Search results for: Knowledge Based Systems

Authors: Luis A. Morales Rosales, Saul E. Pomares Hernandez, Gustavo Rodriguez Gomez

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Synchronous cooperative systems (SCS) bring together users that are geographically distributed and connected through a network to carry out a task. Examples of SCS include Tele- Immersion and Tele-Conferences. In SCS, the coordination is the core of the system, and it has been defined as the act of managing interdependencies between activities performed to achieve a goal. Some of the main problems that SCS present deal with the management of constraints between simultaneous activities and the execution ordering of these activities. In order to resolve these problems, orderings based on Lamport-s happened-before relation have been used, namely, causal, Δ-causal, and causal-total orderings. They mainly differ in the degree of asynchronous execution allowed. One of the most important orderings is the causal order, which establishes that the events must be seen in the cause-effect order as they occur in the system. In this paper we show that for certain SCS (e.g. videoconferences, tele-immersion) where some degradation of the system is allowed, ensuring the causal order is still rigid, which can render negative affects to the system. In this paper, we illustrate how a more relaxed ordering, which we call Fuzzy Causal Order (FCO), is useful for such kind of systems by allowing a more asynchronous execution than the causal order. The benefit of the FCO is illustrated by applying it to a particular scenario of intermedia synchronization of an audio-conference system.

Keywords: Event ordering, fuzzy causal ordering, happenedbefore relation and cooperative systems.

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Authors: N. M. Singh, Jayant Dubey, Ghanshyam Laddha

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State Dependent Riccati Equation (SDRE) approach is a modification of the well studied LQR method. It has the capability of being applied to control nonlinear systems. In this paper the technique has been applied to control the single inverted pendulum (SIP) which represents a rich class of nonlinear underactuated systems. SIP modeling is based on Euler-Lagrange equations. A procedure is developed for judicious selection of weighting parameters and constraint handling. The controller designed by SDRE technique here gives better results than existing controllers designed by energy based techniques.

Keywords: State Dependent Riccati Equation (SDRE), Single Inverted Pendulum (SIP), Linear Quadratic Regulator (LQR)

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Authors: F. Sarabchi, M. E. Kalantari

Abstract:

In this paper, Optimum adaptive loading algorithms are applied to multicarrier system with Space-Time Block Coding (STBC) scheme associated with space-time processing based on singular-value decomposition (SVD) of the channel matrix over Rayleigh fading channels. SVD method has been employed in MIMO-OFDM system in order to overcome subchannel interference. Chaw-s and Compello-s algorithms have been implemented to obtain a bit and power allocation for each subcarrier assuming instantaneous channel knowledge. The adaptive loaded SVD-STBC scheme is capable of providing both full-rate and full-diversity for any number of transmit antennas. The effectiveness of these techniques has demonstrated through the simulation of an Adaptive loaded SVDSTBC system, and the comparison shown that the proposed algorithms ensure better performance in the case of MIMO.

Keywords: OFDM, MIMO, SVD, STBC, Adaptive Loading.

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Authors: M. Soltan Rezaee, M. R. Ghazavi, A. Najafi, W.-H. Liao

Abstract:

Generally, different rods in shaft systems can be misaligned based on the mechanical system usages. These rods can be linked together via U-coupling easily. The system is self-stimulated and may cause instabilities due to the inherent behavior of the coupling. In this study, each rod includes an elastic shaft with an angular stiffness and structural damping. Moreover, the mass of shafts is considered via attached solid disks. The impact of the system architecture and shaft mass on the instability of such mechanism are studied. Stability charts are plotted via a method based on Floquet theory. Eventually, the unstable points have been found and analyzed in detail. The results show that stabilizing the driveline is feasible by changing the system characteristics which include shaft mass and architecture.

Keywords: Coupling, mechanical systems, oscillations, rotating shafts.

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Authors: Kiamran Radjabli

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State Estimator became an intrinsic part of Energy Management Systems (EMS). The SCADA measurements received from the field are processed by the State Estimator in order to accurately determine the actual operating state of the power systems and provide that information to other real-time network applications. All EMS vendors offer a State Estimator functionality in their baseline products. However, setting up and ensuring that State Estimator consistently produces a reliable solution often consumes a substantial engineering effort. This paper provides generic recommendations and describes a simple practical approach to efficient tuning of State Estimator, based on the working experience with major EMS software platforms and consulting projects in many electrical utilities of the USA.

