Search results for: Co-occurrence matrix; Similarity measure.

Authors: Li Jiang, Baoguang Tian

Abstract:

In this paper, we present the preconditioned mixed-type splitting iterative method for solving the linear systems, Ax = b, where A is a Z-matrix. And we give some comparison theorems to show that the convergence rate of the preconditioned mixed-type splitting iterative method is faster than that of the mixed-type splitting iterative method. Finally, we give a numerical example to illustrate our results.

Keywords: Z-matrix, mixed-type splitting iterative method, precondition, comparison theorem, linear system.

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Authors: Mikko Mäkelä, Risto Pöykiö, Gary Watkins, Hannu Nurmesniemi, Olli Dahl

Abstract:

Trace element speciation of an integrated soil amendment matrix was studied with a modified BCR sequential extraction procedure. The analysis included pseudo-total concentration determinations according to USEPA 3051A and relevant physicochemical properties by standardized methods. Based on the results, the soil amendment matrix possessed neutralization capacity comparable to commercial fertilizers. Additionally, the pseudo-total concentrations of all trace elements included in the Finnish regulation for agricultural fertilizers were lower than the respective statutory limit values. According to chemical speciation, the lability of trace elements increased in the following order: Hg < Cr < Co < Cu < As < Zn < Ni < Pb < Cd < V < Mo < Ba. The validity of the BCR approach as a tool for chemical speciation was confirmed by the additional acid digestion phase. Recovery of trace elements during the procedure assured the validity of the approach and indicated good quality of the analytical work.

Keywords: BCR, bioavailability, trace element, industrialresidue, sequential extraction

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Authors: Hong Li, Shou-ming Zhong, Hou-biao Li

Abstract:

In this paper, some brief sufficient conditions for the stability of FO-LTI systems dαx(t) dtα = Ax(t) with the fractional order are investigated when the matrix A and the fractional order α are uncertain or both α and A are uncertain, respectively. In addition, we also relate the stability of a fractional-order system with order 0 < α ≤ 1 to the stability of its equivalent fractional-order system with order 1 ≤ β < 2, the relationship between α and β is presented. Finally, a numeric experiment is given to demonstrate the effectiveness of our results.

Keywords: Interval fractional-order systems, linear matrix inequality (LMI), asymptotical stability.

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Authors: Fadl M. Ba-Alwi, Kamal K. Bharadwaj

Abstract:

In this paper a novel algorithm is proposed that integrates the process of fuzzy hierarchy generation and rule discovery for automated discovery of Production Rules with Fuzzy Hierarchy (PRFH) in large databases.A concept of frequency matrix (Freq) introduced to summarize large database that helps in minimizing the number of database accesses, identification and removal of irrelevant attribute values and weak classes during the fuzzy hierarchy generation.Experimental results have established the effectiveness of the proposed algorithm.

Keywords: Data Mining, Degree of subsumption, Freq matrix, Fuzzy hierarchy.

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Authors: Rihab Gam, Anis Sakly, Faouzi M'sahli

Abstract:

A new strategy of control is formulated for chaos synchronization of non-identical chaotic systems with different orders using the Borne and Gentina practical criterion associated with the Benrejeb canonical arrow form matrix, to drift the stability property of dynamic complex systems. The designed controller ensures that the state variables of controlled chaotic slave systems globally synchronize with the state variables of the master systems, respectively. Numerical simulations are performed to illustrate the efficiency of the proposed method.

Keywords: Synchronization, Non-identical chaotic systems, Different orders, Arrow form matrix.

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Authors: Tim Dunne, Weicheng Li, Chris Cheng, Qi Peng

Abstract:

Deeper petroleum reservoirs are more challenging to exploit due to the high hardness and abrasive characteristics of the formations. A cutting structure that consists of particulate diamond impregnated in a supporting matrix is found to be effective. Diamond impregnated bits are favored in these applications due to the higher thermal stability of the matrix material. The diamond particles scour or abrade away concentric grooves while the rock formation adjacent to the grooves is fractured and removed. The matrix material supporting the diamond will wear away, leaving the superficial dull diamonds to fall out. The matrix material wear will expose other embedded intact sharp diamonds to continue the operation. Minimizing the erosion effect on the matrix is an important design consideration, as the life of the bit can be extended by preventing early diamond pull-out. A careful balancing of the key parameters, such as diamond concentration, tungsten carbide and metal binder must be considered during development. Described herein is the design of experiment for developing and lab testing 8 unique samples. ASTM B611 wear testing was performed to benchmark the material performance against baseline products, with further scanning electron microscopy and microhardness evaluations. The recipe S5 with diamond 25/35 mesh size, narrow size distribution, high concentration blended with fine tungsten carbide and Co-Cu-Fe-P metal binder has the best performance, which shows 19% improvement in the ASTM B611 wear test compared with the reference material. In the field trial, the rate of penetration (ROP) is measured as 15 m/h, compared to 9.5, 7.8, and 6.8 m/h of other commercial impregnated bits in the same formation. A second round of optimizing recipe S5 for a higher wear resistance is further reported.

