Search results for: Analytic Models
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 2707

Search results for: Analytic Models

1117 Generation Scheduling Optimization of Multi-Hydroplants: A Case Study

Authors: Shuangquan Liu, Jinwen Wang, Dada Wang

Abstract:

A case study of the generation scheduling optimization of the multi-hydroplants on the Yuan River Basin in China is reported in this paper. Concerning the uncertainty of the inflows, the long/mid-term generation scheduling (LMTGS) problem is solved by a stochastic model in which the inflows are considered as stochastic variables. For the short-term generation scheduling (STGS) problem, a constraint violation priority is defined in case not all constraints are satisfied. Provided the stage-wise separable condition and low dimensions, the hydroplant-based operational region schedules (HBORS) problem is solved by dynamic programming (DP). The coordination of LMTGS and STGS is presented as well. The feasibility and the effectiveness of the models and solution methods are verified by the numerical results.

Keywords: generation scheduling, multi-hydroplants, optimization.

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1116 Decision Support Framework in Managerial Learning Environment for Organization

Authors: M. Mazhar Manzoor, Nasar.A, A. Sattar

Abstract:

In the open space of decision support system the mental impression of a manager-s decision has been the subject of large importance than the ordinary famous one, when helped by decision support system. Much of this study is an attempt to realize the relation of decision support system usage and decision outcomes that governs the system. For example, several researchers have proposed so many different models to analyze the linkage between decision support system processes and results of decision making. This study draws the important relation of manager-s mental approach with the use of decision support system. The findings of this paper are theoretical attempts to provide Decision Support System (DSS) in a way to exhibit and promote the learning in semi structured area. The proposed model shows the points of one-s learning improvements and maintains a theoretical approach in order to explore the DSS contribution in enhancing the decision forming and governing the system.

Keywords: Decision Support System , Learning Organization,

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1115 2D Numerical Analysis of Sao Paulo Tunnel

Authors: A.H. Akhaveissy

Abstract:

Nonlinear finite element method and Serendipity eight nodes element are used for determining of ground surface settlement due to tunneling. Linear element with elastic behavior is used for modeling of lining. Modified Generalized plasticity model with nonassociated flow rule is applied for analysis of a tunnel in Sao Paulo – Brazil. The tunnel had analyzed by Lades- model with 16 parameters. In this work modified Generalized Plasticity is used with 10 parameters, also Mohr-Coulomb model is used to analysis the tunnel. The results show good agreement with observed results of field data by modified Generalized Plasticity model than other models. The obtained result by Mohr-Coulomb model shows less settlement than other model due to excavation.

Keywords: Non-associated flow rule, Generalized plasticity, tunnel excavation, Excavation method.

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1114 Implementing Activity-Based Costing in Architectural Aluminum Projects: Case Study and Lessons Learned

Authors: Amer Momani, Tarek Al-Hawari, Abdallah Alakayleh

Abstract:

This study explains how to construct an actionable activity-based costing and management system to accurately track and account the total costs of architectural aluminum projects. Two Activity-Based Costing (ABC) models were proposed to accomplish this purpose. First, the learning and development model was introduced to examine how to apply an ABC model in an architectural aluminum firm for the first time and to be familiar with ABC concepts. Second, an actual ABC model was built on the basis of the results of the previous model to accurately trace the actual costs incurred on each project in a year, and to be able to provide a quote with the best trade-off between competitiveness and profitability. The validity of the proposed model was verified on a local architectural aluminum company.

Keywords: Activity-based costing, activity-based management, construction, architectural aluminum.

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1113 Fatigue Life of an Anti-Roll Bar of a Passenger Vehicle

Authors: J. Marzbanrad, A. Yadollahi

Abstract:

In the present paper, Fatigue life assessment of an anti-roll bar component of a passenger vehicle, is investigated by ANSYS 11 software. A stress analysis is also carried out by the finite element technique for the determination of highly stressed regions on the bar. Anti-roll bar is a suspension element used at the front, rear, or at both ends of a car that reduces body roll by resisting any unequal vertical motion between the pair of wheels to which it is connected. As a first stage, fatigue damage models proposed by some well-known references and the corresponding assumptions are discussed and some enhancements are proposed. Then, fracture analysis of an anti-roll bar of an automobile is carried out. The analysed type of the anti-roll bar is especially important as many cases are reported about the fracture after a 100,000 km of travel fatigue and fracture conditions. This paper demonstrates fatigue life of an anti-roll bar and then evaluated by experimental analytically results from other researcher.

