Search results for: multiple robots synchronization

Authors: P. Cermak

Abstract:

This paper shows possibility of extraction Social, Group and Individual Mind from Multiple Agents Rule Bases. Types those Rule bases are selected as two fuzzy systems, namely Mambdani and Takagi-Sugeno fuzzy system. Their rule bases are describing (modeling) agent behavior. Modifying of agent behavior in the time varying environment will be provided by learning fuzzyneural networks and optimization of their parameters with using genetic algorithms in development system FUZNET. Finally, extraction Social, Group and Individual Mind from Multiple Agents Rule Bases are provided by Cognitive analysis and Matching criterion.

Keywords: Mind, Multi-agent system, Cognitive analysis, Fuzzy system, Neural network, Genetic algorithm, Rule base.

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Authors: Mikko Elomaa, Aarne Halme

Abstract:

A novel method using bearing-only SLAM to estimate node positions of a localization network is proposed. A group of simple robots are used to estimate the position of each node. Each node has a unique ID, which it can communicate to a robot close by. Initially the node IDs and positions are unknown. A case example using RFID technology in the localization network is introduced.

Keywords: Localization network, Multi-robot, RFID, SLAM

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Authors: Simon B. N. Thompson

Abstract:

Cortisol is essential to the regulation of the immune system and yawning is a pathological symptom of multiple sclerosis (MS). Electromyography activity (EMG) in the jaw muscles typically rises when the muscles are moved and with yawning is highly correlated with cortisol levels in healthy people. Saliva samples from 59 participants were collected at the start and after yawning, or at the end of the presentation of yawning-provoking stimuli, in the absence of a yawn, together with EMG data and questionnaire data: Hospital Anxiety and Depression Scale, Yawning Susceptibility Scale, General Health Questionnaire, demographic, health details. Exclusion criteria: chronic fatigue, diabetes, fibromyalgia, heart condition, high blood pressure, hormone replacement therapy, multiple sclerosis, stroke. Significant differences were found between the saliva cortisol samples for the yawners, t (23) = -4.263, p = 0.000, as compared with the non-yawners between rest and post-stimuli, which was nonsignificant. Significant evidence was found to support the Thompson Cortisol Hypothesis suggesting that rises in cortisol levels are associated with yawning. Further research is exploring the use of cortisol as an early diagnostic tool for MS. Ethics approval granted and professional code of conduct, confidentiality, and safety issues are approved therein.

Keywords: Cortisol, Multiple Sclerosis, Yawning, Thompson’s Cortisol Hypothesis.

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Authors: Amin Alvani

Abstract:

Multiple sclerosis (MS) is a chronic, often disabling disease in which the immune system attacks the myelin sheath of neurons in the central nervous system. The purpose of this study was to explore the correlation between the Behavioral Inhibition/Approach System (BIS-BAS) and Perceived Stress (PS), while controlling for White Blood Cell (WBC) count. 60 MS patients (36.7% male, 63.3% female; aged 15-65 years) participated in this study. They completed a demographic questionnaire, underwent a complete blood cell (CBC) test, filled out the Behavioral Activation and Behavioral Inhibition Scale (BIS-BAS), and responded to the Perceived Stress Questionnaire (PSS-14). The results indicated a significant relationship between the BAS-Reward Responsiveness (BAS-RR) subscale and PS, particularly in a subset of MS patients with increased WBC counts.

Keywords: Behavioral inhibition/approach system, multiple sclerosis, perceived stress, white blood cell.

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Authors: Hiraku Nunomiya, Takuo Ichiju, Yoshiyuki Higuchi

Abstract:

In the management of industrial waste, conversion from the use of paper invoices to electronic forms is currently under way in developed countries. Difficulties in such computerization include the lack of synchronization between the actual goods and the corresponding data managed by the server. Consequently, a system which utilizes the incorporation of a QR code in connection with the waste material has been developed. The code is read at each stage, from discharge until disposal, and progress at each stage can be easily reported. This system can be linked with Japanese public digital authentication service of waste, taking advantage of its good points, and can be used to submit reports to the regulatory authorities. Its usefulness was confirmed by a verification test, and put into actual practice.