Keywords: Diamond containing material, grit hot press insert, impregnated diamond, insert, rate of penetration, ultrahard formation.

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Authors: Liu Ping

Abstract:

In this paper, for an arbitrary multiplicative functional f from the set of all upper triangular fuzzy matrices to the fuzzy algebra, we prove that there exist a multiplicative functional F and a functional G from the fuzzy algebra to the fuzzy algebra such that the image of an upper triangular fuzzy matrix under f can be represented as the product of all the images of its main diagonal elements under F and other elements under G.

Keywords: Multiplicative functional, triangular fuzzy matrix, fuzzy addition operation, fuzzy multiplication operation.

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Authors: H. D. Ibrahim, H. C. Chinwenyi, H. N. Ude

Abstract:

In this paper, efforts were made to examine and compare the algorithmic iterative solutions of conjugate gradient method as against other methods such as Gauss-Seidel and Jacobi approaches for solving systems of linear equations of the form Ax = b, where A is a real n x n symmetric and positive definite matrix. We performed algorithmic iterative steps and obtained analytical solutions of a typical 3 x 3 symmetric and positive definite matrix using the three methods described in this paper (Gauss-Seidel, Jacobi and Conjugate Gradient methods) respectively. From the results obtained, we discovered that the Conjugate Gradient method converges faster to exact solutions in fewer iterative steps than the two other methods which took much iteration, much time and kept tending to the exact solutions.

Keywords: conjugate gradient, linear equations, symmetric and positive definite matrix, Gauss-Seidel, Jacobi, algorithm

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Authors: Noraini Ahmad, Seripah Awang Kechil, Norma Mohd Basir

Abstract:

The steady coupled dissipative layers, called Marangoni mixed convection boundary layers, in the presence of a magnetic field and solute concentration that are formed along the surface of two immiscible fluids with uniform suction or injection effects is examined. The similarity boundary layer equations are solved numerically using the Runge-Kutta Fehlberg with shooting technique. The Marangoni, buoyancy and external pressure gradient effects that are generated in mixed convection boundary layer flow are assessed. The velocity, temperature and concentration boundary layers thickness decrease with the increase of the magnetic field strength and the injection to suction. For buoyancy-opposed flow, the Marangoni mixed convection parameter enhances the velocity boundary layer but decreases the temperature and concentration boundary layers. However, for the buoyancy-assisted flow, the Marangoni mixed convection parameter decelerates the velocity but increases the temperature and concentration boundary layers.

Keywords: Magnetic field, mixed Marangoni convection, similarity boundary layers, solute concentration.

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Authors: Jeffrey L. Duffany

Abstract:

An optimal solution for a large number of constraint satisfaction problems can be found using the technique of substitution and elimination of variables analogous to the technique that is used to solve systems of equations. A decision function f(A)=max(A2) is used to determine which variables to eliminate. The algorithm can be expressed in six lines and is remarkable in both its simplicity and its ability to find an optimal solution. However it is inefficient in that it needs to square the updated A matrix after each variable elimination. To overcome this inefficiency the algorithm is analyzed and it is shown that the A matrix only needs to be squared once at the first step of the algorithm and then incrementally updated for subsequent steps, resulting in significant improvement and an algorithm complexity of O(n3).

Keywords: Algorithm, complexity, constraint, np-complete.

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Authors: Sunita Jahirabadkar, Parag Kulkarni

Abstract:

Many real-world data sets consist of a very high dimensional feature space. Most clustering techniques use the distance or similarity between objects as a measure to build clusters. But in high dimensional spaces, distances between points become relatively uniform. In such cases, density based approaches may give better results. Subspace Clustering algorithms automatically identify lower dimensional subspaces of the higher dimensional feature space in which clusters exist. In this paper, we propose a new clustering algorithm, ISC – Intelligent Subspace Clustering, which tries to overcome three major limitations of the existing state-of-art techniques. ISC determines the input parameter such as є – distance at various levels of Subspace Clustering which helps in finding meaningful clusters. The uniform parameters approach is not suitable for different kind of databases. ISC implements dynamic and adaptive determination of Meaningful clustering parameters based on hierarchical filtering approach. Third and most important feature of ISC is the ability of incremental learning and dynamic inclusion and exclusions of subspaces which lead to better cluster formation.

