Scholarly

Exploring the Combinatorics of Motif Alignments Foraccurately Computing E-values from P-values

Year: 2009 Volume: 3 Issue: 4 1091 - 1097 Pages

Abstract: In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the E-value as the product of the p-value and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give E-values that significantly diverge from their true values.

A Kernel Classifier using Linearised Bregman Iteration

Year: 2009 Volume: 3 Issue: 4 1087 - 1090 Pages

Authors:
K. A. D. N. K Wimalawarne

Abstract: In this paper we introduce a novel kernel classifier based on a iterative shrinkage algorithm developed for compressive sensing. We have adopted Bregman iteration with soft and hard shrinkage functions and generalized hinge loss for solving l1 norm minimization problem for classification. Our experimental results with face recognition and digit classification using SVM as the benchmark have shown that our method has a close error rate compared to SVM but do not perform better than SVM. We have found that the soft shrinkage method give more accuracy and in some situations more sparseness than hard shrinkage methods.

Hybrid Color-Texture Space for Image Classification

Year: 2009 Volume: 3 Issue: 4 1083 - 1086 Pages

Abstract: This work presents an approach for the construction of a hybrid color-texture space by using mutual information. Feature extraction is done by the Laws filter with SVM (Support Vectors Machine) as a classifier. The classification is applied on the VisTex database and a SPOT HRV (XS) image representing two forest areas in the region of Rabat in Morocco. The result of classification obtained in the hybrid space is compared with the one obtained in the RGB color space.

Scenario Recognition in Modern Building Automation

Year: 2009 Volume: 3 Issue: 4 1074 - 1082 Pages

Abstract: Modern building automation needs to deal with very different types of demands, depending on the use of a building and the persons acting in it. To meet the requirements of situation awareness in modern building automation, scenario recognition becomes more and more important in order to detect sequences of events and to react to them properly. We present two concepts of scenario recognition and their implementation, one based on predefined templates and the other applying an unsupervised learning algorithm using statistical methods. Implemented applications will be described and their advantages and disadvantages will be outlined.

An Ontology Abstract Machine

Year: 2009 Volume: 3 Issue: 4 1062 - 1073 Pages

Abstract: As more people from non-technical backgrounds are becoming directly involved with large-scale ontology development, the focal point of ontology research has shifted from the more theoretical ontology issues to problems associated with the actual use of ontologies in real-world, large-scale collaborative applications. Recently the National Science Foundation funded a large collaborative ontology development project for which a new formal ontology model, the Ontology Abstract Machine (OAM), was developed to satisfy some unique functional and data representation requirements. This paper introduces the OAM model and the related algorithms that enable maintenance of an ontology that supports node-based user access. The successful software implementation of the OAM model and its subsequent acceptance by a large research community proves its validity and its real-world application value.

Increase of Error Detection Effectiveness in the Data Transmission Channels with Pulse-Amplitude Modulation

Year: 2009 Volume: 3 Issue: 4 1057 - 1061 Pages

Authors:
Akram A. Mustafa

Abstract: In this paper an approaches for increasing the effectiveness of error detection in computer network channels with Pulse-Amplitude Modulation (PAM) has been proposed. Proposed approaches are based on consideration of special feature of errors, which are appearances in line with PAM. The first approach consists of CRC modification specifically for line with PAM. The second approach is base of weighted checksums using. The way for checksum components coding has been developed. It has been shown that proposed checksum modification ensure superior digital data control transformation reliability for channels with PAM in compare to CRC.

A Serializability Condition for Multi-step Transactions Accessing Ordered Data

Year: 2009 Volume: 3 Issue: 4 1049 - 1056 Pages

Abstract: In mobile environments, unspecified numbers of transactions arrive in continuous streams. To prove correctness of their concurrent execution a method of modelling an infinite number of transactions is needed. Standard database techniques model fixed finite schedules of transactions. Lately, techniques based on temporal logic have been proposed as suitable for modelling infinite schedules. The drawback of these techniques is that proving the basic serializability correctness condition is impractical, as encoding (the absence of) conflict cyclicity within large sets of transactions results in prohibitively large temporal logic formulae. In this paper, we show that, under certain common assumptions on the graph structure of data items accessed by the transactions, conflict cyclicity need only be checked within all possible pairs of transactions. This results in formulae of considerably reduced size in any temporal-logic-based approach to proving serializability, and scales to arbitrary numbers of transactions.

