Search results for: Gabor features

Authors: Lavanya Srinivasan

Abstract:

Biometric identification is to identify unique features in a person like fingerprints, iris, ear, and voice recognition that need the subject's permission and physical contact. Gait biometric is used to identify the unique gait of the person by extracting moving features. The main advantage of gait biometric to identify the gait of a person at a distance, without any physical contact. In this work, the gait biometric is used for person re-identification. The person walking naturally compared with the same person walking with bag, coat and case recorded using long wave infrared, short wave infrared, medium wave infrared and visible cameras. The videos are recorded in rural and in urban environments. The pre-processing technique includes human identified using You Only Look Once, background subtraction, silhouettes extraction and synthesis Gait Entropy Image by averaging the silhouettes. The moving features are extracted from the Gait Entropy Energy Image. The extracted features are dimensionality reduced by the Principal Component Analysis and recognized using different classifiers. The comparative results with the different classifier show that Linear Discriminant Analysis outperform other classifiers with 95.8% for visible in the rural dataset and 94.8% for longwave infrared in the urban dataset.

Keywords: biometric, gait, silhouettes, You Only Look Once

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Authors: Chan Weng Howe, Mohd Saberi Mohamad

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Protein residue contact map is a compact representation of secondary structure of protein. Due to the information hold in the contact map, attentions from researchers in related field were drawn and plenty of works have been done throughout the past decade. Artificial intelligence approaches have been widely adapted in related works such as neural networks, genetic programming, and Hidden Markov model as well as support vector machine. However, the performance of the prediction was not generalized which probably depends on the data used to train and generate the prediction model. This situation shown the importance of the features or information used in affecting the prediction performance. In this research, support vector machine was used to predict protein residue contact map on different combination of features in order to show and analyze the effectiveness of the features.

Keywords: contact map, protein residue contact, support vector machine, protein structure prediction

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Authors: Baljit Singh Khehra, Amar Partap Singh Pharwaha

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Clusters of Microcalcifications (MCCs) are most frequent symptoms of Ductal Carcinoma in Situ (DCIS) recognized by mammography. Least-Square Support Vector Machine (LS-SVM) is a variant of the standard SVM. In the paper, LS-SVM is proposed as a classifier for classifying MCCs as benign or malignant based on relevant extracted features from enhanced mammogram. To establish the credibility of LS-SVM classifier for classifying MCCs, a comparative evaluation of the relative performance of LS-SVM classifier for different kernel functions is made. For comparative evaluation, confusion matrix and ROC analysis are used. Experiments are performed on data extracted from mammogram images of DDSM database. A total of 380 suspicious areas are collected, which contain 235 malignant and 145 benign samples, from mammogram images of DDSM database. A set of 50 features is calculated for each suspicious area. After this, an optimal subset of 23 most suitable features is selected from 50 features by Particle Swarm Optimization (PSO). The results of proposed study are quite promising.

Keywords: Clusters of Microcalcifications, Ductal Carcinoma in Situ, Least-Square Support Vector Machine, Particle Swarm Optimization.

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Authors: Essam Al-Daoud

Abstract:

A New features are extracted and compared to improve the prediction of protein-protein interactions. The basic idea is to select and use the best set of features from the Tensor matrices that are produced by the frequency vectors of the protein sequences. Three set of features are compared, the first set is based on the indices that are the most common in the interacting proteins, the second set is based on the indices that tend to be common in the interacting and non-interacting proteins, and the third set is constructed by using random indices. Moreover, three encoding strategies are compared; that are based on the amino asides polarity, structure, and chemical properties. The experimental results indicate that the highest accuracy can be obtained by using random indices with chemical properties encoding strategy and support vector machine.

Keywords: protein-protein interactions, random indices, encoding strategies, support vector machine.

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Authors: N. Valliammal, S.N. Geethalakshmi

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This paper describes an optimal approach for feature subset selection to classify the leaves based on Genetic Algorithm (GA) and Kernel Based Principle Component Analysis (KPCA). Due to high complexity in the selection of the optimal features, the classification has become a critical task to analyse the leaf image data. Initially the shape, texture and colour features are extracted from the leaf images. These extracted features are optimized through the separate functioning of GA and KPCA. This approach performs an intersection operation over the subsets obtained from the optimization process. Finally, the most common matching subset is forwarded to train the Support Vector Machine (SVM). Our experimental results successfully prove that the application of GA and KPCA for feature subset selection using SVM as a classifier is computationally effective and improves the accuracy of the classifier.