Keywords: Density based clustering, high dimensional data, subspace clustering, dynamic parameter setting.

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Authors: Somnath Dey, Debasis Samanta

Abstract:

Iris-based biometric authentication is gaining importance in recent times. Iris biometric processing however, is a complex process and computationally very expensive. In the overall processing of iris biometric in an iris-based biometric authentication system, feature processing is an important task. In feature processing, we extract iris features, which are ultimately used in matching. Since there is a large number of iris features and computational time increases as the number of features increases, it is therefore a challenge to develop an iris processing system with as few as possible number of features and at the same time without compromising the correctness. In this paper, we address this issue and present an approach to feature extraction and feature matching process. We apply Daubechies D4 wavelet with 4 levels to extract features from iris images. These features are encoded with 2 bits by quantizing into 4 quantization levels. With our proposed approach it is possible to represent an iris template with only 304 bits, whereas existing approaches require as many as 1024 bits. In addition, we assign different weights to different iris region to compare two iris templates which significantly increases the accuracy. Further, we match the iris template based on a weighted similarity measure. Experimental results on several iris databases substantiate the efficacy of our approach.

Keywords: Iris recognition, biometric, feature processing, patternrecognition, pattern matching.

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Authors: R. Eslami-Farsani, S. M. S. Mousavi Bafrouyi

Abstract:

During past decades, increasing demand of modified Fiber Metal Laminates (FMLs) has stimulated a strong trend towards the development of these structures. FMLs contain several thin layers of metal bonded with composite materials. Characteristics of FMLs such as low specific mass, high bearing strength, impact resistance, corrosion resistance and high fatigue life are attractive. Nowadays, increasing development can be observed to promote the properties of polymer-based composites by nanofillers. By dispersing strong, nanofillers in polymer matrix, modified composites can be developed and tailored to individual applications. On the other hand, the synergic effects of nanoparticles such as graphene and carbon nanotube can significantly improve the mechanical, electrical and thermal properties of nanocomposites. In present paper, the modifying of FMLs by nanofillers and the dispersing of nanoparticles in the polymers matrix are discussed. The evaluations have revealed that this approach is acceptable. Finally, a prospect is presented. This paper will lead to further work on these modified FML species.

Keywords: Fiber metal laminate, nanofiller, polymer matrix, property modification.

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Authors: T. Sakamoto, N. Hori

Abstract:

A multi-rate discrete-time model, whose response agrees exactly with that of a continuous-time original at all sampling instants for any sampling periods, is developed for a linear system, which is assumed to have multiple real eigenvalues. The sampling rates can be chosen arbitrarily and individually, so that their ratios can even be irrational. The state space model is obtained as a combination of a linear diagonal state equation and a nonlinear output equation. Unlike the usual lifted model, the order of the proposed model is the same as the number of sampling rates, which is less than or equal to the order of the original continuous-time system. The method is based on a nonlinear variable transformation, which can be considered as a generalization of linear similarity transformation, which cannot be applied to systems with multiple eigenvalues in general. An example and its simulation result show that the proposed multi-rate model gives exact responses at all sampling instants.

Keywords: Multi-rate discretization, linear systems, triangularization, similarity transformation, diagonalization, exponential transformation, multiple eigenvalues

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Authors: Agus Harjoko, Sri Hartati, Henry Dwiyasa

Abstract:

There have been numerous implementations of security system using biometric, especially for identification and verification cases. An example of pattern used in biometric is the iris pattern in human eye. The iris pattern is considered unique for each person. The use of iris pattern poses problems in encoding the human iris. In this research, an efficient iris recognition method is proposed. In the proposed method the iris segmentation is based on the observation that the pupil has lower intensity than the iris, and the iris has lower intensity than the sclera. By detecting the boundary between the pupil and the iris and the boundary between the iris and the sclera, the iris area can be separated from pupil and sclera. A step is taken to reduce the effect of eyelashes and specular reflection of pupil. Then the four levels Coiflet wavelet transform is applied to the extracted iris image. The modified Hamming distance is employed to measure the similarity between two irises. This research yields the identification success rate of 84.25% for the CASIA version 1.0 database. The method gives an accuracy of 77.78% for the left eyes of MMU 1 database and 86.67% for the right eyes. The time required for the encoding process, from the segmentation until the iris code is generated, is 0.7096 seconds. These results show that the accuracy and speed of the method is better than many other methods.

