Search results for: evolutionary tree

Authors: Wan Chian Li, Justie Su-Tzu Juan, Yi-Chun Wang, Shu-Chuan Chen

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The evolutionary tree is an important topic in bioinformation. In 2006, Chen and Lindsay proposed a new method to build the mixture tree from DNA sequences. Mixture tree is a new type evolutionary tree, and it has two additional information besides the information of ordinary evolutionary tree. One of the information is time parameter, and the other is the set of mutated sites. In 2008, Lin and Juan proposed an algorithm to compute the distance between two mixture trees. Their algorithm computes the distance with only considering the time parameter between two mixture trees. In this paper, we proposes a method to measure the similarity of two mixture trees with considering the set of mutated sites and develops two algorithm to compute the distance between two mixture trees. The time complexity of these two proposed algorithms are O(n2 × max{h(T1), h(T2)}) and O(n2), respectively

Keywords: evolutionary tree, mixture tree, mutated site, distance.

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Authors: Parvinder Singh Sandhu, Sumeet Kaur Sehra, Karmjit Kaur

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Phylogenetic tree is a graphical representation of the evolutionary relationship among three or more genes or organisms. These trees show relatedness of data sets, species or genes divergence time and nature of their common ancestors. Quality of a phylogenetic tree requires parsimony criterion. Various approaches have been proposed for constructing most parsimonious trees. This paper is concerned about calculating and optimizing the changes of state that are needed called Small Parsimony Algorithms. This paper has proposed enhanced small parsimony algorithm to give better score based on number of evolutionary changes needed to produce the observed sequence changes tree and also give the ancestor of the given input.

Keywords: Phylogenetic Analysis, Small Parsimony, EnhancedFitch Algorithm, Enhanced Sakoff Algorithm.

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Authors: Soichi Ogishima, Takeshi Hase, So Nakagawa, Yasuhiro Suzuki, Hiroshi Tanaka

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To understand life as biological system, evolutionary understanding is indispensable. Protein interactions data are rapidly accumulating and are suitable for system-level evolutionary analysis. We have analyzed yeast protein interaction network by both mathematical and biological approaches. In this poster presentation, we inferred the evolutionary birth periods of yeast proteins by reconstructing phylogenetic profile. It has been thought that hub proteins that have high connection degree are evolutionary old. But our analysis showed that hub proteins are entirely evolutionary new. We also examined evolutionary processes of protein complexes. It showed that member proteins of complexes were tend to have appeared in the same evolutionary period. Our results suggested that protein interaction network evolved by modules that form the functional unit. We also reconstructed standardized phylogenetic trees and calculated evolutionary rates of yeast proteins. It showed that there is no obvious correlation between evolutionary rates and connection degrees of yeast proteins.

Keywords: Protein interaction network, evolution, modularity, evolutionary rate, connection degrees.

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Authors: S.L. Loh, S. Salleh, N.H. Sarmin

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A spanning tree of a connected graph is a tree which consists the set of vertices and some or perhaps all of the edges from the connected graph. In this paper, a model for spanning tree transformation of connected graphs into single-row networks, namely Spanning Tree of Connected Graph Modeling (STCGM) will be introduced. Path-Growing Tree-Forming algorithm applied with Vertex-Prioritized is contained in the model to produce the spanning tree from the connected graph. Paths are produced by Path-Growing and they are combined into a spanning tree by Tree-Forming. The spanning tree that is produced from the connected graph is then transformed into single-row network using Tree Sequence Modeling (TSM). Finally, the single-row routing problem is solved using a method called Enhanced Simulated Annealing for Single-Row Routing (ESSR).

Keywords: Graph theory, simulated annealing, single-rowrouting and spanning tree.

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Authors: Deepali Virmani , Satbir Jain

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To meet the demands of wireless sensor networks (WSNs) where data are usually aggregated at a single source prior to transmitting to any distant user, there is a need to establish a tree structure inside any given event region. In this paper , a novel technique to create one such tree is proposed .This tree preserves the energy and maximizes the lifetime of event sources while they are constantly transmitting for data aggregation. The term Decentralized Lifetime Maximizing Tree (DLMT) is used to denote this tree. DLMT features in nodes with higher energy tend to be chosen as data aggregating parents so that the time to detect the first broken tree link can be extended and less energy is involved in tree maintenance. By constructing the tree in such a way, the protocol is able to reduce the frequency of tree reconstruction, minimize the amount of data loss ,minimize the delay during data collection and preserves the energy.

Keywords: branch energy, decentralized, energy level , lifetime, tree energy, wireless sensor networks.