Keywords: Optimization, Feature extraction, Feature subset, Classification, GA, KPCA, SVM and Computation

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Authors: M.Ghazvini, S. A. Monadjemi, N. Movahhedinia, K. Jamshidi

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In this article, a method has been offered to classify normal and defective tiles using wavelet transform and artificial neural networks. The proposed algorithm calculates max and min medians as well as the standard deviation and average of detail images obtained from wavelet filters, then comes by feature vectors and attempts to classify the given tile using a Perceptron neural network with a single hidden layer. In this study along with the proposal of using median of optimum points as the basic feature and its comparison with the rest of the statistical features in the wavelet field, the relational advantages of Haar wavelet is investigated. This method has been experimented on a number of various tile designs and in average, it has been valid for over 90% of the cases. Amongst the other advantages, high speed and low calculating load are prominent.

Keywords: Defect detection, tile and ceramic quality inspection, wavelet transform, classification, neural networks, statistical features.

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Authors: Tomyslav Sledevič, Artūras Serackis, Gintautas Tamulevičius, Dalius Navakauskas

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Paper presents an comparative evaluation of features extraction algorithm for a real-time isolated word recognition system based on FPGA. The Mel-frequency cepstral, linear frequency cepstral, linear predictive and their cepstral coefficients were implemented in hardware/software design. The proposed system was investigated in speaker dependent mode for 100 different Lithuanian words. The robustness of features extraction algorithms was tested recognizing the speech records at different signal to noise rates. The experiments on clean records show highest accuracy for Mel-frequency cepstral and linear frequency cepstral coefficients. For records with 15 dB signal to noise rate the linear predictive cepstral coefficients gives best result. The hard and soft part of the system is clocked on 50 MHz and 100 MHz accordingly. For the classification purpose the pipelined dynamic time warping core was implemented. The proposed word recognition system satisfy the real-time requirements and is suitable for applications in embedded systems.

Keywords: Isolated word recognition, features extraction, MFCC, LFCC, LPCC, LPC, FPGA, DTW.

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Authors: Mohamed Abdel Fattah, Fuji Ren

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This work proposes an approach to address automatic text summarization. This approach is a trainable summarizer, which takes into account several features, including sentence position, positive keyword, negative keyword, sentence centrality, sentence resemblance to the title, sentence inclusion of name entity, sentence inclusion of numerical data, sentence relative length, Bushy path of the sentence and aggregated similarity for each sentence to generate summaries. First we investigate the effect of each sentence feature on the summarization task. Then we use all features score function to train genetic algorithm (GA) and mathematical regression (MR) models to obtain a suitable combination of feature weights. The proposed approach performance is measured at several compression rates on a data corpus composed of 100 English religious articles. The results of the proposed approach are promising.

Keywords: Automatic Summarization, Genetic Algorithm, Mathematical Regression, Text Features.

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

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The recognition of handwritten numeral is an important area of research for its applications in post office, banks and other organizations. This paper presents automatic recognition of handwritten Kannada numerals based on structural features. Five different types of features, namely, profile based 10-segment string, water reservoir; vertical and horizontal strokes, end points and average boundary length from the minimal bounding box are used in the recognition of numeral. The effect of each feature and their combination in the numeral classification is analyzed using nearest neighbor classifiers. It is common to combine multiple categories of features into a single feature vector for the classification. Instead, separate classifiers can be used to classify based on each visual feature individually and the final classification can be obtained based on the combination of separate base classification results. One popular approach is to combine the classifier results into a feature vector and leaving the decision to next level classifier. This method is extended to extract a better information, possibility distribution, from the base classifiers in resolving the conflicts among the classification results. Here, we use fuzzy k Nearest Neighbor (fuzzy k-NN) as base classifier for individual feature sets, the results of which together forms the feature vector for the final k Nearest Neighbor (k-NN) classifier. Testing is done, using different features, individually and in combination, on a database containing 1600 samples of different numerals and the results are compared with the results of different existing methods.

Keywords: Fuzzy k Nearest Neighbor, Multiple Classifiers, Numeral Recognition, Structural features.

