Search results for: String Similarity

Authors: Shih-Yi Chao

Abstract:

The similarity comparison of RNA secondary structures is important in studying the functions of RNAs. In recent years, most existing tools represent the secondary structures by tree-based presentation and calculate the similarity by tree alignment distance. Different to previous approaches, we propose a new method based on maximum clique detection algorithm to extract the maximum common structural elements in compared RNA secondary structures. A new graph-based similarity measurement and maximum common subgraph detection procedures for comparing purely RNA secondary structures is introduced. Given two RNA secondary structures, the proposed algorithm consists of a process to determine the score of the structural similarity, followed by comparing vertices labelling, the labelled edges and the exact degree of each vertex. The proposed algorithm also consists of a process to extract the common structural elements between compared secondary structures based on a proposed maximum clique detection of the problem. This graph-based model also can work with NC-IUB code to perform the pattern-based searching. Therefore, it can be used to identify functional RNA motifs from database or to extract common substructures between complex RNA secondary structures. We have proved the performance of this proposed algorithm by experimental results. It provides a new idea of comparing RNA secondary structures. This tool is helpful to those who are interested in structural bioinformatics.

Keywords: Clique detection, labeled vertices, RNA secondary structures, subgraph, similarity.

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Authors: Hyungkeun Jee, Jooyoung Lee, Dowon Hong

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The most common forensic activity is searching a hard disk for string of data. Nowadays, investigators and analysts are increasingly experiencing large, even terabyte sized data sets when conducting digital investigations. Therefore consecutive searching can take weeks to complete successfully. There are two primary search methods: index-based search and bitwise search. Index-based searching is very fast after the initial indexing but initial indexing takes a long time. In this paper, we discuss a high speed bitwise search model for large-scale digital forensic investigations. We used pattern matching board, which is generally used for network security, to search for string and complex regular expressions. Our results indicate that in many cases, the use of pattern matching board can substantially increase the performance of digital forensic search tools.

Keywords: Digital forensics, search, regular expression.

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Authors: Arturo Aquino, Manuel Emilio Gegundez, Jose Manuel Bravo, Diego Marin

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Retinal vascularity assessment plays an important role in diagnosis of ophthalmic pathologies. The employment of digital images for this purpose makes possible a computerized approach and has motivated development of many methods for automated vascular tree segmentation. Metrics based on contingency tables for binary classification have been widely used for evaluating performance of these algorithms and, concretely, the accuracy has been mostly used as measure of global performance in this topic. However, this metric shows very poor matching with human perception as well as other notable deficiencies. Here, a new similarity function for measuring quality of retinal vessel segmentations is proposed. This similarity function is based on characterizing the vascular tree as a connected structure with a measurable area and length. Tests made indicate that this new approach shows better behaviour than the current one does. Generalizing, this concept of measuring descriptive properties may be used for designing functions for measuring more successfully segmentation quality of other complex structures.

Keywords: Retinal vessel segmentation, quality assessment, performanceevaluation, similarity function.

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

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The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

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In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.

Keywords: Sequence DNA, Relationship of swine, Swineinfluenza, Sequence Similarity

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Authors: Sanghoon Kim, Sun-Tae Chung, Souhwan Jung, Seoungseon Jeon, Jaemin Kim, Seongwon Cho

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In this paper, we propose a face recognition algorithm using AAM and Gabor features. Gabor feature vectors which are well known to be robust with respect to small variations of shape, scaling, rotation, distortion, illumination and poses in images are popularly employed for feature vectors for many object detection and recognition algorithms. EBGM, which is prominent among face recognition algorithms employing Gabor feature vectors, requires localization of facial feature points where Gabor feature vectors are extracted. However, localization method employed in EBGM is based on Gabor jet similarity and is sensitive to initial values. Wrong localization of facial feature points affects face recognition rate. AAM is known to be successfully applied to localization of facial feature points. In this paper, we devise a facial feature point localization method which first roughly estimate facial feature points using AAM and refine facial feature points using Gabor jet similarity-based facial feature localization method with initial points set by the rough facial feature points obtained from AAM, and propose a face recognition algorithm using the devised localization method for facial feature localization and Gabor feature vectors. It is observed through experiments that such a cascaded localization method based on both AAM and Gabor jet similarity is more robust than the localization method based on only Gabor jet similarity. Also, it is shown that the proposed face recognition algorithm using this devised localization method and Gabor feature vectors performs better than the conventional face recognition algorithm using Gabor jet similarity-based localization method and Gabor feature vectors like EBGM.

