Commenced in January 2007
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Edition: International
Paper Count: 6346

Search results for: BER

16 Modeling Biology Inspired Reactive Agents Using X-machines

Authors: George Eleftherakis, Petros Kefalas, Anna Sotiriadou, Evangelos Kehris

Abstract:

Recent advances in both the testing and verification of software based on formal specifications of the system to be built have reached a point where the ideas can be applied in a powerful way in the design of agent-based systems. The software engineering research has highlighted a number of important issues: the importance of the type of modeling technique used; the careful design of the model to enable powerful testing techniques to be used; the automated verification of the behavioural properties of the system; the need to provide a mechanism for translating the formal models into executable software in a simple and transparent way. This paper introduces the use of the X-machine formalism as a tool for modeling biology inspired agents proposing the use of the techniques built around X-machine models for the construction of effective, and reliable agent-based software systems.

Keywords: Biology inspired agent, formal methods, x-machines.

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15 Parallezation Protein Sequence Similarity Algorithms using Remote Method Interface

Authors: Mubarak Saif Mohsen, Zurinahni Zainol, Rosalina Abdul Salam, Wahidah Husain

Abstract:

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

Keywords: Protein sequence algorithm, dynamic programming algorithm, multithread

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14 Improving the Convergence of the Backpropagation Algorithm Using Local Adaptive Techniques

Authors: Z. Zainuddin, N. Mahat, Y. Abu Hassan

Abstract:

Since the presentation of the backpropagation algorithm, a vast variety of improvements of the technique for training a feed forward neural networks have been proposed. This article focuses on two classes of acceleration techniques, one is known as Local Adaptive Techniques that are based on weightspecific only, such as the temporal behavior of the partial derivative of the current weight. The other, known as Dynamic Adaptation Methods, which dynamically adapts the momentum factors, α, and learning rate, η, with respect to the iteration number or gradient. Some of most popular learning algorithms are described. These techniques have been implemented and tested on several problems and measured in terms of gradient and error function evaluation, and percentage of success. Numerical evidence shows that these techniques improve the convergence of the Backpropagation algorithm.

Keywords: Backpropagation, Dynamic Adaptation Methods, Local Adaptive Techniques, Neural networks.

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13 Modeling of Pulping of Sugar Maple Using Advanced Neural Network Learning

Authors: W. D. Wan Rosli, Z. Zainuddin, R. Lanouette, S. Sathasivam

Abstract:

This paper reports work done to improve the modeling of complex processes when only small experimental data sets are available. Neural networks are used to capture the nonlinear underlying phenomena contained in the data set and to partly eliminate the burden of having to specify completely the structure of the model. Two different types of neural networks were used for the application of Pulping of Sugar Maple problem. A three layer feed forward neural networks, using the Preconditioned Conjugate Gradient (PCG) methods were used in this investigation. Preconditioning is a method to improve convergence by lowering the condition number and increasing the eigenvalues clustering. The idea is to solve the modified problem where M is a positive-definite preconditioner that is closely related to A. We mainly focused on Preconditioned Conjugate Gradient- based training methods which originated from optimization theory, namely Preconditioned Conjugate Gradient with Fletcher-Reeves Update (PCGF), Preconditioned Conjugate Gradient with Polak-Ribiere Update (PCGP) and Preconditioned Conjugate Gradient with Powell-Beale Restarts (PCGB). The behavior of the PCG methods in the simulations proved to be robust against phenomenon such as oscillations due to large step size.

Keywords: Convergence, Modeling, Neural Networks, Preconditioned Conjugate Gradient.

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12 Fuzzy Clustering of Categorical Attributes and its Use in Analyzing Cultural Data

Authors: George E. Tsekouras, Dimitris Papageorgiou, Sotiris Kotsiantis, Christos Kalloniatis, Panagiotis Pintelas

Abstract:

We develop a three-step fuzzy logic-based algorithm for clustering categorical attributes, and we apply it to analyze cultural data. In the first step the algorithm employs an entropy-based clustering scheme, which initializes the cluster centers. In the second step we apply the fuzzy c-modes algorithm to obtain a fuzzy partition of the data set, and the third step introduces a novel cluster validity index, which decides the final number of clusters.

