Search results for: Decision Tree learning

Authors: Songlin Yang, Ying Ge

Abstract:

This paper shows that some properties of the decision rules in the literature do not hold by presenting a counterexample. We give sufficient and necessary conditions under which these properties are valid. These results will be helpful when one tries to choose the right decision rules in the research of rough set theory.

Keywords: set, Decision table, Decision rule, coverage factor.

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Authors: R. B. Ibrahim, M. S. Argungu, I. M. Mungadi

Abstract:

It is obvious in this present time, internet has become an indispensable part of human life since its inception. The Internet has provided diverse opportunities to make life so easy for human beings, through the adoption of various channels. Among these channels are email, internet banking, video conferencing, and the like. Email is one of the easiest means of communication hugely accepted among individuals and organizations globally. But over decades the security integrity of this platform has been challenged with malicious activities like Phishing. Email phishing is designed by phishers to fool the recipient into handing over sensitive personal information such as passwords, credit card numbers, account credentials, social security numbers, etc. This activity has caused a lot of financial damage to email users globally which has resulted in bankruptcy, sudden death of victims, and other health-related sicknesses. Although many methods have been proposed to detect email phishing, in this research, the results of multiple machine-learning methods for predicting email phishing have been compared with the use of filter-wrapper feature selection. It is worth noting that all three models performed substantially but one outperformed the other. The dataset used for these models is obtained from Kaggle online data repository, while three classifiers: decision tree, Naïve Bayes, and Logistic regression are ensemble (Bagging) respectively. Results from the study show that the Decision Tree (CART) bagging ensemble recorded the highest accuracy of 98.13% using PEF (Phishing Essential Features). This result further demonstrates the dependability of the proposed model.

Keywords: Ensemble, hybrid, filter-wrapper, phishing.

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Authors: Matthias Kirmse, Uwe Petersohn, Elief Paffrath

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As in today's semiconductor industries test costs can make up to 50 percent of the total production costs, an efficient test error detection becomes more and more important. In this paper, we present a new machine learning approach to test error detection that should provide a faster recognition of test system faults as well as an improved test error recall. The key idea is to learn a classifier ensemble, detecting typical test error patterns in wafer test results immediately after finishing these tests. Since test error detection has not yet been discussed in the machine learning community, we define central problem-relevant terms and provide an analysis of important domain properties. Finally, we present comparative studies reflecting the failure detection performance of three individual classifiers and three ensemble methods based upon them. As base classifiers we chose a decision tree learner, a support vector machine and a Bayesian network, while the compared ensemble methods were simple and weighted majority vote as well as stacking. For the evaluation, we used cross validation and a specially designed practical simulation. By implementing our approach in a semiconductor test department for the observation of two products, we proofed its practical applicability.

Keywords: Ensemble methods, fault detection, machine learning, semiconductor test.

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Authors: Khalil el Hindi

Abstract:

This paper presents a simple and effective method for approximate indexing of instances for instance based learning. The method uses an interval tree to determine a good starting search point for the nearest neighbor. The search stops when an early stopping criterion is met. The method proved to be very effective especially when only the first nearest neighbor is required.

Keywords: Instance based learning, interval trees, the knn algorithm, machine learning.

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Authors: Dejanira Araiza-Illan, Tony J. Dodd

Abstract:

A novel biologically inspired controller for the autonomous navigation of a mobile robot in an evasion task is proposed. The controller takes advantage of the environment by calculating a measure of danger and subsequently choosing the parameters of a reinforcement learning based decision process. Two different reinforcement learning algorithms were used: Qlearning and Sarsa (λ). Simulations show that selecting dynamic parameters reduce the time while executing the decision making process, so the robot can obtain a policy to succeed in an escaping task in a realistic time.

Keywords: Autonomous navigation, mobile robots, reinforcement learning.

