Search results for: spanning tree

Authors: Olli Luoma, Johannes Tuikkala, Olli Nevalainen

Abstract:

In this paper, we propose a novel improvement for the generalized Lloyd Algorithm (GLA). Our algorithm makes use of an M-tree index built on the codebook which makes it possible to reduce the number of distance computations when the nearest code words are searched. Our method does not impose the use of any specific distance function, but works with any metric distance, making it more general than many other fast GLA variants. Finally, we present the positive results of our performance experiments.

Keywords: Clustering, GLA, M-Tree, Vector Quantization .

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Authors: R. Anitha, R. S. Lekshmi

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Graph decompositions are vital in the study of combinatorial design theory. A decomposition of a graph G is a partition of its edge set. An n-sun graph is a cycle Cn with an edge terminating in a vertex of degree one attached to each vertex. In this paper, we define n-sun decomposition of some even order graphs with a perfect matching. We have proved that the complete graph K2n, complete bipartite graph K2n, 2n and the Harary graph H4, 2n have n-sun decompositions. A labeling scheme is used to construct the n-suns.

Keywords: Decomposition, Hamilton cycle, n-sun graph, perfect matching, spanning tree.

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Authors: H.-H. Doh, J.-M. Yu, Y.-J. Kwon, J.-H. Shin, H.-W. Kim, S.-H. Nam, D.-H. Lee

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This paper suggests a decision tree based approach for flexible job shop scheduling with multiple process plans, i.e. each job can be processed through alternative operations, each of which can be processed on alternative machines. The main decision variables are: (a) selecting operation/machine pair; and (b) sequencing the jobs assigned to each machine. As an extension of the priority scheduling approach that selects the best priority rule combination after many simulation runs, this study suggests a decision tree based approach in which a decision tree is used to select a priority rule combination adequate for a specific system state and hence the burdens required for developing simulation models and carrying out simulation runs can be eliminated. The decision tree based scheduling approach consists of construction and scheduling modules. In the construction module, a decision tree is constructed using a four-stage algorithm, and in the scheduling module, a priority rule combination is selected using the decision tree. To show the performance of the decision tree based approach suggested in this study, a case study was done on a flexible job shop with reconfigurable manufacturing cells and a conventional job shop, and the results are reported by comparing it with individual priority rule combinations for the objectives of minimizing total flow time and total tardiness.

Keywords: Flexible job shop scheduling, Decision tree, Priority rules, Case study.

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Authors: J. K. Alhassan, S. A. Lawal

Abstract:

This work is on decision tree-based classification for the disbursement of scholarship. Tree-based data mining classification technique is used in other to determine the generic rule to be used to disburse the scholarship. The system based on the defined rules from the tree is able to determine the class (status) to which an applicant shall belong whether Granted or Not Granted. The applicants that fall to the class of granted denote a successful acquirement of scholarship while those in not granted class are unsuccessful in the scheme. An algorithm that can be used to classify the applicants based on the rules from tree-based classification was also developed. The tree-based classification is adopted because of its efficiency, effectiveness, and easy to comprehend features. The system was tested with the data of National Information Technology Development Agency (NITDA) Abuja, a Parastatal of Federal Ministry of Communication Technology that is mandated to develop and regulate information technology in Nigeria. The system was found working according to the specification. It is therefore recommended for all scholarship disbursement organizations.

Keywords: Decision tree, classification, data mining, scholarship.

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Authors: Salsabil Trabelsi, Zied Elouedi, Khaled Mellouli

Abstract:

The belief decision tree (BDT) approach is a decision tree in an uncertain environment where the uncertainty is represented through the Transferable Belief Model (TBM), one interpretation of the belief function theory. The uncertainty can appear either in the actual class of training objects or attribute values of objects to classify. In this paper, we develop a post-pruning method of belief decision trees in order to reduce size and improve classification accuracy on unseen cases. The pruning of decision tree has a considerable intention in the areas of machine learning.

Keywords: machine learning, uncertainty, belief function theory, belief decision tree, pruning.