Keywords: Convergence, monitoring, performance, state estimator, troubleshooting, tuning, power systems.

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Authors: Ali M. Alakeel

Abstract:

Load balancing in distributed computer systems is the process of redistributing the work load among processors in the system to improve system performance. Most of previous research in using fuzzy logic for the purpose of load balancing has only concentrated in utilizing fuzzy logic concepts in describing processors load and tasks execution length. The responsibility of the fuzzy-based load balancing process itself, however, has not been discussed and in most reported work is assumed to be performed in a distributed fashion by all nodes in the network. This paper proposes a new fuzzy dynamic load balancing algorithm for homogenous distributed systems. The proposed algorithm utilizes fuzzy logic in dealing with inaccurate load information, making load distribution decisions, and maintaining overall system stability. In terms of control, we propose a new approach that specifies how, when, and by which node the load balancing is implemented. Our approach is called Centralized-But-Distributed (CBD).

Keywords: Dynamic load balancing, fuzzy logic, distributed systems, algorithm.

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Authors: M. M. Shahidul Hassan, Omiya Hassan

Abstract:

Bangladesh has set its goal to reach upper middle-income country status by 2024. To attain this status, the country must satisfy the World Bank requirement of achieving minimum Gross National Income (GNI). Number of youth job seekers in the country is increasing. University graduates are looking for decent jobs. So, the vital issue of this country is to understand how the GNI and jobs can be increased. The objective of this paper is to address these issues and find ways to create more job opportunities for youths at home and abroad which will increase the country’s GNI. The paper studies proportion of different goods Bangladesh exported, and also the percentage of employment in different sectors. The data used here for the purpose of analysis have been collected from the available literature. These data are then plotted and analyzed. Through these studies, it is concluded that growth in sectors like agricultural, ready-made garments (RMG), jute industries and fisheries are declining and the business community is not interested in setting up capital-intensive industries. Under this situation, the country needs to explore other business opportunities for a higher economic growth rate. Knowledge can substitute the physical resource. Since the country consists of the large youth population, higher education will play a key role in economic development. It now needs graduates with higher-order skills with innovative quality. Such dispositions demand changes in a university’s curriculum, teaching and assessment method which will function young generations as active learners and creators. By bringing these changes in higher education, a knowledge-based society can be created. The application of such knowledge and creativity will then become the commodity of Bangladesh which will help to reach its goal as an upper middle-income country.

Keywords: Bangladesh, economic sectors, economic growth, higher education, knowledge-based economy, massifcation of higher education, teaching and learning, universities’ role in society.

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Authors: Shattyk Aliyev, Zhakypbek Altayev, Pirimbek Suleimenov, Asset Kuranbek, Zhamila Amirkulova

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Modern civilization has come in recent decades into a new phase in its development, called the information society. The concept of "information society" has become one of the most common. Therefore, the attempt to understand what exactly the society we live in, what are its essential features, and possible future scenarios, is important to the social and philosophical analysis. At the heart of all these deep transformations is more increasing, almost defining role knowledge and information as play substrata of «information society». The mankind opened for itself and actively exploits a new resource – information. Information society puts forward on the arena new type of the power, at the heart of which activity – mastering by a new resource: information and knowledge. The password of the new power – intelligence as synthesis of knowledge, information and communications, the strength of mind, fundamental sociocultural values. In a postindustrial society, the power of knowledge and information is crucial in the management of the company, pushing into the background the influence of money and state coercion.

Keywords: Information society, philosophy of power, management, globalization and innovation.

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Authors: Sofien Chtourou, Mohamed Chtourou, Omar Hammami

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Embedded systems need to respect stringent real time constraints. Various hardware components included in such systems such as cache memories exhibit variability and therefore affect execution time. Indeed, a cache memory access from an embedded microprocessor might result in a cache hit where the data is available or a cache miss and the data need to be fetched with an additional delay from an external memory. It is therefore highly desirable to predict future memory accesses during execution in order to appropriately prefetch data without incurring delays. In this paper, we evaluate the potential of several artificial neural networks for the prediction of instruction memory addresses. Neural network have the potential to tackle the nonlinear behavior observed in memory accesses during program execution and their demonstrated numerous hardware implementation emphasize this choice over traditional forecasting techniques for their inclusion in embedded systems. However, embedded applications execute millions of instructions and therefore millions of addresses to be predicted. This very challenging problem of neural network based prediction of large time series is approached in this paper by evaluating various neural network architectures based on the recurrent neural network paradigm with pre-processing based on the Self Organizing Map (SOM) classification technique.

