Search results for: Jaccard’s similarity measure.
Commenced in January 2007
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Edition: International
Paper Count: 1358

Search results for: Jaccard’s similarity measure.

1238 Computing Entropy for Ortholog Detection

Authors: Hsing-Kuo Pao, John Case

Abstract:

Biological sequences from different species are called or-thologs if they evolved from a sequence of a common ancestor species and they have the same biological function. Approximations of Kolmogorov complexity or entropy of biological sequences are already well known to be useful in extracting similarity information between such sequences -in the interest, for example, of ortholog detection. As is well known, the exact Kolmogorov complexity is not algorithmically computable. In prac-tice one can approximate it by computable compression methods. How-ever, such compression methods do not provide a good approximation to Kolmogorov complexity for short sequences. Herein is suggested a new ap-proach to overcome the problem that compression approximations may notwork well on short sequences. This approach is inspired by new, conditional computations of Kolmogorov entropy. A main contribution of the empir-ical work described shows the new set of entropy-based machine learning attributes provides good separation between positive (ortholog) and nega-tive (non-ortholog) data - better than with good, previously known alter-natives (which do not employ some means to handle short sequences well).Also empirically compared are the new entropy based attribute set and a number of other, more standard similarity attributes sets commonly used in genomic analysis. The various similarity attributes are evaluated by cross validation, through boosted decision tree induction C5.0, and by Receiver Operating Characteristic (ROC) analysis. The results point to the conclu-sion: the new, entropy based attribute set by itself is not the one giving the best prediction; however, it is the best attribute set for use in improving the other, standard attribute sets when conjoined with them.

Keywords: compression, decision tree, entropy, ortholog, ROC.

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1237 Binary Classification Tree with Tuned Observation-based Clustering

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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1236 Unified Fusion Approach with Application to SLAM

Authors: Xinde Li, Xinhan Huang, Min Wang

Abstract:

In this paper, we propose the pre-processor based on the Evidence Supporting Measure of Similarity (ESMS) filter and also propose the unified fusion approach (UFA) based on the general fusion machine coupled with ESMS filter, which improve the correctness and precision of information fusion in any fields of application. Here we mainly apply the new approach to Simultaneous Localization And Mapping (SLAM) of Pioneer II mobile robots. A simulation experiment was performed, where an autonomous virtual mobile robot with sonar sensors evolves in a virtual world map with obstacles. By comparing the result of building map according to the general fusion machine (here DSmT-based fusing machine and PCR5-based conflict redistributor considereded) coupling with ESMS filter and without ESMS filter, it shows the benefit of the selection of the sources as a prerequisite for improvement of the information fusion, and also testifies the superiority of the UFA in dealing with SLAM.

Keywords: DSmT, ESMS filter, SLAM, UFA

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1235 Web Proxy Detection via Bipartite Graphs and One-Mode Projections

Authors: Zhipeng Chen, Peng Zhang, Qingyun Liu, Li Guo

Abstract:

With the Internet becoming the dominant channel for business and life, many IPs are increasingly masked using web proxies for illegal purposes such as propagating malware, impersonate phishing pages to steal sensitive data or redirect victims to other malicious targets. Moreover, as Internet traffic continues to grow in size and complexity, it has become an increasingly challenging task to detect the proxy service due to their dynamic update and high anonymity. In this paper, we present an approach based on behavioral graph analysis to study the behavior similarity of web proxy users. Specifically, we use bipartite graphs to model host communications from network traffic and build one-mode projections of bipartite graphs for discovering social-behavior similarity of web proxy users. Based on the similarity matrices of end-users from the derived one-mode projection graphs, we apply a simple yet effective spectral clustering algorithm to discover the inherent web proxy users behavior clusters. The web proxy URL may vary from time to time. Still, the inherent interest would not. So, based on the intuition, by dint of our private tools implemented by WebDriver, we examine whether the top URLs visited by the web proxy users are web proxies. Our experiment results based on real datasets show that the behavior clusters not only reduce the number of URLs analysis but also provide an effective way to detect the web proxies, especially for the unknown web proxies.

