Search results for: CHAID Decision Tree Algorithm

Authors: Omar F. Hamad, T. Marwala

Abstract:

With optimized bandwidth and latency discrepancy ratios, Node Gain Scores (NGSs) are determined and used as a basis for shaping the max-heap overlay. The NGSs - determined as the respective bandwidth-latency-products - govern the construction of max-heap-form overlays. Each NGS is earned as a synergy of discrepancy ratio of the bandwidth requested with respect to the estimated available bandwidth, and latency discrepancy ratio between the nodes and the source node. The tree leads to enhanceddelivery overlay multicasting – increasing packet delivery which could, otherwise, be hindered by induced packet loss occurring in other schemes not considering the synergy of these parameters on placing the nodes on the overlays. The NGS is a function of four main parameters – estimated available bandwidth, Ba; individual node's requested bandwidth, Br; proposed node latency to its prospective parent (Lp); and suggested best latency as advised by source node (Lb). Bandwidth discrepancy ratio (BDR) and latency discrepancy ratio (LDR) carry weights of α and (1,000 - α ) , respectively, with arbitrary chosen α ranging between 0 and 1,000 to ensure that the NGS values, used as node IDs, maintain a good possibility of uniqueness and balance between the most critical factor between the BDR and the LDR. A max-heap-form tree is constructed with assumption that all nodes possess NGS less than the source node. To maintain a sense of load balance, children of each level's siblings are evenly distributed such that a node can not accept a second child, and so on, until all its siblings able to do so, have already acquired the same number of children. That is so logically done from left to right in a conceptual overlay tree. The records of the pair-wise approximate available bandwidths as measured by a pathChirp scheme at individual nodes are maintained. Evaluation measures as compared to other schemes – Bandwidth Aware multicaSt architecturE (BASE), Tree Building Control Protocol (TBCP), and Host Multicast Tree Protocol (HMTP) - have been conducted. This new scheme generally performs better in terms of trade-off between packet delivery ratio; link stress; control overhead; and end-to-end delays.

Keywords: Overlay multicast, Available bandwidth, Max-heapform overlay, Induced packet loss, Bandwidth-latency product, Node Gain Score (NGS).

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Authors: Watchara Songserm, Teeradej Wuttipornpun

Abstract:

This paper presents a genetic algorithm based permutation and non-permutation scheduling heuristics (GAPNP) to solve a multi-stage finite capacity material requirement planning (FCMRP) problem in automotive assembly flow shop with unrelated parallel machines. In the algorithm, the sequences of orders are iteratively improved by the GA characteristics, whereas the required operations are scheduled based on the presented permutation and non-permutation heuristics. Finally, a linear programming is applied to minimize the total cost. The presented GAPNP algorithm is evaluated by using real datasets from automotive companies. The required parameters for GAPNP are intently tuned to obtain a common parameter setting for all case studies. The results show that GAPNP significantly outperforms the benchmark algorithm about 30% on average.

Keywords: Finite capacity MRP, genetic algorithm, linear programming, flow shop, unrelated parallel machines, application in industries.

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Authors: Michiharu Maeda, Shinya Tsuda

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This paper presents an algorithm of particle swarm optimization with reduction for global optimization problems. Particle swarm optimization is an algorithm which refers to the collective motion such as birds or fishes, and a multi-point search algorithm which finds a best solution using multiple particles. Particle swarm optimization is so flexible that it can adapt to a number of optimization problems. When an objective function has a lot of local minimums complicatedly, the particle may fall into a local minimum. For avoiding the local minimum, a number of particles are initially prepared and their positions are updated by particle swarm optimization. Particles sequentially reduce to reach a predetermined number of them grounded in evaluation value and particle swarm optimization continues until the termination condition is met. In order to show the effectiveness of the proposed algorithm, we examine the minimum by using test functions compared to existing algorithms. Furthermore the influence of best value on the initial number of particles for our algorithm is discussed.

Keywords: Particle swarm optimization, Global optimization, Metaheuristics, Reduction.