Keywords: Address, data set, memory, prediction, recurrentneural network.

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Authors: Enrico Rukzio, George N. Prezerakos, Giovanni Cortese, Eleftherios Koutsoloukas, Sofia Kapellaki

Abstract:

The paper focuses on the area of context modeling with respect to the specification of context-aware systems supporting ubiquitous applications. The proposed approach, followed within the SIMPLICITY IST project, uses a high-level system ontology to derive context models for system components which consequently are mapped to the system's physical entities. For the definition of user and device-related context models in particular, the paper suggests a standard-based process consisting of an analysis phase using the Common Information Model (CIM) methodology followed by an implementation phase that defines 3GPP based components. The benefits of this approach are further depicted by preliminary examples of XML grammars defining profiles and components, component instances, coupled with descriptions of respective ubiquitous applications.

Keywords: 3GPP, context, context-awareness, context model, information model, user model, XML

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Authors: Halizah Awang, Ishak Ramly

Abstract:

Problem-based learning (PBL) is one of the student centered approaches and has been considered by a number of higher educational institutions in many parts of the world as a method of delivery. This paper presents a creative thinking approach for implementing Problem-based Learning in Mechanics of Structure within a Malaysian Polytechnics environment. In the learning process, students learn how to analyze the problem given among the students and sharing classroom knowledge into practice. Further, through this course-s emphasis on problem-based learning, students acquire creative thinking skills and professional skills as they tackle complex, interdisciplinary and real-situation problems. Once the creative ideas are generated, there are useful additional techniques for tender ideas that will grow into a productive concept or solution. The combination of creative skills and technical abilities will enable the students to be ready to “hit-the-ground-running" and produce in industry when they graduate.

Keywords: Creative Thinking Skills, Problem-based Learning, Problem Solving.

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Authors: O. Nouali, A. Saidi, H. Chahrat, A. Krinah, B. Toursel

Abstract:

This article describes a Web pages automatic filtering system. It is an open and dynamic system based on multi agents architecture. This system is built up by a set of agents having each a quite precise filtering task of to carry out (filtering process broken up into several elementary treatments working each one a partial solution). New criteria can be added to the system without stopping its execution or modifying its environment. We want to show applicability and adaptability of the multi-agents approach to the networks information automatic filtering. In practice, most of existing filtering systems are based on modular conception approaches which are limited to centralized applications which role is to resolve static data flow problems. Web pages filtering systems are characterized by a data flow which varies dynamically.

Keywords: Agent, Distributed Artificial Intelligence, Multiagents System, Web pages filtering.

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Authors: R. Chithra, B. Kalaavathi

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E-Learning enables the users to learn at anywhere at any time. In E-Learning systems, authenticating the E-Learning user has security issues. The usage of appropriate communication networks for providing the internet connectivity for E-learning is another challenge. WiMAX networks provide Broadband Wireless Access through the Multicast Broadcast Service so these networks can be most suitable for E-Learning applications. The authentication of E-Learning user is vulnerable to session hijacking problems. The repeated authentication of users can be done to overcome these issues. In this paper, session based Profile Caching Authentication is proposed. In this scheme, the credentials of E-Learning users can be cached at authentication server during the initial authentication through the appropriate subscriber station. The proposed cache based authentication scheme performs fast authentication by using cached user profile. Thus, the proposed authentication protocol reduces the delay in repeated authentication to enhance the security in ELearning.

Keywords: Authentication, E-Learning, WiMAX, Security, Profile caching.

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Authors: Su Xiaohan, Jin Chicheng, Liu Yijing, Burra Venkata Durga Kumar

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Energy-aware scheduling in real-time systems aims to minimize energy consumption, but issues related to resource reservation and timing constraints remain challenges. This study focuses on analyzing two scheduling algorithms, Fair-Share Scheduling (FFS) and Priority-Driven Preemptive Scheduling (PDPS), for solving these issues and energy-aware scheduling in real-time systems. Based on research on both algorithms and the processes of solving two problems, it can be found that FFS ensures fair allocation of resources but needs to improve with an imbalanced system load. And PDPS prioritizes tasks based on criticality to meet timing constraints through preemption but relies heavily on task prioritization and may not be energy efficient. Therefore, improvements to both algorithms with energy-aware features will be proposed. Future work should focus on developing hybrid scheduling techniques that minimize energy consumption through intelligent task prioritization, resource allocation, and meeting time constraints.

