Evolutionary algorithms and HP Model for protein structure prediction

Predição de estruturas de proteínas (PSP) é um problema computacionalmente complexo. Modelos simplificados da molécula proteica (como o Modelo HP) e o uso de Algoritmos Evolutivos (AEs) estão entre as principais técnicas investigadas para PSP. Entretanto, a avaliação de uma estrutura representada pelo Modelo HP considera apenas o número de contatos hidrofóbicos, não possibilitando distinguir entre estruturas com o mesmo número de contatos hidrofóbicos. Neste trabalho, é apresentada uma nova formulação multiobjetivo para PSP em Modelo HP. Duas métricas são avaliadas: o número de contatos hidrofóbicos e a distância entre os aminoácidos hidrofóbicos, as quais são tratados pelo AE Multiobjetivo em Tabelas (AEMT). O algoritmo mostrou-se rápido e robusto

Genetic algorithms applied to phasor estimation and frequency tracking in PMU development.

This paper presents an efficient intelligent tool applied to phasor measurements and frequency tracking\ud of fundamental components for PMU application. The estimation task is modeled as an optimization\ud problem in order to use genetic algorithms to search for optimal solutions. Very promising results are\ud presented. This approach is compared to traditional methods considering the IEEE C37.118 standard\ud and the results show that this intelligent tool offers better performance, especially during transient\ud events, considering traditional methods. The proposed approach is implemented in hardware using\ud FPGAs to take advantage of the intrinsic parallelism of genetic algorithms, making it applicable to realtime\ud estimationsCNPqFAPES

Permutation-based Recombination Operator to Node-depth Encoding

AbstractThe node-depth encoding is a representation for evolutionary algorithms applied to tree problems. Its represents trees by storing the nodes and their depth in a proper ordered list. The original formulation of the node-depth encoding has only mutation operators as the search mechanism. Although the representation has this restriction, it has obtained good results with low convergence. Then, this work proposes a specific recombination operator to improve the convergence of the node-depth encoding representation. These operators are based on recombination for permutation representations. An investigation into the bias and heritability of the proposed recombination operator shows that it has a bias towards stars and low heritability. The performance of node-depth encoding with the proposed operator is investigated for the optimal communication spanning tree problem. The results are presented for benchmark instances in the literature. The use of the recombination operator results in a faster convergence than with only mutation operators

Integrating several subpopulation tables with node-depth encoding and strength Pareto for service restoration in large-scale distribution systems.

Network reconfiguration for service restoration in\ud distribution systems is a combinatorial complex optimization\ud problem that usually involves multiple non-linear constraints and\ud objectives functions. For large scale distribution systems, no exact\ud algorithm has found adequate restoration plans in real-time. On\ud the other hand, the combination of Multi-objective Evolutionary\ud Algorithms (MOEAs) with the Node-Depth Encoding (NDE) has\ud been able to efficiently generate adequate restoration plans for\ud relatively large distribution systems (with thousands of buses\ud and switches). The method called MEAN-NDS results from the\ud combination of NDE with a technique of MOEA based on\ud subpopulation tables and the MOEA called NSGA-II. In order\ud to obtain a more efficient MOEA to treat service restoration\ud problem in large scale distribution systems, this paper proposes\ud a new method, which results from the combination of MEANNDS\ud with the MOEA called SPEA-2. The idea is to improve\ud the capacity of MEAN-NDS to explore both the search and\ud objective spaces. Simulations results with distribution systems\ud ranging from 632 to 1,277 switches, have shown that the proposed\ud method found the configurations of lower switching operations,\ud and explores the space of the objective solutions better than the\ud MEAN-NDS, approximating better the Pareto-optimal front

Editorial

The contemporary technological development refers to new scientific and methodological practices mediated by technologies that converge in interdisciplinary contexts that impact the scientific method and imposes new methodological approaches. Modern science is algorithmic, non-deterministic, self-organizing and intertwines phenomena involving Information and Communication Technologies, (Tecnologias da Informação e Comunicação – TICs).O desenvolvimento tecnológico contemporâneo remete a novas práticas científico-metodológicas mediadas por tecnologias que convergem para contextos interdisciplinares que impactam o método científico e impõe novas posturas metodológicas. A ciência moderna é algorítmica, não determinística, auto organizável e entrelaça fenômenos envolvendo Tecnologias da Informação e Comunicação (TICs)

The effect of intra-urban mobility flows on the spatial heterogeneity of social media activity: investigating the response to rainfall events