An Owl Ontology for Commonkads Template Knowledge Models

Year: 2009 Volume: 3 Issue: 4 1043 - 1048 Pages

Abstract: This paper gives an overview of how an OWL ontology has been created to represent template knowledge models defined in CML that are provided by CommonKADS. CommonKADS is a mature knowledge engineering methodology which proposes the use of template knowledge model for knowledge modelling. The aim of developing this ontology is to present the template knowledge model in a knowledge representation language that can be easily understood and shared in the knowledge engineering community. Hence OWL is used as it has become a standard for ontology and also it already has user friendly tools for viewing and editing.

Two New Low Power High Performance Full Adders with Minimum Gates

Year: 2009 Volume: 3 Issue: 4 1035 - 1042 Pages

Abstract: with increasing circuits- complexity and demand to use portable devices, power consumption is one of the most important parameters these days. Full adders are the basic block of many circuits. Therefore reducing power consumption in full adders is very important in low power circuits. One of the most powerconsuming modules in full adders is XOR/XNOR circuit. This paper presents two new full adders based on two new logic approaches. The proposed logic approaches use one XOR or XNOR gate to implement a full adder cell. Therefore, delay and power will be decreased. Using two new approaches and two XOR and XNOR gates, two new full adders have been implemented in this paper. Simulations are carried out by HSPICE in 0.18μm bulk technology with 1.8V supply voltage. The results show that the ten-transistors proposed full adder has 12% less power consumption and is 5% faster in comparison to MB12T full adder. 9T is more efficient in area and is 24% better than similar 10T full adder in term of power consumption. The main drawback of the proposed circuits is output threshold loss problem.

Texture Based Weed Detection Using Multi Resolution Combined Statistical and Spatial Frequency (MRCSF)

Year: 2009 Volume: 3 Issue: 4 1030 - 1034 Pages

Abstract: Texture classification is a trendy and a catchy technology in the field of texture analysis. Textures, the repeated patterns, have different frequency components along different orientations. Our work is based on Texture Classification and its applications. It finds its applications in various fields like Medical Image Classification, Computer Vision, Remote Sensing, Agricultural Field, and Textile Industry. Weed control has a major effect on agriculture. A large amount of herbicide has been used for controlling weeds in agriculture fields, lawns, golf courses, sport fields, etc. Random spraying of herbicides does not meet the exact requirement of the field. Certain areas in field have more weed patches than estimated. So, we need a visual system that can discriminate weeds from the field image which will reduce or even eliminate the amount of herbicide used. This would allow farmers to not use any herbicides or only apply them where they are needed. A machine vision precision automated weed control system could reduce the usage of chemicals in crop fields. In this paper, an intelligent system for automatic weeding strategy Multi Resolution Combined Statistical & spatial Frequency is used to discriminate the weeds from the crops and to classify them as narrow, little and broad weeds.

A Distributed Cognition Framework to Compare E-Commerce Websites Using Data Envelopment Analysis

Year: 2009 Volume: 3 Issue: 4 1021 - 1029 Pages

Authors:
C. lo Storto

Abstract: This paper presents an approach based on the adoption of a distributed cognition framework and a non parametric multicriteria evaluation methodology (DEA) designed specifically to compare e-commerce websites from the consumer/user viewpoint. In particular, the framework considers a website relative efficiency as a measure of its quality and usability. A website is modelled as a black box capable to provide the consumer/user with a set of functionalities. When the consumer/user interacts with the website to perform a task, he/she is involved in a cognitive activity, sustaining a cognitive cost to search, interpret and process information, and experiencing a sense of satisfaction. The degree of ambiguity and uncertainty he/she perceives and the needed search time determine the effort size – and, henceforth, the cognitive cost amount – he/she has to sustain to perform his/her task. On the contrary, task performing and result achievement induce a sense of gratification, satisfaction and usefulness. In total, 9 variables are measured, classified in a set of 3 website macro-dimensions (user experience, site navigability and structure). The framework is implemented to compare 40 websites of businesses performing electronic commerce in the information technology market. A questionnaire to collect subjective judgements for the websites in the sample was purposely designed and administered to 85 university students enrolled in computer science and information systems engineering undergraduate courses.

