Protein fold recognition using genetic algorithm optimized voting scheme and profile bigram

In biology, identifying the tertiary structure of a protein helps determine its functions. A step towards tertiary structure identification is predicting a protein’s fold. Computational methods have been applied to determine a protein’s fold by assembling information from its structural, physicochemical and/or evolutionary properties. It has been shown that evolutionary information helps improve prediction accuracy. In this study, a scheme is proposed that uses the genetic algorithm (GA) to optimize a weighted voting scheme to improve protein fold recognition. This scheme incorporates k-separated bigram transition probabilities for feature extraction, which are based on the Position Specific Scoring Matrix (PSSM). A set of SVM classifiers are used for initial classification, whereupon their predictions are consolidated using the optimized weighted voting scheme. This scheme has been demonstrated on the Ding and Dubchak (DD), Extended Ding and Dubchak (EDD) and Taguchi and Gromhia (TG) datasets benchmarked data sets

Searching for improvement

Engineering design can be thought of as a search for the best solutions to engineering problems. To perform an effective search, one must distinguish between competing designs and establish a measure of design quality, or fitness. To compare different designs, their features must be adequately described in a well-defined framework, which can mean separating the creative and analytical parts of the design process. By this we mean that a distinction is drawn between coming up with novel design concepts, or architectures, and the process of detailing or refining existing design architecture. In the case of a given design architecture, one can consider the set of all possible designs that could be created by varying its features. If it were possible to measure the fitness of all designs in this set, then one could identify a fitness landscape and search for the best possible solution for this design architecture. In this Chapter, the significance of the interactions between design features in defining the metaphorical fitness landscape is described. This highlights that the efficiency of a search algorithm is inextricably linked to the problem structure (and hence the landscape). Two approaches, namely, Genetic Algorithms (GA) and Robust Engineering Design (RED) are considered in some detail with reference to a case study on improving the design of cardiovascular stents

Computational intelligence approaches to robotics, automation, and control [Volume guest editors]

No abstract available

Metaheuristic design of feedforward neural networks: a review of two decades of research

Over the past two decades, the feedforward neural network (FNN) optimization has been a key interest among the researchers and practitioners of multiple disciplines. The FNN optimization is often viewed from the various perspectives: the optimization of weights, network architecture, activation nodes, learning parameters, learning environment, etc. Researchers adopted such different viewpoints mainly to improve the FNN's generalization ability. The gradient-descent algorithm such as backpropagation has been widely applied to optimize the FNNs. Its success is evident from the FNN's application to numerous real-world problems. However, due to the limitations of the gradient-based optimization methods, the metaheuristic algorithms including the evolutionary algorithms, swarm intelligence, etc., are still being widely explored by the researchers aiming to obtain generalized FNN for a given problem. This article attempts to summarize a broad spectrum of FNN optimization methodologies including conventional and metaheuristic approaches. This article also tries to connect various research directions emerged out of the FNN optimization practices, such as evolving neural network (NN), cooperative coevolution NN, complex-valued NN, deep learning, extreme learning machine, quantum NN, etc. Additionally, it provides interesting research challenges for future research to cope-up with the present information processing era

Development of a multi-objective optimization algorithm based on lichtenberg figures

This doctoral dissertation presents the most important concepts of multi-objective optimization and a systematic review of the most cited articles in the last years of this subject in mechanical engineering. The State of the Art shows a trend towards the use of metaheuristics and the use of a posteriori decision-making techniques to solve engineering problems. This fact increases the demand for algorithms, which compete to deliver the most accurate answers at the lowest possible computational cost. In this context, a new hybrid multi-objective metaheuristic inspired by lightning and Linchtenberg Figures is proposed. The Multi-objective Lichtenberg Algorithm (MOLA) is tested using complex test functions and explicit contrainted engineering problems and compared with other metaheuristics. MOLA outperformed the most used algorithms in the literature: NSGA-II, MOPSO, MOEA/D, MOGWO, and MOGOA. After initial validation, it was applied to two complex and impossible to be analytically evaluated problems. The first was a design case: the multi-objective optimization of CFRP isogrid tubes using the finite element method. The optimizations were made considering two methodologies: i) using a metamodel, and ii) the finite element updating. The last proved to be the best methodology, finding solutions that reduced at least 45.69% of the mass, 18.4% of the instability coefficient, 61.76% of the Tsai-Wu failure index and increased by at least 52.57% the natural frequency. In the second application, MOLA was internally modified and associated with feature selection techniques to become the Multi-objective Sensor Selection and Placement Optimization based on the Lichtenberg Algorithm (MOSSPOLA), an unprecedented Sensor Placement Optimization (SPO) algorithm that maximizes the acquired modal response and minimizes the number of sensors for any structure. Although this is a structural health monitoring principle, it has never been done before. MOSSPOLA was applied to a real helicopter’s main rotor blade using the 7 best-known metrics in SPO. Pareto fronts and sensor configurations were unprecedentedly generated and compared. Better sensor distributions were associated with higher hypervolume and the algorithm found a sensor configuration for each sensor number and metric, including one with 100% accuracy in identifying delamination considering triaxial modal displacements, minimum number of sensors, and noise for all blade sections.Esta tese de doutorado traz os conceitos mais importantes de otimização multi-objetivo e uma revisão sistemática dos artigos mais citados nos últimos anos deste tema em engenharia mecânica. O estado da arte mostra uma tendência no uso de meta-heurísticas e de técnicas de tomada de decisão a posteriori para resolver problemas de engenharia. Este fato aumenta a demanda sobre os algoritmos, que competem para entregar respostas mais precisas com o menor custo computacional possível. Nesse contexto, é proposta uma nova meta-heurística híbrida multi-objetivo inspirada em raios e Figuras de Lichtenberg. O Algoritmo de Lichtenberg Multi-objetivo (MOLA) é testado e comparado com outras metaheurísticas usando funções de teste complexas e problemas restritos e explícitos de engenharia. Ele superou os algoritmos mais utilizados na literatura: NSGA-II, MOPSO, MOEA/D, MOGWO e MOGOA. Após validação, foi aplicado em dois problemas complexos e impossíveis de serem analiticamente otimizados. O primeiro foi um caso de projeto: otimização multi-objetivo de tubos isogrid CFRP usando o método dos elementos finitos. As otimizações foram feitas considerando duas metodologias: i) usando um meta-modelo, e ii) atualização por elementos finitos. A última provou ser a melhor metodologia, encontrando soluções que reduziram pelo menos 45,69% da massa, 18,4% do coeficiente de instabilidade, 61,76% do TW e aumentaram em pelo menos 52,57% a frequência natural. Na segunda aplicação, MOLA foi modificado internamente e associado a técnicas de feature selection para se tornar o Seleção e Alocação ótima de Sensores Multi-objetivo baseado no Algoritmo de Lichtenberg (MOSSPOLA), um algoritmo inédito de Otimização de Posicionamento de Sensores (SPO) que maximiza a resposta modal adquirida e minimiza o número de sensores para qualquer estrutura. Embora isto seja um princípio de Monitoramento da Saúde Estrutural, nunca foi feito antes. O MOSSPOLA foi aplicado na pá do rotor principal de um helicóptero real usando as 7 métricas mais conhecidas em SPO. Frentes de Pareto e configurações de sensores foram ineditamente geradas e comparadas. Melhores distribuições de sensores foram associadas a um alto hipervolume e o algoritmo encontrou uma configuração de sensor para cada número de sensores e métrica, incluindo uma com 100% de precisão na identificação de delaminação considerando deslocamentos modais triaxiais, número mínimo de sensores e ruído para todas as seções da lâmina