Keywords: Biometric, iris recognition, wavelet transform.

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Authors: S. P. Jordan, G. Christian, S. P. Jeffs

Abstract:

Modern composite materials are increasingly being chosen in replacement of heavier metallic material systems within many engineering fields including aerospace and automotive industries. The increasing push towards satisfying environmental targets are fuelling new material technologies and manufacturing processes. This paper will introduce materials and manufacturing processes using metal matrix composites along with manufacturing processes optimized at Alvant Ltd., based in Basingstoke in the UK which offers modern, cost effective, selectively reinforced composites for light-weighting applications within engineering. An overview and introduction into modern optimized manufacturing methods capable of producing viable replacements for heavier metallic and lower temperature capable polymer composites are offered. A review of the capabilities and future applications of this viable material is discussed to highlight the potential involved in further optimization of old manufacturing techniques, to fully realize the potential to lightweight material using cost-effective methods.

Keywords: Aluminum matrix composites, light-weighting, hybrid squeeze casting, strategically placed reinforcements.

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Authors: M. V. Sudhamani, C. R. Venugopal

Abstract:

Content-based Image Retrieval (CBIR) aims at searching image databases for specific images that are similar to a given query image based on matching of features derived from the image content. This paper focuses on a low-dimensional color based indexing technique for achieving efficient and effective retrieval performance. In our approach, the color features are extracted using the mean shift algorithm, a robust clustering technique. Then the cluster (region) mode is used as representative of the image in 3-D color space. The feature descriptor consists of the representative color of a region and is indexed using a spatial indexing method that uses *R -tree thus avoiding the high-dimensional indexing problems associated with the traditional color histogram. Alternatively, the images in the database are clustered based on region feature similarity using Euclidian distance. Only representative (centroids) features of these clusters are indexed using *R -tree thus improving the efficiency. For similarity retrieval, each representative color in the query image or region is used independently to find regions containing that color. The results of these methods are compared. A JAVA based query engine supporting query-by- example is built to retrieve images by color.

Keywords: Content-based, indexing, cluster, region.

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Authors: Roslinda Nazar, Amin Noor, Khamisah Jafar, Ioan Pop

Abstract:

In this paper, the steady laminar three-dimensional boundary layer flow and heat transfer of a copper (Cu)-water nanofluid in the vicinity of a permeable shrinking flat surface in an otherwise quiescent fluid is studied. The nanofluid mathematical model in which the effect of the nanoparticle volume fraction is taken into account is considered. The governing nonlinear partial differential equations are transformed into a system of nonlinear ordinary differential equations using a similarity transformation which is then solved numerically using the function bvp4c from Matlab. Dual solutions (upper and lower branch solutions) are found for the similarity boundary layer equations for a certain range of the suction parameter. A stability analysis has been performed to show which branch solutions are stable and physically realizable. The numerical results for the skin friction coefficient and the local Nusselt number as well as the velocity and temperature profiles are obtained, presented and discussed in detail for a range of various governing parameters.

Keywords: Heat Transfer, Nanofluid, Shrinking Surface, Stability Analysis, Three-Dimensional Flow.

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Authors: S. Sarumathi, P. Ranjetha, C. Saraswathy, M. Vaishnavi, S. Geetha

Abstract:

Clustering is an unsupervised learning technique for aggregating data objects into meaningful classes so that intra cluster similarity is maximized and inter cluster similarity is minimized in data mining. However, no single clustering algorithm proves to be the most effective in producing the best result. As a result, a new challenging technique known as the cluster ensemble approach has blossomed in order to determine the solution to this problem. For the cluster analysis issue, this new technique is a successful approach. The cluster ensemble's main goal is to combine similar clustering solutions in a way that achieves the precision while also improving the quality of individual data clustering. Because of the massive and rapid creation of new approaches in the field of data mining, the ongoing interest in inventing novel algorithms necessitates a thorough examination of current techniques and future innovation. This paper presents a comparative analysis of various cluster ensemble approaches, including their methodologies, formal working process, and standard accuracy and error rates. As a result, the society of clustering practitioners will benefit from this exploratory and clear research, which will aid in determining the most appropriate solution to the problem at hand.