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Authors: Rosshairy Abd Rahman, Chooi-Leng Ang, Razamin Ramli

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Feed is one of the factors which play an important role in determining a successful development of an aquaculture industry. It is always critical to produce the best aquaculture diet at a minimum cost in order to trim down the operational cost and gain more profit. However, the feed mix problem becomes increasingly difficult since many issues need to be considered simultaneously. Thus, the purpose of this paper is to review the current techniques used by nutritionist and researchers to tackle the issues. Additionally, this paper introduce an enhance algorithm which is deemed suitable to deal with all the issues arise. The proposed technique refers to Hybrid Genetic Algorithm which is expected to obtain the minimum cost diet for farmed animal, while satisfying nutritional requirements. Hybrid GA technique with artificial bee algorithm is expected to reduce the penalty function and provide a better solution for the feed mix problem.

Keywords: Artificial bee algorithm, feed mix problem, hybrid genetic algorithm.

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Authors: Ágnes Bogárdi-Mészöly, Takeshi Hashimoto, Shohei Yokoyama, Hiroshi Ishikawa

Abstract:

The spread of Web 2.0 has caused user-generated content explosion. Users can tag resources to describe and organize them. Tag clouds provide rough impression of relative importance of each tag within overall cloud in order to facilitate browsing among numerous tags and resources. The goal of our paper is to enrich visualization of tag clouds. A font distribution algorithm has been proposed to calculate a novel metric based on frequency and content, and to classify among classes from this metric based on power law distribution and percentages. The suggested algorithm has been validated and verified on the tag cloud of a real-world thesis portal.

Keywords: Tag cloud, font distribution algorithm, frequency-based, content-based, power law.

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Authors: Mouataz Zreika, Maria Estela Varua

Abstract:

Stock investment decisions are often made based on current events of the global economy and the analysis of historical data. Conversely, visual representation could assist investors’ gain deeper understanding and better insight on stock market trends more efficiently. The trend analysis is based on long-term data collection. The study adopts a hybrid method that combines the Clustering algorithm and Force-directed algorithm to overcome the scalability problem when visualizing large data. This method exemplifies the potential relationships between each stock, as well as determining the degree of strength and connectivity, which will provide investors another understanding of the stock relationship for reference. Information derived from visualization will also help them make an informed decision. The results of the experiments show that the proposed method is able to produced visualized data aesthetically by providing clearer views for connectivity and edge weights.

Keywords: Clustering, force-directed, graph drawing, stock investment analysis.

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Authors: N. Dahraoui, M. Boulakroune, D. Benatia

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In this paper, the improvement by deconvolution of the depth resolution in Secondary Ion Mass Spectrometry (SIMS) analysis is considered. Indeed, we have developed a new Tikhonov- Miller deconvolution algorithm where a priori model of the solution is included. This is a denoisy and pre-deconvoluted signal obtained from: firstly, by the application of wavelet shrinkage algorithm, secondly by the introduction of the obtained denoisy signal in an iterative deconvolution algorithm. In particular, we have focused the light on the effect of the iterations number on the evolution of the deconvoluted signals. The SIMS profiles are multilayers of Boron in Silicon matrix.

Keywords: DRF, in-depth resolution, multiresolution deconvolution, SIMS, wavelet shrinkage.

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Authors: Pavel Shcherban, Viktoria Ivanova, Alexander Neprokin, Vladislav Golovanov

Abstract:

Currently, LLC «Lukoil-Kaliningradmorneft» is implementing a comprehensive program for the development of offshore fields of the Kaliningrad region. This is largely associated with the depletion of the resource base of land in the region, as well as the positive results of geological investigation surrounding the Baltic Sea area and the data on the volume of hydrocarbon recovery from a single offshore field are working on the Kaliningrad region – D-6 «Kravtsovskoye».The article analyzes the main stages of the LLC «Lukoil-Kaliningradmorneft»’s development program for the development of the hydrocarbon resources of the region's shelf and suggests an optimization algorithm that allows managing a multi-criteria process of development of shelf deposits. The algorithm is formed on the basis of the problem of sequential decision making, which is a section of dynamic programming. Application of the algorithm during the consolidation of the initial data, the elaboration of project documentation, the further exploration and development of offshore fields will allow to optimize the complex of technical and technological solutions and increase the economic efficiency of the field development project implemented by LLC «Lukoil-Kaliningradmorneft».

Keywords: Offshore fields of hydrocarbons of the Baltic Sea, Development of offshore oil and gas fields, Optimization of the field development scheme, Solution of multi-criteria tasks in the oil and gas complex, Quality management of technical and technological processes.