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Authors: Qiang Yang, Ping-An Du

Abstract:

Group decision making with multiple attribute has attracted intensive concern in the decision analysis area. This paper assumes that the contributions of all the decision makers (DMs) are not equal to the decision process based on different knowledge and experience in group setting. The aim of this paper is to develop a novel approach to determine weights of DMs in the group decision making problems. In this paper, the weights of DMs are determined in the group decision environment via angle cosine and projection method. First of all, the average decision of all individual decisions is defined as the ideal decision. After that, we define the weight of each decision maker (DM) by aggregating the angle cosine and projection between individual decision and ideal decision with associated direction indicator μ. By using the weights of DMs, all individual decisions are aggregated into a collective decision. Further, the preference order of alternatives is ranked in accordance with the overall row value of collective decision. Finally, an example in a chemical company is provided to illustrate the developed approach.

Keywords: Angel cosine, ideal decision, projection method, weights of decision makers.

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Authors: J. Yang, Y. Ma, X. Zhang, S. Li, Y. Zhang

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The traditional k-means algorithm has been widely used as a simple and efficient clustering method. However, the algorithm often converges to local minima for the reason that it is sensitive to the initial cluster centers. In this paper, an algorithm for selecting initial cluster centers on the basis of minimum spanning tree (MST) is presented. The set of vertices in MST with same degree are regarded as a whole which is used to find the skeleton data points. Furthermore, a distance measure between the skeleton data points with consideration of degree and Euclidean distance is presented. Finally, MST-based initialization method for the k-means algorithm is presented, and the corresponding time complexity is analyzed as well. The presented algorithm is tested on five data sets from the UCI Machine Learning Repository. The experimental results illustrate the effectiveness of the presented algorithm compared to three existing initialization methods.

Keywords: Degree, initial cluster center, k-means, minimum spanning tree.

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Authors: Taylan Kabbani, Ekrem Duman

Abstract:

Deep Reinforcement Learning (DRL) algorithms can scale to previously intractable problems. The automation of profit generation in the stock market is possible using DRL, by combining  the financial assets price ”prediction” step and the ”allocation” step of the portfolio in one unified process to produce fully autonomous systems capable of interacting with its environment to make optimal decisions through trial and error. This work represents a DRL model to generate profitable trades in the stock market, effectively overcoming the limitations of supervised learning approaches. We formulate the trading problem as a Partially observed Markov Decision Process (POMDP) model, considering the constraints imposed by the stock market, such as liquidity and transaction costs. We then solved the formulated POMDP problem using the Twin Delayed Deep Deterministic Policy Gradient (TD3) algorithm and achieved a 2.68 Sharpe ratio on the test dataset. From the point of view of stock market forecasting and the intelligent decision-making mechanism, this paper demonstrates the superiority of DRL in financial markets over other types of machine learning and proves its credibility and advantages of strategic decision-making.

Keywords: Autonomous agent, deep reinforcement learning, MDP, sentiment analysis, stock market, technical indicators, twin delayed deep deterministic policy gradient.

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Authors: Tessy Badriyah, Jim S. Briggs, Dave R. Prytherch

Abstract:

It is well known that Logistic Regression is the gold standard method for predicting clinical outcome, especially predicting risk of mortality. In this paper, the Decision Tree method has been proposed to solve specific problems that commonly use Logistic Regression as a solution. The Biochemistry and Haematology Outcome Model (BHOM) dataset obtained from Portsmouth NHS Hospital from 1 January to 31 December 2001 was divided into four subsets. One subset of training data was used to generate a model, and the model obtained was then applied to three testing datasets. The performance of each model from both methods was then compared using calibration (the χ2 test or chi-test) and discrimination (area under ROC curve or c-index). The experiment presented that both methods have reasonable results in the case of the c-index. However, in some cases the calibration value (χ2) obtained quite a high result. After conducting experiments and investigating the advantages and disadvantages of each method, we can conclude that Decision Trees can be seen as a worthy alternative to Logistic Regression in the area of Data Mining.

Keywords: Decision Trees, Logistic Regression, clinical outcome, risk of mortality.