Keywords: Anti-roll bar, Fracture, Fatigue life, Random loading

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1112 Contact Stress Analysis of Spur Gear Teeth Pair

Authors: Ali Raad Hassan

Abstract:

Contact stress analysis between two spur gear teeth was considered in different contact positions, representing a pair of mating gears during rotation. A programme has been developed to plot a pair of teeth in contact. This programme was run for each 3° of pinion rotation from the first location of contact to the last location of contact to produce 10 cases. Each case was represented a sequence position of contact between these two teeth. The programme gives graphic results for the profiles of these teeth in each position and location of contact during rotation. Finite element models were made for these cases and stress analysis was done. The results were presented and finite element analysis results were compared with theoretical calculations, wherever available.

Keywords: Contact stress, Spur gear, Contact ratio, Finite elements

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1111 Terrain Classification for Ground Robots Based on Acoustic Features

Authors: Bernd Kiefer, Abraham Gebru Tesfay, Dietrich Klakow

Abstract:

The motivation of our work is to detect different terrain types traversed by a robot based on acoustic data from the robot-terrain interaction. Different acoustic features and classifiers were investigated, such as Mel-frequency cepstral coefficient and Gamma-tone frequency cepstral coefficient for the feature extraction, and Gaussian mixture model and Feed forward neural network for the classification. We analyze the system’s performance by comparing our proposed techniques with some other features surveyed from distinct related works. We achieve precision and recall values between 87% and 100% per class, and an average accuracy at 95.2%. We also study the effect of varying audio chunk size in the application phase of the models and find only a mild impact on performance.

Keywords: Terrain classification, acoustic features, autonomous robots, feature extraction.

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1110 Testing of Materials for Rapid Prototyping Fused Deposition Modelling Technology

Authors: L. Novakova-Marcincinova, J. Novak-Marcincin

Abstract:

Paper presents knowledge about types of test in area of materials properties of selected methods of rapid prototyping technologies. In today used rapid prototyping technologies for production of models and final parts are used materials in initial state as solid, liquid or powder material structure. In solid state are used various forms such as pellets, wire or laminates. Basic range materials include paper, nylon, wax, resins, metals and ceramics. In Fused Deposition Modeling (FDM) rapid prototyping technology are mainly used as basic materials ABS (Acrylonitrile Butadiene Styrene), polyamide, polycarbonate, polyethylene and polypropylene. For advanced FDM applications are used special materials as silicon nitrate, PZT (Piezoceramic Material - Lead Zirconate Titanate), aluminium oxide, hydroxypatite and stainless steel.

Keywords: Rapid prototyping, materials, testing of materials.

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1109 Multidisciplinary and Multilevel Design Methodology of Unmanned Aerial Vehicles Using Enhanced Collaborative Optimization

Authors: Pedro F. Albuquerque, Pedro V. Gamboa, Miguel A. Silvestre

Abstract:

The present work describes the implementation of the Enhanced Collaborative Optimization (ECO) multilevel architecture with a gradient-based optimization algorithm with the aim of performing a multidisciplinary design optimization of a generic unmanned aerial vehicle with morphing technologies. The concepts of weighting coefficient and dynamic compatibility parameter are presented for the ECO architecture. A routine that calculates the aircraft performance for the user defined mission profile and vehicle’s performance requirements has been implemented using low fidelity models for the aerodynamics, stability, propulsion, weight, balance and flight performance. A benchmarking case study for evaluating the advantage of using a variable span wing within the optimization methodology developed is presented.

Keywords: Multidisciplinary, Multilevel, Morphing, Enhanced Collaborative Optimization (ECO).

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1108 Decoupled Scheduling in Meta Environment

Authors: Ponsy R.K. Sathia Bhama, Thamarai Selvi Soma Sundaram, R. Sivakama Sundari, R. Bakiyalakshmi, K. Thamizharasi

Abstract:

Grid scheduling is the process of mapping grid jobs to resources over multiple administrative domains. Traditionally, application-level schedulers have been tightly integrated with the application itself and were not easily applied to other applications. This design is generic that decouples the scheduler core (the search procedure) from the application-specific (e.g. application performance models) and platform-specific (e.g. collection of resource information) components used by the search procedure. In this decoupled approach the application details are not revealed completely to broker, but customer will give the application to resource provider for execution. In a decoupled approach, apart from scheduling, the resource selection can be performed independently in order to achieve scalability.