Keywords: Energy-aware scheduling, fair-share scheduling, priority-driven preemptive scheduling, real-time systems, optimization, resource reservation, timing constraints.

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Authors: Y. Benjelloun Touimi, N. Faddouli, S. Bennani, M. Khalidi Idrissi

Abstract:

The pedagogy project has been proven as an active learning method, which is used to develop learner-s skills and knowledge.The use of technology in the learning world, has filed several gaps in the implementation of teaching methods, and online evaluation of learners. However, the project methodology presents challenges in the assessment of learners online. Indeed, interoperability between E-learning platforms (LMS) is one of the major challenges of project-based learning assessment. Firstly, we have reviewed the characteristics of online assessment in the context of project-based teaching. We addressed the constraints encountered during the peer evaluation process. Our approach is to propose a meta-model, which will describe a language dedicated to the conception of peer assessment scenario in project-based learning. Then we illustrate our proposal by an instantiation of the meta-model through a business process in a scenario of collaborative assessment on line.

Keywords: Online project based learning, meta-model, peer assessment process.

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Authors: Mohsen Hayati, Yazdan Shirvany

Abstract:

In this paper, the application of neural networks to study the design of short-term load forecasting (STLF) Systems for Illam state located in west of Iran was explored. One important architecture of neural networks named Multi-Layer Perceptron (MLP) to model STLF systems was used. Our study based on MLP was trained and tested using three years (2004-2006) data. The results show that MLP network has the minimum forecasting error and can be considered as a good method to model the STLF systems.

Keywords: Artificial neural networks, Forecasting, Multi-layer perceptron.

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Authors: Jean-Pierre Dubois, Jihad S. Daba, H. Karam, J. Abdallah

Abstract:

Tsunami early detection and warning systems have proved to be of ultimate importance, especially after the destructive tsunami that hit Japan in March 2012. Such systems are crucial to inform the authorities of any risk of a tsunami and of the degree of its danger in order to make the right decision and notify the public of the actions they need to take to save their lives. The purpose of this research is to enhance existing tsunami detection and warning systems. We first propose an automated and miniaturized model of an early tsunami detection and warning system. The model for the operation of a tsunami warning system is simulated using the data acquisition toolbox of Matlab and measurements acquired from specified internet pages due to the lack of the required real-life sensors, both seismic and hydrologic, and building a graphical user interface for the system. In the second phase of this work, we implement various satellite image filtering schemes to enhance the acquired synthetic aperture radar images of the tsunami affected region that are masked by speckle noise. This enables us to conduct a post-tsunami damage extent study and calculate the percentage damage. We conclude by proposing improvements to the existing telecommunication infrastructure of existing warning tsunami systems using a migration to IP-based networks and fiber optics links.

Keywords: Detection, GIS, GSN, GTS, GPS, speckle noise, synthetic aperture radar, tsunami, wiener filter.

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Authors: B. O. Diyaolu, O. O. Oyerinde

Abstract:

This study examined the effect of sexuality education training programs on the knowledge and practice of sexual risk behavior among secondary school adolescents in Ibadan North Local Government area of Oyo State. A total of 105 students were sampled from two schools in the Local Government area. 70 students constituted the experimental group while 35 constituted the control group. Pretest-Posttest control group quasi-experimental design was adopted. A self-developed questionnaire was used to test participants’ knowledge and practice of sexual risk behavior before and after the training (α = .62, .82 and .74). Analysis indicated a significant effect of sexuality education training on participants’ knowledge and practice of sexual risk behavior, a significant gender difference in knowledge of sexual risk behavior but no significant age and gender difference in the practice of sexual risk behavior. It was thus concluded that sexuality education should be taught in schools and emphasized at homes with no age or gender restrictions.

Keywords: Early adolescent, health risk, sexual risk behavior, sexuality education.

