Search results for: Local fitting binary

Authors: Omer Nebil Yaveroglu, Tolga Can

Abstract:

In this study, a high accuracy protein-protein interaction prediction method is developed. The importance of the proposed method is that it only uses sequence information of proteins while predicting interaction. The method extracts phylogenetic profiles of proteins by using their sequence information. Combining the phylogenetic profiles of two proteins by checking existence of homologs in different species and fitting this combined profile into a statistical model, it is possible to make predictions about the interaction status of two proteins. For this purpose, we apply a collection of pattern recognition techniques on the dataset of combined phylogenetic profiles of protein pairs. Support Vector Machines, Feature Extraction using ReliefF, Naive Bayes Classification, K-Nearest Neighborhood Classification, Decision Trees, and Random Forest Classification are the methods we applied for finding the classification method that best predicts the interaction status of protein pairs. Random Forest Classification outperformed all other methods with a prediction accuracy of 76.93%

Keywords: Protein Interaction Prediction, Phylogenetic Profile, SVM , ReliefF, Decision Trees, Random Forest Classification

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Authors: Adil AL-Rammahi

Abstract:

When we prefer to make the data secure from various attacks and fore integrity of data, we must encrypt the data before it is transmitted or stored. This paper introduces a new effective and lossless image encryption algorithm using a natural logarithmic function. The new algorithm encrypts an image through a three stage process. In the first stage, a reference natural logarithmic function is generated as the foundation for the encryption image. The image numeral matrix is then analyzed to five integer numbers, and then the numbers’ positions are transformed to matrices. The advantages of this method is useful for efficiently encrypting a variety of digital images, such as binary images, gray images, and RGB images without any quality loss. The principles of the presented scheme could be applied to provide complexity and then security for a variety of data systems such as image and others.

Keywords: Linear Systems, Image Encryption, Calculus.

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Authors: Tarek Aboueldahab

Abstract:

In this paper, we propose a new hybrid learning model for stock market indices prediction by adding a passive congregation term to the standard hybrid model comprising Particle Swarm Optimization (PSO) with Genetic Algorithm (GA) operators in training Neural Networks (NN). This new passive congregation term is based on the cooperation between different particles in determining new positions rather than depending on the particles selfish thinking without considering other particles positions, thus it enables PSO to perform both the local and global search instead of only doing the local search. Experiment study carried out on the most famous European stock market indices in both long term and short term prediction shows significantly the influence of the passive congregation term in improving the prediction accuracy compared to standard hybrid model.

Keywords: Global Search, Hybrid Model, Passive Congregation, Stock Market Prediction.

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Authors: Mehdi Kheradmand, Mehdi Azhdary Moghaddam, Abdolreza Zahiri, Khalil Ghorbani

Abstract:

In modeling phenomena, the presence of local conditions may cause the use of a general relation not to produce good results and thus fail to demonstrate local changes. If possible, identifying homogenous limits and providing simple linear relations for each of these limits will increase the accuracy of models. Accordingly, the models are divided into simpler and smaller problems to solve complicated problems, and the obtained answers will be combined. This simple idea can be applied to decision tree models. For this aim, the input data values are divided into several sub-intervals or sub-regions, and an appropriate model is extracted for an appropriate model or equation. This research proposes the M5 decision tree method as a solution to accurately compute the flow discharge in meandering compound channels.

Keywords: Stage-discharge relationship, decision tree, M5 decision tree model, meandering compound channels.

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Authors: Ranjan Sarukkalige, Dinushi Gamage

Abstract:

The aim of this study was to develop a storm water quality improvement strategy plan (WQISP) which assists managers and decision makers of local city councils in enhancing their activities to improve regional water quality. City of Gosnells in Western Australia has been considered as a case study. The procedure on developing the WQISP consists of reviewing existing water quality data, identifying water quality issues in the study areas and developing a decision making tool for the officers, managers and decision makers. It was found that land use type is the main factor affecting the water quality. Therefore, activities, sources and pollutants related to different land use types including residential, industrial, agricultural and commercial are given high importance during the study. Semi-structured interviews were carried out with coordinators of different management sections of the regional councils in order to understand the associated management framework and issues. The issues identified from these interviews were used in preparing the decision making tool. Variables associated with the defined “value versus threat" decision making tool are obtained from the intensive literature review. The main recommendations provided for improvement of water quality in local city councils, include non-structural, structural and management controls and potential impacts of climate change.