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Authors: J. K. Shrestha, A. Benta, R. B. Lopes, N. Lopes

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This work provides a practical method for the development of rural road networks in rural areas of developing countries. The proposed methodology enables to determine obligatory points in the rural road network maximizing the number of settlements that have access to basic services within a given maximum distance. The proposed methodology is simple and practical, hence, highly applicable to real-world scenarios, as demonstrated in the definition of the road network for the rural areas of Nepal.

Keywords: Minimum spanning tree, nodal points, rural road network.

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Authors: B. Bakır, İ. Batmaz, F. A. Güntürkün, İ. A. İpekçi, G. Köksal, N. E. Özdemirel

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The main aim of this study is to identify the most influential variables that cause defects on the items produced by a casting company located in Turkey. To this end, one of the items produced by the company with high defective percentage rates is selected. Two approaches-the regression analysis and decision treesare used to model the relationship between process parameters and defect types. Although logistic regression models failed, decision tree model gives meaningful results. Based on these results, it can be claimed that the decision tree approach is a promising technique for determining the most important process variables.

Keywords: Casting industry, decision tree algorithm C5.0, logistic regression, quality improvement.

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

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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: S. Ghorbani, N. I. Polushin

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The machinability of workpieces (AISI 1045 Steel, AA2024 aluminum alloy, A48-class30 gray cast iron) in turning operation has been carried out using different types of cutting tool (conventional, cutting tool with holes in toolholder and cutting tool filled up with composite material) under dry conditions on a turning machine at different stages of spindle speed (630-1000 rpm), feed rate (0.05-0.075 mm/rev), depth of cut (0.05-0.15 mm) and tool overhang (41-65 mm). Experimentation was performed as per Taguchi’s orthogonal array. To evaluate the relative importance of factors affecting surface roughness the single decision tree (SDT), Decision tree forest (DTF) and Group method of data handling (GMDH) were applied.

Keywords: Decision Tree Forest, GMDH, surface roughness, taguchi method, turning process.

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Authors: S. Ghorbani, N. I. Polushin

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In this study, an approach to identify factors affecting on surface roughness in a machining process is presented. This study is based on 81 data about surface roughness over a wide range of cutting tools (conventional, cutting tool with holes, cutting tool with composite material), workpiece materials (AISI 1045 Steel, AA2024 aluminum alloy, A48-class30 gray cast iron), spindle speed (630-1000 rpm), feed rate (0.05-0.075 mm/rev), depth of cut (0.05-0.15 mm) and tool overhang (41-65 mm). A single decision tree (SDT) analysis was done to identify factors for predicting a model of surface roughness, and the CART algorithm was employed for building and evaluating regression tree. Results show that a single decision tree is better than traditional regression models with higher rate and forecast accuracy and strong value.

Keywords: Cutting condition, surface roughness, decision tree, CART algorithm.

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Authors: S. Sowmyayani, V. Murugan

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With the advent of three-dimension (3D) technology, there are lots of research in converting 2D images to 3D images. The main difference between 2D and 3D is the visual illusion of depth in 3D images. In the recent era, there are more depth estimation techniques. The objective of this paper is to convert 2D images to 3D images with less computation time. For this, the input image is divided into blocks from which the depth information is obtained. Having the depth information, a depth map is generated. Then the 3D image is warped using the original image and the depth map. The proposed method is tested on Make3D dataset and NYU-V2 dataset. The experimental results are compared with other recent methods. The proposed method proved to work with less computation time and good accuracy.

Keywords: Depth map, 3D image warping, image rendering, bilateral filter, minimum spanning tree.

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Authors: Mahesh Pal

Abstract:

In recent years, a number of works proposing the combination of multiple classifiers to produce a single classification have been reported in remote sensing literature. The resulting classifier, referred to as an ensemble classifier, is generally found to be more accurate than any of the individual classifiers making up the ensemble. As accuracy is the primary concern, much of the research in the field of land cover classification is focused on improving classification accuracy. This study compares the performance of four ensemble approaches (boosting, bagging, DECORATE and random subspace) with a univariate decision tree as base classifier. Two training datasets, one without ant noise and other with 20 percent noise was used to judge the performance of different ensemble approaches. Results with noise free data set suggest an improvement of about 4% in classification accuracy with all ensemble approaches in comparison to the results provided by univariate decision tree classifier. Highest classification accuracy of 87.43% was achieved by boosted decision tree. A comparison of results with noisy data set suggests that bagging, DECORATE and random subspace approaches works well with this data whereas the performance of boosted decision tree degrades and a classification accuracy of 79.7% is achieved which is even lower than that is achieved (i.e. 80.02%) by using unboosted decision tree classifier.