Keywords: Meta, grid scheduling, application-level scheduler, decouple, scheduler core and performance model.

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1107 Tongue Diagnosis System Based on PCA and SVM

Authors: Jin-Woong Park, Sun-Kyung Kang, Sung-Tae Jung

Abstract:

In this study, we propose a tongue diagnosis method which detects the tongue from face image and divides the tongue area into six areas, and finally generates tongue coating ratio of each area. To detect the tongue area from face image, we use ASM as one of the active shape models. Detected tongue area is divided into six areas widely used in the Korean traditional medicine and the distribution of tongue coating of the six areas is examined by SVM(Support Vector Machine). For SVM, we use a 3-dimensional vector calculated by PCA(Principal Component Analysis) from a 12-dimentional vector consisting of RGB, HIS, Lab, and Luv. As a result, we detected the tongue area stably using ASM and found that PCA and SVM helped raise the ratio of tongue coating detection.

Keywords: Active Shape Model, Principal Component Analysis, Support Vector Machine, Tongue diagnosis

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1106 Impovement of a Label Extraction Method for a Risk Search System

Authors: Shigeaki Sakurai, Ryohei Orihara

Abstract:

This paper proposes an improvement method of classification efficiency in a classification model. The model is used in a risk search system and extracts specific labels from articles posted at bulletin board sites. The system can analyze the important discussions composed of the articles. The improvement method introduces ensemble learning methods that use multiple classification models. Also, it introduces expressions related to the specific labels into generation of word vectors. The paper applies the improvement method to articles collected from three bulletin board sites selected by users and verifies the effectiveness of the improvement method.

Keywords: Text mining, Risk search system, Corporate reputation, Bulletin board site, Ensemble learning

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1105 A New Muscle Architecture Model with Non-Uniform Distribution of Muscle Fiber Types

Authors: Javier Navallas, Armando Malanda, Luis Gila, Javier Rodriguez, Ignacio Rodriguez

Abstract:

According to previous studies, some muscles present a non-homogeneous spatial distribution of its muscle fiber types and motor unit types. However, available muscle models only deal with muscles with homogeneous distributions. In this paper, a new architecture muscle model is proposed to permit the construction of non-uniform distributions of muscle fibers within the muscle cross section. The idea behind is the use of a motor unit placement algorithm that controls the spatial overlapping of the motor unit territories of each motor unit type. Results show the capabilities of the new algorithm to reproduce arbitrary muscle fiber type distributions.

Keywords: muscle model, muscle architecture, motor unit, EMG simulation.

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1104 Using Degree of Adaptive (DOA) Model for Partner Selection in Supply Chain

Authors: Habibollah Javanmard

Abstract:

In order to reduce cost, increase quality, and for timely supplying production systems has considerably taken the advantages of supply chain management and these advantages are also competitive. Selection of appropriate supplier has an important role in improvement and efficiency of systems. The models of supplier selection which have already been used by researchers have considered selection one or more suppliers from potential suppliers but in this paper selecting one supplier as partner from one supplier that have minimum one period supplying to buyer is considered. This paper presents a conceptual model for partner selection and application of Degree of Adoptive (DOA) model for final selection. The attributes weight in this model is prepared through AHP model. After making the descriptive model, determining the attributes and measuring the parameters of the adaptive is examined in an auto industry of Iran(Zagross Khodro co.) and results are presented.

Keywords: Partnership, Degree of Adaptive, AHP, SupplyChain.

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1103 A Performance Model for Designing Network in Reverse Logistic

Authors: S. Dhib, S. A. Addouche, T. Loukil, A. Elmhamedi

Abstract:

In this paper, a reverse supply chain network is investigated for a decision making. This decision is surrounded by complex flows of returned products, due to the increasing quantity, the type of returned products and the variety of recovery option products (reuse, recycling, and refurbishment). The most important problem in the reverse logistic network (RLN) is to orient returned products to the suitable type of recovery option. However, returned products orientations from collect sources to the recovery disposition have not well considered in performance model. In this study, we propose a performance model for designing a network configuration on reverse logistics. Conceptual and analytical models are developed with taking into account operational, economic and environmental factors on designing network.