Keywords: Categorical data, cultural data, fuzzy logic clustering, fuzzy c-modes, cluster validity index.

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11 Morphing Human Faces: Automatic Control Points Selection and Color Transition

Authors: Stephen Karungaru, Minoru Fukumi, Norio Akamatsu

Abstract:

In this paper, we propose a morphing method by which face color images can be freely transformed. The main focus of this work is the transformation of one face image to another. This method is fully automatic in that it can morph two face images by automatically detecting all the control points necessary to perform the morph. A face detection neural network, edge detection and medium filters are employed to detect the face position and features. Five control points, for both the source and target images, are then extracted based on the facial features. Triangulation method is then used to match and warp the source image to the target image using the control points. Finally color interpolation is done using a color Gaussian model that calculates the color for each particular frame depending on the number of frames used. A real coded Genetic algorithm is used in both the image warping and color blending steps to assist in step size decisions and speed up the morphing. This method results in ''very smooth'' morphs and is fast to process.

Keywords: color transition, genetic algorithms morphing, warping

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10 On the Noise Distance in Robust Fuzzy C-Means

Authors: M. G. C. A. Cimino, G. Frosini, B. Lazzerini, F. Marcelloni

Abstract:

In the last decades, a number of robust fuzzy clustering algorithms have been proposed to partition data sets affected by noise and outliers. Robust fuzzy C-means (robust-FCM) is certainly one of the most known among these algorithms. In robust-FCM, noise is modeled as a separate cluster and is characterized by a prototype that has a constant distance δ from all data points. Distance δ determines the boundary of the noise cluster and therefore is a critical parameter of the algorithm. Though some approaches have been proposed to automatically determine the most suitable δ for the specific application, up to today an efficient and fully satisfactory solution does not exist. The aim of this paper is to propose a novel method to compute the optimal δ based on the analysis of the distribution of the percentage of objects assigned to the noise cluster in repeated executions of the robust-FCM with decreasing values of δ . The extremely encouraging results obtained on some data sets found in the literature are shown and discussed.

Keywords: noise prototype, robust fuzzy clustering, robustfuzzy C-means

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9 Forecasting Enrollment Model Based on First-Order Fuzzy Time Series

Authors: Melike Şah, Konstantin Y.Degtiarev

Abstract:

This paper proposes a novel improvement of forecasting approach based on using time-invariant fuzzy time series. In contrast to traditional forecasting methods, fuzzy time series can be also applied to problems, in which historical data are linguistic values. It is shown that proposed time-invariant method improves the performance of forecasting process. Further, the effect of using different number of fuzzy sets is tested as well. As with the most of cited papers, historical enrollment of the University of Alabama is used in this study to illustrate the forecasting process. Subsequently, the performance of the proposed method is compared with existing fuzzy time series time-invariant models based on forecasting accuracy. It reveals a certain performance superiority of the proposed method over methods described in the literature.

Keywords: Forecasting, fuzzy time series, linguistic values, student enrollment, time-invariant model.

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8 Design of Gain Scheduled Fuzzy PID Controller

Authors: Leehter Yao, Chin-Chin Lin

Abstract:

An adaptive fuzzy PID controller with gain scheduling is proposed in this paper. The structure of the proposed gain scheduled fuzzy PID (GS_FPID) controller consists of both fuzzy PI-like controller and fuzzy PD-like controller. Both of fuzzy PI-like and PD-like controllers are weighted through adaptive gain scheduling, which are also determined by fuzzy logic inference. A modified genetic algorithm called accumulated genetic algorithm is designed to learn the parameters of fuzzy inference system. In order to learn the number of fuzzy rules required for the TSK model, the fuzzy rules are learned in an accumulated way. In other words, the parameters learned in the previous rules are accumulated and updated along with the parameters in the current rule. It will be shown that the proposed GS_FPID controllers learned by the accumulated GA perform well for not only the regular linear systems but also the higher order and time-delayed systems.

Keywords: Gain scheduling, fuzzy PID controller, adaptive control, genetic algorithm.