Keywords: Storm water quality, Storm water Management, Land use, Strategy plan

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Authors: Jutta Hämmerle-Uhl, Georg Penn, Gerhard Pötzelsberger, Andreas Uhl

Abstract:

Iris codes contain bits with different entropy. This work investigates different strategies to reduce the size of iris code templates with the aim of reducing storage requirements and computational demand in the matching process. Besides simple subsampling schemes, also a binary multi-resolution representation as used in the JBIG hierarchical coding mode is assessed. We find that iris code template size can be reduced significantly while maintaining recognition accuracy. Besides, we propose a two-stage identification approach, using small-sized iris code templates in a pre-selection stage, and full resolution templates for final identification, which shows promising recognition behaviour.

Keywords: Iris recognition, compact iris code, fast matching, best bits, pre-selection identification, two-stage identification.

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Authors: J.Morris, D.Allinson, J.Harrison, K.J. Lomas

Abstract:

The UK Government has emphasized the role of Local Authorities as a key player in its flagship residential energy efficiency strategies, by identifying and targeting areas for energy efficiency improvements. Residential energy consumption in England is characterized by significant geographical variation in energy demand, which makes centralized targeting of areas for energy efficiency intervention difficult. This paper draws on research which aims to understand how demographic, social, economic, urban form and climatic factors influence the geographical variations in English residential gas consumption. The paper reports the findings of a multiple regression model that shows how 64% of the geographical variation in residential gas consumption is accounted for by variations in these factors. Results from this study, after further refinement and validation, can be used by Local Authorities to identify areas within their boundaries that have higher than expected gas consumption, these may be prime targets for energy efficiency initiatives.

Keywords: UK Housing, Heating Energy, Socio-Economics, Statistical Modelling

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Authors: M. Alauddin, T. Tsujimoto

Abstract:

Dynamicity of stream channels along with environmental concern is the key issue to address in lowland rivers like Jamuna in Bangladesh. The groins are important structures in attaining the improved river environment, but their effective functioning is not evident yet with the present design. Considering the present demands, an approach through modification of groin configurations is planned to function more natural way in dynamic lowland rivers. Four different configurations including the conventional one are considered in the study, and the changes in hydro- and morpho-dynamics affected by various structures are investigated in the laboratory. Results show that the modified combined groin favors gradual deceleration of flow towards the channel side and minimizes local scour noticeably. This favors stable regular channel and improve environmental functions.

Keywords: Lowland river, dynamicity, river environment, groin configuration, local scour.

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Authors: M. P. Amado, C. V. Santos, E. B. Moura, V.G. Silva

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Urban planning, in particular on protected landscape areas, demands an increasing role of public participation within the frame of the efficiency of sustainable planning process. The development of urban planning actions in Protected Landscape areas, as Sintra-Cascais Natural Park, should perform a methodological process that is structured over distinct sequential stages, providing the development of a continuous, interactive, integrated and participative planning. From the start of Malveira da Serra and Janes Plan process, several public participation actions were promoted, in order to involve the local agents, stakeholders and the population in the decision of specific local key issues and define the appropriate priorities within the goals and strategies previously settled. As a result, public participation encouraged an innovative process that guarantees the efficiency of sustainable urban planning and promotes a sustainable new way of living in community.

Keywords: Protected landscape areas, Public participation, Sustainable development, Sustainable planning, Urban planning.

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Authors: Alessandra Battisti, Silvia Cimini

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This article stands in the context of rural communities in Brazil, where, like many others emerging countries, the overwhelming increasing markets and the overcrowded cities are leaving behind informal settlements based on obsolete agricultural economies and techniques. The pilot project for the community of Goiabeira reflects the attempt to imagine a development model that privileges the actual improvement of living conditions, the education and training, the social inclusion and participation of the dwellers of rural communities. Through the inclusion of operative public space, the aim is for them to become self-sustaining, encouraging the use of local resources for appropriate architectural, ecological and energy technologies and devices, that are efficient, affordable and foster community participation, in the respect of the surrounding environment.

Keywords: Economical development, environment conservation, local resources, participation and social inclusion.