Keywords: Ensemble learning, decision tree, remote sensingclassification.

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Authors: N. A. Ibrahim, A. Kudus, I. Daud, M. R. Abu Bakar

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Competing risks survival data that comprises of more than one type of event has been used in many applications, and one of these is in clinical study (e.g. in breast cancer study). The decision tree method can be extended to competing risks survival data by modifying the split function so as to accommodate two or more risks which might be dependent on each other. Recently, researchers have constructed some decision trees for recurrent survival time data using frailty and marginal modelling. We further extended the method for the case of competing risks. In this paper, we developed the decision tree method for competing risks survival time data based on proportional hazards for subdistribution of competing risks. In particular, we grow a tree by using deviance statistic. The application of breast cancer data is presented. Finally, to investigate the performance of the proposed method, simulation studies on identification of true group of observations were executed.

Keywords: Competing risks, Decision tree, Simulation, Subdistribution Proportional Hazard.

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Authors: Dewan Md. Farid, Nguyen Huu Hoa, Jerome Darmont, Nouria Harbi, Mohammad Zahidur Rahman

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In this paper, we present a new learning algorithm for anomaly based network intrusion detection using improved self adaptive naïve Bayesian tree (NBTree), which induces a hybrid of decision tree and naïve Bayesian classifier. The proposed approach scales up the balance detections for different attack types and keeps the false positives at acceptable level in intrusion detection. In complex and dynamic large intrusion detection dataset, the detection accuracy of naïve Bayesian classifier does not scale up as well as decision tree. It has been successfully tested in other problem domains that naïve Bayesian tree improves the classification rates in large dataset. In naïve Bayesian tree nodes contain and split as regular decision-trees, but the leaves contain naïve Bayesian classifiers. The experimental results on KDD99 benchmark network intrusion detection dataset demonstrate that this new approach scales up the detection rates for different attack types and reduces false positives in network intrusion detection.

Keywords: Detection rates, false positives, network intrusiondetection, naïve Bayesian tree.

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Authors: M. H. Ahmad, A. A. A. Jamil, H. Ahmad, M. A. M. Piah, A. Darus, Y. Z. Arief, N. Bashir

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The use of synthetic retardants in polymeric insulated cables is not uncommon in the high voltage engineering to study electrical treeing phenomenon. However few studies on organic materials for the same investigation have been carried. .This paper describes the study on the effects of Oil Palm Empty Fruit Bunch (OPEFB) microfiller on the tree initiation and propagation in silicone rubber with different weight percentages (wt %) of filler to insulation bulk material. The weight percentages used were 0 wt % and 1 wt % respectively. It was found that the OPEFB retards the propagation of the electrical treeing development. For tree inception study, the addition of 1(wt %) OPEFB has increase the tree inception voltage of silicone rubber. So, OPEFB is a potential retardant to the initiation and growth of electrical treeing occurring in polymeric materials for high voltage application. However more studies on the effects of physical and electrical properties of OPEFB as a tree retardant material are required.

Keywords: Oil palm empty fruit bunch, electrical tree, siliconerubber, fillers.

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Authors: F. S. Eguakun, T. C. Nkwor

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Trees in the university environment are uniquely position; however, they can also present a millstone to the infrastructure and humans they coexist with. The numerous benefits of trees can be negated due to poor tree health and anthropogenic activities and as such can become hazardous. The study aims at evaluating the hazardous status of avenue trees in University of Port Harcourt. Data were collected from all the avenue trees within the selected major roads in the University. Tree growth variables were measured and health condition of the avenue trees were assessed as an indicator of some structural defects. The hazard status of the avenue trees was determined. Several tree species were used as avenue trees in the University however, Azadirachta indica (81%) was found to be most abundant. The result shows that only 0.3% avenue tree species was found to pose severe harzard in Abuja part of the University. Most avenue trees (55.2%) were rated as medium hazard status. Due to the danger and risk associated with hazardous trees, the study recommends that good and effective management strategies be implemented so as to prevent future damages from trees with small or medium hazard status.

