Search results for: semantics similarity.

Authors: N. Greco, S. Impedovo, R.Modugno, G. Pirlo

Abstract:

This paper presents a new technique for generating sets of synthetic classifiers to evaluate abstract-level combination methods. The sets differ in terms of both recognition rates of the individual classifiers and degree of similarity. For this purpose, each abstract-level classifier is considered as a random variable producing one class label as the output for an input pattern. From the initial set of classifiers, new slightly different sets are generated by applying specific operators, which are defined at the purpose. Finally, the sets of synthetic classifiers have been used to estimate the performance of combination methods for abstract-level classifiers. The experimental results demonstrate the effectiveness of the proposed approach.

Keywords: Abstract-level Classifier, Dempster-Shafer Rule, Multi-expert Systems, Similarity Index, System Evaluation

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Authors: Loai AbdAllah, Mahmoud Kaiyal

Abstract:

Missing values in real-world datasets are a common problem. Many algorithms were developed to deal with this problem, most of them replace the missing values with a fixed value that was computed based on the observed values. In our work, we used a distance function based on Bhattacharyya distance to measure the distance between objects with missing values. Bhattacharyya distance, which measures the similarity of two probability distributions. The proposed distance distinguishes between known and unknown values. Where the distance between two known values is the Mahalanobis distance. When, on the other hand, one of them is missing the distance is computed based on the distribution of the known values, for the coordinate that contains the missing value. This method was integrated with Wikaya, a digital health company developing a platform that helps to improve prevention of chronic diseases such as diabetes and cancer. In order for Wikaya’s recommendation system to work distance between users need to be measured. Since there are missing values in the collected data, there is a need to develop a distance function distances between incomplete users profiles. To evaluate the accuracy of the proposed distance function in reflecting the actual similarity between different objects, when some of them contain missing values, we integrated it within the framework of k nearest neighbors (kNN) classifier, since its computation is based only on the similarity between objects. To validate this, we ran the algorithm over diabetes and breast cancer datasets, standard benchmark datasets from the UCI repository. Our experiments show that kNN classifier using our proposed distance function outperforms the kNN using other existing methods.

Keywords: Missing values, distance metric, Bhattacharyya distance.

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Authors: Mustafa Yorgancılar, Emine Atalay, Necdet Akgün, Ali Topal

Abstract:

In this study, polymerase chain reaction based Inter-simple sequence repeat (ISSR) from DNA fingerprinting techniques were used to investigate the genetic relationships among barley crossbreed genotypes in Turkey. It is important that selection based on the genetic base in breeding programs via ISSR, in terms of breeding time. 14 ISSR primers generated a total of 97 bands, of which 81 (83.35%) were polymorphic. The highest total resolution power (RP) value was obtained from the F2 (0.53) and M16 (0.51) primers. According to the ISSR result, the genetic similarity index changed between 0.64–095; Lane 3 with Line 6 genotypes were the closest, while Line 36 were the most distant ones. The ISSR markers were found to be promising for assessing genetic diversity in barley crossbreed genotypes.

Keywords: Barley, crossbreed, genetic similarity, ISSR.

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Authors: Huynh Quyet Thang, Vo Sy Nam

Abstract:

Schema matching plays a key role in many different applications, such as schema integration, data integration, data warehousing, data transformation, E-commerce, peer-to-peer data management, ontology matching and integration, semantic Web, semantic query processing, etc. Manual matching is expensive and error-prone, so it is therefore important to develop techniques to automate the schema matching process. In this paper, we present a solution for XML schema automated matching problem which produces semantic mappings between corresponding schema elements of given source and target schemas. This solution contributed in solving more comprehensively and efficiently XML schema automated matching problem. Our solution based on combining linguistic similarity, data type compatibility and structural similarity of XML schema elements. After describing our solution, we present experimental results that demonstrate the effectiveness of this approach.

Keywords: XML Schema, Schema Matching, SemanticMatching, Automatic XML Schema Matching.

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Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

Abstract:

Development of a method to estimate gene functions is an important task in bioinformatics. One of the approaches for the annotation is the identification of the metabolic pathway that genes are involved in. Since gene expression data reflect various intracellular phenomena, those data are considered to be related with genes’ functions. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning.