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Authors: Ichiro Mukai

Abstract:

The purpose of this study is to investigate whether firms applying International Financial Reporting Standards (IFRS), provide high-quality and comparable earnings information that is useful for decision making of information users relative to firms applying local Generally Accepted Accounting Principles (GAAP). Focus is placed on the earnings quality of listed firms in several developed countries: Australia, Canada, France, Germany, Japan, the United Kingdom (UK), and the United States (US). Except for Japan and the US, the adoption of IFRS is mandatory for listed firms in these countries. In Japan, the application of IFRS is allowed for specific listed firms. In the US, the foreign firms listed on the US securities market are permitted to apply IFRS but the listed domestic firms are prohibited from doing so. In this paper, the differences in earnings quality are compared between firms applying local GAAP and those applying IFRS in each country and industry category, and the reasons of differences in earnings quality are analyzed using various factors. The results show that, although the earnings quality of firms applying IFRS is higher than that of firms applying local GAAP, this varies with country and industry category. Thus, even if a single set of global accounting standards is used for all listed firms worldwide, it is difficult to establish comparability of financial information among global firms. These findings imply that various circumstances surrounding firms, industries, and countries etc. influence business operations and affect the differences in earnings quality.

Keywords: Accruals, earnings quality, IFRS, information comparability.

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Authors: Yousra Zakaria Ahmed, Ahmed El Gendy, Salah El Haggar

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In this paper, our methodology to assess sustainability of wastewater treatment technologies in Egypt is presented. The preliminary list of factors to be considered, as well as their ranking listed. The factors include, but are not limited to pollutants removal efficiency and energy consumption under the environmental dimension, construction cost, operation and maintenance costs and required land area cost under the economic dimension and public acceptance, noise and generating job opportunities for local residents. This methodology is intended to be a user-friendly screening tool to support the decision making process when investigating different wastewater treatment technologies in Egypt. Based on the research work results presented in this paper, it can be generally concluded that the categorization of some of the social and environmental aspects of sustainability is subjective and highly dependent on the local conditions and researchers’ background.

Keywords: Sustainability, wastewater treatment, sustainability assessment, Egypt.

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Authors: Xingyu Pan, Laure Tougne

Abstract:

For recognizing coins, the graved release date is important information to identify precisely its monetary type. However, reading characters in coins meets much more obstacles than traditional character recognition tasks in the other fields, such as reading scanned documents or license plates. To address this challenging issue in a numismatic context, we propose a training-free approach dedicated to detection and recognition of the release date of the coin. In the first step, the date zone is detected by comparing histogram features; in the second step, a topology-based algorithm is introduced to recognize coin numbers with various font types represented by binary gradient map. Our method obtained a recognition rate of 92% on synthetic data and of 44% on real noised data.

Keywords: Coin, detection, character recognition, topology.

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Authors: Gholamreza Zarei, Hossein Shamsi, Farjam Fazeli

Abstract:

This study carried out to determine the effect of plant densities on some agronomic characteristics of four safflower cultivars in spring planting. The experiment was conducted at Yazd, Iran- using a factorial in a randomized complete block design with four replications. Cultivars were including Arak, IL, Asteria and Local and plant densities were 10, 13.3, 20 and 40 plant/m2. Number of seeds/head, number of heads/plant, HI, 1000-seed weight and seed yield significantly decreased as planting density increased. With increasing planting density, LAI, plant height, first branch height and biological yield increased. The highest seed yield was obtained in 13.3 plant/m2 (2167 kg/ha). There were significant differences between cultivars. Local cv. had higher seed yield than the other cultivars mainly due to higher heads/plant and seeds/head.

Keywords: safflower, plant density, cultivar

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Authors: M. S. Ahmed, F. A. Mohammad

Abstract:

The aim of this paper is to perform experimental modal analysis (EMA) of reinforced concrete (RC) square slabs. EMA is the process of determining the modal parameters (Natural Frequencies, damping factors, modal vectors) of a structure from a set of frequency response functions FRFs (curve fitting). Although, experimental modal analysis (or modal testing) has grown steadily in popularity since the advent of the digital FFT spectrum analyzer in the early 1970’s, studying all types of members and materials using such method have not yet been well documented. Therefore, in this work, experimental tests were conducted on RC square slab specimens of dimensions 600mm x 600mmx 40mm. Experimental analysis was based on freely supported boundary condition. Moreover, impact testing as a fast and economical means of finding the modes of vibration of a structure was used during the experiments. In addition, Pico Scope 6 device and MATLAB software were used to acquire data, analyze and plot Frequency Response Function (FRF). The experimental natural frequencies which were extracted from measurements exhibit good agreement with analytical predictions. It is showed that EMA method can be usefully employed to investigate the dynamic behavior of RC slabs.

Keywords: Natural frequencies, Mode shapes, Modal analysis, RC slabs.