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Authors: Sudipta Majumdar

Abstract:

This paper presents a method for identification of a linear time invariant (LTI) autonomous all pole system using singular value decomposition. The novelty of this paper is two fold: First, MUSIC algorithm for estimating complex frequencies from real measurements is proposed. Secondly, using the proposed algorithm, we can identify the coefficients of differential equation that determines the LTI system by switching off our input signal. For this purpose, we need only to switch off the input, apply our complex MUSIC algorithm and determine the coefficients as symmetric polynomials in the complex frequencies. This method can be applied to unstable system and has higher resolution as compared to time series solution when, noisy data are used. The classical performance bound, Cramer Rao bound (CRB), has been used as a basis for performance comparison of the proposed method for multiple poles estimation in noisy exponential signal.

Keywords: MUSIC algorithm, Cramer Rao bound, frequency estimation.

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Authors: Elham Jelodari Mamaghani, Christian Prins, Haoxun Chen

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In this paper, there is concentration on collaborative transportation planning (CTP) among multiple carriers with pickup and delivery requests and time windows. This problem is a vehicle routing problem with constraints from standard vehicle routing problems and new constraints from a real-world application. In the problem, each carrier has a finite number of vehicles, and each request is a pickup and delivery request with time window. Moreover, each carrier has reserved requests, which must be served by itself, whereas its exchangeable requests can be outsourced to and served by other carriers. This collaboration among carriers can help them to reduce total transportation costs. A mixed integer programming model is proposed to the problem. To solve the model, a hybrid algorithm that combines Genetic Algorithm and Simulated Annealing (GASA) is proposed. This algorithm takes advantages of GASA at the same time. After tuning the parameters of the algorithm with the Taguchi method, the experiments are conducted and experimental results are provided for the hybrid algorithm. The results are compared with those obtained by a commercial solver. The comparison indicates that the GASA significantly outperforms the commercial solver.

Keywords: Centralized collaborative transportation, collaborative transportation with pickup and delivery, collaborative transportation with time windows, hybrid algorithm of GA and SA.

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Authors: Morteza Moazami-Goudarzi, Mohammad H. Moradi, Ali Taheri

Abstract:

In this paper we introduce an effective ECG compression algorithm based on two dimensional multiwavelet transform. Multiwavelets offer simultaneous orthogonality, symmetry and short support, which is not possible with scalar two-channel wavelet systems. These features are known to be important in signal processing. Thus multiwavelet offers the possibility of superior performance for image processing applications. The SPIHT algorithm has achieved notable success in still image coding. We suggested applying SPIHT algorithm to 2-D multiwavelet transform of2-D arranged ECG signals. Experiments on selected records of ECG from MIT-BIH arrhythmia database revealed that the proposed algorithm is significantly more efficient in comparison with previously proposed ECG compression schemes.

Keywords: ECG signal compression, multi-rateprocessing, 2-D Multiwavelet, Prefiltering.

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Authors: Satyendra Pratap Singh, S. P. Singh

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This paper presents a methodology using Gravitational Search Algorithm for optimal placement of Phasor Measurement Units (PMUs) in order to achieve complete observability of the power system. The objective of proposed algorithm is to minimize the total number of PMUs at the power system buses, which in turn minimize installation cost of the PMUs. In this algorithm, the searcher agents are collection of masses which interact with each other using Newton’s laws of gravity and motion. This new Gravitational Search Algorithm based method has been applied to the IEEE 14-bus, IEEE 30-bus and IEEE 118-bus test systems. Case studies reveal optimal number of PMUs with better observability by proposed method.

Keywords: Gravitational Search Algorithm (GSA), Law of Motion, Law of Gravity, Observability, Phasor Measurement Unit.

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Authors: Pınar Tüfekçi, Yılmaz Kılıçaslan

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In this paper we present a computational model for pronominal anaphora resolution in Turkish. The model is based on Hobbs’ Naїve Algorithm [4, 5, 6], which exploits only the surface syntax of sentences in a given text.

Keywords: Anaphora Resolution, Pronoun Resolution, Syntax based Algorithms, Naїve Algorithm.

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Authors: Xun Ge, Jianhua Gong

Abstract:

 

ankings for output of Chinese main agricultural commodity in the world for 1978, 1980, 1990, 2000, 2006, 2007 and 2008 have been released in United Nations FAO Database. Unfortunately, where the ranking of output of Chinese cotton lint in the world for 2008 was missed. This paper uses sequential data mining methods with decision rules filling this gap. This new data mining method will be help to give a further improvement for United Nations FAO Database.