Keywords: Bipartite graph, clustering, one-mode projection, web proxy detection.

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1234 Improving Topic Quality of Scripts by Using Scene Similarity Based Word Co-Occurrence

Authors: Yunseok Noh, Chang-Uk Kwak, Sun-Joong Kim, Seong-Bae Park

Abstract:

Scripts are one of the basic text resources to understand broadcasting contents. Topic modeling is the method to get the summary of the broadcasting contents from its scripts. Generally, scripts represent contents descriptively with directions and speeches, and provide scene segments that can be seen as semantic units. Therefore, a script can be topic modeled by treating a scene segment as a document. Because scene segments consist of speeches mainly, however, relatively small co-occurrences among words in the scene segments are observed. This causes inevitably the bad quality of topics by statistical learning method. To tackle this problem, we propose a method to improve topic quality with additional word co-occurrence information obtained using scene similarities. The main idea of improving topic quality is that the information that two or more texts are topically related can be useful to learn high quality of topics. In addition, more accurate topical representations lead to get information more accurate whether two texts are related or not. In this paper, we regard two scene segments are related if their topical similarity is high enough. We also consider that words are co-occurred if they are in topically related scene segments together. By iteratively inferring topics and determining semantically neighborhood scene segments, we draw a topic space represents broadcasting contents well. In the experiments, we showed the proposed method generates a higher quality of topics from Korean drama scripts than the baselines.

Keywords: Broadcasting contents, generalized P´olya urn model, scripts, text similarity, topic model.

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1233 Error-Robust Nature of Genome Profiling Applied for Clustering of Species Demonstrated by Computer Simulation

Authors: Shamim Ahmed Koichi Nishigaki

Abstract:

Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.

Keywords: Fluctuation, Genome profiling (GP), Pattern similarity score (PaSS), Robustness, Spiddos-shift.

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1232 A Survey of Model Comparison Strategies and Techniques in Model Driven Engineering

Authors: Junaid Rashid, Waqar Mehmood, Muhammad Wasif Nisar

Abstract:

This survey paper shows the recent state of model comparison as it’s applies to Model Driven engineering. In Model Driven Engineering to calculate the difference between the models is a very important and challenging task. There are number of tasks involved in model differencing that firstly starts with identifying and matching the elements of the model. In this paper, we discuss how model matching is accomplished, the strategies, techniques and the types of the model. We also discuss the future direction. We found out that many of the latest model comparison strategies are geared near enabling Meta model and similarity based matching. Therefore model versioning is the most dominant application of the model comparison. Recently to work on comparison for versioning has begun to deteriorate, giving way to different applications. Ultimately there is wide change among the tools in the measure of client exertion needed to perform model comparisons, as some require more push to encourage more sweeping statement and expressive force.

Keywords: Model comparison, model clone detection, model versioning, EMF Model, model diff.

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1231 Applications of Rough Set Decompositions in Information Retrieval

Authors: Chen Wu, Xiaohua Hu

Abstract:

This paper proposes rough set models with three different level knowledge granules in incomplete information system under tolerance relation by similarity between objects according to their attribute values. Through introducing dominance relation on the discourse to decompose similarity classes into three subclasses: little better subclass, little worse subclass and vague subclass, it dismantles lower and upper approximations into three components. By using these components, retrieving information to find naturally hierarchical expansions to queries and constructing answers to elaborative queries can be effective. It illustrates the approach in applying rough set models in the design of information retrieval system to access different granular expanded documents. The proposed method enhances rough set model application in the flexibility of expansions and elaborative queries in information retrieval.

Keywords: Incomplete information system, Rough set model, tolerance relation, dominance relation, approximation, decomposition, elaborative query.