Keywords: Infectious Waste, Electronic Manifest, Real Time Management, QR code.

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Authors: Bradley Christensen, Kevin T. McCusker, Daniel J. Gauthier, Daniel Kumor, Venkat Chandar, P. G. Kwiat

Abstract:

We report on a high-speed quantum cryptography system that utilizes simultaneous entanglement in polarization and in “time-bins". With multiple degrees of freedom contributing to the secret key, we can achieve over ten bits of random entropy per detected coincidence. In addition, we collect from multiple spots o the downconversion cone to further amplify the data rate, allowing usto achieve over 10 Mbits of secure key per second.

Keywords: Downconversion, Hyper-entanglement, Quantum Cryptography

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Authors: Shengqi Yu, Jinwei Zhao

Abstract:

This paper presents a kind of analog circuit based temperature control system, which is mainly composed by threshold control signal circuit, synchronization signal circuit and trigger pulse circuit. Firstly, the temperature feedback signal function is realized by temperature sensor TS503F3950E. Secondly, the main control circuit forms the cycle controlled pulse signal to control the thyristor switching model. Finally two reverse paralleled thyristors regulate the output power by their switching state. In the consequence, this is a modernized and energy-saving domestic electric heating system.

Keywords: Time base circuit, automatic control, zero-crossing trigger, temperature control.

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Authors: Dariusz Barbucha, Piotr Jedrzejowicz

Abstract:

The paper proposes and validates a new method of solving instances of the vehicle routing problem (VRP). The approach is based on a multiple agent system paradigm. The paper contains the VRP formulation, an overview of the multiple agent environment used and a description of the proposed implementation. The approach is validated experimentally. The experiment plan and the discussion of experiment results follow.

Keywords: multi-agent systems, population-based methods, vehiclerouting problem.

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Authors: C. Ardil

Abstract:

Fighter aircraft selection is one of the most critical strategies for defense multiple criteria decision-making analysis to increase the decisive power of air defense and its superior power in the defense strategy. Vague set theory is an adequate approach for modeling vagueness, uncertainty, and imprecision in decision-making problems. This study integrates vague set theory and the technique for order of preference by similarity to ideal solution (TOPSIS) to support fighter aircraft selection. The proposed method is applied in the selection of fighter aircraft for the Air Force. In the proposed approach, the ratings of alternatives and the importance weights of criteria for fighter aircraft selection are represented by the vague set theory. Finally, an illustrative example for fighter aircraft selection is given to demonstrate the applicability and effectiveness of the proposed approach. The fighter aircraft candidates were selected under six criteria including costability, payloadability, maneuverability, speedability, stealthility, and survivability. Analysis results show that the best fighter aircraft is selected with the highest closeness coefficient value. The proposed method can also be applied to solve other multiple criteria decision analysis problems. 

Keywords: fighter aircraft selection, vague set theory, fuzzy set theory, neutrosophic set theory, multiple criteria decision making analysis, MCDMA, TOPSIS

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Authors: Ibrahim M. Hussain

Abstract:

Three new algorithms based on minimization of autocorrelation of transmitted symbols and the SLM approach which are computationally less demanding have been proposed. In the first algorithm, autocorrelation of complex data sequence is minimized to a value of 1 that results in reduction of PAPR. Second algorithm generates multiple random sequences from the sequence generated in the first algorithm with same value of autocorrelation i.e. 1. Out of these, the sequence with minimum PAPR is transmitted. Third algorithm is an extension of the second algorithm and requires minimum side information to be transmitted. Multiple sequences are generated by modifying a fixed number of complex numbers in an OFDM data sequence using only one factor. The multiple sequences represent the same data sequence and the one giving minimum PAPR is transmitted. Simulation results for a 256 subcarrier OFDM system show that significant reduction in PAPR is achieved using the proposed algorithms.