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Authors: Daningsih Sulaeman, Achmad Sjarmidi, Djoko T. Iskandar

Abstract:

Komodo National Park can be associated with the implementation of ecotourism program. The result of Principal Components Analysis is synthesized, tested, and compared to the basic concept of ecotourism with some field adjustments. Principal aspects of professional management should involve ecotourism and wildlife welfare. The awareness should be focused on the future of the Natural Park as 7^th Wonder Natural Heritage and its wildlife components, free from human wastes and beneficial to wildlife and local people. According to perceptions and expectations of visitors from various results of tourism programs, the visitor’s perceptions showed that the tourism management in Komodo National Park should pay more attention to visitor's satisfaction and expectation and gives positive impact directly to the ecosystem sustainability, local community and transparency to the conservation program.

Keywords: 7th Wonders of Nature, Ecotourism, Komodo dragon, visitor’s perceptions, wildlife management.

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Authors: S. Ishak, M. G. Nasuruddin

Abstract:

This paper looks at healing performances as ethnographic expressions of local knowledge and culture embedded within the Malay psyche and gemeinschaft. As society develops and progresses, these healing performances are caught within conflicting trajectories which become compounded by the contestations of tradition, religious concerns, locality and modernity. As exemplifications of the Malay ethos, these performances practice common rituals, cater to the innate needs of the practitioners and serve the targeted, closed, local community. This paper traces the ethnographic methods in documenting these practices as rituals of healing in a post-modern world. It delineates the ethnographic concepts used to analyze these rituals, and to semiotically read the varied binarial oppositions and juxtapositions. The paper concludes by highlighting the reconciliatory processes involved in maintaining these ritual performances as exemplifications of the Malay ethos playing an important role in the re-aligning, re-balancing and healing of the Malay community’s psyche.

Keywords: Angin/winds, Semangat/spirits, Traditional Theatres, Trance.

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Authors: Ahmet Tekcan, Arzu Özkoç

Abstract:

Let D = 1 be a positive non-square integer and let δ = √D or 1+√D 2 be a real quadratic irrational with trace t =δ + δ and norm n = δδ. Let γ = P+δ Q be a quadratic irrational for positive integers P and Q. Given a quadratic irrational γ, there exist a quadratic ideal Iγ = [Q, δ + P] and an indefinite quadratic form Fγ(x, y) = Q(x−γy)(x−γy) of discriminant Δ = t 2−4n. In the first section, we give some preliminaries form binary quadratic forms, quadratic irrationals and quadratic ideals. In the second section, we obtain some results on γ, Iγ and Fγ for some specific values of Q and P.

Keywords: Quadratic irrationals, quadratic ideals, indefinite quadratic forms, extended modular group.

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Authors: Meng-Hui Chen, Pei-Chann Chang, Wei-Hsiu Huang

Abstract:

Artificial Immune System is adopted as a Heuristic Algorithm to solve the combinatorial problems for decades. Nevertheless, many of these applications took advantage of the benefit for applications but seldom proposed approaches for enhancing the efficiency. In this paper, we continue the previous research to develop a Self-evolving Artificial Immune System II via coordinating the T and B cell in Immune System and built a block-based artificial chromosome for speeding up the computation time and better performance for different complexities of problems. Through the design of Plasma cell and clonal selection which are relative the function of the Immune Response. The Immune Response will help the AIS have the global and local searching ability and preventing trapped in local optima. From the experimental result, the significant performance validates the SEAIS II is effective when solving the permutation flows-hop problems.

Keywords: Artificial Immune System, Clonal Selection, Immune Response, Permutation Flow-shop Scheduling Problems

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Authors: N. Maksimentseva

Abstract:

The issue of public administration in subsoil use, renewal and protection is of high importance for Ukraine since it is strongly linked to energy security of the state as well as it shall facilitate the people of Ukraine to efficiently implement its propitiatory rights towards natural resources and redistribution of national wealth. As it is stipulated in the Article 11 of the Subsoil Code of Ukraine (the Code) the authorities that administer the industry are limited to central executive bodies and local governments. In particular, it is stipulated in the Code that the Ukraine’s Cabinet of Ministers carries out public administration in geological exploration, production and protection of subsoil. Other state bodies of public administration include central public authority responsible for state environmental protection policies; central public authority in charge of implementation of state geological exploration and efficient subsoil use policies; central authority in charge of state health and safety control policies. There are also public authorities in the Autonomous Republic of Crimea; local executive bodies and other state authorities and local self-government authorities in compliance with laws of Ukraine. This article is devoted to the analysis of the legal relations in the area of public administration of subsoil use, renewal and protection in Ukraine. The main approaches to study the essence of legal relations in the named area as well as its tasks, functions and methods are analyzed. It is concluded in this article that legal relationship in the field of public administration of subsoil use, renewal and protection is characterized by specifics of its task (development of natural resources).