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Authors: Kwangjin Hong, Chulhan Lee, Keechul Jung, Kyoungsu Oh

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For the communication between human and computer in an interactive computing environment, the gesture recognition is studied vigorously. Therefore, a lot of studies have proposed efficient methods about the recognition algorithm using 2D camera captured images. However, there is a limitation to these methods, such as the extracted features cannot fully represent the object in real world. Although many studies used 3D features instead of 2D features for more accurate gesture recognition, the problem, such as the processing time to generate 3D objects, is still unsolved in related researches. Therefore we propose a method to extract the 3D features combined with the 3D object reconstruction. This method uses the modified GPU-based visual hull generation algorithm which disables unnecessary processes, such as the texture calculation to generate three kinds of 3D projection maps as the 3D feature: a nearest boundary, a farthest boundary, and a thickness of the object projected on the base-plane. In the section of experimental results, we present results of proposed method on eight human postures: T shape, both hands up, right hand up, left hand up, hands front, stand, sit and bend, and compare the computational time of the proposed method with that of the previous methods.

Keywords: Fast 3D Feature Extraction, Gesture Recognition, Computer Vision.

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Authors: I. M. Sur, A. M. Chirila-Babau, T. Gabor, V. Micle

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This paper shows researches in order to extract Cr, Cu and Ni from the polluted soils. Research is based on preliminary studies regarding the usage of Thiobacillus ferrooxidans bacterium (9K medium) for bioleaching of soil polluted with heavy metal (Cu, Cr and Ni). The microorganisms (Thiobacillus ferooxidans) selected directly from polluted soil samples were used in this experimental work. Soil samples used in the experimental research were taken from an area polluted with heavy metals from Romania. The soil samples are subjected to the cleaning process using the 9K medium solution (20 mL and 40 mL, respectively), stirred 200 rpm for 20 hours at a controlled temperature (30 ˚C). During the experiment (0, 2, 4, 8 and 20 h), liquid samples have been extracted and analyzed using the Atomic Absorption Spectrophotometer AA-6800 (AAS) in order to determine the Cr, Cu and Ni concentration. Experiments led to the conclusion that these soils can be depolluted by bioleaching, being a biological treatment method involving the use of microorganisms to favor the extraction of Cr, Cu and Ni from polluted soils.

Keywords: Bioleaching, extraction, microorganisms, polluted soil, Thiobacillus ferooxidans.

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Authors: Peter A. Bibby

Abstract:

Research has suggested that implicit learning tasks may rely on episodic processing to generate above chance performance on the standard classification tasks. The current research examines the invariant features task (McGeorge and Burton, 1990) and argues that such episodic processing is indeed important. The results of the experiment suggest that both rejection and similarity strategies are used by participants in this task to simultaneously reject unfamiliar items and to accept (falsely) familiar items. Primarily these decisions are based on the presence of low or high frequency goal based features of the stimuli presented in the incidental learning phase. It is proposed that a goal based analysis of the incidental learning task provides a simple step in understanding which features of the episodic processing are most important for explaining the match between incidental, implicit learning and test performance.

Keywords: Episodic processing, incidental learning, implicitlearning, invariant learning.

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Authors: R. K. Chaurasiya, N. D. Londhe, S. Ghosh

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The study of the electrical signals produced by neural activities of human brain is called Electroencephalography. In this paper, we propose an automatic and efficient EEG signal classification approach. The proposed approach is used to classify the EEG signal into two classes: epileptic seizure or not. In the proposed approach, we start with extracting the features by applying Discrete Wavelet Transform (DWT) in order to decompose the EEG signals into sub-bands. These features, extracted from details and approximation coefficients of DWT sub-bands, are used as input to Principal Component Analysis (PCA). The classification is based on reducing the feature dimension using PCA and deriving the supportvectors using Support Vector Machine (SVM). The experimental are performed on real and standard dataset. A very high level of classification accuracy is obtained in the result of classification.

Keywords: Discrete Wavelet Transform, Electroencephalogram, Pattern Recognition, Principal Component Analysis, Support Vector Machine.

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Authors: Shu-Lu Hsu, Jeffrey C. F. Tai, Yi-Han Wang

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The purpose of this study is to understand how consumers react to a company's promotional offers with mobile applications (APP) as premiums. This paper presents the results of an experimental study where five features of APP were involved: the cost (free/discounted) for earning APP, the relationship between APP and the promoted product, the perceived usefulness, the perceived ease of use, and the perceived playfulness of APP in the context of light foods purchase. The results support that the above features, except perceived ease of use, have substantial influences on consumers' intention to adopt the APP. Among the five features, the cost for earning APP has the most impact on the adopting intention of APP. The study also found a positive influence of adopting intention of APP on the consumer's purchase intention of the promoted product. Thus, APP-based premiums may enhance the consumer's purchase intention of a company's promoted products.