Keywords: Aperiodic autocorrelation, OFDM, PAPR, SLM, wireless communication.

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Authors: San Nah Sze, Wei King Tiong

Abstract:

The multiple traveling salesman problem (mTSP) can be used to model many practical problems. The mTSP is more complicated than the traveling salesman problem (TSP) because it requires determining which cities to assign to each salesman, as well as the optimal ordering of the cities within each salesman's tour. Previous studies proposed that Genetic Algorithm (GA), Integer Programming (IP) and several neural network (NN) approaches could be used to solve mTSP. This paper compared the results for mTSP, solved with Genetic Algorithm (GA) and Nearest Neighbor Algorithm (NNA). The number of cities is clustered into a few groups using k-means clustering technique. The number of groups depends on the number of salesman. Then, each group is solved with NNA and GA as an independent TSP. It is found that k-means clustering and NNA are superior to GA in terms of performance (evaluated by fitness function) and computing time.

Keywords: Multiple Traveling Salesman Problem, GeneticAlgorithm, Nearest Neighbor Algorithm, k-Means Clustering.

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Authors: N. Promsuwanna, P. Uthansakul, M. Uthansakul

Abstract:

The Carrier Frequency Offset (CFO) due to timevarying fading channel is the main cause of the loss of orthogonality among OFDM subcarriers which is linked to inter-carrier interference (ICI). Hence, it is necessary to precisely estimate and compensate the CFO. Especially for mobile broadband communications, CFO and channel gain also have to be estimated and tracked to maintain the system performance. Thus, synchronization pilots are embedded in every OFDM symbol to track the variations. In this paper, we present the pilot scheme for both channel and CFO estimation where channel estimation process can be carried out with only one OFDM symbol. Additional, the proposed pilot scheme also provides better performance in CFO estimation comparing with the conventional orthogonal pilot scheme due to the increasing of signal-tointerference ratio.

Keywords: MIMO, OFDM, carrier frequency offset, channel, estimation.

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Authors: Mehdi Hosseinzadeh, Somayyeh Jafarali Jassbi, Keivan Navi

Abstract:

Residue Number System (RNS) is a modular representation and is proved to be an instrumental tool in many digital signal processing (DSP) applications which require high-speed computations. RNS is an integer and non weighted number system; it can support parallel, carry-free, high-speed and low power arithmetic. A very interesting correspondence exists between the concepts of Multiple Valued Logic (MVL) and Residue Number Arithmetic. If the number of levels used to represent MVL signals is chosen to be consistent with the moduli which create the finite rings in the RNS, MVL becomes a very natural representation for the RNS. There are two concerns related to the application of this Number System: reaching the most possible speed and the largest dynamic range. There is a conflict when one wants to resolve both these problem. That is augmenting the dynamic range results in reducing the speed in the same time. For achieving the most performance a method is considere named “One-Hot Residue Number System" in this implementation the propagation is only equal to one transistor delay. The problem with this method is the huge increase in the number of transistors they are increased in order m² . In real application this is practically impossible. In this paper combining the Multiple Valued Logic and One-Hot Residue Number System we represent a new method to resolve both of these two problems. In this paper we represent a novel design of an OHRNS-based adder circuit. This circuit is useable for Multiple Valued Logic moduli, in comparison to other RNS design; this circuit has considerably improved the number of transistors and power consumption.

Keywords: Computer Arithmetic, Residue Number System, Multiple Valued Logic, One-Hot, VLSI.