Keywords: Legal relations, public administration, Subsoil Code of Ukraine, subsoil use, renewal and protection.

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Authors: Ikhwan Hakim, Bruno Parolin

Abstract:

This paper investigates the spatial structure of employment in the Jakarta Metropolitan Area (JMA), with reference to the concept of the Southeast Asian extended metropolitan region (EMR). A combination of factor analysis and local Getis-Ord (Gi*) hot-spot analysis is used to identify clusters of employment in the region, including those of the urban and agriculture sectors. Spatial statistical analysis is further used to probe the spatial association of identified employment clusters with their surroundings on several dimensions, including the spatial association between the central business district (CBD) in Jakarta city on employment density in the region, the spatial impacts of urban expansion on population growth and the degree of urban-rural interaction. The degree of spatial interaction for the whole JMA is measured by the patterns of commuting trips destined to the various employment clusters. Results reveal the strong role of the urban core of Jakarta, and the regional CBD, as the centre for mixed job sectors such as retail, wholesale, services and finance. Manufacturing and local government services, on the other hand, form corridors radiating out of the urban core, reaching out to the agriculture zones in the fringes. Strong associations between the urban expansion corridors and population growth, and urban-rural mix, are revealed particularly in the eastern and western parts of JMA. Metropolitan wide commuting patterns are focussed on the urban core of Jakarta and the CBD, while relatively local commuting patterns are shown to be prevalent for the employment corridors.

Keywords: Jakarta Metropolitan Area, Southeast Asian EMR, spatial association, spatial statistics, spatial structure.

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Authors: Ashwani K. Rana, Narottam Chand, Vinod Kapoor

Abstract:

This paper presents a new compact analytical model of the gate leakage current in high-k based nano scale MOSFET by assuming a two-step inelastic trap-assisted tunneling (ITAT) process as the conduction mechanism. This model is based on an inelastic trap-assisted tunneling (ITAT) mechanism combined with a semiempirical gate leakage current formulation in the BSIM 4 model. The gate tunneling currents have been calculated as a function of gate voltage for different gate dielectrics structures such as HfO2, Al2O3 and Si3N4 with EOT (equivalent oxide thickness) of 1.0 nm. The proposed model is compared and contrasted with santaurus simulation results to verify the accuracy of the model and excellent agreement is found between the analytical and simulated data. It is observed that proposed analytical model is suitable for different highk gate dielectrics simply by adjusting two fitting parameters. It was also shown that gate leakages reduced with the introduction of high-k gate dielectric in place of SiO2.

Keywords: Analytical model, High-k gate dielectrics, inelastic trap assisted tunneling, metal–oxide–semiconductor (MOS) devices.

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Authors: S. Ghafoori, A. Al-Harbi, B. Al-Ajmi, A. Al-Shaalan, A. Al-Ajmi, M. Ali Juma

Abstract:

Seismic methods play an important role in the exploration for hydrocarbon reservoirs. However, the success of the method depends strongly on the reliability of the measured or predicted information regarding the velocity of sound in the media. Speed of sound has been used to study the thermodynamic properties of fluids. In this study, experimental data are reported and analyzed on the speed of sound in toluene and octane binary mixture. Three-factor three-level Box-Benhkam design is used to determine the significance of each factor, the synergetic effects of the factors, and the most significant factors on speed of sound. The developed mathematical model and statistical analysis provided a critical analysis of the simultaneous interactive effects of the independent variables indicating that the developed quadratic models were highly accurate and predictive.

Keywords: Experimental design, octane, speed of sound, toluene.

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Authors: Jing Zhao, Yoshiharu Ishikawa, Chuan Xiao, Kento Sugiura

Abstract:

In order to analyze large-scale scientific data, research on data exploration and visualization has gained popularity. In this paper, we focus on the exploration and visualization of scientific simulation data, and define a spatial V-Optimal histogram for data summarization. We propose histogram construction algorithms based on a general binary hierarchical partitioning as well as a more specific one, the l-grid partitioning. For effective data summarization and efficient data visualization in scientific data analysis, we propose an optimal algorithm as well as a heuristic algorithm for histogram construction. To verify the effectiveness and efficiency of the proposed methods, we conduct experiments on the massive evacuation simulation data.