Keywords: Reverse logistics, Network design, Performance model, Open loop configuration.

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1102 Electronic Auction Market in Croatia

Authors: Bojan Korizma, Zeljko Panian

Abstract:

Online auctions are not very popular in Croatia. The main reason for this is a very limited number of services which can be used by Croatian users. Until recent times, even selling through the most popular online auction site eBay wasn't possible because PayPal services could not make payment to bank or debit card accounts in Croatia. Furthermore, many foreign sellers do not offer delivery of their products to Croatia which means that large quantities of goods initially offered on such sites are not available. With that in mind, it is necessary to analyze the buying and selling habits of Croatian users and existing online auction sites, both Croatian and foreign, and create a model for new domestic site. This site will have to exploit every positive aspect of existing models and neutralize every negative perception indicated by users in the survey so that, hopefully, it would attract new users.

Keywords: online auction, eBay, safe payment, product delivery

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1101 A Preliminary Study for Design of Automatic Block Reallocation Algorithm with Genetic Algorithm Method in the Land Consolidation Projects

Authors: Tayfun Çay, Yaşar İnceyol, Abdurrahman Özbeyaz

Abstract:

Land reallocation is one of the most important steps in land consolidation projects. Many different models were proposed for land reallocation in the literature such as Fuzzy Logic, block priority based land reallocation and Spatial Decision Support Systems. A model including four parts is considered for automatic block reallocation with genetic algorithm method in land consolidation projects. These stages are preparing data tables for a project land, determining conditions and constraints of land reallocation, designing command steps and logical flow chart of reallocation algorithm and finally writing program codes of Genetic Algorithm respectively. In this study, we designed the first three steps of the considered model comprising four steps.

Keywords: Genetic algorithm, land consolidation, landholding, land reallocation.

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1100 Simulation of Dynamics of a Permanent Magnet Linear Actuator

Authors: Ivan Yatchev, Ewen Ritchie

Abstract:

Comparison of two approaches for the simulation of the dynamic behaviour of a permanent magnet linear actuator is presented. These are full coupled model, where the electromagnetic field, electric circuit and mechanical motion problems are solved simultaneously, and decoupled model, where first a set of static magnetic filed analysis is carried out and then the electric circuit and mechanical motion equations are solved employing bi-cubic spline approximations of the field analysis results. The results show that the proposed decoupled model is of satisfactory accuracy and gives more flexibility when the actuator response is required to be estimated for different external conditions, e.g. external circuit parameters or mechanical loads.

Keywords: Coupled problems, dynamic models, finite elementanalysis, linear actuators, permanent magnets.

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1099 Effects of Nanolayer Structure and Brownian Motion of Particles in Thermal Conductivity Enhancement of Nanofluids

Authors: M. Izadi, S. Hossainpour, D. Jalali-Vahid

Abstract:

Nanofluids are novel fluids that are going to have an important role in future industrial thermal device designs. Studies are being predominantly conducted on the mechanism of these heat transfers. The key to this attraction is in the increase in thermal conductivity brought about by the Nanofluids compared with the base fluid. Different models have been proposed for calculation of effective thermal conduction that has been gradually modified. In this investigation effect of nanolayer structure and Brownian motion of particles are studied and a new modified thermal conductivity model is proposed. Temperature, concentration, nanolayer thickness and particle size are taken as variables and their effect are studied simultaneously on the thermal conductivity of the fluids, showing the concentration of the nanoparticles to affect the nanolayer thickness which also affects the Brownian motion.

Keywords: Relative thermal conductivity, Brownian motion, Nanolayer structure.

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1098 Dynamic Interaction Network to Model the Interactive Patterns of International Stock Markets

Authors: Laura Lukmanto, Harya Widiputra, Lukas

Abstract:

Studies in economics domain tried to reveal the correlation between stock markets. Since the globalization era, interdependence between stock markets becomes more obvious. The Dynamic Interaction Network (DIN) algorithm, which was inspired by a Gene Regulatory Network (GRN) extraction method in the bioinformatics field, is applied to reveal important and complex dynamic relationship between stock markets. We use the data of the stock market indices from eight countries around the world in this study. Our results conclude that DIN is able to reveal and model patterns of dynamic interaction from the observed variables (i.e. stock market indices). Furthermore, it is also found that the extracted network models can be utilized to predict movement of the stock market indices with a considerably good accuracy.

