Improvements in the score matrix calculation method using parallel score estimating algorithm

The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.

Optimizing urban traffic flow using genetic algorithm with petri net analysis as fitness function

This paper describes a new methodology adopted for urban traffic stream optimization. By using Petri net analysis as fitness function of a Genetic Algorithm, an entire urban road network is controlled in real time. With the advent of new technologies that have been published, particularly focusing on communications among vehicles and roads infrastructures, we consider that vehicles can provide their positions and their destinations to a central server so that it is able to calculate the best route for one of them. Our tests concentrate on comparisons between the proposed approach and other algorithms that are currently used for the same purpose, being possible to conclude that our algorithm optimizes traffic in a relevant manner.

MR-Radix: a multi-relational data mining algorithm

Background: Once multi-relational approach has emerged as an alternative for analyzing structured data such as relational databases, since they allow applying data mining in multiple tables directly, thus avoiding expensive joining operations and semantic losses, this work proposes an algorithm with multi-relational approach. Methods: Aiming to compare traditional approach performance and multi-relational for mining association rules, this paper discusses an empirical study between PatriciaMine - an traditional algorithm - and its corresponding multi-relational proposed, MR-Radix. Results: This work showed advantages of the multi-relational approach in performance over several tables, which avoids the high cost for joining operations from multiple tables and semantic losses. The performance provided by the algorithm MR-Radix shows faster than PatriciaMine, despite handling complex multi-relational patterns. The utilized memory indicates a more conservative growth curve for MR-Radix than PatriciaMine, which shows the increase in demand of frequent items in MR-Radix does not result in a significant growth of utilized memory like in PatriciaMine. Conclusion: The comparative study between PatriciaMine and MR-Radix confirmed efficacy of the multi-relational approach in data mining process both in terms of execution time and in relation to memory usage. Besides that, the multi-relational proposed algorithm, unlike other algorithms of this approach, is efficient for use in large relational databases.

Reconfiguration of radial electric power distribution system via a scatter search algorithm

In this paper, to solve the reconfiguration problem of radial distribution systems a scatter search, which is a metaheuristic-based algorithm, is proposed. In the codification process of this algorithm a structure called node-depth representation is used. It then, via the operators and from the electrical power system point of view, results finding only radial topologies. In order to show the effectiveness, usefulness, and the efficiency of the proposed method, a commonly used test system, 135-bus, and a practical system, a part of Sao Paulo state's distribution network, 7052 bus, are conducted. Results confirm the efficiency of the proposed algorithm that can find high quality solutions satisfying all the physical and operational constraints of the problem.

Multiobjective Genetic Algorithm applied to dengue control

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A self-learning simulated annealing algorithm for global optimizations of electromagnetic devices

A self-learning simulated annealing algorithm is developed by combining the characteristics of simulated annealing and domain elimination methods. The algorithm is validated by using a standard mathematical function and by optimizing the end region of a practical power transformer. The numerical results show that the CPU time required by the proposed method is about one third of that using conventional simulated annealing algorithm.