Keywords: Simulation data, data summarization, spatial histograms, exploration and visualization.

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Authors: Vakhtang Charaia

Abstract:

The article focuses on the role of FDI in Georgia’s economic development for the last decade. To attract as much FDI as possible a proper investment climate should be on the place - institutional, policy and regulatory environment. Well developed investment climate is the chance and motivation for both, local economy and foreign companies, to generate maximum income, create new work places and improve the quality of life. FDI trend is one of the best indicators of country’s economic sustainability and its attractiveness. Especially for small and developing countries, the amount of FDI matters, therefore most of such countries are trying to compete with each other through improving their investment climate according to different world famous indexes. As a result of impressive reforms since 2003, Georgian economy was benefited with large invasion of FDI, however the level of per capita GDP is still law in comparison to Eastern European countries and it should be improved. The main idea of the paper is to show a real linkage between FDI and employment ration, on the case of Georgian economy.

Keywords: Foreign Direct Investment, Sustainable Development, Corruption, Employment/Unemployment.

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Authors: Sang-Soo Kim, Seong-Bae Park, Sang-Jo Lee

Abstract:

In this paper, we propose a method of resolving dependency ambiguities of Korean subordinate clauses based on Support Vector Machines (SVMs). Dependency analysis of clauses is well known to be one of the most difficult tasks in parsing sentences, especially in Korean. In order to solve this problem, we assume that the dependency relation of Korean subordinate clauses is the dependency relation among verb phrase, verb and endings in the clauses. As a result, this problem is represented as a binary classification task. In order to apply SVMs to this problem, we selected two kinds of features: static and dynamic features. The experimental results on STEP2000 corpus show that our system achieves the accuracy of 73.5%.

Keywords: Dependency analysis, subordinate clauses, binaryclassification, support vector machines.

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Authors: Youssef Chahir, Messaoud Mostefai, Salah Khodja

Abstract:

This paper presents the development of a 2D visual marker, derived from a recent patented work in the field of numbering systems. The proposed fiducial uses a group of projective invariant straight-line patterns, easily detectable and remotely recognizable. Based on an efficient data coding scheme, the developed marker enables producing a large panel of unique real time identifiers with highly distinguishable patterns. The proposed marker Incorporates simultaneously decimal and binary information, making it readable by both humans and machines. This important feature opens up new opportunities for the development of efficient visual human-machine communication and monitoring protocols. Extensive experiment tests validate the robustness of the marker against acquisition and geometric distortions.

Keywords: visual marker, projective invariants, distance map, level set

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Authors: Il Young Song, Du Yong Kim, Vladimir Shin

Abstract:

This paper reports on a receding horizon filtering for mobile robot systems with cross-correlated sensor noises and uncertainties. Also, the effect of uncertain parameters in the state of the tracking error model performance is considered. A distributed fusion receding horizon filter is proposed. The distributed fusion filtering algorithm represents the optimal linear combination of the local filters under the minimum mean square error criterion. The derivation of the error cross-covariances between the local receding horizon filters is the key of this paper. Simulation results of the tracking mobile robot-s motion demonstrate high accuracy and computational efficiency of the distributed fusion receding horizon filter.

Keywords: Distributed fusion, fusion formula, Kalman filter, multisensor, receding horizon, wheeled mobile robot

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Authors: Paola Lecca, Lorenzo Dematte

Abstract:

Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.

Keywords: Reaction-diffusion systems, Fick's law, stochastic simulation algorithm.

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Authors: Paul O'Leary, Matthew Harker

Abstract:

This paper presents unified theory for local (Savitzky- Golay) and global polynomial smoothing. The algebraic framework can represent any polynomial approximation and is seamless from low degree local, to high degree global approximations. The representation of the smoothing operator as a projection onto orthonormal basis functions enables the computation of: the covariance matrix for noise propagation through the filter; the noise gain and; the frequency response of the polynomial filters. A virtually perfect Gram polynomial basis is synthesized, whereby polynomials of degree d = 1000 can be synthesized without significant errors. The perfect basis ensures that the filters are strictly polynomial preserving. Given n points and a support length ls = 2m + 1 then the smoothing operator is strictly linear phase for the points xi, i = m+1. . . n-m. The method is demonstrated on geometric surfaces data lying on an invariant 2D lattice.

Keywords: Gram polynomials, Savitzky-Golay Smoothing, Discrete Polynomial Moments

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