Keywords: Face Recognition, AAM, Gabor features, EBGM.

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Authors: C. S. Sastry, Saurabh Jain, Ashish Mishra

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Image retrieval is a topic where scientific interest is currently high. The important steps associated with image retrieval system are the extraction of discriminative features and a feasible similarity metric for retrieving the database images that are similar in content with the search image. Gabor filtering is a widely adopted technique for feature extraction from the texture images. The recently proposed sparsity promoting l1-norm minimization technique finds the sparsest solution of an under-determined system of linear equations. In the present paper, the l1-norm minimization technique as a similarity metric is used in image retrieval. It is demonstrated through simulation results that the l1-norm minimization technique provides a promising alternative to existing similarity metrics. In particular, the cases where the l1-norm minimization technique works better than the Euclidean distance metric are singled out.

Keywords: l1-norm minimization, content based retrieval, modified Gabor function.

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Authors: Ahmad Fadel Klaib, Zurinahni Zainol, Nurul Hashimah Ahamed, Rosma Ahmad, Wahidah Hussin

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Bioinformatics and Cheminformatics use computer as disciplines providing tools for acquisition, storage, processing, analysis, integrate data and for the development of potential applications of biological and chemical data. A chemical database is one of the databases that exclusively designed to store chemical information. NMRShiftDB is one of the main databases that used to represent the chemical structures in 2D or 3D structures. SMILES format is one of many ways to write a chemical structure in a linear format. In this study we extracted Antimicrobial Structures in SMILES format from NMRShiftDB and stored it in our Local Data Warehouse with its corresponding information. Additionally, we developed a searching tool that would response to user-s query using the JME Editor tool that allows user to draw or edit molecules and converts the drawn structure into SMILES format. We applied Quick Search algorithm to search for Antimicrobial Structures in our Local Data Ware House.

Keywords: Exact String-matching Algorithms, NMRShiftDB, SMILES Format, Antimicrobial Structures.

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Authors: Timothee G. Leleu

Abstract:

A new technique of topological multi-scale analysis is introduced. By performing a clustering recursively to build a hierarchy, and analyzing the co-scale and intra-scale similarities, an Iterated Function System can be extracted from any data set. The study of fractals shows that this method is efficient to extract self-similarities, and can find elegant solutions the inverse problem of building fractals. The theoretical aspects and practical implementations are discussed, together with examples of analyses of simple fractals.

Keywords: hierarchical clustering, multi-scale analysis, Similarity hashing.

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Authors: Matthias Dehmer, Frank Emmert Streib, Jürgen Kilian, Andreas Zulauf

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Methods for organizing web data into groups in order to analyze web-based hypertext data and facilitate data availability are very important in terms of the number of documents available online. Thereby, the task of clustering web-based document structures has many applications, e.g., improving information retrieval on the web, better understanding of user navigation behavior, improving web users requests servicing, and increasing web information accessibility. In this paper we investigate a new approach for clustering web-based hypertexts on the basis of their graph structures. The hypertexts will be represented as so called generalized trees which are more general than usual directed rooted trees, e.g., DOM-Trees. As a important preprocessing step we measure the structural similarity between the generalized trees on the basis of a similarity measure d. Then, we apply agglomerative clustering to the obtained similarity matrix in order to create clusters of hypertext graph patterns representing navigation structures. In the present paper we will run our approach on a data set of hypertext structures and obtain good results in Web Structure Mining. Furthermore we outline the application of our approach in Web Usage Mining as future work.

Keywords: Clustering methods, graph-based patterns, graph similarity, hypertext structures, web structure mining

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Hany T. Alashwal, Rohayanti Hassan, FarhanMohamed

Abstract:

The most important property of the Gene Ontology is the terms. These control vocabularies are defined to provide consistent descriptions of gene products that are shareable and computationally accessible by humans, software agent, or other machine-readable meta-data. Each term is associated with information such as definition, synonyms, database references, amino acid sequences, and relationships to other terms. This information has made the Gene Ontology broadly applied in microarray and proteomic analysis. However, the process of searching the terms is still carried out using traditional approach which is based on keyword matching. The weaknesses of this approach are: ignoring semantic relationships between terms, and highly depending on a specialist to find similar terms. Therefore, this study combines semantic similarity measure and genetic algorithm to perform a better retrieval process for searching semantically similar terms. The semantic similarity measure is used to compute similitude strength between two terms. Then, the genetic algorithm is employed to perform batch retrievals and to handle the situation of the large search space of the Gene Ontology graph. The computational results are presented to show the effectiveness of the proposed algorithm.