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Authors: Emilia Nercissians

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Neoclassical and functionalist explanations of self organization in multiagent systems have been criticized on several accounts including unrealistic explication of overadapted agents and failure to resolve problems of externality. The paper outlines a more elaborate and dynamic model that is capable of resolving these dilemmas. An illustrative example where behavioral diversity is cobred in a repeated nonzero sum task via evolutionary computing is presented.

Keywords: evolutionary stability, externalities, neofunctionalism, prisoners' dilemma.

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Authors: Sung-Hae Jun, Kyung-Whan Oh

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Statistical learning theory was developed by Vapnik. It is a learning theory based on Vapnik-Chervonenkis dimension. It also has been used in learning models as good analytical tools. In general, a learning theory has had several problems. Some of them are local optima and over-fitting problems. As well, statistical learning theory has same problems because the kernel type, kernel parameters, and regularization constant C are determined subjectively by the art of researchers. So, we propose an evolutionary statistical learning theory to settle the problems of original statistical learning theory. Combining evolutionary computing into statistical learning theory, our theory is constructed. We verify improved performances of an evolutionary statistical learning theory using data sets from KDD cup.

Keywords: Evolutionary computing, Local optima, Over-fitting, Statistical learning theory

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Authors: Amitava Chakraborty, Sudip Kumar De, Ranjan Dasgupta

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Point quad tree is considered as one of the most common data organizations to deal with spatial data & can be used to increase the efficiency for searching the point features. As the efficiency of the searching technique depends on the height of the tree, arbitrary insertion of the point features may make the tree unbalanced and lead to higher time of searching. This paper attempts to design an algorithm to make a nearly balanced quad tree. Point pattern analysis technique has been applied for this purpose which shows a significant enhancement of the performance and the results are also included in the paper for the sake of completeness.

Keywords: Algorithm, Height balanced tree, Point patternanalysis, Point quad tree.

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Authors: José Maria A. Pangilinan, Gerrit K. Janssens

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This paper presents an overview of the multiobjective shortest path problem (MSPP) and a review of essential and recent issues regarding the methods to its solution. The paper further explores a multiobjective evolutionary algorithm as applied to the MSPP and describes its behavior in terms of diversity of solutions, computational complexity, and optimality of solutions. Results show that the evolutionary algorithm can find diverse solutions to the MSPP in polynomial time (based on several network instances) and can be an alternative when other methods are trapped by the tractability problem.

Keywords: Multiobjective evolutionary optimization, geneticalgorithms, shortest paths.

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Authors: Alberto Hananel

Abstract:

The aim of this work is to modelize the occlusion of a person with temporomandibular disorders as an evolutionary equation and approach its solution by the construction and characterizing of discrete variational splines. To formulate the problem, certain boundary conditions have been considered. After showing the existence and the uniqueness of the solution of such a problem, a convergence result of a discrete variational evolutionary spline is shown. A stress analysis of the occlusion of a human jaw with temporomandibular disorders by finite elements is carried out in FreeFem++ in order to prove the validity of the presented method.

Keywords: Approximation, evolutionary PDE, finite element method, temporomandibular disorders, variational spline.

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Authors: Gökhan Silahtaroğlu

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Decision tree algorithms have very important place at classification model of data mining. In literature, algorithms use entropy concept or gini index to form the tree. The shape of the classes and their closeness to each other some of the factors that affect the performance of the algorithm. In this paper we introduce a new decision tree algorithm which employs data (attribute) folding method and variation of the class variables over the branches to be created. A comparative performance analysis has been held between the proposed algorithm and C4.5.

Keywords: Classification, decision tree, split, pruning, entropy, gini.

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Authors: Bhed Bahadur Bista

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Network layer multicast, i.e. IP multicast, even after many years of research, development and standardization, is not deployed in large scale due to both technical (e.g. upgrading of routers) and political (e.g. policy making and negotiation) issues. Researchers looked for alternatives and proposed application/overlay multicast where multicast functions are handled by end hosts, not network layer routers. Member hosts wishing to receive multicast data form a multicast delivery tree. The intermediate hosts in the tree act as routers also, i.e. they forward data to the lower hosts in the tree. Unlike IP multicast, where a router cannot leave the tree until all members below it leave, in overlay multicast any member can leave the tree at any time thus disjoining the tree and disrupting the data dissemination. All the disrupted hosts have to rejoin the tree. This characteristic of the overlay multicast causes multicast tree unstable, data loss and rejoin overhead. In this paper, we propose that each node sets its leaving time from the tree and sends join request to a number of nodes in the tree. The nodes in the tree will reject the request if their leaving time is earlier than the requesting node otherwise they will accept the request. The node can join at one of the accepting nodes. This makes the tree more stable as the nodes will join the tree according to their leaving time, earliest leaving time node being at the leaf of the tree. Some intermediate nodes may not follow their leaving time and leave earlier than their leaving time thus disrupting the tree. For this, we propose a proactive recovery mechanism so that disrupted nodes can rejoin the tree at predetermined nodes immediately. We have shown by simulation that there is less overhead when joining the multicast tree and the recovery time of the disrupted nodes is much less than the previous works. Keywords