Keywords: complex dynamic relationship, dynamic interaction network, interactive stock markets, stock market interdependence.

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1097 A MATLAB Simulink Library for Transient Flow Simulation of Gas Networks

Authors: M. Behbahani-Nejad, A. Bagheri

Abstract:

An efficient transient flow simulation for gas pipelines and networks is presented. The proposed transient flow simulation is based on the transfer function models and MATLABSimulink. The equivalent transfer functions of the nonlinear governing equations are derived for different types of the boundary conditions. Next, a MATLAB-Simulink library is developed and proposed considering any boundary condition type. To verify the accuracy and the computational efficiency of the proposed simulation, the results obtained are compared with those of the conventional finite difference schemes (such as TVD, method of lines, and other finite difference implicit and explicit schemes). The effects of the flow inertia and the pipeline inclination are incorporated in this simulation. It is shown that the proposed simulation has a sufficient accuracy and it is computationally more efficient than the other methods.

Keywords: Gas network, MATLAB-Simulink, transfer functions, transient flow.

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1096 Simultaneous Determination of Reference Free-Stream Temperature and Convective Heat Transfer Coefficient

Authors: Giho Jeong, Sooin Jeong, Kuisoon Kim

Abstract:

It is very important to determine reference temperature when convective temperature because it should be used to calculate the temperature potential. This paper deals with the development of a new method that can determine heat transfer coefficient and reference free stream temperature simultaneously, based on transient heat transfer experiments with using two narrow band thermo-tropic liquid crystals (TLC's). The method is validated through error analysis in terms of the random uncertainties in the measured temperatures. It is shown how the uncertainties in heat transfer coefficient and free stream temperature can be reduced. The general method described in this paper is applicable to many heat transfer models with unknown free stream temperature.

Keywords: Heat transfer coefficient, Thermo-tropic LiquidCrystal (TLC), Free stream temperature.

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1095 Optimal Sizing of SSSC Controllers to Minimize Transmission Loss and a Novel Model of SSSC to Study Transient Response

Authors: A. M. El-Zonkoly

Abstract:

In this paper, based on steady-state models of Flexible AC Transmission System (FACTS) devices, the sizing of static synchronous series compensator (SSSC) controllers in transmission network is formed as an optimization problem. The objective of this problem is to reduce the transmission losses in the network. The optimization problem is solved using particle swarm optimization (PSO) technique. The Newton-Raphson load flow algorithm is modified to consider the insertion of the SSSC devices in the network. A numerical example, illustrating the effectiveness of the proposed algorithm, is introduced. In addition, a novel model of a 3- phase voltage source converter (VSC) that is suitable for series connected FACTS a controller is introduced. The model is verified by simulation using Power System Blockset (PSB) and Simulink software.

Keywords: FACTS, Modeling, PSO, SSSC, Transmission lossreduction.

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1094 An Algorithm of Regulation of Glucose-Insulin Concentration in the Blood

Authors: B. Selma, S. Chouraqui

Abstract:

The pancreas is an elongated organ that extends across the abdomen, below the stomach. In addition, it secretes certain enzymes that aid in food digestion. The pancreas also manufactures hormones responsible for regulating blood glucose levels. In the present paper, we propose a mathematical model to study the homeostasis of glucose and insulin in healthy human, and a simulation of this model, which depicts the physiological events after a meal, will be represented in ordinary humans. The aim of this paper is to design an algorithm which regulates the level of glucose in the blood. The algorithm applied the concept of expert system for performing an algorithm control in the form of an "active" used to prescribe the rate of insulin infusion. By decomposing the system into subsystems, we have developed parametric models of each subsystem by using a forcing function strategy. The results showed a performance of the control system.

Keywords: Modeling, algorithm, regulation, glucose-insulin, blood, control system.

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1093 Project Portfolio Management Phases: A Technique for Strategy Alignment

Authors: Amaral, António, Araújo, Madalena

Abstract:

This paper seeks to give a general idea of the universe of project portfolio management, from its multidisciplinary nature, to the many challenges it raises, passing through the different techniques, models and tools used to solve the multiple problems known. It is intended to contribute to the clarification, with great depth, of the impacts and relationships involved in managing the projects- portfolio. It aims at proposing a technique for the project alignment with the organisational strategy, in order to select projects that later on will be considered in the analysis and selection of the portfolio. We consider the development of a methodology for assessing the project alignment index very relevant in the global market scenario. It can help organisations to gain a greater awareness of market dynamics, speed up the decision process and increase its consistency, thus enabling the strategic alignment and the improvement of the organisational performance.