Keywords: Gene Ontology, Semantic similarity measure, Genetic algorithm, Ontology search

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Authors: Haider A Ramadhan, Khalil Shihab

Abstract:

Clustering techniques have been used by many intelligent software agents to group similar access patterns of the Web users into high level themes which express users intentions and interests. However, such techniques have been mostly focusing on one salient feature of the Web document visited by the user, namely the extracted keywords. The major aim of these techniques is to come up with an optimal threshold for the number of keywords needed to produce more focused themes. In this paper we focus on both keyword and similarity thresholds to generate themes with concentrated themes, and hence build a more sound model of the user behavior. The purpose of this paper is two fold: use distance based clustering methods to recognize overall themes from the Proxy log file, and suggest an efficient cut off levels for the keyword and similarity thresholds which tend to produce more optimal clusters with better focus and efficient size.

Keywords: Data mining, knowledge discovery, clustering, dataanalysis, Web log analysis, theme based searching.

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Authors: Ahmed A. A. Radwan, Bahgat A. Abdel Latef, Abdel Mgeid A. Ali, Osman A. Sadek

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This study investigates the use of genetic algorithms in information retrieval. The method is shown to be applicable to three well-known documents collections, where more relevant documents are presented to users in the genetic modification. In this paper we present a new fitness function for approximate information retrieval which is very fast and very flexible, than cosine similarity fitness function.

Keywords: Cosine similarity, Fitness function, Genetic Algorithm, Information Retrieval, Query learning.

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Authors: Mounira Taileb, Sid Lamrous, Sami Touati

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In order to accelerate the similarity search in highdimensional database, we propose a new hierarchical indexing method. It is composed of offline and online phases. Our contribution concerns both phases. In the offline phase, after gathering the whole of the data in clusters and constructing a hierarchical index, the main originality of our contribution consists to develop a method to construct bounding forms of clusters to avoid overlapping. For the online phase, our idea improves considerably performances of similarity search. However, for this second phase, we have also developed an adapted search algorithm. Our method baptized NOHIS (Non-Overlapping Hierarchical Index Structure) use the Principal Direction Divisive Partitioning (PDDP) as algorithm of clustering. The principle of the PDDP is to divide data recursively into two sub-clusters; division is done by using the hyper-plane orthogonal to the principal direction derived from the covariance matrix and passing through the centroid of the cluster to divide. Data of each two sub-clusters obtained are including by a minimum bounding rectangle (MBR). The two MBRs are directed according to the principal direction. Consequently, the nonoverlapping between the two forms is assured. Experiments use databases containing image descriptors. Results show that the proposed method outperforms sequential scan and SRtree in processing k-nearest neighbors.

Keywords: K-nearest neighbour search, multi-dimensional indexing, multimedia databases, similarity search.

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Authors: S. Hellam, Y. Oulahrir, F. El Mounchid, A. Sadiq, S. Mbarki

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In this paper, we propose a method for three-dimensional (3-D)-model indexing based on defining a new descriptor, which we call new descriptor using spherical harmonics. The purpose of the method is to minimize, the processing time on the database of objects models and the searching time of similar objects to request object. Firstly we start by defining the new descriptor using a new division of 3-D object in a sphere. Then we define a new distance which will be used in the search for similar objects in the database.

Keywords: 3D indexation, spherical harmonic, similarity of 3D objects.

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Authors: Ozan Mut, Mehmet Göktürk

Abstract:

Matching algorithms have significant importance in speaker recognition. Feature vectors of the unknown utterance are compared to feature vectors of the modeled speakers as a last step in speaker recognition. A similarity score is found for every model in the speaker database. Depending on the type of speaker recognition, these scores are used to determine the author of unknown speech samples. For speaker verification, similarity score is tested against a predefined threshold and either acceptance or rejection result is obtained. In the case of speaker identification, the result depends on whether the identification is open set or closed set. In closed set identification, the model that yields the best similarity score is accepted. In open set identification, the best score is tested against a threshold, so there is one more possible output satisfying the condition that the speaker is not one of the registered speakers in existing database. This paper focuses on closed set speaker identification using a modified version of a well known matching algorithm. The results of new matching algorithm indicated better performance on YOHO international speaker recognition database.

Keywords: Automatic Speaker Recognition, Voice Recognition, Pattern Recognition, Digital Audio Signal Processing.

