Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Optimización del sistema de transporte en el colegio The English School

La optimización de sistemas y modelos se ha convertido en uno de los factores más importantes a la hora de buscar la mayor eficiencia de un proceso. Este concepto no es ajeno al transporte escolar, ambiente que cambia constantemente al ritmo de las necesidades de sus clientes, y que responde ante una fuerte responsabilidad frente a sus usuarios, los niños que hacen uso del servicio, en cuanto al cumplimiento de tiempos y seguridad, mientras busca constantemente la reducción de costos. Este proyecto expone las problemáticas presentadas en The English School en esta área y propone un modelo de optimización simple que permitirá notables mejoras en términos de tiempos y costos, de tal forma que genere beneficios para la institución en términos financieros y de satisfacción al cliente. Por medio de la implementación de este modelo será posible identificar errores comunes del proceso, se identificarán soluciones prácticas de fácil aplicación en el manejo del transporte y se presentarán los resultados obtenidos en la muestra utilizada para desarrollar el proyecto.

PSO assisted NURB Neural Network Identification

A system identification algorithm is introduced for Hammerstein systems that are modelled using a non-uniform rational B-spline (NURB) neural network. The proposed algorithm consists of two successive stages. First the shaping parameters in NURB network are estimated using a particle swarm optimization (PSO) procedure. Then the remaining parameters are estimated by the method of the singular value decomposition (SVD). Numerical examples are utilized to demonstrate the efficacy of the proposed approach.

An elastic net orthogonal forward regression algorithm

In this paper we propose an efficient two-level model identification method for a large class of linear-in-the-parameters models from the observational data. A new elastic net orthogonal forward regression (ENOFR) algorithm is employed at the lower level to carry out simultaneous model selection and elastic net parameter estimation. The two regularization parameters in the elastic net are optimized using a particle swarm optimization (PSO) algorithm at the upper level by minimizing the leave one out (LOO) mean square error (LOOMSE). Illustrative examples are included to demonstrate the effectiveness of the new approaches.

Online modeling with tunable RBF network

In this paper, we propose a novel online modeling algorithm for nonlinear and nonstationary systems using a radial basis function (RBF) neural network with a fixed number of hidden nodes. Each of the RBF basis functions has a tunable center vector and an adjustable diagonal covariance matrix. A multi-innovation recursive least square (MRLS) algorithm is applied to update the weights of RBF online, while the modeling performance is monitored. When the modeling residual of the RBF network becomes large in spite of the weight adaptation, a node identified as insignificant is replaced with a new node, for which the tunable center vector and diagonal covariance matrix are optimized using the quantum particle swarm optimization (QPSO) algorithm. The major contribution is to combine the MRLS weight adaptation and QPSO node structure optimization in an innovative way so that it can track well the local characteristic in the nonstationary system with a very sparse model. Simulation results show that the proposed algorithm has significantly better performance than existing approaches.

Elastic-net prefiltering for two-class classification

A two-stage linear-in-the-parameter model construction algorithm is proposed aimed at noisy two-class classification problems. The purpose of the first stage is to produce a prefiltered signal that is used as the desired output for the second stage which constructs a sparse linear-in-the-parameter classifier. The prefiltering stage is a two-level process aimed at maximizing a model's generalization capability, in which a new elastic-net model identification algorithm using singular value decomposition is employed at the lower level, and then, two regularization parameters are optimized using a particle-swarm-optimization algorithm at the upper level by minimizing the leave-one-out (LOO) misclassification rate. It is shown that the LOO misclassification rate based on the resultant prefiltered signal can be analytically computed without splitting the data set, and the associated computational cost is minimal due to orthogonality. The second stage of sparse classifier construction is based on orthogonal forward regression with the D-optimality algorithm. Extensive simulations of this approach for noisy data sets illustrate the competitiveness of this approach to classification of noisy data problems.

Efficiency of evolutionary algorithms in water network pipe sizing

The pipe sizing of water networks via evolutionary algorithms is of great interest because it allows the selection of alternative economical solutions that meet a set of design requirements. However, available evolutionary methods are numerous, and methodologies to compare the performance of these methods beyond obtaining a minimal solution for a given problem are currently lacking. A methodology to compare algorithms based on an efficiency rate (E) is presented here and applied to the pipe-sizing problem of four medium-sized benchmark networks (Hanoi, New York Tunnel, GoYang and R-9 Joao Pessoa). E numerically determines the performance of a given algorithm while also considering the quality of the obtained solution and the required computational effort. From the wide range of available evolutionary algorithms, four algorithms were selected to implement the methodology: a PseudoGenetic Algorithm (PGA), Particle Swarm Optimization (PSO), a Harmony Search and a modified Shuffled Frog Leaping Algorithm (SFLA). After more than 500,000 simulations, a statistical analysis was performed based on the specific parameters each algorithm requires to operate, and finally, E was analyzed for each network and algorithm. The efficiency measure indicated that PGA is the most efficient algorithm for problems of greater complexity and that HS is the most efficient algorithm for less complex problems. However, the main contribution of this work is that the proposed efficiency ratio provides a neutral strategy to compare optimization algorithms and may be useful in the future to select the most appropriate algorithm for different types of optimization problems.

