Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome

<p>Abstract</p> <p>Background</p> <p>Fourier transforms and their associated power spectra are used for detecting periodicities and protein-coding genes and is generally regarded as a well established technique. Many of the periodicities which have been found with this method are quite well understood such as the periodicity of 3 nt which is associated to codon usage. But what is the origin of the peculiar frequency multiples <it>k</it>/21 which were reported for a tiny section of chromosome 2 in <it>P. falciparum</it>? Are these present in other chromosomes and perhaps in related organisms? And how should we interpret fractional periodicities in genomes?</p> <p>Results</p> <p>We applied the binary indicator power spectrum to all chromosomes of <it>P. falciparum</it>, and found that the frequency overtones <it>k</it>/21 are present only in non-coding sections. We did not find such frequency overtones in any other related genomes. Furthermore, the frequency overtones were identified as artifacts of the way the genome is encoded into a numerical sequence, that is, they are frequency aliases. By choosing a different way to encode the sequence the overtones do not appear. In view of these results, we revisited early applications of this technique to proteins where frequency overtones were reported.</p> <p>Conclusions</p> <p>Some authors hinted recently at the possibility of mapping artifacts and frequency aliases in power spectra. However, in the case of <it>P. falciparum</it> the frequency aliases are particularly strong and can mask the 1/3 frequency which is used for gene detecting. This shows that albeit being a well known technique, with a long history of application in proteins, few researchers seem to be aware of the problems represented by frequency aliases.</p

Lyapunov design of a simple step-size adaptation strategy based on success

A simple success-based step-size adaptation rule for singleparent Evolution Strategies is formulated, and the setting of the corresponding parameters is considered. Theoretical convergence on the class of strictly unimodal functions of one variable that are symmetric around the optimum is investigated using a stochastic Lyapunov function method developed by Semenov and Terkel [5] in the context of martingale theory. General expressions for the conditional expectations of the next values of step size and distance to the optimum under (1 +, λ)-selection are analytically derived, and an appropriate Lyapunov function is constructed. Convergence rate upper bounds, as well as adaptation parameter values, are obtained through numerical optimization for increasing values of λ. By selecting the number of offspring that minimizes the bound on the convergence rate with respect to the number of function evaluations, all strategy parameter values result from the analysis

CardNutri:A Software of Weekly Menus Nutritional Elaboration for Scholar Feeding Applying Evolutionary Computation

This paper aims to present and evaluate a software that uses an evolutionary strategy to design weekly nutritional menus for School Feeding. The software ensures the nutritional needs of students and also minimizes the total cost of the menu. We based our nutritional needs on the Brazilian National School Feeding Programme (PNAE). This program takes into account: (i) the age of the student; (ii) some preparations issues as color, consistency and, variety; and also (iii) the maximum amount to be paid per meal. Our software generates, in less than five minutes, a set of menus, and the nutritionist can choose the menu that suits his/her best. We evaluate our algorithm using the Weighted-Sum approach, and our results show that the obtained 5-days menus using the proposed methodology not only comply with the restrictions imposed by the authorities but also produce inexpensive and healthy menus. We also appraise the software itself using an opinion pool among nine nutritionists. The professionals considered our software above expectations

A strategy for clustering students minimizing the number of bus stops for solving the school bus routing problem

In this work we tackle the bus stop selection step for the School Bus Routing Problem (SBRP). Our goal is to minimize the number of bus stops in order to assign all students to a bus stop respecting a home-to-bus-stop walking distance constraint. Our strategy creates a large number of possible bus stops points in a road network and uses a pseudo-random constructive heuristic algorithm to assign students to a bus stops. Our approach is tested on a real georeferenced data of a Brazilian city and is compared with a different methodology. Results demonstrate that the proposed approach is able to find good solutions for this optimization problem. Besides, the higher the number of possible points to install bus stops, the smaller is the number of bus stops required to attend all students

A GRASP-based heuristic for allocating the roadside infrastructure maximizing the number of distinct vehicles experiencing contact opportunities

In this work the allocation of Roadside Units (RSUs) in a V2I network is modeled as a Maximum Coverage Problem. The main objective is to maximize the number of distinct vehicles contacting the infrastructure. Two different approaches are presented to solve the problem. The first one is an ILP model that can found optimal solutions or give sharp upper and lower bounds for the problem. The second one is a GRASP-based heuristic that can found close-to-optimal solutions. The GRASP-based heuristic is compared with a previous work achieving better results. Furthermore, a new metric to measure the efficiency of a Deployment strategy is presented