Keywords: Mobile Application, Premium, Sales Promotion, TAM.

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Authors: Mahesh Pal

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This paper proposes to use ETM+ multispectral data and panchromatic band as well as texture features derived from the panchromatic band for land cover classification. Four texture features including one 'internal texture' and three GLCM based textures namely correlation, entropy, and inverse different moment were used in combination with ETM+ multispectral data. Two data sets involving combination of multispectral, panchromatic band and its texture were used and results were compared with those obtained by using multispectral data alone. A decision tree classifier with and without boosting were used to classify different datasets. Results from this study suggest that the dataset consisting of panchromatic band, four of its texture features and multispectral data was able to increase the classification accuracy by about 2%. In comparison, a boosted decision tree was able to increase the classification accuracy by about 3% with the same dataset.

Keywords: Internal texture; GLCM; decision tree; boosting; classification accuracy.

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Authors: Chaitanya Chawla, Divya Panwar, Gurneesh Singh Anand, M. P. S Bhatia

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This paper presents a deep-learning mechanism for classifying computer generated images and photographic images. The proposed method accounts for a convolutional layer capable of automatically learning correlation between neighbouring pixels. In the current form, Convolutional Neural Network (CNN) will learn features based on an image's content instead of the structural features of the image. The layer is particularly designed to subdue an image's content and robustly learn the sensor pattern noise features (usually inherited from image processing in a camera) as well as the statistical properties of images. The paper was assessed on latest natural and computer generated images, and it was concluded that it performs better than the current state of the art methods.

Keywords: Image forensics, computer graphics, classification, deep learning, convolutional neural networks.

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Authors: Assel S. Issabekova, Olga A. Berillo, Vladimir A. Khailenko, Shara A. Atambayeva, Mireille Regnier, Anatoly T. Ivachshenko

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Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed. Functional regions of mRNA were shown to be significantly heterogenous according to the number of binding sites of miRNA and to the location density of these sites.

Keywords: 5'UTR, 3'UTR, CDS, miRNA, target mRNA

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Authors: Timothy E. Frank, Josh R. Aldred, Sophie B. Boulware, Michelle K. Cabonce, Justin H. White

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Materials degrade at different rates in different environments depending on factors such as temperature, aridity, salinity, and solar radiation. Therefore, predicting asset longevity depends, in part, on the environmental conditions to which the asset is exposed. Heating, ventilation, and air conditioning (HVAC) systems are critical to building operations yet are responsible for a significant proportion of their energy consumption. HVAC energy use increases substantially with slight operational inefficiencies. Understanding the environmental influences on HVAC degradation in detail will inform maintenance schedules and capital investment, reduce energy use, and increase lifecycle management efficiency. HVAC inspection records spanning 14 years from 21 locations across the United States were compiled and associated with the climate conditions to which they were exposed. Three environmental features were explored in this study: average high temperature, average low temperature, and annual precipitation, as well as four non-environmental features. Initial insights showed no correlations between individual features and the rate of HVAC component degradation. Using neighborhood component analysis, however, the most critical features related to degradation were identified. Two models were considered, and results varied between them. However, longitude and latitude emerged as potentially the best predictors of average HVAC component degradation. Further research is needed to evaluate additional environmental features, increase the resolution of the environmental data, and develop more robust models to achieve more conclusive results.

Keywords: Climate, infrastructure degradation, HVAC, neighborhood component analysis.

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Authors: Emad E Abdallah, A.F. Otoom, ArwaSaqer, Ola Abu-Aisheh, Diana Omari, Ghadeer Salem

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As emails communications have no consistent authentication procedure to ensure the authenticity, we present an investigation analysis approach for detecting forged emails based on Random Forests and Naïve Bays classifiers. Instead of investigating the email headers, we use the body content to extract a unique writing style for all the possible suspects. Our approach consists of four main steps: (1) The cybercrime investigator extract different effective features including structural, lexical, linguistic, and syntactic evidence from previous emails for all the possible suspects, (2) The extracted features vectors are normalized to increase the accuracy rate. (3) The normalized features are then used to train the learning engine, (4) upon receiving the anonymous email (M); we apply the feature extraction process to produce a feature vector. Finally, using the machine learning classifiers the email is assigned to one of the suspects- whose writing style closely matches M. Experimental results on real data sets show the improved performance of the proposed method and the ability of identifying the authors with a very limited number of features.