Estratégias de aplicações sequenciais e paralelas da metaheurística otimização por enxame de partículas ao problema do caixeiro viajante

Particle Swarm Optimization is a metaheuristic that arose in order to simulate the behavior of a number of birds in flight, with its random movement locally, but globally determined. This technique has been widely used to address non-liner continuous problems and yet little explored in discrete problems. This paper presents the operation of this metaheuristic, and propose strategies for implementation of optimization discret problems as form of execution parallel as sequential. The computational experiments were performed to instances of the TSP, selected in the library TSPLIB contenct to 3038 nodes, showing the improvement of performance of parallel methods for their sequential versions, in executation time and results

Análise e otimização de superfícies seletivas de Frequência utilizando redes neurais artificiais e algoritmos de otimização natural

The bidimensional periodic structures called frequency selective surfaces have been well investigated because of their filtering properties. Similar to the filters that work at the traditional radiofrequency band, such structures can behave as band-stop or pass-band filters, depending on the elements of the array (patch or aperture, respectively) and can be used for a variety of applications, such as: radomes, dichroic reflectors, waveguide filters, artificial magnetic conductors, microwave absorbers etc. To provide high-performance filtering properties at microwave bands, electromagnetic engineers have investigated various types of periodic structures: reconfigurable frequency selective screens, multilayered selective filters, as well as periodic arrays printed on anisotropic dielectric substrates and composed by fractal elements. In general, there is no closed form solution directly from a given desired frequency response to a corresponding device; thus, the analysis of its scattering characteristics requires the application of rigorous full-wave techniques. Besides that, due to the computational complexity of using a full-wave simulator to evaluate the frequency selective surface scattering variables, many electromagnetic engineers still use trial-and-error process until to achieve a given design criterion. As this procedure is very laborious and human dependent, optimization techniques are required to design practical periodic structures with desired filter specifications. Some authors have been employed neural networks and natural optimization algorithms, such as the genetic algorithms and the particle swarm optimization for the frequency selective surface design and optimization. This work has as objective the accomplishment of a rigorous study about the electromagnetic behavior of the periodic structures, enabling the design of efficient devices applied to microwave band. For this, artificial neural networks are used together with natural optimization techniques, allowing the accurate and efficient investigation of various types of frequency selective surfaces, in a simple and fast manner, becoming a powerful tool for the design and optimization of such structures

Análise e síntese de antenas e superfícies seletivas de frequência utilizando computação evolucionária e inteligência de enxames

The frequency selective surfaces, or FSS (Frequency Selective Surfaces), are structures consisting of periodic arrays of conductive elements, called patches, which are usually very thin and they are printed on dielectric layers, or by openings perforated on very thin metallic surfaces, for applications in bands of microwave and millimeter waves. These structures are often used in aircraft, missiles, satellites, radomes, antennae reflector, high gain antennas and microwave ovens, for example. The use of these structures has as main objective filter frequency bands that can be broadcast or rejection, depending on the specificity of the required application. In turn, the modern communication systems such as GSM (Global System for Mobile Communications), RFID (Radio Frequency Identification), Bluetooth, Wi-Fi and WiMAX, whose services are highly demanded by society, have required the development of antennas having, as its main features, and low cost profile, and reduced dimensions and weight. In this context, the microstrip antenna is presented as an excellent choice for communications systems today, because (in addition to meeting the requirements mentioned intrinsically) planar structures are easy to manufacture and integration with other components in microwave circuits. Consequently, the analysis and synthesis of these devices mainly, due to the high possibility of shapes, size and frequency of its elements has been carried out by full-wave models, such as the finite element method, the method of moments and finite difference time domain. However, these methods require an accurate despite great computational effort. In this context, computational intelligence (CI) has been used successfully in the design and optimization of microwave planar structures, as an auxiliary tool and very appropriate, given the complexity of the geometry of the antennas and the FSS considered. The computational intelligence is inspired by natural phenomena such as learning, perception and decision, using techniques such as artificial neural networks, fuzzy logic, fractal geometry and evolutionary computation. This work makes a study of application of computational intelligence using meta-heuristics such as genetic algorithms and swarm intelligence optimization of antennas and frequency selective surfaces. Genetic algorithms are computational search methods based on the theory of natural selection proposed by Darwin and genetics used to solve complex problems, eg, problems where the search space grows with the size of the problem. The particle swarm optimization characteristics including the use of intelligence collectively being applied to optimization problems in many areas of research. The main objective of this work is the use of computational intelligence, the analysis and synthesis of antennas and FSS. We considered the structures of a microstrip planar monopole, ring type, and a cross-dipole FSS. We developed algorithms and optimization results obtained for optimized geometries of antennas and FSS considered. To validate results were designed, constructed and measured several prototypes. The measured results showed excellent agreement with the simulated. Moreover, the results obtained in this study were compared to those simulated using a commercial software has been also observed an excellent agreement. Specifically, the efficiency of techniques used were CI evidenced by simulated and measured, aiming at optimizing the bandwidth of an antenna for wideband operation or UWB (Ultra Wideband), using a genetic algorithm and optimizing the bandwidth, by specifying the length of the air gap between two frequency selective surfaces, using an optimization algorithm particle swarm