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1230 Segmentation of Gray Scale Images of Dropwise Condensation on Textured Surfaces

Authors: Helene Martin, Solmaz Boroomandi Barati, Jean-Charles Pinoli, Stephane Valette, Yann Gavet

Abstract:

In the present work we developed an image processing algorithm to measure water droplets characteristics during dropwise condensation on pillared surfaces. The main problem in this process is the similarity between shape and size of water droplets and the pillars. The developed method divides droplets into four main groups based on their size and applies the corresponding algorithm to segment each group. These algorithms generate binary images of droplets based on both their geometrical and intensity properties. The information related to droplets evolution during time including mean radius and drops number per unit area are then extracted from the binary images. The developed image processing algorithm is verified using manual detection and applied to two different sets of images corresponding to two kinds of pillared surfaces.

Keywords: Dropwise condensation, textured surface, image processing, watershed.

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1229 Application of Intuitionistic Fuzzy Cross Entropy Measure in Decision Making for Medical Diagnosis

Authors: Shikha Maheshwari, Amit Srivastava

Abstract:

In medical investigations, uncertainty is a major challenging problem in making decision for doctors/experts to identify the diseases with a common set of symptoms and also has been extensively increasing in medical diagnosis problems. The theory of cross entropy for intuitionistic fuzzy sets (IFS) is an effective approach in coping uncertainty in decision making for medical diagnosis problem. The main focus of this paper is to propose a new intuitionistic fuzzy cross entropy measure (IFCEM), which aid in reducing the uncertainty and doctors/experts will take their decision easily in context of patient’s disease. It is shown that the proposed measure has some elegant properties, which demonstrates its potency. Further, it is also exemplified in detail the efficiency and utility of the proposed measure by using a real life case study of diagnosis the disease in medical science.

Keywords: Intuitionistic fuzzy cross entropy (IFCEM), intuitionistic fuzzy set (IFS), medical diagnosis, uncertainty.

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1228 A Numerical Solution Based On Operational Matrix of Differentiation of Shifted Second Kind Chebyshev Wavelets for a Stefan Problem

Authors: Rajeev, N. K. Raigar

Abstract:

In this study, one dimensional phase change problem (a Stefan problem) is considered and a numerical solution of this problem is discussed. First, we use similarity transformation to convert the governing equations into ordinary differential equations with its boundary conditions. The solutions of ordinary differential equation with the associated boundary conditions and interface condition (Stefan condition) are obtained by using a numerical approach based on operational matrix of differentiation of shifted second kind Chebyshev wavelets. The obtained results are compared with existing exact solution which is sufficiently accurate.

Keywords: Operational matrix of differentiation, Similarity transformation, Shifted second kind Chebyshev wavelets, Stefan problem.

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1227 Generation of Photo-Mosaic Images through Block Matching and Color Adjustment

Authors: Hae-Yeoun Lee

Abstract:

Mosaic refers to a technique that makes image by gathering lots of small materials in various colors. This paper presents an automatic algorithm that makes the photo-mosaic image using photos. The algorithm is composed of 4 steps: partition and feature extraction, block matching, redundancy removal and color adjustment. The input image is partitioned in the small block to extract feature. Each block is matched to find similar photo in database by comparing similarity with Euclidean difference between blocks. The intensity of the block is adjusted to enhance the similarity of image by replacing the value of light and darkness with that of relevant block. Further, the quality of image is improved by minimizing the redundancy of tiles in the adjacent blocks. Experimental results support that the proposed algorithm is excellent in quantitative analysis and qualitative analysis.

Keywords: Photo-mosaic, Euclidean distance, Block matching, Intensity adjustment.

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1226 A Bootstrap's Reliability Measure on Tests of Hypotheses

Authors: Al Jefferson J. Pabelic, Dennis A. Tarepe

Abstract:

Bootstrapping has gained popularity in different tests of hypotheses as an alternative in using asymptotic distribution if one is not sure of the distribution of the test statistic under a null hypothesis. This method, in general, has two variants – the parametric and the nonparametric approaches. However, issues on reliability of this method always arise in many applications. This paper addresses the issue on reliability by establishing a reliability measure in terms of quantiles with respect to asymptotic distribution, when this is approximately correct. The test of hypotheses used is Ftest. The simulated results show that using nonparametric bootstrapping in F-test gives better reliability than parametric bootstrapping with relatively higher degrees of freedom.