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Authors: C. Ardil

Abstract:

This paper presents a multiple criteria decision making analysis technique for selecting fighter aircraft for the national air force. The selection of military aircraft is a process consisting of contradictory goals and objectives. When a modern air force needs to choose fighter aircraft to upgrade existing fleets, a multiple criteria decision making analysis and scenario planning for defense acquisition has been put forward. The selection of fighter aircraft for the air defense force is a strategic decision making process, since the purchase or lease of fighter jets, maintenance and operating costs and having a fleet is the biggest cost for the air force. Multiple criteria decision making analysis methods are effectively applied to facilitate decision making from various available options. The selection criteria were determined using the literature on the problem of fighter aircraft selection. The selection of fighter aircraft to be purchased for the air defense forces is handled using a multiple criteria decision making analysis technique that also determines a suitable methodological approach for the defense procurement and fleet upgrade planning process. The aim of this study is to originate an approach to evaluate fighter aircraft alternatives, Su-35, F-35, and TF-X (MMU), based on technique for order preference by similarity to ideal solution (TOPSIS).

Keywords: Fighter Aircraft, Fighter Aircraft Selection, Technique for Order Preference by Similarity to Ideal Solution, TOPSIS, Multiple Criteria Decision Making, Multiple Criteria Decision Making Analysis, MCDMA, Su-35, F-35, TF-X (MMU)

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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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Authors: Frank Emmert-Streib, Matthias Dehmer, Jing Liu, Max Muhlhauser

Abstract:

The major objective of this paper is to introduce a new method to select genes from DNA microarray data. As criterion to select genes we suggest to measure the local changes in the correlation graph of each gene and to select those genes whose local changes are largest. More precisely, we calculate the correlation networks from DNA microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to tumor progression. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth. This indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, generalized trees, graph alignment, DNA microarray data, cervical cancer.

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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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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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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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Authors: Lubna Eljabu, Mohammad Etemad, Stan Matwin

Abstract:

Port authorities have many challenges in congested ports to allocate their resources to provide a safe and secure loading/unloading procedure for cargo vessels. Selecting a destination port is the decision of a vessel master based on many factors such as weather, wavelength and changes of priorities. Having access to a tool which leverages Automatic Identification System (AIS) messages to monitor vessel’s movements and accurately predict their next destination port promotes an effective resource allocation process for port authorities. In this research, we propose a method, namely, Reference Route of Trajectory (RRoT) to assist port authorities in predicting inflow and outflow traffic in their local environment by monitoring AIS messages. Our RRo method creates a reference route based on historical AIS messages. It utilizes some of the best trajectory similarity measures to identify the destination of a vessel using their recent movement. We evaluated five different similarity measures such as Discrete Frechet Distance (DFD), Dynamic Time ´ Warping (DTW), Partial Curve Mapping (PCM), Area between two curves (Area) and Curve length (CL). Our experiments show that our method identifies the destination port with an accuracy of 98.97% and an f-measure of 99.08% using Dynamic Time Warping (DTW) similarity measure.

Keywords: Spatial temporal data mining, trajectory mining, trajectory similarity, resource optimization.

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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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Authors: Walid Cherif

Abstract:

Data mining has, over recent years, seen big advances because of the spread of internet, which generates everyday a tremendous volume of data, and also the immense advances in technologies which facilitate the analysis of these data. In particular, classification techniques are a subdomain of Data Mining which determines in which group each data instance is related within a given dataset. It is used to classify data into different classes according to desired criteria. Generally, a classification technique is either statistical or machine learning. Each type of these techniques has its own limits. Nowadays, current data are becoming increasingly heterogeneous; consequently, current classification techniques are encountering many difficulties. This paper defines new measure functions to quantify the resemblance between instances and then combines them in a new approach which is different from actual algorithms by its reliability computations. Results of the proposed approach exceeded most common classification techniques with an f-measure exceeding 97% on the IRIS Dataset.

Keywords: Data mining, knowledge discovery, machine learning, similarity measurement, supervised classification.

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Authors: K. Sakthivel, R. Nallusamy, C. Kavitha

Abstract:

The system is designed to show images which are related to the query image. Extracting color, texture, and shape features from an image plays a vital role in content-based image retrieval (CBIR). Initially RGB image is converted into HSV color space due to its perceptual uniformity. From the HSV image, Color features are extracted using block color histogram, texture features using Haar transform and shape feature using Fuzzy C-means Algorithm. Then, the characteristics of the global and local color histogram, texture features through co-occurrence matrix and Haar wavelet transform and shape are compared and analyzed for CBIR. Finally, the best method of each feature is fused during similarity measure to improve image retrieval effectiveness and accuracy.

Keywords: Color Histogram, Haar Wavelet Transform, Fuzzy C-means, Co-occurrence matrix; Similarity measure.