Desenvolvimento de um Algoritmo de Decomposição Híbrido Bioinspirado Baseado em Baleias e Estratégias de Evolução Diferencial para Otimização Multiobjetivo

A Multiobjective Optimization Problem (MOP) requires the optimization of several objective functions simultaneously, usually in conflict with each other. One of the most efficient algorithms for solving MOPs is MOEA/D (Multiobjective Evolutionary Algorithm Based on Decomposition), which decomposes a MOP into single-objective optimization subproblems and solves them using information from neighboring subproblems. MOEA/D variants with other evolutionary operators have emerged over the years, improving their efficiency in various MOPs. Recently, the IWOA (Improved Whale Optimization Algorithm) was proposed, an optimization algorithm bioinspired by the whale hunting method hybridized with Differential Evolution, which presented excellent results in single-objective optimization problems. This work proposes the MOEA/D-IWOA algorithm, which associates characteristics of the evolutionary operators of the IWOA to MOEA/D. Computational experiments were accomplished to analyze the performance of the MOEA/D-IWOA in benchmark MOPs suites. The results were compared with those obtained by the MOEA/D, Non-dominated Sorting Genetic Algorithm II (NSGA-II), Third Evolution Step of Generalized Differential Evolution (GDE3), Improving the Strength Pareto Evolutionary Algorithm (SPEA2), and Indicator-Based Evolutionary Algorithm (IBEA) algorithms in the Hypervolume and Inverted Generational Distance Plus (IGD+) indicators. The MOEA/D-IWOA proved to be competitive, with a good performance profile, in addition to presenting the best results in some POMs.Um Problema de Otimização Multiobjetivo (POM) requer a otimização de várias funções objetivo simultaneamente, geralmente conflitantes entre si. Um dos algoritmos mais eficientes para resolver POMs é o MOEA/D (Multiobjective Evolutionary Algorithm Based on Decomposition), que decompõe um POM em subproblemas de otimização monobjetivo, isto é, com uma única função objetivo a ser minimizada, e os resolve usando informações de subproblemas vizinhos. Variantes do MOEA/D com outros operadores evolutivos surgiram ao longo dos anos, melhorando sua eficiência em diversos POMs. Recentemente foi proposto o IWOA (Improved Whale Optimization Algorithm), um algoritmo de otimização bioinspirado no método de caça das baleias hibridizado com Evolução Diferencial que apresentou ótimos resultados em problemas de otimização monobjetivo. Esse trabalho propõe o algoritmo MOEA/D-IWOA, que extende o IWOA para resolver POMs associando características dos seus operadores evolutivos ao MOEA/D. Experimentos computacionais para analisar o desempenho do MOEA/D-IWOA em POMs benchmark foram realizados e os resultados comparados aos obtidos pelos algoritmos bem conhecidos da literatura, a saber, MOEA/D, Non-dominated Sorting Genetic Algorithm II (NSGA-II), Third Evolution Step of Generalized Differential Evolution (GDE3), Improving the Strength Pareto Evolutionary Algorithm (SPEA2) e Indicator-Based Evolutionary Algorithm (IBEA) nos indicadores Hypervolume e Inverted Generational Distance Plus (IGD+). O MOEA/D-IWOA se mostrou competitivo, com bom perfil de desempenho, além de apresentar os melhores resultados em alguns POMs

Solving security constrained optimal power flow problems:a hybrid evolutionary approach

A hybrid population-based metaheuristic, Hybrid Canonical Differential Evolutionary Particle Swarm Optimization (hC-DEEPSO), is applied to solve Security Constrained Optimal Power Flow (SCOPF) problems. Despite the inherent difficulties of tackling these real-world problems, they must be solved several times a day taking into account operation and security conditions. A combination of the C-DEEPSO metaheuristic coupled with a multipoint search operator is proposed to better exploit the search space in the vicinity of the best solution found so far by the current population in the first stages of the search process. A simple diversity mechanism is also applied to avoid premature convergence and to escape from local optima. A experimental design is devised to fine-tune the parameters of the proposed algorithm for each instance of the SCOPF problem. The effectiveness of the proposed hC-DEEPSO is tested on the IEEE 57-bus, IEEE 118-bus and IEEE 300-bus standard systems. The numerical results obtained by hC-DEEPSO are compared with other evolutionary methods reported in the literature to prove the potential and capability of the proposed hC-DEEPSO for solving the SCOPF at acceptable economical and technical levels