Keywords: F-test, nonparametric bootstrapping, parametric bootstrapping, reliability measure, tests of hypotheses.

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1225 Robust Image Registration Based on an Adaptive Normalized Mutual Information Metric

Authors: Huda Algharib, Amal Algharib, Hanan Algharib, Ali Mohammad Alqudah

Abstract:

Image registration is an important topic for many imaging systems and computer vision applications. The standard image registration techniques such as Mutual information/ Normalized mutual information -based methods have a limited performance because they do not consider the spatial information or the relationships between the neighbouring pixels or voxels. In addition, the amount of image noise may significantly affect the registration accuracy. Therefore, this paper proposes an efficient method that explicitly considers the relationships between the adjacent pixels, where the gradient information of the reference and scene images is extracted first, and then the cosine similarity of the extracted gradient information is computed and used to improve the accuracy of the standard normalized mutual information measure. Our experimental results on different data types (i.e. CT, MRI and thermal images) show that the proposed method outperforms a number of image registration techniques in terms of the accuracy.

Keywords: Image registration, mutual information, image gradients, Image transformations.

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1224 Optimal Convolutive Filters for Real-Time Detection and Arrival Time Estimation of Transient Signals

Authors: Michal Natora, Felix Franke, Klaus Obermayer

Abstract:

Linear convolutive filters are fast in calculation and in application, and thus, often used for real-time processing of continuous data streams. In the case of transient signals, a filter has not only to detect the presence of a specific waveform, but to estimate its arrival time as well. In this study, a measure is presented which indicates the performance of detectors in achieving both of these tasks simultaneously. Furthermore, a new sub-class of linear filters within the class of filters which minimize the quadratic response is proposed. The proposed filters are more flexible than the existing ones, like the adaptive matched filter or the minimum power distortionless response beamformer, and prove to be superior with respect to that measure in certain settings. Simulations of a real-time scenario confirm the advantage of these filters as well as the usefulness of the performance measure.

Keywords: Adaptive matched filter, minimum variance distortionless response, beam forming, Capon beam former, linear filters, performance measure.

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1223 A Study on Finding Similar Document with Multiple Categories

Authors: R. Saraçoğlu, N. Allahverdi

Abstract:

Searching similar documents and document management subjects have important place in text mining. One of the most important parts of similar document research studies is the process of classifying or clustering the documents. In this study, a similar document search approach that includes discussion of out the case of belonging to multiple categories (multiple categories problem) has been carried. The proposed method that based on Fuzzy Similarity Classification (FSC) has been compared with Rocchio algorithm and naive Bayes method which are widely used in text mining. Empirical results show that the proposed method is quite successful and can be applied effectively. For the second stage, multiple categories vector method based on information of categories regarding to frequency of being seen together has been used. Empirical results show that achievement is increased almost two times, when proposed method is compared with classical approach.

Keywords: Document similarity, Fuzzy classification, Multiple categories, Text mining.

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1222 Video-Based Face Recognition Based On State-Space Model

Authors: Cheng-Chieh Chiang, Yi-Chia Chan, Greg C. Lee

Abstract:

This paper proposes a video-based framework for face recognition to identify which faces appear in a video sequence. Our basic idea is like a tracking task - to track a selection of person candidates over time according to the observing visual features of face images in video frames. Hence, we employ the state-space model to formulate video-based face recognition by dividing this problem into two parts: the likelihood and the transition measures. The likelihood measure is to recognize whose face is currently being observed in video frames, for which two-dimensional linear discriminant analysis is employed. The transition measure estimates the probability of changing from an incorrect recognition at the previous stage to the correct person at the current stage. Moreover, extra nodes associated with head nodes are incorporated into our proposed state-space model. The experimental results are also provided to demonstrate the robustness and efficiency of our proposed approach.

Keywords: 2DLDA, face recognition, state-space model, likelihood measure, transition measure.

