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.

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.

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

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

Arquitetura multiagente baseada em nuvem de partículas para hibridização de metaheurísticas

This thesis proposes an architecture of a new multiagent system framework for hybridization of metaheuristics inspired on the general Particle Swarm Optimization framework (PSO). The main contribution is to propose an effective approach to solve hard combinatory optimization problems. The choice of PSO as inspiration was given because it is inherently multiagent, allowing explore the features of multiagent systems, such as learning and cooperation techniques. In the proposed architecture, particles are autonomous agents with memory and methods for learning and making decisions, using search strategies to move in the solution space. The concepts of position and velocity originally defined in PSO are redefined for this approach. The proposed architecture was applied to the Traveling Salesman Problem and to the Quadratic Assignment Problem, and computational experiments were performed for testing its effectiveness. The experimental results were promising, with satisfactory performance, whereas the potential of the proposed architecture has not been fully explored. For further researches, the proposed approach will be also applied to multiobjective combinatorial optimization problems, which are closer to real-world problems. In the context of applied research, we intend to work with both students at the undergraduate level and a technical level in the implementation of the proposed architecture in real-world problems

Uma abordagem por nuvem de partículas para problemas de otimização combinatória

Combinatorial optimization problems have the goal of maximize or minimize functions defined over a finite domain. Metaheuristics are methods designed to find good solutions in this finite domain, sometimes the optimum solution, using a subordinated heuristic, which is modeled for each particular problem. This work presents algorithms based on particle swarm optimization (metaheuristic) applied to combinatorial optimization problems: the Traveling Salesman Problem and the Multicriteria Degree Constrained Minimum Spanning Tree Problem. The first problem optimizes only one objective, while the other problem deals with many objectives. In order to evaluate the performance of the algorithms proposed, they are compared, in terms of the quality of the solutions found, to other approaches

Identificação e comparação entre controle preditivo com modelo não linear e PI sintonizados com PSO em sistema de separação gravitacional de águia-óleo

The separation methods are reduced applications as a result of the operational costs, the low output and the long time to separate the uids. But, these treatment methods are important because of the need for extraction of unwanted contaminants in the oil production. The water and the concentration of oil in water should be minimal (around 40 to 20 ppm) in order to take it to the sea. Because of the need of primary treatment, the objective of this project is to study and implement algorithms for identification of polynomial NARX (Nonlinear Auto-Regressive with Exogenous Input) models in closed loop, implement a structural identification, and compare strategies using PI control and updated on-line NARX predictive models on a combination of three-phase separator in series with three hydro cyclones batteries. The main goal of this project is to: obtain an optimized process of phase separation that will regulate the system, even in the presence of oil gushes; Show that it is possible to get optimized tunings for controllers analyzing the mesh as a whole, and evaluate and compare the strategies of PI and predictive control applied to the process. To accomplish these goals a simulator was used to represent the three phase separator and hydro cyclones. Algorithms were developed for system identification (NARX) using RLS(Recursive Least Square), along with methods for structure models detection. Predictive Control Algorithms were also implemented with NARX model updated on-line, and optimization algorithms using PSO (Particle Swarm Optimization). This project ends with a comparison of results obtained from the use of PI and predictive controllers (both with optimal state through the algorithm of cloud particles) in the simulated system. Thus, concluding that the performed optimizations make the system less sensitive to external perturbations and when optimized, the two controllers show similar results with the assessment of predictive control somewhat less sensitive to disturbances

Feature selection through gravitational search algorithm

In this paper we deal with the problem of feature selection by introducing a new approach based on Gravitational Search Algorithm (GSA). The proposed algorithm combines the optimization behavior of GSA together with the speed of Optimum-Path Forest (OPF) classifier in order to provide a fast and accurate framework for feature selection. Experiments on datasets obtained from a wide range of applications, such as vowel recognition, image classification and fraud detection in power distribution systems are conducted in order to asses the robustness of the proposed technique against Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA) and a Particle Swarm Optimization (PSO)-based algorithm for feature selection.