Keywords: Network layer multicast, Fault Resilience, IP multicast

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Authors: Monica Chiş

Abstract:

Software metric is a measure of some property of a piece of software or its specification. The aim of this paper is to present an application of evolutionary decision trees in software engineering in order to classify the software modules that have or have not one or more reported defects. For this some metrics are used for detecting the class of modules with defects or without defects.

Keywords: Evolutionary decision trees, decision trees, softwaremetrics.

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Authors: Konstantinos Metaxiotis, Konstantinos Liagkouras

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The objective of this study is to examine the performance of three well-known multiobjective evolutionary algorithms for solving optimization problems. The first algorithm is the Non-dominated Sorting Genetic Algorithm-II (NSGA-II), the second one is the Strength Pareto Evolutionary Algorithm 2 (SPEA-2), and the third one is the Multiobjective Evolutionary Algorithms based on decomposition (MOEA/D). The examined multiobjective algorithms are analyzed and tested on the ZDT set of test functions by three performance metrics. The results indicate that the NSGA-II performs better than the other two algorithms based on three performance metrics.

Keywords: MOEAs, Multiobjective optimization, ZDT test functions, performance metrics.

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Authors: Krishnamoorthi Makkithaya, N. V. Subba Reddy, U. Dinesh Acharya

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As the number of networked computers grows, intrusion detection is an essential component in keeping networks secure. Various approaches for intrusion detection are currently being in use with each one has its own merits and demerits. This paper presents our work to test and improve the performance of a new class of decision tree c-fuzzy decision tree to detect intrusion. The work also includes identifying best candidate feature sub set to build the efficient c-fuzzy decision tree based Intrusion Detection System (IDS). We investigated the usefulness of c-fuzzy decision tree for developing IDS with a data partition based on horizontal fragmentation. Empirical results indicate the usefulness of our approach in developing the efficient IDS.

Keywords: Data mining, Decision tree, Feature selection, Fuzzyc- means clustering, Intrusion detection.

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Authors: Maciej Norberciak

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Timetabling problems are often hard and timeconsuming to solve. Most of the methods of solving them concern only one problem instance or class. This paper describes a universal method for solving large, highly constrained timetabling problems from different domains. The solution is based on evolutionary algorithm-s framework and operates on two levels – first-level evolutionary algorithm tries to find a solution basing on given set of operating parameters, second-level algorithm is used to establish those parameters. Tabu search is employed to speed up the solution finding process on first level. The method has been used to solve three different timetabling problems with promising results.

Keywords: Evolutionary algorithms, tabu search, timetabling.

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Authors: Hairulliza M. Judi, Soon Y. Chee

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This paper discusses the landscape design that could increase energy efficiency in a house. By planting trees in a house compound, the tree shades prevent direct sunlight from heating up the building, and it enables cooling off the surrounding air. The requirement for air-conditioning could be minimized and the air quality could be improved. During the life time of a tree, the saving cost from the mentioned benefits could be up to US $ 200 for each tree. The project intends to visually describe the landscape design in a house compound that could enhance energy efficiency and consequently lead to energy saving. The house compound model was developed in three dimensions by using AutoCAD 2005, the animation was programmed by using LightWave 3D softwares i.e. Modeler and Layout to display the tree shadings in the wall. The visualization was executed on a VRML Pad platform and implemented on a web environment.

Keywords: Tree planting, tree shading, energy efficiency, visualization.

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Authors: M. Umabharathi, S. Vijayabaskar

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Evolutionary Fuzzy PID Speed Controller for Permanent Magnet Synchronous Motor (PMSM) is developed to achieve the Speed control of PMSM in Closed Loop operation and to deal with the existence of transients. Consider a Fuzzy PID control design problem, based on common control Engineering Knowledge. If the transient error is big, that Good transient performance can be obtained by increasing the P and I gains and decreasing the D gains. To autotune the control parameters of the Fuzzy PID controller, the Evolutionary Algorithms (EA) are developed. EA based Fuzzy PID controller provides better speed control and guarantees the closed loop stability. The Evolutionary Fuzzy PID controller can be implemented in real time Applications without any concern about instabilities that leads to system failure or damage.