Keywords: Ranking, output of the main agricultural commodity, gross domestic product, decision table, information system, data mining, decision rule

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Authors: Chia-Hung Chen, Shangyao Yan

Abstract:

The solution algorithm, based on Lagrangian relaxation, a sub-gradient method and a heuristic to find the upper bound of the solution, is proposed to solve the coordinated fleet routing and flight scheduling problems. Numerical tests are performed to evaluate the proposed algorithm using real operating data from two Taiwan airlines. The test results indicate that the solution algorithm is a significant improvement over those obtained with CPLEX, consequently they could be useful for allied airlines to solve coordinated fleet routing and flight scheduling problems.

Keywords: Coordinated flight scheduling, multiple commodity network flow problem, Lagrangian relaxation.

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Authors: Nien-Zheng Yew, Kung-Ming Tiong, Su-Ting Yong

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Number Link is a Japanese logic puzzle where pairs of same numbers are connected using lines. Number Link can be regarded as a dynamic multiple travelers, multiple entries and exits maze, where the walls and passages are dynamically changing as the travelers move. In this paper, we apply the Tremaux’s algorithm to solve Number Link puzzles of size 8x8, 10x10 and 15x20. The algorithm works well and produces a solution for puzzles of size 8x8 and 10x10. However, solving a puzzle of size 15x20 requires high computer processing power and is time consuming.

Keywords: Number Link, maze, puzzle, Tremaux’s algorithm

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Authors: Christiono Utomo, Arazi Idrus, Madzlan Napiah, Mohd. Faris Khamidi

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This paper presents a conceptual model of agreement options on negotiation support for civil engineering decision. The negotiation support facilitates the solving of group choice decision making problems in civil engineering decision to reduce the impact of mud volcano disaster in Sidoarjo, Indonesia. The approach based on application of analytical hierarchy process (AHP) method for multi criteria decision on three level of decision hierarchy. Decisions for reducing impact is very complicated since many parties involved in a critical time. Where a number of stakeholders are involved in choosing a single alternative from a set of solution alternatives, there are different concern caused by differing stakeholder preferences, experiences, and background. Therefore, a group choice decision support is required to enable each stakeholder to evaluate and rank the solution alternatives before engaging into negotiation with the other stakeholders. Such civil engineering solutions as alternatives are referred to as agreement options that are determined by identifying the possible stakeholder choice, followed by determining the optimal solution for each group of stakeholder. Determination of the optimal solution is based on a game theory model of n-person general sum game with complete information that involves forming coalitions among stakeholders.

Keywords: Agreement options, AHP, agent, negotiation, multicriteria, game theory, and coalition.

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Authors: Deepanshu Kaushal, T. Shanmuganantham

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This paper draws a comparison between two microstrip patch antennas having different ground structures. The designs utilize 45 mm x 40 mm x 1.6 mm FR4 epoxy substrate (relative permittivity of 4.4 and dielectric loss tangent of 0.02) and CPW feeding technique. The design 1 uses conducting partial ground plates along the two sides of the radiating X’mas tree shaped patch. The design 2 utilizes an X’mas tree shaped slotted ground structure that features a circular radiating patch. A comparative analysis of results of both designs has been carried. The two designs are intended to serve the fixed satellite applications in X and Ku band respectively.

Keywords: CPW feed, partial ground structures, slotted ground structures, fixed satellite applications.

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Authors: Xun Ge

Abstract:

Recently, X. Ge and J. Qian investigated some relations between higher mathematics scores and calculus scores (resp. linear algebra scores, probability statistics scores) for Chinese university students. Based on rough-set theory, they established an information system S = (U,CuD,V, f). In this information system, higher mathematics score was taken as a decision attribute and calculus score, linear algebra score, probability statistics score were taken as condition attributes. They investigated importance of each condition attribute with respective to decision attribute and strength of each condition attribute supporting decision attribute. In this paper, we give further investigations for this issue. Based on the above information system S = (U, CU D, V, f), we analyze the decision rules between condition and decision granules. For each x E U, we obtain support (resp. strength, certainty factor, coverage factor) of the decision rule C —>x D, where C —>x D is the decision rule induced by x in S = (U, CU D, V, f). Results of this paper gives new analysis of on higher mathematics scores for Chinese university students, which can further lead Chinese university students to raise higher mathematics scores in Chinese graduate student entrance examination.

