence-energetics-function mapping of the specificity landscape of the Hepatitis C Virus (HCV) NS3/4A protease, whose function — site-specific cleavages of the viral polyprotein — is a key determinant of viral fitness. We elucidate the cleavability of 3.2 million substrate variants by the HCV protease and find extensive clustering of cleavable and uncleavable motifs in sequence space indicating mutational robustness, and thereby providing a plausible molecular mechanism to buffer the effects of low replicative fidelity of this RNA virus. Specificity landscapes of known drug-resistant variants are similarly clustered. Our results highlight the key and constraining role of molecular-level energetics in shaping plateau-like fitness landscapes from quasispecies theory.

Effective Algorithms for Scheduling Workflow Tasks on Mobile Clouds

2020 ◽  
Vol 29 (16) ◽  
pp. 2050255
Author(s):  
Heng Li ◽  
Yaoqin Zhu ◽  
Meng Zhou ◽  
Yun Dong
Keyword(s):  
Mobile Devices ◽  
Solution Space ◽  
Iterated Local Search ◽  
Mobile Cloud ◽  
Local Optimum ◽  
Perturbation Operator ◽  
Evolutionary Mechanisms ◽  
Local Optima ◽  
Np Hard Problem ◽  
Workflow Tasks

In mobile cloud computing, the computing resources of mobile devices can be integrated to execute complicated applications, in order to tackle the problem of insufficient resources of mobile devices. Such applications are, in general, characterized as workflows. Scheduling workflow tasks on a mobile cloud system consisting of heterogeneous mobile devices is a NP-hard problem. In this paper, intelligent algorithms, e.g., particle swarm optimization (PSO) and simulated annealing (SA), are widely used to solve this problem. However, both PSO and SA suffer from the limitation of easily being trapped into local optima. Since these methods rely on their evolutionary mechanisms to explore new solutions in solution space, the search procedure converges once getting stuck in local optima. To address this limitation, in this paper, we propose two effective metaheuristic algorithms that incorporate the iterated local search (ILS) strategy into PSO and SA algorithms, respectively. In case that the intelligent algorithm converges to a local optimum, the proposed algorithms use a perturbation operator to explore new solutions and use the newly explored solutions to start a new round of evolution in the solution space. This procedure is iterated until no better solutions can be explored. Experimental results show that by incorporating the ILS strategy, our proposed algorithms outperform PSO and SA in reducing workflow makespans. In addition, the perturbation operator is beneficial for improving the effectiveness of scheduling algorithms in exploring high-quality scheduling solutions.

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