Keywords: Evolutionary Algorithm (EA), Fuzzy system, Genetic Algorithm (GA), Membership, Permanent Magnet Synchronous Motor (PMSM).

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Authors: Zhu Jiaming, Yu Mengna

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In this article, models based on quantitative analysis, physical geometry and regression analysis are established, by using analytic hierarchy process analysis, fuzzy cluster analysis, fuzzy photographic and data fitting. The reasons of various leaf shapes among different species and the differences between the leaf shapes on same tree have been solved by using software, such as Eviews, VB and Matlab. We also successfully estimate the leaf mass of a tree and the correlation with the tree profile.

Keywords: Leaf shape; Mass; Fuzzy cluster; Regression analysis; Eviews; Matlab

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Authors: Asha Rani, Christian Micheloni, Gian Luca Foresti

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In this paper, a neural tree (NT) classifier having a simple perceptron at each node is considered. A new concept for making a balanced tree is applied in the learning algorithm of the tree. At each node, if the perceptron classification is not accurate and unbalanced, then it is replaced by a new perceptron. This separates the training set in such a way that almost the equal number of patterns fall into each of the classes. Moreover, each perceptron is trained only for the classes which are present at respective node and ignore other classes. Splitting nodes are employed into the neural tree architecture to divide the training set when the current perceptron node repeats the same classification of the parent node. A new error function based on the depth of the tree is introduced to reduce the computational time for the training of a perceptron. Experiments are performed to check the efficiency and encouraging results are obtained in terms of accuracy and computational costs.

Keywords: Neural Tree, Pattern Classification, Perceptron, Splitting Nodes.

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Authors: Kiyoshi Sawada, Takashi Mitsuishi

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This paper proposes a model of adding relations between members of the same level in a pyramid organization structure which is a complete K-ary tree such that the communication of information between every member in the organization becomes the most efficient. When edges between one node and every other node with the same depth N in a complete K-ary tree of height H are added, an optimal depth N* = H is obtained by minimizing the total path length which is the sum of lengths of shortest paths between every pair of all nodes.

Keywords: complete K-ary tree, organization structure, shortest path

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Authors: Mourad Ykhlef, Hebah ElGibreen

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Mining Sequential Patterns in large databases has become an important data mining task with broad applications. It is an important task in data mining field, which describes potential sequenced relationships among items in a database. There are many different algorithms introduced for this task. Conventional algorithms can find the exact optimal Sequential Pattern rule but it takes a long time, particularly when they are applied on large databases. Nowadays, some evolutionary algorithms, such as Particle Swarm Optimization and Genetic Algorithm, were proposed and have been applied to solve this problem. This paper will introduce a new kind of hybrid evolutionary algorithm that combines Genetic Algorithm (GA) with Particle Swarm Optimization (PSO) to mine Sequential Pattern, in order to improve the speed of evolutionary algorithms convergence. This algorithm is referred to as SP-GAPSO.

Keywords: Genetic Algorithm, Hybrid Evolutionary Algorithm, Particle Swarm Optimization algorithm, Sequential Pattern mining.

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Authors: Mounira Taileb, Sami Touati

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In Content-Based Image Retrieval systems it is important to use an efficient indexing technique in order to perform and accelerate the search in huge databases. The used indexing technique should also support the high dimensions of image features. In this paper we present the hierarchical index NOHIS-tree (Non Overlapping Hierarchical Index Structure) when we scale up to very large databases. We also present a study of the influence of clustering on search time. The performance test results show that NOHIS-tree performs better than SR-tree. Tests also show that NOHIS-tree keeps its performances in high dimensional spaces. We include the performance test that try to determine the number of clusters in NOHIS-tree to have the best search time.

Keywords: High-dimensional indexing, k-nearest neighborssearch.

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Authors: Ha T. Pham, Shuichi Miyagawa

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Ongoing landscape transformation is one of the major causes behind disappearance of traditional landscapes, and lead to species and resource loss. Tree in paddy fields in the northeast of Thailand is one of those traditional landscapes. Using three different historical time layers, we acknowledged the severe deforestation and rapid urbanization happened in the region. Despite the general thinking of decline in tree density as consequences, the heterogeneous trend of changes in total tree density in three studied landscapes denied the hypothesis that number of trees in paddy field depend on the length of land use practice. On the other hand, due to selection of planting new trees on levees, existence of trees in paddy field now relies on their values for human use. Besides, changes in land use and landscape structure had a significant impact on decision of which tree density level is considered as suitable for the landscape.

Keywords: Aerial photographs, land use change, traditional landscape, tree in paddy fields.