Keywords: Project Portfolio Management Cycle, Project Portfolio Selection, Resource Assignment, Strategy Alignment technique

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1092 Extracting Tongue Shape Dynamics from Magnetic Resonance Image Sequences

Authors: María S. Avila-García, John N. Carter, Robert I. Damper

Abstract:

An important problem in speech research is the automatic extraction of information about the shape and dimensions of the vocal tract during real-time speech production. We have previously developed Southampton dynamic magnetic resonance imaging (SDMRI) as an approach to the solution of this problem.However, the SDMRI images are very noisy so that shape extraction is a major challenge. In this paper, we address the problem of tongue shape extraction, which poses difficulties because this is a highly deforming non-parametric shape. We show that combining active shape models with the dynamic Hough transform allows the tongue shape to be reliably tracked in the image sequence.

Keywords: Vocal tract imaging, speech production, active shapemodels, dynamic Hough transform, object tracking.

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1091 Research on Weakly Hard Real-Time Constraints and Their Boolean Combination to Support Adaptive QoS

Authors: Xiangbin Zhu

Abstract:

Advances in computing applications in recent years have prompted the demand for more flexible scheduling models for QoS demand. Moreover, in practical applications, partly violated temporal constraints can be tolerated if the violation meets certain distribution. So we need extend the traditional Liu and Lanland model to adapt to these circumstances. There are two extensions, which are the (m, k)-firm model and Window-Constrained model. This paper researches on weakly hard real-time constraints and their combination to support QoS. The fact that a practical application can tolerate some violations of temporal constraint under certain distribution is employed to support adaptive QoS on the open real-time system. The experiment results show these approaches are effective compared to traditional scheduling algorithms.

Keywords: Weakly Hard Real-Time, Real-Time, Scheduling, Quality of Service.

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1090 Performance Analysis of Artificial Neural Network with Decision Tree in Prediction of Diabetes Mellitus

Authors: J. K. Alhassan, B. Attah, S. Misra

Abstract:

Human beings have the ability to make logical decisions. Although human decision - making is often optimal, it is insufficient when huge amount of data is to be classified. Medical dataset is a vital ingredient used in predicting patient’s health condition. In other to have the best prediction, there calls for most suitable machine learning algorithms. This work compared the performance of Artificial Neural Network (ANN) and Decision Tree Algorithms (DTA) as regards to some performance metrics using diabetes data. WEKA software was used for the implementation of the algorithms. Multilayer Perceptron (MLP) and Radial Basis Function (RBF) were the two algorithms used for ANN, while RegTree and LADTree algorithms were the DTA models used. From the results obtained, DTA performed better than ANN. The Root Mean Squared Error (RMSE) of MLP is 0.3913 that of RBF is 0.3625, that of RepTree is 0.3174 and that of LADTree is 0.3206 respectively.

Keywords: Artificial neural network, classification, decision tree, diabetes mellitus.

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1089 Modelling Silica Optical Fibre Reliability: A Software Application

Authors: I. Severin, M. Caramihai, R. El Abdi, M. Poulain, A. Avadanii

Abstract:

In order to assess optical fiber reliability in different environmental and stress conditions series of testing are performed simulating overlapping of chemical and mechanical controlled varying factors. Each series of testing may be compared using statistical processing: i.e. Weibull plots. Due to the numerous data to treat, a software application has appeared useful to interpret selected series of experiments in function of envisaged factors. The current paper presents a software application used in the storage, modelling and interpretation of experimental data gathered from optical fibre testing. The present paper strictly deals with the software part of the project (regarding the modelling, storage and processing of user supplied data).

Keywords: Optical fibres, computer aided analysis, data models, data processing, graphical user interfaces.

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1088 Exploring the Combinatorics of Motif Alignments Foraccurately Computing E-values from P-values

Authors: T. Kjosmoen, T. Ryen, T. Eftestøl

Abstract:

In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the E-value as the product of the p-value and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give E-values that significantly diverge from their true values.

Keywords: Motif alignment, combinatorics, p-value, E-value, OOPS, ZOOPS, ANR.

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