Keywords: Clustering, cluster ensemble methods, consensus function, data mining, unsupervised learning.

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Authors: Rozilawati Binti Dollah, Masaki Aono

Abstract:

Classifying biomedical literature is a difficult and challenging task, especially when a large number of biomedical articles should be organized into a hierarchical structure. In this paper, we present an approach for classifying a collection of biomedical text abstracts downloaded from Medline database with the help of ontology alignment. To accomplish our goal, we construct two types of hierarchies, the OHSUMED disease hierarchy and the Medline abstract disease hierarchies from the OHSUMED dataset and the Medline abstracts, respectively. Then, we enrich the OHSUMED disease hierarchy before adapting it to ontology alignment process for finding probable concepts or categories. Subsequently, we compute the cosine similarity between the vector in probable concepts (in the “enriched" OHSUMED disease hierarchy) and the vector in Medline abstract disease hierarchies. Finally, we assign category to the new Medline abstracts based on the similarity score. The results obtained from the experiments show the performance of our proposed approach for hierarchical classification is slightly better than the performance of the multi-class flat classification.

Keywords: Biomedical literature, hierarchical text classification, ontology alignment, text mining.

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Authors: Peyman Sindareh Esfahani, Jeffery Kurt Pieper

Abstract:

In this paper, the problem of robust model predictive control (MPC) for discrete-time linear systems in linear fractional transformation form with structured uncertainty and norm-bounded disturbance is investigated. The problem of minimization of the cost function for MPC design is converted to minimization of the worst case of the cost function. Then, this problem is reduced to minimization of an upper bound of the cost function subject to a terminal inequality satisfying the l₂-norm of the closed loop system. The characteristic of the linear fractional transformation system is taken into account, and by using some mathematical tools, the robust predictive controller design problem is turned into a linear matrix inequality minimization problem. Afterwards, a formulation which includes an integrator to improve the performance of the proposed robust model predictive controller in steady state condition is studied. The validity of the approaches is illustrated through a robust control benchmark problem.

Keywords: Linear fractional transformation, linear matrix inequality, robust model predictive control, state feedback control.

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Authors: Pil Un Kim, Yunjung Lee, Gihyoun Lee, Jin Ho Cho, Myoung Nam Kim

Abstract:

In this paper, the vessel inscribed trigonometry (VITM) for the vessel progression orientation (VPO) is proposed in the two-dimensional fundus image. The VPO is a major factor in the optic disc (OD) detection which is a basic process in the retina analysis. To measure the VPO, skeletons of vessel are used. First, the vessels are classified into three classes as vessel end, vessel branch and vessel stem. And the chain code maps of VS are generated. Next, two farthest neighborhoods of each point on VS are searched by the proposed angle restriction. Lastly, a gradient of the straight line between two farthest neighborhoods is estimated to measure the VPO. VITM is validated by comparing with manual results and 2D Gaussian templates. It is confirmed that VPO of the proposed mensuration is correct enough to detect OD from the results of experiment which applied VITM to detect OD in fundus images.

Keywords: Angle measurement, Optic disc, Retina vessel, Vessel progression orientation.

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Authors: M. M. Doroodmand, Z.Tahvildar, M. H.Sheikhi

Abstract:

novel and simple method is introduced for rapid and highly efficient water treatment by reverse osmosis (RO) method using multi-walled carbon nanotubes (MWCNTs) / polyacrylonitrile (PAN) polymer as a flexible, highly efficient, reusable and semi-permeable mixed matrix membrane (MMM). For this purpose, MWCNTs were directly synthesized and on-line purified by chemical vapor deposition (CVD) process, followed by directing the MWCNT bundles towards an ultrasonic bath, in which PAN polymer was simultaneously suspended inside a solid porous silica support in water at temperature to ~70 οC. Fabrication process of MMM was finally completed by hot isostatic pressing (HIP) process. In accordance with the analytical figures of merit, the efficiency of fabricated MMM was ~97%. The rate of water treatment process was also evaluated to 6.35 L min-1. The results reveal that, the CNT-based MMM is suitable for rapid treatment of different forms of industrial, sea, drinking and well water samples.