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Authors: Li Shoutao, Gordon Lee

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Evolutionary robotics is concerned with the design of intelligent systems with life-like properties by means of simulated evolution. Approaches in evolutionary robotics can be categorized according to the control structures that represent the behavior and the parameters of the controller that undergo adaptation. The basic idea is to automatically synthesize behaviors that enable the robot to perform useful tasks in complex environments. The evolutionary algorithm searches through the space of parameterized controllers that map sensory perceptions to control actions, thus realizing a specific robotic behavior. Further, the evolutionary algorithm maintains and improves a population of candidate behaviors by means of selection, recombination and mutation. A fitness function evaluates the performance of the resulting behavior according to the robot-s task or mission. In this paper, the focus is in the use of genetic algorithms to solve a multi-objective optimization problem representing robot behaviors; in particular, the A-Compander Law is employed in selecting the weight of each objective during the optimization process. Results using an adaptive fitness function show that this approach can efficiently react to complex tasks under variable environments.

Keywords: adaptive fuzzy neural inference, evolutionary tuning

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Authors: Jan Rychtar, Brian Stadler

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We study how the outcome of evolutionary dynamics on graphs depends on a randomness on the graph structure. We gradually change the underlying graph from completely regular (e.g. a square lattice) to completely random. We find that the fixation probability increases as the randomness increases; nevertheless, the increase is not significant and thus the fixation probability could be estimated by the known formulas for underlying regular graphs.

Keywords: evolutionary dynamics, small-world networks

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Authors: Konstantin Movsovic, Emanuele Stomeo, Tatiana Kalganova

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The evolutionary design of electronic circuits, or evolvable hardware, is a discipline that allows the user to automatically obtain the desired circuit design. The circuit configuration is under the control of evolutionary algorithms. Several researchers have used evolvable hardware to design electrical circuits. Every time that one particular algorithm is selected to carry out the evolution, it is necessary that all its parameters, such as mutation rate, population size, selection mechanisms etc. are tuned in order to achieve the best results during the evolution process. This paper investigates the abilities of evolution strategy to evolve digital logic circuits based on programmable logic array structures when different mutation rates are used. Several mutation rates (fixed and variable) are analyzed and compared with each other to outline the most appropriate choice to be used during the evolution of combinational logic circuits. The experimental results outlined in this paper are important as they could be used by every researcher who might need to use the evolutionary algorithm to design digital logic circuits.

Keywords: Evolvable hardware, evolutionary algorithm, digitallogic circuit, mutation rate.

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Authors: Yasmin Mohd Yacob, Harsa A. Mat Sakim, Nor Ashidi Mat Isa

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Feature selection study is gaining importance due to its contribution to save classification cost in terms of time and computation load. In search of essential features, one of the methods to search the features is via the decision tree. Decision tree act as an intermediate feature space inducer in order to choose essential features. In decision tree-based feature selection, some studies used decision tree as a feature ranker with a direct threshold measure, while others remain the decision tree but utilized pruning condition that act as a threshold mechanism to choose features. This paper proposed threshold measure using Manhattan Hierarchical Cluster distance to be utilized in feature ranking in order to choose relevant features as part of the feature selection process. The result is promising, and this method can be improved in the future by including test cases of a higher number of attributes.

Keywords: Feature ranking, decision tree, hierarchical cluster, Manhattan distance.

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Authors: Ulrike Völlinger, Erik Lehmann, Rainer Stark

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The intention of this paper is, to help the user of evolutionary algorithms to adapt them easier to their problem at hand. For a lot of problems in the technical field it is not necessary to reach an optimum solution, but to reach a good solution in time. In many cases the solution is undetermined or there doesn-t exist a method to determine the solution. For these cases an evolutionary algorithm can be useful. This paper intents to give the user rules of thumb with which it is easier to decide if the problem is suitable for an evolutionary algorithm and how to design them.

Keywords: Multi criteria optimization, Memetic algorithms

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Authors: Tawee Chimsuk, Surapong Auwatanamongkol

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Machine Translation (MT) between the Thai and English languages has been a challenging research topic in natural language processing. Most research has been done on English to Thai machine translation, but not the other way around. This paper presents a Thai to English Machine Translation System that translates a Thai sentence into interlingua of a Thai LFG tree using LFG grammar and a bottom up parser. The Thai LFG tree is then transformed into the corresponding English LFG tree by pattern matching and node transformation. Finally, an equivalent English sentence is created using structural information prescribed by the English LFG tree. Based on results of experiments designed to evaluate the performance of the proposed system, it can be stated that the system has been proven to be effective in providing a useful translation from Thai to English.

Keywords: Interlingua, LFG grammar, Machine translation, Pattern matching.

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