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Authors: Abhijit Mitra, C. Ardil

Abstract:

We investigate efficient spreading codes for transmitter based techniques of code division multiple access (CDMA) systems. The channel is considered to be known at the transmitter which is usual in a time division duplex (TDD) system where the channel is assumed to be the same on uplink and downlink. For such a TDD/CDMA system, both bitwise and blockwise multiuser transmission schemes are taken up where complexity is transferred to the transmitter side so that the receiver has minimum complexity. Different spreading codes are considered at the transmitter to spread the signal efficiently over the entire spectrum. The bit error rate (BER) curves portray the efficiency of the codes in presence of multiple access interference (MAI) as well as inter symbol interference (ISI).

Keywords: Code division multiple access, time division duplex, transmitter technique, precoding, pre-rake, rake, spreading code.

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Authors: Abdelouahab Errida, Bouchra Lotfi, Elalami Semma

Abstract:

In this paper, we try to address the topic of multiple change management by adopting an engineered research methodology, conducted within a Moroccan company during its implementation of several change projects that aim at improving its supply chain management performance. Firstly, we present the key concepts related to our research, namely change management, multiproject management and supply chain management. Then, we try to assess how the change management and multi-project management are applied in this company. Finally, we try to propose an approach that will help managers in dealing with multiple change projects. This approach proposes to integrate change management, project management and multi-project management for managing change projects according to three organizational levels: executive level, project portfolio level and change project level.

Keywords: Change management, multi-project management, project management, change portfolio, supply chain management.

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Authors: Huiming Peng, Jianguo Wen, Hongwei Li, Jeff Chang, Xiaobo Zhou

Abstract:

NFκB activation plays a crucial role in anti-apoptotic responses in response to the apoptotic signaling during tumor necrosis factor (TNFa) stimulation in Multiple Myeloma (MM). Although several drugs have been found effective for the treatment of MM by mainly inhibiting NFκB pathway, there are no any quantitative or qualitative results of comparison assessment on inhibition effect between different single drugs or drug combinations. Computational modeling is becoming increasingly indispensable for applied biological research mainly because it can provide strong quantitative predicting power. In this study, a novel computational pathway modeling approach is employed to comparably assess the inhibition effects of specific single drugs and drug combinations on the NFκB pathway in MM, especially the prediction of synergistic drug combinations.

Keywords: Computational modeling, drug combination, inhibition effect, multiple myeloma, NFkB pathway.

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Authors: C. Ardil

Abstract:

Aircraft selection decisions can be challenging due to their multidimensional and interdisciplinary nature. They involve multiple stakeholders with conflicting objectives and numerous alternative options with uncertain outcomes. This study focuses on the analysis of aerial firefighting aircraft that can be chosen for the Air Fire Service to extinguish forest fires. To make such a selection, the characteristics of the fire zones must be considered, and the capability to manage the logistics involved in such operations, as well as the purchase and maintenance of the aircraft, must be determined. The selection of firefighting aircraft is particularly complex because they have longer fleet lives and require more demanding operation and maintenance than scheduled passenger air service. This paper aims to use the fuzzy proximity measure method to select the most appropriate aerial firefighting aircraft based on decision criteria using multiple attribute decision making analysis. Following fuzzy decision analysis, the most suitable aerial firefighting aircraft is ranked and determined for the Air Fire Service.

Keywords: Aerial firefighting aircraft selection, multiple criteria decision making, fuzzy sets, standard fuzzy sets, determinate fuzzy sets, indeterminate fuzzy sets, proximity measure method, Minkowski distance family function, Hausdorff distance function, MCDM, PMM, PMM-F

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Authors: Rama Debbarma, Debanjan Das

Abstract:

The performance of multiple tuned mass dampers to mitigate the seismic vibration of structures considering real time history data is investigated in this paper. Three different real earthquake time history data like Kobe, Imperial Valley and Mammoth Lake are taken in the present study. The multiple tuned mass dampers (MTMD) are distributed at each storey. For comparative study, single tuned mass damper (STMD) is installed at top of the similar structure. This study is conducted for a fixed mass ratio (5%) and fixed damping ratio (5%) of structures. Numerical study is performed to evaluate the effectiveness of MTMDs and overall system performance. The displacement, acceleration, base shear and storey drift are obtained for both combined system (structure with MTMD and structure with STMD) for all earthquakes. The same responses are also obtained for structure without damper system. From obtained results, it is investigated that the MTMD configuration is more effective for controlling the seismic response of the primary system with compare to STMD configuration.