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Authors: Heejung Lee

Abstract:

To offer a large variety of products while maintaining low costs, high speed, and high quality in a mass customization product development environment, platform based product development has much benefit and usefulness in many industry fields. This paper proposes a product configuration strategy by similarity measure, incorporating the knowledge engineering principles such as product information model, ontology engineering, and formal concept analysis.

Keywords: Platform, product family, ontology, formal concept analysis.

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Authors: N. Bachok, N. L. Aleng, N. M. Arifin, A. Ishak, N. Senu

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The problem of laminar fluid flow which results from the shrinking of a permeable surface in a nanofluid has been investigated numerically. The model used for the nanofluid incorporates the effects of Brownian motion and thermophoresis. A similarity solution is presented which depends on the mass suction parameter S, Prandtl number Pr, Lewis number Le, Brownian motion number Nb and thermophoresis number Nt. It was found that the reduced Nusselt number is decreasing function of each dimensionless number.

Keywords: Boundary layer, Nanofluid, Shrinking sheet, Brownian motion, Thermophoresis, Similarity solution.

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Authors: Mohamed Ali

Abstract:

The boundary layer flow and heat transfer on a stretched surface moving with prescribed skin friction is studied for permeable surface. The surface temperature is assumed to vary inversely with the vertical direction x for n = -1. The skin friction at the surface scales as (x-1/2) at m = 0. The constants m and n are the indices of the power law velocity and temperature exponent respectively. Similarity solutions are obtained for the boundary layer equations subject to power law temperature and velocity variation. The effect of various governing parameters, such as the buoyancy parameter λ and the suction/injection parameter fw for air (Pr = 0.72) are studied. The choice of n and m ensures that the used similarity solutions are x independent. The results show that, assisting flow (λ > 0) enhancing the heat transfer coefficient along the surface for any constant value of fw. Furthermore, injection increases the heat transfer coefficient but suction reduces it at constant λ.

Keywords: Stretching surface, Boundary layers, Prescribed skin friction, Suction or injection, similarity solutions, buoyancy effects.

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Authors: Okay Gunes

Abstract:

In this article, a new method is proposed for the measuring of well-being inequality through a model composed of superimposing satisfaction waves. The displacement of households’ satisfactory state (i.e. satisfaction) is defined in a satisfaction string. The duration of the satisfactory state for a given period is measured in order to determine the relationship between utility and total satisfactory time, itself dependent on the density and tension of each satisfaction string. Thus, individual cardinal total satisfaction values are computed by way of a one-dimensional form for scalar sinusoidal (harmonic) moving wave function, using satisfaction waves with varying amplitudes and frequencies which allow us to measure wellbeing inequality. One advantage to using satisfaction waves is the ability to show that individual utility and consumption amounts would probably not commute; hence, it is impossible to measure or to know simultaneously the values of these observables from the dataset. Thus, we crystallize the problem by using a Heisenberg-type uncertainty resolution for self-adjoint economic operators. We propose to eliminate any estimation bias by correlating the standard deviations of selected economic operators; this is achieved by replacing the aforementioned observed uncertainties with households’ perceived uncertainties (i.e. corrected standard deviations) obtained through the logarithmic psychophysical law proposed by Weber and Fechner.

Keywords: Heisenberg Uncertainty Principle, superimposing satisfaction waves, Weber–Fechner law, well-being inequality.

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Authors: Min-Hsun Kuo, Yun-Shiow Chen

Abstract:

The running logs of a process hold valuable information about its executed activity behavior and generated activity logic structure. Theses informative logs can be extracted, analyzed and utilized to improve the efficiencies of the process's execution and conduction. One of the techniques used to accomplish the process improvement is called as process mining. To mine similar processes is such an improvement mission in process mining. Rather than directly mining similar processes using a single comparing coefficient or a complicate fitness function, this paper presents a simplified heuristic process mining algorithm with two similarity comparisons that are able to relatively conform the activity logic sequences (traces) of mining processes with those of a normalized (regularized) one. The relative process conformance is to find which of the mining processes match the required activity sequences and relationships, further for necessary and sufficient applications of the mined processes to process improvements. One similarity presented is defined by the relationships in terms of the number of similar activity sequences existing in different processes; another similarity expresses the degree of the similar (identical) activity sequences among the conforming processes. Since these two similarities are with respect to certain typical behavior (activity sequences) occurred in an entire process, the common problems, such as the inappropriateness of an absolute comparison and the incapability of an intrinsic information elicitation, which are often appeared in other process conforming techniques, can be solved by the relative process comparison presented in this paper. To demonstrate the potentiality of the proposed algorithm, a numerical example is illustrated.