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7 [email protected]: Intelligent Home Control and Simulation

Authors: Berardina De Carolis, Giovanni Cozzolongo

Abstract:

In this paper, we present [email protected], a multiagent system aiming at modeling, controlling and simulating the behavior of an intelligent house. The developed system aims at providing to architects, designers and psychologists a simulation and control tool for understanding which is the impact of embedded and pervasive technology on people daily life. In this vision, the house is seen as an environment made up of independent and distributed devices, controlled by agents, interacting to support user's goals and tasks.

Keywords: Ambient intelligence, agent-based systems, influence diagrams.

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6 Computational Method for Annotation of Protein Sequence According to Gene Ontology Terms

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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5 Automated ECG Segmentation Using Piecewise Derivative Dynamic Time Warping

Authors: Ali Zifan, Sohrab Saberi, Mohammad Hassan Moradi, Farzad Towhidkhah

Abstract:

Electrocardiogram (ECG) segmentation is necessary to help reduce the time consuming task of manually annotating ECG's. Several algorithms have been developed to segment the ECG automatically. We first review several of such methods, and then present a new single lead segmentation method based on Adaptive piecewise constant approximation (APCA) and Piecewise derivative dynamic time warping (PDDTW). The results are tested on the QT database. We compared our results to Laguna's two lead method. Our proposed approach has a comparable mean error, but yields a slightly higher standard deviation than Laguna's method.

Keywords: Adaptive Piecewise Constant Approximation, Dynamic programming, ECG segmentation, Piecewise Derivative Dynamic Time Warping.

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4 Protein-Protein Interaction Detection Based on Substring Sensitivity Measure

Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

Abstract:

Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

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3 Affine Projection Algorithm with Variable Data-Reuse Factor

Authors: ChangWoo Lee, Young Kow Lee, Sung Jun Ban, SungHoo Choi, Sang Woo Kim

Abstract:

This paper suggests a new Affine Projection (AP) algorithm with variable data-reuse factor using the condition number as a decision factor. To reduce computational burden, we adopt a recently reported technique which estimates the condition number of an input data matrix. Several simulations show that the new algorithm has better performance than that of the conventional AP algorithm.

Keywords: Affine projection algorithm, variable data-reuse factor, condition number, convergence rate, misalignment.

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2 Gene Network Analysis of PPAR-γ: A Bioinformatics Approach Using STRING

Authors: S. Bag, S. Ramaiah, P. Anitha, K. M. Kumar, P. Lavanya, V. Sivasakhthi, A. Anbarasu

Abstract:

Gene networks present a graphical view at the level of gene activities and genetic functions and help us to understand complex interactions in a meaningful manner. In the present study, we have analyzed the gene interaction of PPAR-γ (peroxisome proliferator-activated receptor gamma) by search tool for retrieval of interacting genes. We find PPAR-γ is highly networked by genetic interactions with 10 genes: RXRA (retinoid X receptor, alpha), PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha), NCOA1 (nuclear receptor coactivator 1), NR0B2 (nuclear receptor subfamily 0, group B, member 2), HDAC3 (histone deacetylase 3), MED1 (mediator complex subunit 1), INS (insulin), NCOR2 (nuclear receptor co-repressor 2), PAX8 (paired box 8), ADIPOQ (adiponectin) and it augurs well for the fact that obesity and several other metabolic disorders are inter related.

Keywords: Gene networks, NCOA1, PPARγ, PPARGC1A, RXRA.

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1 The Number of Rational Points on Elliptic Curves y2 = x3 + a3 on Finite Fields

Authors: Musa Demirci, Nazlı Yıldız İkikardeş, Gökhan Soydan, İsmail Naci Cangül

Abstract:

In this work, we consider the rational points on elliptic curves over finite fields Fp. We give results concerning the number of points Np,a on the elliptic curve y2 ≡ x3 +a3(mod p) according to whether a and x are quadratic residues or non-residues. We use two lemmas to prove the main results first of which gives the list of primes for which -1 is a quadratic residue, and the second is a result from [1]. We get the results in the case where p is a prime congruent to 5 modulo 6, while when p is a prime congruent to 1 modulo 6, there seems to be no regularity for Np,a.

Keywords: Elliptic curves over finite fields, rational points, quadratic residue.

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