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Authors: Ali E. Abbas

Abstract:

This paper summarizes some of the discussions that occurred in a workshop in West Virginia, U.S.A which was sponsored by the National Science Foundation (NSF) in February 2016. The goal of the workshop was to explore the opportunities and challenges for applying systems engineering in large enterprises, and some of the issues that still persist. The main topics of the discussion included challenges with elaboration and abstraction in large systems, interfacing physical and social systems, and the need for axiomatic frameworks for large enterprises. We summarize these main points of discussion drawing parallels with decision making in organizations to instigate research in these discussion areas.

Keywords: Decision analysis, systems engineering, framing, value creation.

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Authors: Kriangkrai Maneerat, Chutima Prommak

Abstract:

This paper presents an analysis of the localization accuracy of indoor positioning systems using Cramer-s rule via IEEE 802.15.4 wireless sensor networks. The objective is to study the impact of the methods used to convert the received signal strength into the distance that is used to compute the object location in the wireless indoor positioning system. Various methods were tested and the localization accuracy was analyzed. The experimental results show that the method based on the empirical data measured in the non line-of-sight (NLOS) environment yield the highest localization accuracy; with the minimum error distance less than 3 m.

Keywords: Indoor positioning systems, localization accuracy, wireless networks, Cramer's rule.

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Authors: Batin Latif Aylak, Bernd Noche

Abstract:

Overhead conveyor systems satisfy by their simple
construction, wide application range and their full compatibility with
other manufacturing systems, which are designed according to
international standards. Ultra-light overhead conveyor systems are
rope-based conveying systems with individually driven vehicles. The
vehicles can move automatically on the rope and this can be realized
by energy and signals. Crossings are realized by switches. Overhead
conveyor systems are particularly used in the automotive industry but
also at post offices. Overhead conveyor systems always must be
integrated with a logistical process by finding the best way for a
cheaper material flow and in order to guarantee precise and fast
workflows. With their help, any transport can take place without
wasting ground and space, without excessive company capacity, lost
or damaged products, erroneous delivery, endless travels and without
wasting time. Ultra-light overhead conveyor systems provide optimal
material flow, which produces profit and saves time. This article
illustrates the advantages of the structure of the ultra-light overhead
conveyor systems in logistics applications and explains the steps of
their system design. After an illustration of the steps, currently
available systems on the market will be shown by means of their
technical characteristics. Due to their simple construction, demands
to an ultra-light overhead conveyor system will be illustrated.

Keywords: Logistics, material flow, overhead conveyor.

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Authors: B. G. Sampath, K. C. R. Perera, W. A. S. I. Wijesuriya, V. P. C. Dassanayake

Abstract:

In this paper the design, development and testing of a stabilizer control system for a Quad-rotor is presented which is focused on the maneuverability. The mechanical design is performed along with the design of the controlling algorithm which is devised using fuzzy logic controller. The inputs for the system are the angular positions and angular rates of the Quad-rotor relative to three axes. Then the output data is filtered from an accelerometer and a gyroscope through a Kalman filter. In the development of the stability controlling system Mandani fuzzy model is incorporated. The results prove that the fuzzy based stabilizer control system is superior in high dynamic disturbances compared to the traditional systems which use PID integrated stabilizer control systems.

Keywords: Fuzzy stabilizer, maneuverability, PID, Quad-rotor.

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Authors: Volker Heierhoff, Aurilla Aurelie Bechina Arntzen, Gerrit Muller

Abstract:

It well recognized that one feature that makes a successful company is its ability to successfully align its business goals with its information communication technologies platform. Enterprise Resource Planning (ERP) systems contribute to achieve better performance by integrating various business functions and providing support for information flows. However, the technological systems complexity is known to prevent the business users to exploit in an efficient way the Enterprise Resource Planning Systems (ERP). This paper aims to investigate the role of training in improving the usage of ERP systems. To this end, we have designed an instrument survey to employees of a Norwegian multinational global provider of technology solutions. Based on the analysis of collected data, we have delineated a training model that could be high relevance for both researchers and practitioners as a step towards a better understanding of ERP system implementation.

Keywords: Business User Training, Enterprise resource planning system, Global consulting company, Role and responsibilities

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Authors: M. Pourgholi, V.J.Majd

Abstract:

This paper addresses parameter and state estimation problem in the presence of the perturbation of observer gain bounded input disturbances for the Lipschitz systems that are linear in unknown parameters and nonlinear in states. A new nonlinear adaptive resilient observer is designed, and its stability conditions based on Lyapunov technique are derived. The gain for this observer is derived systematically using linear matrix inequality approach. A numerical example is provided in which the nonlinear terms depend on unmeasured states. The simulation results are presented to show the effectiveness of the proposed method.