Keywords: process mining, process similarity, artificial intelligence, process conformance.

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Authors: Jehad Al Dallal

Abstract:

Class cohesion is an important object-oriented software quality attributes, and it refers to the degree of relatedness of class attributes and methods. Several class cohesion measures are proposed in the literature, and the impact of considering the special methods (i.e., constructors, destructors, and access and delegation methods) in cohesion calculation is not thoroughly theoretically studied for most of them. In this paper, we address this issue for three popular similarity-based class cohesion measures. For each of the considered measures we theoretically study the impact of including or excluding special methods on the values that are obtained by applying the measure. This study is based on analyzing the definitions and formulas that are proposed for the measures. The results show that including/excluding special methods has a considerable effect on the obtained cohesion values and that this effect varies from one measure to another. The study shows the importance of considering the types of methods that have to be accounted for when proposing a similarity-based cohesion measure.

Keywords: Object-oriented class, software quality, class cohesion measure, class cohesion, special methods.

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Authors: E. Al Daoud

Abstract:

The purpose of computing the similarity and the diversity in the species is to trace the process of evolution and to find the relationship between the species and discover the unique, the special, the common and the universal proteins. The proteins of the whole genome of 40 species are compared with the cronobacter genome which is used as reference genome. More than 3 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 172 proteins in cronobacter genome which have insignificant hits in other species, 116 significant proteins in the all tested species with very high score value and 129 common proteins in the plants but have insignificant hits in mammals, birds, fishes, and insects.

Keywords: Genome, species, blastp, conserved genes, cronobacter.

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Authors: M. M. Kassem, A. S. Rashed

Abstract:

The time dependent progress of a chemical reaction over a flat horizontal plate is here considered. The problem is solved through the group similarity transformation method which reduces the number of independent by one and leads to a set of nonlinear ordinary differential equation. The problem shows a singularity at the chemical reaction order n=1 and is analytically solved through the perturbation method. The behavior of the process is then numerically investigated for n≠1 and different Schmidt numbers. Graphical results for the velocity and concentration of chemicals based on the analytical and numerical solutions are presented and discussed.

Keywords: Time dependent, chemical convection, grouptransformation method, perturbation method.

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Authors: P. Ashok, G. M. Kadhar Nawaz

Abstract:

Rough set theory is used to handle uncertainty and incomplete information by applying two accurate sets, Lower approximation and Upper approximation. In this paper, the rough clustering algorithms are improved by adopting the Similarity, Dissimilarity–Similarity and Entropy based initial centroids selection method on three different clustering algorithms namely Entropy based Rough K-Means (ERKM), Similarity based Rough K-Means (SRKM) and Dissimilarity-Similarity based Rough K-Means (DSRKM) were developed and executed by yeast dataset. The rough clustering algorithms are validated by cluster validity indexes namely Rand and Adjusted Rand indexes. An experimental result shows that the ERKM clustering algorithm perform effectively and delivers better results than other clustering methods. Outlier detection is an important task in data mining and very much different from the rest of the objects in the clusters. Entropy based Rough Outlier Factor (EROF) method is seemly to detect outlier effectively for yeast dataset. In rough K-Means method, by tuning the epsilon (ᶓ) value from 0.8 to 1.08 can detect outliers on boundary region and the RKM algorithm delivers better results, when choosing the value of epsilon (ᶓ) in the specified range. An experimental result shows that the EROF method on clustering algorithm performed very well and suitable for detecting outlier effectively for all datasets. Further, experimental readings show that the ERKM clustering method outperformed the other methods.

Keywords: Clustering, Entropy, Outlier, Rough K-Means, validity index.

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Authors: Lenka Krulikovská, Jaroslav Polec

Abstract:

In this paper we present a method of abrupt cut detection with a novel logic of frames- comparison. Actual frame is compared with its motion estimated prediction instead of comparison with successive frame. Four different similarity metrics were employed to estimate the resemblance of compared frames. Obtained results were evaluated by standard used measures of test accuracy and compared with existing approach. Based on the results, we claim the proposed method is more effective and Pearson correlation coefficient obtained the best results among chosen similarity metrics.

Keywords: Abrupt cut, mutual information, shot cut detection, Pearson correlation coefficient.