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1221 Real Time Speed Estimation of Vehicles

Authors: Azhar Hussain, Kashif Shahzad, Chunming Tang

Abstract:

this paper gives a novel approach towards real-time speed estimation of multiple traffic vehicles using fuzzy logic and image processing techniques with proper arrangement of camera parameters. The described algorithm consists of several important steps. First, the background is estimated by computing median over time window of specific frames. Second, the foreground is extracted using fuzzy similarity approach (FSA) between estimated background pixels and the current frame pixels containing foreground and background. Third, the traffic lanes are divided into two parts for both direction vehicles for parallel processing. Finally, the speeds of vehicles are estimated by Maximum a Posterior Probability (MAP) estimator. True ground speed is determined by utilizing infrared sensors for three different vehicles and the results are compared to the proposed algorithm with an accuracy of ± 0.74 kmph.

Keywords: Defuzzification, Fuzzy similarity approach, lane cropping, Maximum a Posterior Probability (MAP) estimator, Speed estimation

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1220 A Rigid Point Set Registration of Remote Sensing Images Based on Genetic Algorithms and Hausdorff Distance

Authors: F. Meskine, N. Taleb, M. Chikr El-Mezouar, K. Kpalma, A. Almhdie

Abstract:

Image registration is the process of establishing point by point correspondence between images obtained from a same scene. This process is very useful in remote sensing, medicine, cartography, computer vision, etc. Then, the task of registration is to place the data into a common reference frame by estimating the transformations between the data sets. In this work, we develop a rigid point registration method based on the application of genetic algorithms and Hausdorff distance. First, we extract the feature points from both images based on the algorithm of global and local curvature corner. After refining the feature points, we use Hausdorff distance as similarity measure between the two data sets and for optimizing the search space we use genetic algorithms to achieve high computation speed for its inertial parallel. The results show the efficiency of this method for registration of satellite images.

Keywords: Feature extraction, Genetic algorithms, Hausdorff distance, Image registration, Point registration.

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1219 Prediction of Research Topics Using Ensemble of Best Predictors from Similar Dataset

Authors: Indra Budi, Rizal Fathoni Aji, Agus Widodo

Abstract:

Prediction of future research topics by using time series analysis either statistical or machine learning has been conducted previously by several researchers. Several methods have been proposed to combine the forecasting results into single forecast. These methods use fixed combination of individual forecast to get the final forecast result. In this paper, quite different approach is employed to select the forecasting methods, in which every point to forecast is calculated by using the best methods used by similar validation dataset. The dataset used in the experiment is time series derived from research report in Garuda, which is an online sites belongs to the Ministry of Education in Indonesia, over the past 20 years. The experimental result demonstrates that the proposed method may perform better compared to the fix combination of predictors. In addition, based on the prediction result, we can forecast emerging research topics for the next few years.

Keywords: Combination, emerging topics, ensemble, forecasting, machine learning, prediction, research topics, similarity measure, time series.

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1218 On Generalized Exponential Fuzzy Entropy

Authors: Rajkumar Verma, Bhu Dev Sharma

Abstract:

In the present communication, the existing measures of fuzzy entropy are reviewed. A generalized parametric exponential fuzzy entropy is defined.Our study of the four essential and some other properties of the proposed measure, clearly establishes the validity of the measure as an entropy.

Keywords: fuzzy sets, fuzzy entropy, exponential entropy, exponential fuzzy entropy.

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1217 Effect of Neighborhood Size on Negative Weights in Punctual Kriging Based Image Restoration

Authors: Asmatullah Chaudhry, Anwar M. Mirza

Abstract:

We present a general comparison of punctual kriging based image restoration for different neighbourhood sizes. The formulation of the technique under consideration is based on punctual kriging and fuzzy concepts for image restoration in spatial domain. Three different neighbourhood windows are considered to estimate the semivariance at different lags for studying its effect in reduction of negative weights resulted in punctual kriging, consequently restoration of degraded images. Our results show that effect of neighbourhood size higher than 5x5 on reduction in negative weights is insignificant. In addition, image quality measures, such as structure similarity indices, peak signal to noise ratios and the new variogram based quality measures; show that 3x3 window size gives better performance as compared with larger window sizes.

Keywords: Image restoration, punctual kriging, semi-variance, structure similarity index, negative weights in punctual kriging.