Local Curvelet Based Classification Using Linear Discriminant Analysis for Face Recognition

Year: 2009 Volume: 3 Issue: 4 1015 - 1020 Pages

Abstract: In this paper, an efficient local appearance feature extraction method based the multi-resolution Curvelet transform is proposed in order to further enhance the performance of the well known Linear Discriminant Analysis(LDA) method when applied to face recognition. Each face is described by a subset of band filtered images containing block-based Curvelet coefficients. These coefficients characterize the face texture and a set of simple statistical measures allows us to form compact and meaningful feature vectors. The proposed method is compared with some related feature extraction methods such as Principal component analysis (PCA), as well as Linear Discriminant Analysis LDA, and independent component Analysis (ICA). Two different muti-resolution transforms, Wavelet (DWT) and Contourlet, were also compared against the Block Based Curvelet-LDA algorithm. Experimental results on ORL, YALE and FERET face databases convince us that the proposed method provides a better representation of the class information and obtains much higher recognition accuracies.

Information Extraction from Unstructured and Ungrammatical Data Sources for Semantic Annotation

Year: 2009 Volume: 3 Issue: 4 1006 - 1014 Pages

Abstract: The internet has become an attractive avenue for global e-business, e-learning, knowledge sharing, etc. Due to continuous increase in the volume of web content, it is not practically possible for a user to extract information by browsing and integrating data from a huge amount of web sources retrieved by the existing search engines. The semantic web technology enables advancement in information extraction by providing a suite of tools to integrate data from different sources. To take full advantage of semantic web, it is necessary to annotate existing web pages into semantic web pages. This research develops a tool, named OWIE (Ontology-based Web Information Extraction), for semantic web annotation using domain specific ontologies. The tool automatically extracts information from html pages with the help of pre-defined ontologies and gives them semantic representation. Two case studies have been conducted to analyze the accuracy of OWIE.

A General Framework for Modeling Replicated Real-Time Database

Year: 2009 Volume: 3 Issue: 4 999 - 1005 Pages

Abstract: There are many issues that affect modeling and designing real-time databases. One of those issues is maintaining consistency between the actual state of the real-time object of the external environment and its images as reflected by all its replicas distributed over multiple nodes. The need to improve the scalability is another important issue. In this paper, we present a general framework to design a replicated real-time database for small to medium scale systems and maintain all timing constrains. In order to extend the idea for modeling a large scale database, we present a general outline that consider improving the scalability by using an existing static segmentation algorithm applied on the whole database, with the intent to lower the degree of replication, enables segments to have individual degrees of replication with the purpose of avoiding excessive resource usage, which all together contribute in solving the scalability problem for DRTDBS.

Performance of Histogram-Based Skin Colour Segmentation for Arms Detection in Human Motion Analysis Application

Year: 2009 Volume: 3 Issue: 4 993 - 998 Pages

Abstract: Arms detection is one of the fundamental problems in human motion analysis application. The arms are considered as the most challenging body part to be detected since its pose and speed varies in image sequences. Moreover, the arms are usually occluded with other body parts such as the head and torso. In this paper, histogram-based skin colour segmentation is proposed to detect the arms in image sequences. Six different colour spaces namely RGB, rgb, HSI, TSL, SCT and CIELAB are evaluated to determine the best colour space for this segmentation procedure. The evaluation is divided into three categories, which are single colour component, colour without luminance and colour with luminance. The performance is measured using True Positive (TP) and True Negative (TN) on 250 images with manual ground truth. The best colour is selected based on the highest TN value followed by the highest TP value.