Keywords: Avenue tree, hazard status, inventory, urban.

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Authors: A. Boveiri Monji, H. Yousefnia, S. Zolghadri, B. Salimi

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The main goal of this paper was to make use of green reagents as a substitute of perilous synthetic reagents and organic solvents for spectrophotometric determination of hafnium(IV). The extracts taken from six different kinds of tree leaves including Acer negundo, Ficus carica, Cerasus avium, Chimonanthus, Salix babylonica and Pinus brutia, were applied as green reagents for the experiments. In 6-M hydrochloric acid, hafnium reacted with the reagent to form a yellow product and showed maximum absorbance at 421 nm. Among tree leaves, Chimonanthus showed satisfactory results with a molar absorptivity value of 0.61 × 10⁴ l mol^-1 cm^-1 and the method was linear in the 0.3-9 µg mL ^-1 concentration range. The detection limit value was 0.064 µg mL^-1. The proposed method was simple, low cost, clean, and selective.

Keywords: Spectrophotometric determination, tree leaves, synthetic reagents, hafnium.

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Authors: B.-Y.-S. Lau, Y.-C.-T. Jonathan, M.-S. Alias

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Heritage trees are natural large, individual trees with exceptionally value due to association with age or event or distinguished people. In Malaysia, there is an abundance of tropical heritage trees throughout the country. It is essential to set up a repository of heritage trees to prevent valuable trees from being cut down. In this cross domain study, a web-based online expert system namely the Heritage Tree Expert Assessment and Classification (HTEAC) is developed and deployed for public to nominate potential heritage trees. Based on the nomination, tree care experts or arborists would evaluate and verify the nominated trees as heritage trees. The expert system automatically rates the approved heritage trees according to pre-defined grades via Delphi technique. Features and usability test of the expert system are presented. Preliminary result is promising for the system to be used as a full scale public system.

Keywords: Arboriculture, Delphi, expert system, heritage tree, urban forestry.

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Authors: Miloš Šeda

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In this paper, we deal with the Steiner tree problem (STP) on a graph in which a fuzzy number, instead of a real number, is assigned to each edge. We propose a modification of the shortest paths approximation based on the fuzzy shortest paths (FSP) evaluations. Since a fuzzy min operation using the extension principle leads to nondominated solutions, we propose another approach to solving the FSP using Cheng's centroid point fuzzy ranking method.

Keywords: Steiner tree, single shortest path problem, fuzzyranking, binary heap, priority queue.

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Authors: Do Phuc, Nguyen Thi Kim Phung

Abstract:

In this paper, we represent protein structure by using graph. A protein structure database will become a graph database. Each graph is represented by a spectral vector. We use Jacobi rotation algorithm to calculate the eigenvalues of the normalized Laplacian representation of adjacency matrix of graph. To measure the similarity between two graphs, we calculate the Euclidean distance between two graph spectral vectors. To cluster the graphs, we use M-tree with the Euclidean distance to cluster spectral vectors. Besides, M-tree can be used for graph searching in graph database. Our proposal method was tested with graph database of 100 graphs representing 100 protein structures downloaded from Protein Data Bank (PDB) and we compare the result with the SCOP hierarchical structure.

Keywords: Eigenvalues, m-tree, graph database, protein structure, spectra graph theory.