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Authors: Yasser F. Hassan

Abstract:

Deep learning structure is a branch of machine learning science and greet achievement in research and applications. Cellular neural networks are regarded as array of nonlinear analog processors called cells connected in a way allowing parallel computations. The paper discusses how to use deep learning structure for representing neural cellular automata model. The proposed learning technique in cellular automata model will be examined from structure of deep learning. A deep automata neural cellular system modifies each neuron based on the behavior of the individual and its decision as a result of multi-level deep structure learning. The paper will present the architecture of the model and the results of simulation of approach are given. Results from the implementation enrich deep neural cellular automata system and shed a light on concept formulation of the model and the learning in it.

Keywords: Cellular automata, neural cellular automata, deep learning, classification.

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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

Abstract:

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: Maziar Ahmad Sharbafi, Caro Lucas, Abolfazel Toroghi Haghighat, Omid AmirGhiasvand, Omid Aghazade

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RoboCup Rescue simulation as a large-scale Multi agent system (MAS) is one of the challenging environments for keeping coordination between agents to achieve the objectives despite sensing and communication limitations. The dynamicity of the environment and intensive dependency between actions of different kinds of agents make the problem more complex. This point encouraged us to use learning-based methods to adapt our decision making to different situations. Our approach is utilizing reinforcement leaning. Using learning in rescue simulation is one of the current ways which has been the subject of several researches in recent years. In this paper we present an innovative learning method implemented for Police Force (PF) Agent. This method can cope with the main difficulties that exist in other learning approaches. Different methods used in the literature have been examined. Their drawbacks and possible improvements have led us to the method proposed in this paper which is fast and accurate. The Brain Emotional Learning Based Intelligent Controller (BELBIC) is our solution for learning in this environment. BELBIC is a physiologically motivated approach based on a computational model of amygdale and limbic system. The paper presents the results obtained by the proposed approach, showing the power of BELBIC as a decision making tool in complex and dynamic situation.

Keywords: Emotional learning, rescue, simulation environment, RoboCup, multi-agent system.

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Authors: Maruto Masserie Sardadi, Mohd Shafry bin Mohd Rahim, Zahabidin Jupri, Daut bin Daman

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The latest Geographic Information System (GIS) technology makes it possible to administer the spatial components of daily “business object," in the corporate database, and apply suitable geographic analysis efficiently in a desktop-focused application. We can use wireless internet technology for transfer process in spatial data from server to client or vice versa. However, the problem in wireless Internet is system bottlenecks that can make the process of transferring data not efficient. The reason is large amount of spatial data. Optimization in the process of transferring and retrieving data, however, is an essential issue that must be considered. Appropriate decision to choose between R-tree and Quadtree spatial data indexing method can optimize the process. With the rapid proliferation of these databases in the past decade, extensive research has been conducted on the design of efficient data structures to enable fast spatial searching. Commercial database vendors like Oracle have also started implementing these spatial indexing to cater to the large and diverse GIS. This paper focuses on the decisions to choose R-tree and quadtree spatial indexing using Oracle spatial database in mobile GIS application. From our research condition, the result of using Quadtree and R-tree spatial data indexing method in one single spatial database can save the time until 42.5%.

Keywords: Indexing, Mobile GIS, MapViewer, Oracle SpatialDatabase.

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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: Mohammad Shahid Jamil, Mohamed Chabi

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In this study, students’ learning has been investigated and satisfaction in one of the course offered at Qatar University Foundation Program. Innovative teaching has been implied methodology that emphasizes on enhancing students’ thinking skills, decision making, and problem solving skills. Some interesting results were found which could be used to further improvement of the teaching methodology. In Fall 2012 in Foundation Program Math department at Qatar University has started implementing new ways of teaching Math by introducing MyMathLab (MML) as an innovative interactive tool in addition of the use Blackboard to support standard teaching such as Discussion board in Virtual class to engage students outside of classroom and to enhance independent, active learning that promote students’ critical thinking skills, decision making, and problem solving skills through the learning process.

Keywords: Blackboard, MyMathLab, study plan, discussion board, critical thinking, active and independent learning, problem solving.