Keywords: Rough set, support, strength, certainty factor, coverage factor.

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Authors: R. C. Joshi, Shashikala Tapaswi

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The paper proposes an approach using genetic algorithm for computing the region based image similarity. The image is denoted using a set of segmented regions reflecting color and texture properties of an image. An image is associated with a family of image features corresponding to the regions. The resemblance of two images is then defined as the overall similarity between two families of image features, and quantified by a similarity measure, which integrates properties of all the regions in the images. A genetic algorithm is applied to decide the most plausible matching. The performance of the proposed method is illustrated using examples from an image database of general-purpose images, and is shown to produce good results.

Keywords: Image Features, color descriptor, segmented classes, texture descriptors, genetic algorithm.

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Authors: Nabilah Filzah Mohd Radzuan, Andi Putra, Zalinda Othman, Azuraliza Abu Bakar, Abdul Razak Hamdan

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Precipitation forecast is important in avoid incident of natural disaster which can cause loss in involved area. This review paper involves three techniques from artificial intelligence namely logistic regression, decisions tree, and random forest which used in making precipitation forecast. These combination techniques through VAR model in finding advantages and strength for every technique in forecast process. Data contains variables from rain domain. Adaptation of artificial intelligence techniques involved on rain domain enables the process to be easier and systematic for precipitation forecast.

Keywords: Logistic regression, decisions tree, random forest, VAR model.

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Authors: Jian Shi, Baoguo Yu, Haonan Jia, Meng Liu, Ping Huang

Abstract:

Adapting to the flexibility of war, a large number of guided weapons launch from aircraft. Therefore, the inertial navigation system loaded in the weapon needs to undergo an alignment process in the air. This article proposes the following methods to the problem of inaccurate modeling of the system under large misalignment angles, the accuracy reduction of filtering caused by outliers, and the noise changes in GPS signals: first, considering the large misalignment errors of Strapdown Inertial Navigation System (SINS)/GPS, a more accurate model is made rather than to make a small-angle approximation, and the Unscented Kalman Filter (UKF) algorithms are used to estimate the state; then, taking into account the impact of GPS noise changes on the fine alignment algorithm, the innovation adaptive filtering algorithm is introduced to estimate the GPS’s noise in real-time; at the same time, in order to improve the anti-interference ability of the air fine alignment algorithm, a robust filtering algorithm based on outlier detection is combined with the air fine alignment algorithm to improve the robustness of the algorithm. The algorithm can improve the alignment accuracy and robustness under interference conditions, which is verified by simulation.

Keywords: Air alignment, fine alignment, inertial navigation system, integrated navigation system, UKF.

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Authors: Faruq A. Al-Omari, Nabeel I. Al-Fayoumi

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In this paper, we present a new algorithm for clustering data in large datasets using image processing approaches. First the dataset is mapped into a binary image plane. The synthesized image is then processed utilizing efficient image processing techniques to cluster the data in the dataset. Henceforth, the algorithm avoids exhaustive search to identify clusters. The algorithm considers only a small set of the data that contains critical boundary information sufficient to identify contained clusters. Compared to available data clustering techniques, the proposed algorithm produces similar quality results and outperforms them in execution time and storage requirements.

Keywords: Data clustering, Data mining, Image-mapping, Pattern discovery, Predictive analysis.

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Authors: Debashree Guha, Debjani Chakraborty

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The aim of this paper is to adopt a compromise ratio (CR) methodology for fuzzy multi-attribute single-expert decision making proble. In this paper, the rating of each alternative has been described by linguistic terms, which can be expressed as triangular fuzzy numbers. The compromise ratio method for fuzzy multi-attribute single expert decision making has been considered here by taking the ranking index based on the concept that the chosen alternative should be as close as possible to the ideal solution and as far away as possible from the negative-ideal solution simultaneously. From logical point of view, the distance between two triangular fuzzy numbers also is a fuzzy number, not a crisp value. Therefore a fuzzy distance measure, which is itself a fuzzy number, has been used here to calculate the difference between two triangular fuzzy numbers. Now in this paper, with the help of this fuzzy distance measure, it has been shown that the compromise ratio is a fuzzy number and this eases the problem of the decision maker to take the decision. The computation principle and the procedure of the compromise ratio method have been described in detail in this paper. A comparative analysis of the compromise ratio method previously proposed [1] and the newly adopted method have been illustrated with two numerical examples.