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Authors: Chunling Cong, Chris.P.Tsokos

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The objective of the present research manuscript is to perform parametric, nonparametric, and decision tree analysis to evaluate two treatments that are being used for breast cancer patients. Our study is based on utilizing real data which was initially used in “Tamoxifen with or without breast irradiation in women of 50 years of age or older with early breast cancer" [1], and the data is supplied to us by N.A. Ibrahim “Decision tree for competing risks survival probability in breast cancer study" [2]. We agree upon certain aspects of our findings with the published results. However, in this manuscript, we focus on relapse time of breast cancer patients instead of survival time and parametric analysis instead of semi-parametric decision tree analysis is applied to provide more precise recommendations of effectiveness of the two treatments with respect to reoccurrence of breast cancer.

Keywords: decision tree, breast cancer treatments, parametricanalysis, non-parametric analysis

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Authors: R. Vishnu Priya, A. Vadivel

Abstract:

Sequential pattern mining is a challenging task in data mining area with large applications. One among those applications is mining patterns from weblog. Recent times, weblog is highly dynamic and some of them may become absolute over time. In addition, users may frequently change the threshold value during the data mining process until acquiring required output or mining interesting rules. Some of the recently proposed algorithms for mining weblog, build the tree with two scans and always consume large time and space. In this paper, we build Revised PLWAP with Non-frequent Items (RePLNI-tree) with single scan for all items. While mining sequential patterns, the links related to the nonfrequent items are not considered. Hence, it is not required to delete or maintain the information of nodes while revising the tree for mining updated transactions. The algorithm supports both incremental and interactive mining. It is not required to re-compute the patterns each time, while weblog is updated or minimum support changed. The performance of the proposed tree is better, even the size of incremental database is more than 50% of existing one. For evaluation purpose, we have used the benchmark weblog dataset and found that the performance of proposed tree is encouraging compared to some of the recently proposed approaches.

Keywords: Sequential pattern mining, weblog, frequent and non-frequent items, incremental and interactive mining.

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Authors: F. Tajarrod, G. Latif-Shabgahi

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Fault tree analysis is a well-known method for reliability and safety assessment of engineering systems. In the last 3 decades, a number of methods have been introduced, in the literature, for automatic construction of fault trees. The main difference between these methods is the starting model from which the tree is constructed. This paper presents a new methodology for the construction of static and dynamic fault trees from a system Simulink model. The method is introduced and explained in detail, and its correctness and completeness is experimentally validated by using an example, taken from literature. Advantages of the method are also mentioned.

Keywords: Fault tree, Simulink, Standby Sparing and Redundancy

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Authors: Suguru Ochiai, Toru Yabuki, Yoshiki Yamaguchi, Yuetsu Kodama

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In this paper, we propose a Connect6 solver which adopts a hybrid approach based on a tree-search algorithm and image processing techniques. The solver must deal with the complicated computation and provide high performance in order to make real-time decisions. The proposed approach enables the solver to be implemented on a single Spartan-6 XC6SLX45 FPGA produced by XILINX without using any external devices. The compact implementation is achieved through image processing techniques to optimize a tree-search algorithm of the Connect6 game. The tree search is widely used in computer games and the optimal search brings the best move in every turn of a computer game. Thus, many tree-search algorithms such as Minimax algorithm and artificial intelligence approaches have been widely proposed in this field. However, there is one fundamental problem in this area; the computation time increases rapidly in response to the growth of the game tree. It means the larger the game tree is, the bigger the circuit size is because of their highly parallel computation characteristics. Here, this paper aims to reduce the size of a Connect6 game tree using image processing techniques and its position symmetric property. The proposed solver is composed of four computational modules: a two-dimensional checkmate strategy checker, a template matching module, a skilful-line predictor, and a next-move selector. These modules work well together in selecting next moves from some candidates and the total amount of their circuits is small. The details of the hardware design for an FPGA implementation are described and the performance of this design is also shown in this paper.