Keywords: Mixed Matrix Membrane, Carbon Nanostructures, Chemical Vapour Deposition, Hot Isostatic Pressing

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Authors: C. Ardil

Abstract:

This article presents a multiple criteria evaluation approach to uncertainty, vagueness, and imprecision analysis for ranking alternatives with fuzzy data for decision making using the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS). The fighter aircraft evaluation and selection decision making problem is modeled in a fuzzy environment with triangular fuzzy numbers. The fuzzy decision information related to the fighter aircraft selection problem is taken into account in ordering the alternatives and selecting the best candidate. The basic fuzzy TOPSIS procedure steps transform fuzzy decision matrices into matrices of alternatives evaluated according to all decision criteria. A practical numerical example illustrates the proposed approach to the fighter aircraft selection problem.

Keywords: triangular fuzzy number (TFN), multiple criteria decision making analysis, decision making, aircraft selection, MCDMA, fuzzy TOPSIS

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Authors: Jiashang Jiang, Yongxin Yuan

Abstract:

In this paper we develop an efficient numerical method for the finite-element model updating of damped gyroscopic systems based on incomplete complex modal measured data. It is assumed that the analytical mass and stiffness matrices are correct and only the damping and gyroscopic matrices need to be updated. By solving a constrained optimization problem, the optimal corrected symmetric damping matrix and skew-symmetric gyroscopic matrix complied with the required eigenvalue equation are found under a weighted Frobenius norm sense.

Keywords: Model updating, damped gyroscopic system, partially prescribed spectral information.

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Authors: Supachai Supmak, Yachai Limpiyakorn

Abstract:

Mutation testing can be applied for the quality assessment of test cases. Prioritization of mutation test generation has been a critical element of the industry practice that would contribute to the evaluation of test cases. The industry generally delivers the product under the condition of time to the market and thus, inevitably sacrifices software testing tasks, even though many test cases are required for software verification. This paper presents an approach of applying a social network centrality measure, PageRank, to prioritize mutation test generation. The source code with the highest values of PageRank, will be focused first when developing their test cases as these modules are vulnerable for defects or anomalies which may cause the consequent defects in many other associated modules. Moreover, the approach would help identify the reducible test cases in the test suite, still maintaining the same criteria as the original number of test cases.

Keywords: Software testing, mutation test, network centrality measure, test case prioritization.

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Authors: Vitalice K. Oduol, C. Ardil

Abstract:

A method is presented for obtaining the error probability for block codes. The method is based on the eigenvalueeigenvector properties of the code correlation matrix. It is found that under a unary transformation and for an additive white Gaussian noise environment, the performance evaluation of a block code becomes a one-dimensional problem in which only one eigenvalue and its corresponding eigenvector are needed in the computation. The obtained error rate results show remarkable agreement between simulations and analysis.

Keywords: bit error rate, block codes, code correlation matrix, eigenstructure, soft-decision decoding, weight vector.

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Authors: Wen-Lung Huang, Shih-Pin Chen

Abstract:

This paper investigates the optimization problem of multi-product aggregate production planning (APP) with fuzzy data. From a comprehensive viewpoint of conserving the fuzziness of input information, this paper proposes a method that can completely describe the membership function of the performance measure. The idea is based on the well-known Zadeh-s extension principle which plays an important role in fuzzy theory. In the proposed solution procedure, a pair of mathematical programs parameterized by possibility level a is formulated to calculate the bounds of the optimal performance measure at a . Then the membership function of the optimal performance measure is constructed by enumerating different values of a . Solutions obtained from the proposed method contain more information, and can offer more chance to achieve the feasible disaggregate plan. This is helpful to the decision-maker in practical applications.

Keywords: fuzzy data, aggregate production planning, membership function, parametric programming

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Authors: Ghada Badr, Arwa Alturki

Abstract:

The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: Alignment, RNA secondary structure, pairwise, component-based, data mining.

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Authors: Elragig Aiman, Dreiwi Hanan, Townley Stuart, Elmabrook Idriss

Abstract:

In this paper, we reconsider the analysis of the Oregonator model. We highlight an error in this analysis which leads to an incorrect depiction of the parameter region in which diffusion driven instability is possible. We believe that the cause of the oversight is the complexity of stability analyses based on eigenvalues and the dependence on parameters of matrix minors appearing in stability calculations. We regenerate the parameter space where Turing patterns can be seen, and we use the common Lyapunov function (CLF) approach, which is numerically reliable, to further confirm the dependence of the results on diffusion coefficients intensities.

Keywords: Diffusion driven instability, common Lyapunov function (CLF), turing pattern, positive-definite matrix.

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