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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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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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Authors: K. Nirmala Devi, V. Murali Bhaskaran

Abstract:

Traditional document representation for classification follows Bag of Words (BoW) approach to represent the term weights. The conventional method uses the Vector Space Model (VSM) to exploit the statistical information of terms in the documents and they fail to address the semantic information as well as order of the terms present in the documents. Although, the phrase based approach follows the order of the terms present in the documents rather than semantics behind the word. Therefore, a semantic concept based approach is used in this paper for enhancing the semantics by incorporating the ontology information. In this paper a novel method is proposed to forecast the intraday stock market price directional movement based on the sentiments from Twitter and money control news articles. The stock market forecasting is a very difficult and highly complicated task because it is affected by many factors such as economic conditions, political events and investor’s sentiment etc. The stock market series are generally dynamic, nonparametric, noisy and chaotic by nature. The sentiment analysis along with wisdom of crowds can automatically compute the collective intelligence of future performance in many areas like stock market, box office sales and election outcomes. The proposed method utilizes collective sentiments for stock market to predict the stock price directional movements. The collective sentiments in the above social media have powerful prediction on the stock price directional movements as up/down by using Granger Causality test.

Keywords: Bag of Words, Collective Sentiments, Ontology, Semantic relations, Sentiments, Social media, Stock Prediction, Twitter, Vector Space Model and wisdom of crowds.

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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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Authors: Elmi Abu Bakar, Tetsuo Miyake, Zhong Zhang, Takashi Imamura

Abstract:

Knowing the geometrical object pose of products in manufacturing line before robot manipulation is required and less time consuming for overall shape measurement. In order to perform it, the information of shape representation and matching of objects is become required. Objects are compared with its descriptor that conceptually subtracted from each other to form scalar metric. When the metric value is smaller, the object is considered closed to each other. Rotating the object from static pose in some direction introduce the change of value in scalar metric value of boundary information after feature extraction of related object. In this paper, a proposal method for indexing technique for retrieval of 3D geometrical models based on similarity between boundaries shapes in order to measure 3D CAD object pose using object shape feature matching for Computer Aided Testing (CAT) system in production line is proposed. In experimental results shows the effectiveness of proposed method.

Keywords: CAD, rendering, feature extraction, feature classification.

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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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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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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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Authors: Yun Bai

Abstract:

This paper is to investigate the impplementation of security mechanism in object oriented database system. Formal methods plays an essential role in computer security due to its powerful expressiveness and concise syntax and semantics. In this paper, both issues of specification and implementation in database security environment will be considered; and the database security is achieved through the development of an efficient implementation of the specification without compromising its originality and expressiveness.

Keywords: database security, authorization policy, logic basedspecification

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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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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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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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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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Authors: Francesco Maiorana

Abstract:

In this paper a one-dimension Self Organizing Map algorithm (SOM) to perform feature selection is presented. The algorithm is based on a first classification of the input dataset on a similarity space. From this classification for each class a set of positive and negative features is computed. This set of features is selected as result of the procedure. The procedure is evaluated on an in-house dataset from a Knowledge Discovery from Text (KDT) application and on a set of publicly available datasets used in international feature selection competitions. These datasets come from KDT applications, drug discovery as well as other applications. The knowledge of the correct classification available for the training and validation datasets is used to optimize the parameters for positive and negative feature extractions. The process becomes feasible for large and sparse datasets, as the ones obtained in KDT applications, by using both compression techniques to store the similarity matrix and speed up techniques of the Kohonen algorithm that take advantage of the sparsity of the input matrix. These improvements make it feasible, by using the grid, the application of the methodology to massive datasets.

Keywords: Clustering algorithm, Data mining, Feature selection, Grid, Kohonen Self Organizing Map.

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Authors: Lae-Jeong Park, Jung-Ho Moon

Abstract:

People detection from images has a variety of applications such as video surveillance and driver assistance system, but is still a challenging task and more difficult in crowded environments such as shopping malls in which occlusion of lower parts of human body often occurs. Lack of the full-body information requires more effective features than common features such as HOG. In this paper, new features are introduced that exploits global self-symmetry (GSS) characteristic in head-shoulder patterns. The features encode the similarity or difference of color histograms and oriented gradient histograms between two vertically symmetric blocks. The domain-specific features are rapid to compute from the integral images in Viola-Jones cascade-of-rejecters framework. The proposed features are evaluated with our own head-shoulder dataset that, in part, consists of a well-known INRIA pedestrian dataset. Experimental results show that the GSS features are effective in reduction of false alarmsmarginally and the gradient GSS features are preferred more often than the color GSS ones in the feature selection.

Keywords: Pedestrian detection, cascade of rejecters, feature extraction, self-symmetry, HOG.

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