Keywords: Compromise ratio method, Fuzzy multi-attributesingle-expert decision making, Fuzzy number, Linguistic variable

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Authors: Na Li

Abstract:

This paper describes a new measuring algorithm for three-dimensional (3-D) braided composite material .Braided angle is an important parameter of braided composites. The objective of this paper is to present an automatic measuring system. In the paper, the algorithm is performed by using vcµ6.0 language on PC. An advanced filtered algorithm for image of 3-D braided composites material performs has been developed. The procedure is completely automatic and relies on the gray scale information content of the images and their local wavelet transform modulus maxims. Experimental results show that the proposed method is feasible. The algorithm was tested on both carbon-fiber and glass-fiber performs.

Keywords: Three-Dimensional composite material, Mathematical morphology.

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Authors: Kassem Saleh

Abstract:

Decision Support System (DSS) are interactive software systems that are built to assist the management of an organization in the decision making process when faced with nonroutine problems in a specific application domain. Non-functional requirements (NFRs) for a DSS deal with the desirable qualities and restrictions that the DSS functionalities must satisfy. Unlike the functional requirements, which are tangible functionalities provided by the DSS, NFRs are often hidden and transparent to DSS users but affect the quality of the provided functionalities. NFRs are often overlooked or added later to the system in an ad hoc manner, leading to a poor overall quality of the system. In this paper, we discuss the development of NFRs as part of the requirements engineering phase of the system development life cycle of DSSs. To help eliciting NFRs, we provide a comprehensive taxonomy of NFRs for DSSs.

Keywords: Decision support system, Development, Elicitation, Non-functional requirements, Taxonomy

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Authors: Harpreet Singh Dhillon, Abhijit Mitra

Abstract:

A reduced-bit multiplication algorithm based on the ancient Vedic multiplication formulae is proposed in this paper. Both the Vedic multiplication formulae, Urdhva tiryakbhyam and Nikhilam, are first discussed in detail. Urdhva tiryakbhyam, being a general multiplication formula, is equally applicable to all cases of multiplication. It is applied to the digital arithmetic and is shown to yield a multiplier architecture which is very similar to the popular array multiplier. Due to its structure, it leads to a high carry propagation delay in case of multiplication of large numbers. Nikhilam Sutra, on the other hand, is more efficient in the multiplication of large numbers as it reduces the multiplication of two large numbers to that of two smaller numbers. The framework of the proposed algorithm is taken from this Sutra and is further optimized by use of some general arithmetic operations such as expansion and bit-shifting to take advantage of bit-reduction in multiplication. We illustrate the proposed algorithm by reducing a general 4x4-bit multiplication to a single 2 x 2-bit multiplication operation.

Keywords: Multiplication, algorithm, Vedic mathematics, digital arithmetic, reduced-bit.

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Authors: Yuji Kageyama, Shin Nagata, Tatsuya Takino, Izuru Nomura, Hiroyuki Kamata

Abstract:

In previous study, technique to estimate a self-location by using a lunar image is proposed.We consider the improvement of the conventional method in consideration of FPGA implementationin this paper. Specifically, we introduce Artificial Bee Colony algorithm for reduction of search time.In addition, we use fixed point arithmetic to enable high-speed operation on FPGA.

Keywords: SLIM, Artificial Bee Colony Algorithm, Location Estimate.

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Authors: Jorge Cardoso

Abstract:

Workflow Management Systems (WfMS) alloworganizations to streamline and automate business processes and reengineer their structure. One important requirement for this type of system is the management and computation of the Quality of Service(QoS) of processes and workflows. Currently, a range of Web processes and workflow languages exist. Each language can be characterized by the set of patterns they support. Developing andimplementing a suitable and generic algorithm to compute the QoSof processes that have been designed using different languages is a difficult task. This is because some patterns are specific to particular process languages and new patterns may be introduced in future versions of a language. In this paper, we describe an adaptive algorithm implemented to cope with these two problems. The algorithm is called adaptive since it can be dynamically changed as the patterns of a process language also change.

Keywords: quality of service, web processes, workflows, web services

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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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