Although it is acknowledged that urban inequalities can lead to biases in the production of social media data, there is a lack of studies which make an assessment of the effects of intra-urban movements in real-world urban analytics applications, based on social media. This study investigates the spatial heterogeneity of social media with regard to the regular intra-urban movements of residents by means of a case study of rainfall-related Twitter activity in São Paulo, Brazil. We apply a spatial autoregressive model that uses population and income as covariates and intra-urban mobility flows as spatial weights to explain the spatial distribution of the social response to rainfall events in Twitter vis-à-vis rainfall radar data. Results show high spatial heterogeneity in the response of social media to rainfall events, which is linked to intra-urban inequalities. Our model performance (R2=0.80) provides evidence that urban mobility flows and socio-economic indicators are significant factors to explain the spatial heterogeneity of thematic spatiotemporal patterns extracted from social media. Therefore, urban analytics research and practice should consider not only the influence of socio-economic profile of neighborhoods but also the spatial interaction introduced by intra-urban mobility flows to account for spatial heterogeneity when using social media data

Food security:reflections on a complex problem

RESUMO. O combate à má alimentação em todas as suas formas, que também se expressa na epidemia da obesidade, é uma das prioridades da Agenda 2030 e dos Objetivos de Desenvolvimento Sustentável. Este artigo traz elementos sobre insegurança alimentar no Brasil, a partir de temas relativos ao crescimento populacional, mudanças climáticas, biodiversidade e sistemas alimentares tradicionais e regenerativos; trata também do papel dos movimentos sociais para a garantia do Direito Humano à Alimentação Adequada. O Grupo de Pesquisa em Nutrição e Pobreza, o Saúde Planetária Brasil, e o Centro de Inteligência Artificial (C4AI) - Eixo AgriBio, entendem que a retomada organizada e sistêmica das frentes apontadas neste artigo de posicionamento, pode constituir um caminho para a articulação entre pesquisa, serviço e políticas públicas na direção do combate à fome e às demais manifestações da má alimentação, enquanto problema complexo prioritário para a garantia do bem-estar social

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research

Energy restoration in distribution systems by evolutionary algorithm associated with graph chains

O trabalho proposto enfoca a obtenção de planos de restabelecimento de energia de forma automática para a reenergização de redes de distribuição de energia elétrica. Assim sendo, consideram-se situações que deixam regiões do sistema sem energia. A interrupção do serviço pode ser causada por falhas no circuito de distribuição ou pela necessidade de isolar zonas do mesmo para serviços de manutenção. O restabelecimento do fornecimento da energia aos consumidores é um problema com múltiplos objetivos, alguns deles conflitantes. O problema de restabelecimento envolve funções cujas características, em geral, dificultam o uso das técnicas de programação matemática para obter planos de restabelecimento. Além disso, as propostas usando tais metodologias de programação são afetadas intensamente pelo problema de explosão combinatória. Os Algoritmos Evolucionários (AEs) têm apresentado resultados animadores para esse problema. Contudo, tais algoritmos ainda apresentam dificuldades para a rápida obtenção de planos de restabelecimento para redes de tamanho real (grande porte) de maneira a tornar possível sua aplicação em tempo real. Este trabalho propõe uma nova técnica baseada em AEs para o problema de restabelecimento. Essa proposta envolve também um nova forma de representar computacionalmente as redes de distribuição e de modificar a configuração das mesmas. Também é proposto um fluxo de carga específico para ser utilizado com a nova representação. Diversos testes são apresentados utilizando redes com diferentes tamanhos, no intuito de se avaliar a potencialidade da técnica proposta.The proposed research focus on the automatic elaboration of plans for service restoration in electrical distribution systems. So this research considers situations that leave network regions out-of-service. The service interruption may be caused by faults in the distribution circuit or by isolation of circuit zones for maintenance task. The restoration of the energy supply to the consumers is a multiobjective problem, with a certain degree of conflict. The restoration problem considers functions whose characteristics, in general, difficult the use of mathematical programming techniques to obtain restoration plans. Moreover, the approaches using such functions are intensively affected by the combinatorial explosion problem. The Evolutionary Algorithms have shown relevant results for this problem. Nevertheless, these techniques still have difficulties to obtain restoration plans, in a fast manner, for real size networks (i.e., large size). This work proposes a new methodology based on Evolutionary Algorithms. This approach involves also a new way to computationally represent distribution networks and to modify the network configurations. A specific load flow to be used with the new representation is also proposed. Severals tests are shown, using networks with different sizes, to evaluate the potential of the proposed technique