Keywords: Adaptive observer, linear matrix inequality, nonlinear systems, nonlinear observer, resilient observer, robust estimation.

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Authors: Elin Cahyaningsih, Dana Indra Sensuse, Wahyu Catur Wibowo, Sofiyanti Indriasari

Abstract:

Bureaucracy reform program drives Indonesian government to change their management to enhance their organizational performance. Information technology became one of strategic plan that organization tried to improve. Knowledge management system is one of information system that supporting knowledge management implementation in government which categorized as people perspective, because this system has high dependency in human interaction and participation. Strategic plan for developing knowledge management system can be determine using some of information system strategic methods. This research conducted to define type of strategic method of information system, stage of activity each method, strength and weakness. Literature review methods used to identify and classify strategic methods of information system, differentiate method type, categorize common activities, strength and weakness. Result of this research are determine and compare six strategic information system methods, Balanced Scorecard and Risk Analysis believe as common strategic method that usually used and have the highest excellence strength.

Keywords: Knowledge management system, balanced scorecard, five force, risk analysis, gap analysis, value chain analysis, SWOT analysis.

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Authors: M. R. Aghaebrahimi, S. H. Zahiri, M. Amiri

Abstract:

In this paper a data miner based on the learning automata is proposed and is called LA-miner. The LA-miner extracts classification rules from data sets automatically. The proposed algorithm is established based on the function optimization using learning automata. The experimental results on three benchmarks indicate that the performance of the proposed LA-miner is comparable with (sometimes better than) the Ant-miner (a data miner algorithm based on the Ant Colony optimization algorithm) and CNZ (a well-known data mining algorithm for classification).

Keywords: Data mining, Learning automata, Classification rules, Knowledge discovery.

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Authors: Roberto Boselli, Mirko Cesarini, Mario Mezzanzanica

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The paper is concerned with relationships between SSME and ICTs and focuses on the role of Web 2.0 tools in the service development process. The research presented aims at exploring how collaborative technologies can support and improve service processes, highlighting customer centrality and value coproduction. The core idea of the paper is the centrality of user participation and the collaborative technologies as enabling factors; Wikipedia is analyzed as an example. The result of such analysis is the identification and description of a pattern characterising specific services in which users collaborate by means of web tools with value co-producers during the service process. The pattern of collaborative co-production concerning several categories of services including knowledge based services is then discussed.

Keywords: Service Interaction Patterns, Services Science, Web2.0 tools, Service Development Process.

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Authors: Daniel F. Garcia, Diego Gonzalez

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This paper shows a simple and effective approach to the design and implementation of Industrial Information Systems (IIS) oriented to control the characteristics of each individual product manufactured in a production line and also their manufacturing conditions. The particular products considered in this work are large steel strips that are coiled just after their manufacturing. However, the approach is directly applicable to coiled strips in other industries, like paper, textile, aluminum, etc. These IIS provide very detailed information of each manufactured product, which complement the general information managed by the ERP system of the production line. In spite of the high importance of this type of IIS to guarantee and improve the quality of the products manufactured in many industries, there are very few works about them in the technical literature. For this reason, this paper represents an important contribution to the development of this type of IIS, providing guidelines for their design, implementation and exploitation.

Keywords: Data storage, industrial information systems, measurement systems integration, signal acquisition.

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Authors: Chidentree Treesatayapun

Abstract:

A direct adaptive controller for a class of unknown nonlinear discrete-time systems is presented in this article. The proposed controller is constructed by fuzzy rules emulated network (FREN). With its simple structure, the human knowledge about the plant is transferred to be if-then rules for setting the network. These adjustable parameters inside FREN are tuned by the learning mechanism with time varying step size or learning rate. The variation of learning rate is introduced by main theorem to improve the system performance and stabilization. Furthermore, the boundary of adjustable parameters is guaranteed through the on-line learning and membership functions properties. The validation of the theoretical findings is represented by some illustrated examples.

Keywords: Neuro-Fuzzy, learning algorithm, nonlinear discrete time.

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Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

Abstract:

A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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