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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

Abstract:

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: N. Paparisteidi, D. Rodamitou

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This article focuses on the skills development and path planning of students studying computer science at EPITECH: French private institute of higher education. We examine students’ points of view and experience in a blended learning model based on a skills development curriculum. The study is based on the collection of four main categories of data: semi-participant observation, distribution of questionnaires, interviews, and analysis of internal school databases. The findings seem to indicate that a skills-based program on active learning enables students to develop their learning strategies as well as their personal skills and to actively engage in the creation of their career path and contribute to providing additional information to curricula planners and decision-makers about learning design in higher education.

Keywords: Active learning, blended learning, higher education, skills development.

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Authors: R. Vishnu Priya, A. Vadivel

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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: S. Kotsiantis, E. Koumanakos, D. Tzelepis, V. Tampakas

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This paper explores the effectiveness of machine learning techniques in detecting firms that issue fraudulent financial statements (FFS) and deals with the identification of factors associated to FFS. To this end, a number of experiments have been conducted using representative learning algorithms, which were trained using a data set of 164 fraud and non-fraud Greek firms in the recent period 2001-2002. The decision of which particular method to choose is a complicated problem. A good alternative to choosing only one method is to create a hybrid forecasting system incorporating a number of possible solution methods as components (an ensemble of classifiers). For this purpose, we have implemented a hybrid decision support system that combines the representative algorithms using a stacking variant methodology and achieves better performance than any examined simple and ensemble method. To sum up, this study indicates that the investigation of financial information can be used in the identification of FFS and underline the importance of financial ratios.

Keywords: Machine learning, stacking, classifier.

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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: R. Sharma, M. Gopal

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This paper presents a new problem solving approach that is able to generate optimal policy solution for finite-state stochastic sequential decision-making problems with high data efficiency. The proposed algorithm iteratively builds and improves an approximate Markov Decision Process (MDP) model along with cost-to-go value approximates by generating finite length trajectories through the state-space. The approach creates a synergy between an approximate evolving model and approximate cost-to-go values to produce a sequence of improving policies finally converging to the optimal policy through an intelligent and structured search of the policy space. The approach modifies the policy update step of the policy iteration so as to result in a speedy and stable convergence to the optimal policy. We apply the algorithm to a non-holonomic mobile robot control problem and compare its performance with other Reinforcement Learning (RL) approaches, e.g., a) Q-learning, b) Watkins Q(λ), c) SARSA(λ).

Keywords: Markov Decision Process (MDP), Mobile robot, Policy iteration, Simulation.

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Authors: Hyun-Woo Cho

Abstract:

The early diagnostic decision making in industrial processes is absolutely necessary to produce high quality final products. It helps to provide early warning for a special event in a process, and finding its assignable cause can be obtained. This work presents a hybrid diagnostic schmes for batch processes. Nonlinear representation of raw process data is combined with classification tree techniques. The nonlinear kernel-based dimension reduction is executed for nonlinear classification decision boundaries for fault classes. In order to enhance diagnosis performance for batch processes, filtering of the data is performed to get rid of the irrelevant information of the process data. For the diagnosis performance of several representation, filtering, and future observation estimation methods, four diagnostic schemes are evaluated. In this work, the performance of the presented diagnosis schemes is demonstrated using batch process data.

Keywords: Diagnostics, batch process, nonlinear representation, data filtering, multivariate statistical approach

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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: Ilyes Jenhani, Salem Benferhat, Zied Elouedi

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This paper investigates the issue of building decision trees from data with imprecise class values where imprecision is encoded in the form of possibility distributions. The Information Affinity similarity measure is introduced into the well-known gain ratio criterion in order to assess the homogeneity of a set of possibility distributions representing instances-s classes belonging to a given training partition. For the experimental study, we proposed an information affinity based performance criterion which we have used in order to show the performance of the approach on well-known benchmarks.

Keywords: Data mining from uncertain data, Decision Trees, Possibility Theory.

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Authors: Khaddouja Boujenfa, Nadia Essoussi, Mohamed Limam

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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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