Keywords: Earthquake, multiple tuned mass dampers, single tuned mass damper, time history.

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Authors: Ksenija Dumičić, Anita Čeh Časni, Irena Palić

Abstract:

This paper examines economic and Information and Communication Technology (ICT) development influence on recently increasing Internet purchases by individuals for European Union member states. After a growing trend for Internet purchases in EU27 was noticed, all possible regression analysis was applied using nine independent variables in 2011. Finally, two linear regression models were studied in detail. Conducted simple linear regression analysis confirmed the research hypothesis that the Internet purchases in analyzed EU countries is positively correlated with statistically significant variable Gross Domestic Product per capita (GDPpc). Also, analyzed multiple linear regression model with four regressors, showing ICT development level, indicates that ICT development is crucial for explaining the Internet purchases by individuals, confirming the research hypothesis.

Keywords: European Union, Internet purchases, multiple linear regression model, outlier

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Authors: Young Hee Geum

Abstract:

We propose the numerical method defined by

xn+1 = xn − λ[f(xn − μh(xn))/]f'(xn) , n ∈ N,

and determine the control parameter λ and μ to converge cubically. In addition, we derive the asymptotic error constant. Applying this proposed scheme to various test functions, numerical results show a good agreement with the theory analyzed in this paper and are proven using Mathematica with its high-precision computability.

Keywords: Asymptotic error constant, iterative method , multiple root, root-finding.

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Authors: C. Ardil

Abstract:

In this paper, the comparison of composite programming and compromise programming for the aircraft selection problem is discussed using the multiple criteria decision analysis method. The decision making process requires the prior definition and fulfillment of certain factors, especially when it comes to complex areas such as aircraft selection problems. The proposed technique gives more efficient results by extending the composite programming and compromise programming, which are widely used in modeling multiple criteria decisions. The proposed model is applied to a practical decision problem for evaluating and selecting aircraft problems.A selection of aircraft was made based on the proposed approach developed in the field of multiple criteria decision making. The model presented is solved by using the following methods: composite programming, and compromise programming. The importance values of the weight coefficients of the criteria are calculated using the mean weight method. The evaluation and ranking of aircraft are carried out using the composite programming and compromise programming methods. In order to determine the stability of the model and the ability to apply the developed composite programming and compromise programming approach, the paper analyzes its sensitivity, which involves changing the value of the coefficient λ and q in the first part. The second part of the sensitivity analysis relates to the application of different multiple criteria decision making methods, composite programming and compromise programming. In addition, in the third part of the sensitivity analysis, the Spearman correlation coefficient of the ranks obtained was calculated which confirms the applicability of all the proposed approaches.

Keywords: composite programming, compromise programming, additive weighted model, multiplicative weighted model, multiple criteria decision making analysis, MCDMA, aircraft selection

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Authors: Khin Thandar Lwin, Than Htike, Zaw Min Naing

Abstract:

This paper introduces an intelligent system, which can be applied in the monitoring of vehicle speed using a single camera. The ability of motion tracking is extremely useful in many automation problems and the solution to this problem will open up many future applications. One of the most common problems in our daily life is the speed detection of vehicles on a highway. In this paper, a novel technique is developed to track multiple moving objects with their speeds being estimated using a sequence of video frames. Field test has been conducted to capture real-life data and the processed results were presented. Multiple object problems and noisy in data are also considered. Implementing this system in real-time is straightforward. The proposal can accurately evaluate the position and the orientation of moving objects in real-time. The transformations and calibration between the 2D image and the actual road are also considered.