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1216 Parallezation Protein Sequence Similarity Algorithms using Remote Method Interface

Authors: Mubarak Saif Mohsen, Zurinahni Zainol, Rosalina Abdul Salam, Wahidah Husain

Abstract:

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

Keywords: Protein sequence algorithm, dynamic programming algorithm, multithread

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1215 OCIRS: An Ontology-based Chinese Idioms Retrieval System

Authors: Hu Haibo, Tu Chunmei, Fu Chunlei, Fu Li, Mao Fan, Ma Yuan

Abstract:

Chinese Idioms are a type of traditional Chinese idiomatic expressions with specific meanings and stereotypes structure which are widely used in classical Chinese and are still common in vernacular written and spoken Chinese today. Currently, Chinese Idioms are retrieved in glossary with key character or key word in morphology or pronunciation index that can not meet the need of searching semantically. OCIRS is proposed to search the desired idiom in the case of users only knowing its meaning without any key character or key word. The user-s request in a sentence or phrase will be grammatically analyzed in advance by word segmentation, key word extraction and semantic similarity computation, thus can be mapped to the idiom domain ontology which is constructed to provide ample semantic relations and to facilitate description logics-based reasoning for idiom retrieval. The experimental evaluation shows that OCIRS realizes the function of searching idioms via semantics, obtaining preliminary achievement as requested by the users.

Keywords: Chinese idiom, idiom retrieval, semantic searching, ontology, semantics similarity.

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1214 Composite Programming for Electric Passenger Car Selection in Multiple Criteria Decision Making

Authors: C. Ardil

Abstract:

This paper discusses the use of the composite programming method to identify the optimum electric passenger automobile in multiple criteria decision making. With the composite programming approach, a set of alternatives are compared using an optimality measure that gauges how far apart they are from the optimum solution. In this paper, some key factors (range, battery, engine, maximum speed, acceleration) that customers should consider while purchasing an electric passenger car for daily use are discussed. A numerical illustration is provided to demonstrate the validity and applicability of the proximity measure approach

Keywords: electric passenger car selection, multiple criteria decision making, proximity measure method, composite programming, entropic weight method

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1213 Detecting Remote Protein Evolutionary Relationships via String Scoring Method

Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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1212 Computational Analysis of Potential Inhibitors Selected Based On Structural Similarity for the Src SH2 Domain

Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

Abstract:

The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: Nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation.

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1211 Computational Method for Annotation of Protein Sequence According to Gene Ontology Terms

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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1210 A New Measure of Herding Behavior: Derivation and Implications

Authors: Amina Amirat, Abdelfettah Bouri

Abstract:

If price and quantity are the fundamental building blocks of any theory of market interactions, the importance of trading volume in understanding the behavior of financial markets is clear. However, while many economic models of financial markets have been developed to explain the behavior of prices -predictability, variability, and information content- far less attention has been devoted to explaining the behavior of trading volume. In this article, we hope to expand our understanding of trading volume by developing a new measure of herding behavior based on a cross sectional dispersion of volumes betas. We apply our measure to the Toronto stock exchange using monthly data from January 2000 to December 2002. Our findings show that the herd phenomenon consists of three essential components: stationary herding, intentional herding and the feedback herding.

Keywords: Herding behavior, market return, trading volume.

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1209 Military Combat Aircraft Selection Using Trapezoidal Fuzzy Numbers with the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS)

Authors: C. Ardil

Abstract:

This article presents a new approach to uncertainty, vagueness, and imprecision analysis for ranking alternatives with fuzzy data for decision making using the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS). In the proposed approach, fuzzy decision information related to the aircraft selection problem is taken into account in ranking the alternatives and selecting the best one. The basic procedural step is to transform the fuzzy decision matrices into matrices of alternatives evaluated according to all decision criteria. A numerical example illustrates the proposed approach for the military combat aircraft selection problem.

Keywords: trapezoidal fuzzy numbers, multiple criteria decision making analysis, decision making, aircraft selection, MCDMA, fuzzy TOPSIS

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