Bounds on Reliability of Parallel Computer Interconnection Systems

Year: 2009 Volume: 3 Issue: 4 987 - 992 Pages

Abstract: The evaluation of residual reliability of large sized parallel computer interconnection systems is not practicable with the existing methods. Under such conditions, one must go for approximation techniques which provide the upper bound and lower bound on this reliability. In this context, a new approximation method for providing bounds on residual reliability is proposed here. The proposed method is well supported by two algorithms for simulation purpose. The bounds on residual reliability of three different categories of interconnection topologies are efficiently found by using the proposed method

DACS3:Embedding Individual Ant Behavior in Ant Colony System

Year: 2009 Volume: 3 Issue: 4 981 - 986 Pages

Abstract: Ants are fascinating creatures that demonstrate the ability to find food and bring it back to their nest. Their ability as a colony, to find paths to food sources has inspired the development of algorithms known as Ant Colony Systems (ACS). The principle of cooperation forms the backbone of such algorithms, commonly used to find solutions to problems such as the Traveling Salesman Problem (TSP). Ants communicate to each other through chemical substances called pheromones. Modeling individual ants- ability to manipulate this substance can help an ACS find the best solution. This paper introduces a Dynamic Ant Colony System with threelevel updates (DACS3) that enhance an existing ACS. Experiments were conducted to observe single ant behavior in a colony of Malaysian House Red Ants. Such behavior was incorporated into the DACS3 algorithm. We benchmark the performance of DACS3 versus DACS on TSP instances ranging from 14 to 100 cities. The result shows that the DACS3 algorithm can achieve shorter distance in most cases and also performs considerably faster than DACS.

Semi-Automatic Trend Detection in Scholarly Repository Using Semantic Approach

Year: 2009 Volume: 3 Issue: 4 978 - 980 Pages

Abstract: Currently WWW is the first solution for scholars in finding information. But, analyzing and interpreting this volume of information will lead to researchers overload in pursuing their research. Trend detection in scientific publication retrieval systems helps scholars to find relevant, new and popular special areas by visualizing the trend of input topic. However, there are few researches on trend detection in scientific corpora while their proposed models do not appear to be suitable. Previous works lack of an appropriate representation scheme for research topics. This paper describes a method that combines Semantic Web and ontology to support advance search functions such as trend detection in the context of scholarly Semantic Web system (SSWeb).

Face Recognition Using Eigen face Coefficients and Principal Component Analysis

Year: 2009 Volume: 3 Issue: 4 973 - 977 Pages

Abstract: Face Recognition is a field of multidimensional applications. A lot of work has been done, extensively on the most of details related to face recognition. This idea of face recognition using PCA is one of them. In this paper the PCA features for Feature extraction are used and matching is done for the face under consideration with the test image using Eigen face coefficients. The crux of the work lies in optimizing Euclidean distance and paving the way to test the same algorithm using Matlab which is an efficient tool having powerful user interface along with simplicity in representing complex images.

A study of Cancer-related MicroRNAs through Expression Data and Literature Search

Year: 2009 Volume: 3 Issue: 4 970 - 972 Pages

Abstract: MicroRNAs (miRNAs) are a class of non-coding RNAs that hybridize to mRNAs and induce either translation repression or mRNA cleavage. Recently, it has been reported that miRNAs could possibly play an important role in human diseases. By integrating miRNA target genes, cancer genes, miRNA and mRNA expression profiles information, a database is developed to link miRNAs to cancer target genes. The database provides experimentally verified human miRNA target genes information, including oncogenes and tumor suppressor genes. In addition, fragile sites information for miRNAs, and the strength of the correlation of miRNA and its target mRNA expression level for nine tissue types are computed, which serve as an indicator for suggesting miRNAs could play a role in human cancer. The database is freely accessible at http://ppi.bioinfo.asia.edu.tw/mirna_target/index.html.

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