Keywords: Motion Estimation, Image Analyses, Speed Detection

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Authors: Sara Sharifi Rad, Hassan Haghighi

Abstract:

Due to important issues, such as deadlock, starvation, communication, non-deterministic behavior and synchronization, concurrent systems are very complex, sensitive, and error-prone. Thus ensuring reliability and accuracy of these systems is very essential. Therefore, there has been a big interest in the formal specification of concurrent programs in recent years. Nevertheless, some features of concurrent systems, such as dynamic process creation, scheduling and starvation have not been specified formally yet. Also, some other features have been specified partially and/or have been described using a combination of several different formalisms and methods whose integration needs too much effort. In other words, a comprehensive and integrated specification that could cover all aspects of concurrent systems has not been provided yet. Thus, this paper makes two major contributions: firstly, it provides a comprehensive formal framework to specify all well-known features of concurrent systems. Secondly, it provides an integrated specification of these features by using just a single formal notation, i.e., the Z language.

Keywords: Concurrent systems, Formal methods, Formal specification, Z language

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Authors: S Hariharan, K Chaitanya, P Muthuchidambaranathan

Abstract:

The IEEE 802.22 working group aims to drive the Digital Video Broadcasting-Terrestrial (DVB-T) bands for data communication to the rural area without interfering the TV broadcast. In this paper, we arrive at a closed-form expression for average detection probability of Fusion center (FC) with multiple antenna over the κ − μ fading channel model. We consider a centralized cooperative multiple antenna network for reporting. The DVB-T samples forwarded by the secondary user (SU) were combined using Maximum ratio combiner at FC, an energy detection is performed to make the decision. The fading effects of the channel degrades the detection probability of the FC, a generalized independent and identically distributed (IID) κ − μ and an additive white Gaussian noise (AWGN) channel is considered for reporting and sensing respectively. The proposed system performance is verified through simulation results.

Keywords: IEEE 802.22, Cooperative spectrum sensing, Multiple antenna, κ − μ .

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Authors: S. Deswal, M. Pal

Abstract:

Presently various computational techniques are used in modeling and analyzing environmental engineering data. In the present study, an intra-comparison of polynomial and radial basis kernel functions based on Support Vector Regression and, in turn, an inter-comparison with Multi Linear Regression has been attempted in modeling mass transfer capacity of vertical (θ = 90O) and inclined (θ multiple plunging jets (varying from 1 to 16 numbers). The data set used in this study consists of four input parameters with a total of eighty eight cases, forty four each for vertical and inclined multiple plunging jets. For testing, tenfold cross validation was used. Correlation coefficient values of 0.971 and 0.981 along with corresponding root mean square error values of 0.0025 and 0.0020 were achieved by using polynomial and radial basis kernel functions based Support Vector Regression respectively. An intra-comparison suggests improved performance by radial basis function in comparison to polynomial kernel based Support Vector Regression. Further, an inter-comparison with Multi Linear Regression (correlation coefficient = 0.973 and root mean square error = 0.0024) reveals that radial basis kernel functions based Support Vector Regression performs better in modeling and estimating mass transfer by multiple plunging jets.

Keywords: Mass transfer, multiple plunging jets, polynomial and radial basis kernel functions, Support Vector Regression.

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Authors: An Chen, Huilin Ye

Abstract:

Mining sequential patterns from large customer transaction databases has been recognized as a key research topic in database systems. However, the previous works more focused on mining sequential patterns at a single concept level. In this study, we introduced concept hierarchies into this problem and present several algorithms for discovering multiple-level sequential patterns based on the hierarchies. An experiment was conducted to assess the performance of the proposed algorithms. The performances of the algorithms were measured by the relative time spent on completing the mining tasks on two different datasets. The experimental results showed that the performance depends on the characteristics of the datasets and the pre-defined threshold of minimal support for each level of the concept hierarchy. Based on the experimental results, some suggestions were also given for how to select appropriate algorithm for a certain datasets.