Keywords: Digital investigation, cybercrimes, emails forensics, anonymous emails, writing style, and authorship analysis

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Authors: Zhankuliyeva S. A.

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This article considers the main features of party construction in the course of political modernization of Kazakhstan. Along with consideration of party construction author analyzed how the transformation of the party system was fulfilled in Kazakhstan. Besides the basic stages in the course of party construction were explained by the author. The statistical data is cited.

Keywords: elections, multi-party system, party construction, political pluralism, political party, Republic of Kazakhstan (RK)

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Authors: Hemashree Bordoloi, Kandarpa Kumar Sarma

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Rotation or tilt present in an image capture by digital means can be detected and corrected using Artificial Neural Network (ANN) for application with a Face Recognition System (FRS). Principal Component Analysis (PCA) features of faces at different angles are used to train an ANN which detects the rotation for an input image and corrected using a set of operations implemented using another system based on ANN. The work also deals with the recognition of human faces with features from the foreheads, eyes, nose and mouths as decision support entities of the system configured using a Generalized Feed Forward Artificial Neural Network (GFFANN). These features are combined to provide a reinforced decision for verification of a person-s identity despite illumination variations. The complete system performing facial image rotation detection, correction and recognition using re-enforced decision support provides a success rate in the higher 90s.

Keywords: Rotation, Face, Recognition, ANN.

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Authors: Xiaoli Shen, Yuehui Chen

Abstract:

Interactions among proteins are the basis of various life events. So, it is important to recognize and research protein interaction sites. A control set that contains 149 protein molecules were used here. Then 10 features were extracted and 4 sample sets that contained 9 sliding windows were made according to features. These 4 sample sets were calculated by Radial Basis Functional neutral networks which were optimized by Particle Swarm Optimization respectively. Then 4 groups of results were obtained. Finally, these 4 groups of results were integrated by decision fusion (DF) and Genetic Algorithm based Selected Ensemble (GASEN). A better accuracy was got by DF and GASEN. So, the integrated methods were proved to be effective.

Keywords: protein interaction sites, features, sliding windows, radial basis functional neutral networks, genetic algorithm basedselected ensemble.

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Authors: M. Bastanfard, S. Jafari, B.Jalaeian

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Ultrasound images are very useful diagnostic tool to distinguish benignant from malignant masses of the breast. However, there is a considerable overlap between benignancy and malignancy in ultrasonic images which makes it difficult to interpret. In this paper, a new noise removal algorithm was used to improve the images and classification process. The masses are classified by wavelet transform's coefficients, morphological and textural features as a novel feature set for this goal. The Bayesian estimation theory is used to classify the tissues in three classes according to their features.

Keywords: Bayesian estimation theory, breast, ultrasound, wavelet.

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Authors: Ismail Baniadam, Nafisa Tadayyon, Javid Fereidoni

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This study aimed to investigate medical students’ attitudes toward some teachers’ talking features regarding their gender in the Iranian context. To do so, 60 male and 60 female medical students of Urmia University of Medical Sciences (UMSU) participated in the research. A researcher made Likert-type questionnaire which was initially piloted and was used to gather the data. Comparing the four different factors regarding the features of teacher talk, it was revealed that visual and extra-linguistic information factor, Lexical and syntactic familiarity, Speed of speech, and the use of Persian language had the highest to the lowest mean score, respectively. It was also indicated that female students rather than male students were significantly more in favor of speed of speech and lexical and syntactic familiarity.

Keywords: Attitude, gender, medical student, teacher talk.

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Authors: Hee-Jeong Ahn, Kee-Won Kim, Seung-Hoon Kim

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The knowledge of the relationship between characters can help readers to understand the overall story or plot of the literary fiction. In this paper, we present a method for extracting the specific relationship between characters from a Korean literary fiction. Generally, methods for extracting relationships between characters in text are statistical or computational methods based on the sentence distance between characters without considering Korean linguistic features. Furthermore, it is difficult to extract the relationship with direction from text, such as one-sided love, because they consider only the weight of relationship, without considering the direction of the relationship. Therefore, in order to identify specific relationships between characters, we propose a statistical method considering linguistic features, such as syntactic patterns and speech verbs in Korean. The result of our method is represented by a weighted directed graph of the relationship between the characters. Furthermore, we expect that proposed method could be applied to the relationship analysis between characters of other content like movie or TV drama.

Keywords: Data mining, Korean linguistic feature, literary fiction, relationship extraction.