Keywords: Connect6, pattern matching, game-tree reduction, hardware direct computation

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Authors: Riad S. Jabri

Abstract:

Pattern matching based on regular tree grammars have been widely used in many areas of computer science. In this paper, we propose a pattern matcher within the framework of code generation, based on a generic and a formalized approach. According to this approach, parsers for regular tree grammars are adapted to a general pattern matching solution, rather than adapting the pattern matching according to their parsing behavior. Hence, we first formalize the construction of the pattern matches respective to input trees drawn from a regular tree grammar in a form of the so-called match trees. Then, we adopt a recently developed generic parser and tightly couple its parsing behavior with such construction. In addition to its generality, the resulting pattern matcher is characterized by its soundness and efficient implementation. This is demonstrated by the proposed theory and by the derived algorithms for its implementation. A comparison with similar and well-known approaches, such as the ones based on tree automata and LR parsers, has shown that our pattern matcher can be applied to a broader class of grammars, and achieves better approximation of pattern matches in one pass. Furthermore, its use as a machine code selector is characterized by a minimized overhead, due to the balanced distribution of the cost computations into static ones, during parser generation time, and into dynamic ones, during parsing time.

Keywords: Bottom-up automata, Code selection, Pattern matching, Regular tree grammars, Match trees.

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Authors: Ber-Lin Yu, Jie Cui, Hong Cheng, Zhengfeng Yu

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A sign pattern is a matrix whose entries belong to the set {+,−, 0}. An n-by-n sign pattern A is said to allow an eventually positive matrix if there exist some real matrices A with the same sign pattern as A and a positive integer k0 such that Ak > 0 for all k ≥ k0. It is well known that identifying and classifying the n-by-n sign patterns that allow an eventually positive matrix are posed as two open problems. In this article, the tree sign patterns of small order that allow an eventually positive matrix are classified completely.

Keywords: Eventually positive matrix, sign pattern, tree.

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Authors: Khaddouja Boujenfa, Nadia Essoussi, Mohamed Limam

Abstract:

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

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

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Authors: Maythapolnun Athimethphat, Boontarika Lerteerawong

Abstract:

There are several approaches for handling multiclass classification. Aside from one-against-one (OAO) and one-against-all (OAA), hierarchical classification technique is also commonly used. A binary classification tree is a hierarchical classification structure that breaks down a k-class problem into binary sub-problems, each solved by a binary classifier. In each node, a set of classes is divided into two subsets. A good class partition should be able to group similar classes together. Many algorithms measure similarity in term of distance between class centroids. Classes are grouped together by a clustering algorithm when distances between their centroids are small. In this paper, we present a binary classification tree with tuned observation-based clustering (BCT-TOB) that finds a class partition by performing clustering on observations instead of class centroids. A merging step is introduced to merge any insignificant class split. The experiment shows that performance of BCT-TOB is comparable to other algorithms.

Keywords: multiclass classification, hierarchical classification, binary classification tree, clustering, observation-based clustering

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Authors: Hossein Mirzaee, Farhad Besharati

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Solar sunspot rotation, latitudinal bands are studied based on intelligent computation methods. A combination of image fusion method with together tree decomposition is used to obtain quantitative values about the latitudes of trajectories on sun surface that sunspots rotate around them. Daily solar images taken with SOlar and Heliospheric (SOHO) satellite are fused for each month separately .The result of fused image is decomposed with Quad Tree decomposition method in order to achieve the precise information about latitudes of sunspot trajectories. Such analysis is useful for gathering information about the regions on sun surface and coordinates in space that is more expose to solar geomagnetic storms, tremendous flares and hot plasma gases permeate interplanetary space and help human to serve their technical systems. Here sunspot images in September, November and October in 2001 are used for studying the magnetic behavior of sun.

Keywords: Quad tree decomposition, sunspot image.

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Authors: Chyn Liaw, Chun-Wei Tung, Shinn-Jang Ho, Shinn-Ying Ho

Abstract:

The γ-turns play important roles in protein folding and molecular recognition. The prediction and analysis of γ-turn types are important for both protein structure predictions and better understanding the characteristics of different γ-turn types. This study proposed a physicochemical property-based decision tree (PPDT) method to interpretably predict γ-turn types. In addition to the good prediction performance of PPDT, three simple and human interpretable IF-THEN rules are extracted from the decision tree constructed by PPDT. The identified informative physicochemical properties and concise rules provide a simple way for discriminating and understanding γ-turn types.

Keywords: Classification and regression tree (CART), γ-turn, Physicochemical properties, Protein secondary structure.

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