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Authors: M. F. Miah, K. M. A. Zinnah, M. J. Raihan, H. Ali, M. N. Naser

Abstract:

As genetic diversity is most important for existing, breeding and production of any fish; this study was undertaken for investigating genetic diversity of freshwater mud eel, Monopterus cuchia at population level where three ecological populations such as flooded area of Sylhet (P1), open water of Moulvibazar (P2) and open water of Sunamganj (P3) districts of Bangladesh were considered. Four arbitrary RAPD primers (OPB-12, C0-4, B-03 and OPB-08) were screened and RAPD banding patterns were analyzed among the populations considering 15 individuals of each population. In total 174, 138 and 149 bands were detected in the populations of P1, P2 and P3 respectively; however, each primer revealed less number of bands in each population. 100% polymorphic loci were recorded in P2 and P3 whereas only one monomorphic locus was observed in P1, recorded 97.5% polymorphism. Different genetic parameters such as inter-individual pairwise similarity, genetic distance, Nei genetic similarity, linkage distances, cluster analysis and allelic information, etc. were considered for measuring genetic diversity. The average inter-individual pairwise similarity was recorded 2.98, 1.47 and 1.35 in P1, P2 and P3 respectively. Considering genetic distance analysis, the highest distance 1 was recorded in P2 and P3 and the lowest genetic distance 0.444 was found in P2. The average Nei genetic similarity was observed 0.19, 0.16 and 0.13 in P1, P2 and P3, respectively; however, the average linkage distance was recorded 24.92, 17.14 and 15.28 in P1, P3 and P2 respectively. Based on linkage distance, genetic clusters were generated in three populations where 6 clades and 7 clusters were found in P1, 3 clades and 5 clusters were observed in P2 and 4 clades and 7 clusters were detected in P3. In addition, allelic information was observed where the frequency of p and q alleles were observed 0.093 and 0.907 in P1, 0.076 and 0.924 in P2, 0.074 and 0.926 in P3 respectively. The average gene diversity was observed highest in P2 (0.132) followed by P3 (0.131) and P1 (0.121) respectively.

Keywords: Genetic diversity, Monopterus cuchia, population, RAPD, Bangladesh.

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Authors: Yogesh Gupta, Ashish Saini, A.K. Saxena

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Information retrieval has become an important field of study and research under computer science due to explosive growth of information available in the form of full text, hypertext, administrative text, directory, numeric or bibliographic text. The research work is going on various aspects of information retrieval systems so as to improve its efficiency and reliability. This paper presents a comprehensive study, which discusses not only emergence and evolution of information retrieval but also includes different information retrieval models and some important aspects such as document representation, similarity measure and query expansion.

Keywords: Information Retrieval, query expansion, similarity measure, query expansion, vector space model.

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Authors: Jia-Rong Yeh, Tzu-Yu Lin, Jiann-Shing Shieh, Yun Chen

Abstract:

A mammal-s body can be seen as a blood vessel with complex tunnels. When heart pumps blood periodically, blood runs through blood vessels and rebounds from walls of blood vessels. Blood pressure signals can be measured with complex but periodic patterns. When an artery is clamped during a surgical operation, the spectrum of blood pressure signals will be different from that of normal situation. In this investigation, intestinal artery clamping operations were conducted to a pig for simulating the situation of intestinal blocking during a surgical operation. Similarity theory is a convenient and easy tool to prove that patterns of blood pressure signals of intestinal artery blocking and unblocking are surely different. And, the algorithm of Hilbert Huang Transform can be applied to extract the character parameters of blood pressure pattern. In conclusion, the patterns of blood pressure signals of two different situations, intestinal artery blocking and unblocking, can be distinguished by these character parameters defined in this paper.

Keywords: Blood pressure, spectrum, intestinal artery, similarity theory and Hilbert Huang Transform.

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Authors: M. Das Gupta, S. Banerjee

Abstract:

Content Based Image Retrieval (CBIR) coupled with Case Based Reasoning (CBR) is a paradigm that is becoming increasingly popular in the diagnosis and therapy planning of medical ailments utilizing the digital content of medical images. This paper presents a survey of some of the promising approaches used in the detection of abnormalities in retina images as well in mammographic screening and detection of regions of interest in MRI scans of the brain. We also describe our proposed algorithm to detect hard exudates in fundus images of the retina of Diabetic Retinopathy patients.

Keywords: Case based reasoning, Exudates, Retina image, Similarity based retrieval.

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