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Authors: Thashmee Karunaratne, Henrik Böstrom

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Logic based methods for learning from structured data is limited w.r.t. handling large search spaces, preventing large-sized substructures from being considered by the resulting classifiers. A novel approach to learning from structured data is introduced that employs a structure transformation method, called finger printing, for addressing these limitations. The method, which generates features corresponding to arbitrarily complex substructures, is implemented in a system, called DIFFER. The method is demonstrated to perform comparably to an existing state-of-art method on some benchmark data sets without requiring restrictions on the search space. Furthermore, learning from the union of features generated by finger printing and the previous method outperforms learning from each individual set of features on all benchmark data sets, demonstrating the benefit of developing complementary, rather than competing, methods for structure classification.

Keywords: Machine learning, Structure classification, Propositionalization.

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Authors: E. Oguz, Yıldız, A., Hayırsever, F.

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The purpose of the present study is to determine the level of reading habit of future classroom teachers, to discuss the obtained results according to their socio-demographic features and to define the factors which are influential on taking up reading in the context of future teachers experiences. The target population of the study consists of the fourth grade students at 62 faculties of education, department of classroom teaching from Turkish state universities. The sampling of the study consists of the fourth grade students from seven faculties of education, department of classroom teaching from each region. In the study, in the first and the second aspects, there will be a questionnaire to be developed concerning the measurement of future teachers level of reading habits and their socio-demographic features. The questionnaire was applied to all the students in the sample.

Keywords: Reading, Reading Habits, Teachers

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Authors: S. Balaji, M. Rajaram, Y. Harold Robinson, E. Golden Julie

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Delay Tolerant Networks (DTN) which have sufficient state information include trajectory and contact information, to protect routing efficiency. However, state information is dynamic and hard to obtain without a global and/or long-term collection process. To deal with these problems, the internal social features of each node are introduced in the network to perform the routing process. This type of application is motivated from several human contact networks where people contact each other more frequently if they have more social features in common. Two unique processes were developed for this process; social feature extraction and multipath routing. The routing method then becomes a hypercube–based feature matching process. Furthermore, the effectiveness of multipath routing is evaluated and compared to that of single-path routing.

Keywords: Delay tolerant networks, entropy, human contact networks, hyper cubes, multipath Routing, social features.

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Authors: I. Omerhodzic, S. Avdakovic, A. Nuhanovic, K. Dizdarevic

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In this paper, a wavelet-based neural network (WNN) classifier for recognizing EEG signals is implemented and tested under three sets EEG signals (healthy subjects, patients with epilepsy and patients with epileptic syndrome during the seizure). First, the Discrete Wavelet Transform (DWT) with the Multi-Resolution Analysis (MRA) is applied to decompose EEG signal at resolution levels of the components of the EEG signal (δ, θ, α, β and γ) and the Parseval-s theorem are employed to extract the percentage distribution of energy features of the EEG signal at different resolution levels. Second, the neural network (NN) classifies these extracted features to identify the EEGs type according to the percentage distribution of energy features. The performance of the proposed algorithm has been evaluated using in total 300 EEG signals. The results showed that the proposed classifier has the ability of recognizing and classifying EEG signals efficiently.

Keywords: Epilepsy, EEG, Wavelet transform, Energydistribution, Neural Network, Classification.

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Authors: Chia-Ta Tsai, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Shinn-Ying Ho

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Prediction of bacterial virulent protein sequences can give assistance to identification and characterization of novel virulence-associated factors and discover drug/vaccine targets against proteins indispensable to pathogenicity. Gene Ontology (GO) annotation which describes functions of genes and gene products as a controlled vocabulary of terms has been shown effectively for a variety of tasks such as gene expression study, GO annotation prediction, protein subcellular localization, etc. In this study, we propose a sequence-based method Virulent-GO by mining informative GO terms as features for predicting bacterial virulent proteins. Each protein in the datasets used by the existing method VirulentPred is annotated by using BLAST to obtain its homologies with known accession numbers for retrieving GO terms. After investigating various popular classifiers using the same five-fold cross-validation scheme, Virulent-GO using the single kind of GO term features with an accuracy of 82.5% is slightly better than VirulentPred with 81.8% using five kinds of sequence-based features. For the evaluation of independent test, Virulent-GO also yields better results (82.0%) than VirulentPred (80.7%). When evaluating single kind of feature with SVM, the GO term feature performs much well, compared with each of the five kinds of features.

Keywords: Bacterial virulence factors, GO terms, prediction, protein sequence.

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