Keywords: Data Mining, Multiple-Level Sequential Pattern, Concept Hierarchy, Customer Transaction Database.

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Authors: N. Parimala, P. Pahwa

Abstract:

OLAP uses multidimensional structures, to provide access to data for analysis. Traditionally, OLAP operations are more focused on retrieving data from a single data mart. An exception is the drill across operator. This, however, is restricted to retrieving facts on common dimensions of the multiple data marts. Our concern is to define further operations while retrieving data from multiple data marts. Towards this, we have defined six operations which coalesce data marts. While doing so we consider the common as well as the non-common dimensions of the data marts.

Keywords: Data warehouse, Dimension, OLAP, Star Schema.

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Authors: Saher Ali Al-Sabbah, See Ching Mey, Ong Saw Lan

Abstract:

This article addresses the procedures to validate the Arabic version of Multiple Intelligence Development Assessment Scale (MIDAS). The content validity was examined based on the experts- judgments on the MIDAS-s items in the Arabic version. The content of eleven items in the Arabic version of MIDAS was modified to match the Arabic context. Then a translation from original English version of MIDAS into Arabic language was performed. The reliability of the Arabic MIDAS was calculated based on test and retest method and found to be 0.85 for the overall MIDAS and for the different subscales ranging between 0.78 - 0.87. The examination of construct validity for the overall Arabic MIDAS and its subscales was established by using Winsteps program version 6 based on Rasch model in order to fit the items into the Arabic context. The findings indicated that, the eight subscales in Arabic version of MIDAS scale have a unidimensionality, and the total number of kept items in the overall scale is 108 items.

Keywords: Rasch-Model, validation, multiple intelligence, and MIDAS scale.

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Authors: G. Büyüközkan , O. Feyzioglu, Z. Vardaloglu

Abstract:

Collaborative planning, forecasting and replenishment (CPFR) coordinates the various supply chain management activities including production and purchase planning, demand forecasting and inventory replenishment between supply chain trading partners. This study proposes a systematic way of analyzing CPFR supporting factors using fuzzy cognitive map (FCM) approach. FCMs have proven particularly useful for solving problems in which a number of decision variables and uncontrollable variables are causally interrelated. Hence the FCMs of CPFR are created to show the relationships between the factors that influence on effective implementation of CPFR in the supply chain.

Keywords: Collaborative planning, forecasting and replenishment, fuzzy cognitive map, information sharing, decision synchronization, incentive alignment.

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Authors: Khaddouja Boujenfa, Nadia Essoussi, Mohamed Limam

Abstract:

Multiple sequence alignment is a fundamental part in many bioinformatics applications such as phylogenetic analysis. Many alignment methods have been proposed. Each method gives a different result for the same data set, and consequently generates a different phylogenetic tree. Hence, the chosen alignment method affects the resulting tree. However in the literature, there is no evaluation of multiple alignment methods based on the comparison of their phylogenetic trees. This work evaluates the following eight aligners: ClustalX, T-Coffee, SAGA, MUSCLE, MAFFT, DIALIGN, ProbCons and Align-m, based on their phylogenetic trees (test trees) produced on a given data set. The Neighbor-Joining method is used to estimate trees. Three criteria, namely, the dNNI, the dRF and the Id_Tree are established to test the ability of different alignment methods to produce closer test tree compared to the reference one (true tree). Results show that the method which produces the most accurate alignment gives the nearest test tree to the reference tree. MUSCLE outperforms all aligners with respect to the three criteria and for all datasets, performing particularly better when sequence identities are within 10-20%. It is followed by T-Coffee at lower sequence identity (<10%), Align-m at 20-30% identity, and ClustalX and ProbCons at 30-50% identity. Also, it is noticed that when sequence identities are higher (>30%), trees scores of all methods become similar.

Keywords: Multiple alignment methods, phylogenetic trees, Neighbor-Joining method, Robinson-Foulds distance.

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