Otimização de superfícies seletivas de frequência com elementos pré-fractais utilizando rede neural MLP e algoritmos de busca populacional

This thesis describes design methodologies for frequency selective surfaces (FSSs) composed of periodic arrays of pre-fractals metallic patches on single-layer dielectrics (FR4, RT/duroid). Shapes presented by Sierpinski island and T fractal geometries are exploited to the simple design of efficient band-stop spatial filters with applications in the range of microwaves. Initial results are discussed in terms of the electromagnetic effect resulting from the variation of parameters such as, fractal iteration number (or fractal level), fractal iteration factor, and periodicity of FSS, depending on the used pre-fractal element (Sierpinski island or T fractal). The transmission properties of these proposed periodic arrays are investigated through simulations performed by Ansoft DesignerTM and Ansoft HFSSTM commercial softwares that run full-wave methods. To validate the employed methodology, FSS prototypes are selected for fabrication and measurement. The obtained results point to interesting features for FSS spatial filters: compactness, with high values of frequency compression factor; as well as stable frequency responses at oblique incidence of plane waves. This thesis also approaches, as it main focus, the application of an alternative electromagnetic (EM) optimization technique for analysis and synthesis of FSSs with fractal motifs. In application examples of this technique, Vicsek and Sierpinski pre-fractal elements are used in the optimal design of FSS structures. Based on computational intelligence tools, the proposed technique overcomes the high computational cost associated to the full-wave parametric analyzes. To this end, fast and accurate multilayer perceptron (MLP) neural network models are developed using different parameters as design input variables. These neural network models aim to calculate the cost function in the iterations of population-based search algorithms. Continuous genetic algorithm (GA), particle swarm optimization (PSO), and bees algorithm (BA) are used for FSSs optimization with specific resonant frequency and bandwidth. The performance of these algorithms is compared in terms of computational cost and numerical convergence. Consistent results can be verified by the excellent agreement obtained between simulations and measurements related to FSS prototypes built with a given fractal iteration

Técnicas de computação natural para segmentação de imagens médicas

Image segmentation is one of the image processing problems that deserves special attention from the scientific community. This work studies unsupervised methods to clustering and pattern recognition applicable to medical image segmentation. Natural Computing based methods have shown very attractive in such tasks and are studied here as a way to verify it's applicability in medical image segmentation. This work treats to implement the following methods: GKA (Genetic K-means Algorithm), GFCMA (Genetic FCM Algorithm), PSOKA (PSO and K-means based Clustering Algorithm) and PSOFCM (PSO and FCM based Clustering Algorithm). Besides, as a way to evaluate the results given by the algorithms, clustering validity indexes are used as quantitative measure. Visual and qualitative evaluations are realized also, mainly using data given by the BrainWeb brain simulator as ground truth

Maximização da penetração da geração distribuída através do algoritmo de otimização nuvem de partículas

This work develops a methodology for defining the maximum active power being injected into predefined nodes in the studied distribution networks, considering the possibility of multiple accesses of generating units. The definition of these maximum values is obtained from an optimization study, in which further losses should not exceed those of the base case, i.e., without the presence of distributed generation. The restrictions on the loading of the branches and voltages of the system are respected. To face the problem it is proposed an algorithm, which is based on the numerical method called particle swarm optimization, applied to the study of AC conventional load flow and optimal load flow for maximizing the penetration of distributed generation. Alternatively, the Newton-Raphson method was incorporated to resolution of the load flow. The computer program is performed with the SCILAB software. The proposed algorithm is tested with the data from the IEEE network with 14 nodes and from another network, this one from the Rio Grande do Norte State, at a high voltage (69 kV), with 25 nodes. The algorithm defines allowed values of nominal active power of distributed generation, in percentage terms relative to the demand of the network, from reference values

Avaliacao de dados de secagem de suspensoes de polpas de frutas em leito de jorro com alimentacao intermitente

The objective of this work was the development and improvement of the mathematical models based on mass and heat balances, representing the drying transient process fruit pulp in spouted bed dryer with intermittent feeding. Mass and energy balance for drying, represented by a system of differential equations, were developed in Fortran language and adapted to the condition of intermittent feeding and mass accumulation. Were used the DASSL routine (Differential Algebraic System Solver) for solving the differential equation system and used a heuristic optimization algorithm in parameter estimation, the Particle Swarm algorithm. From the experimental data food drying, the differential models were used to determine the quantity of water and the drying air temperature at the exit of a spouted bed and accumulated mass of powder in the dryer. The models were validated using the experimental data of drying whose operating conditions, air temperature, flow rate and time intermittency, varied within the limits studied. In reviewing the results predicted, it was found that these models represent the experimental data of the kinetics of production and accumulation of powder and humidity and air temperature at the outlet of the dryer