Search results for: Similarity based retrieval.

Authors: Hager Kammoun, Jean Charles Lamirel, Mohamed Ben Ahmed

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In this paper, a model for an information retrieval system is proposed which takes into account that knowledge about documents and information need of users are dynamic. Two methods are combined, one qualitative or symbolic and the other quantitative or numeric, which are deemed suitable for many clustering contexts, data analysis, concept exploring and knowledge discovery. These two methods may be classified as inductive learning techniques. In this model, they are introduced to build “long term" knowledge about past queries and concepts in a collection of documents. The “long term" knowledge can guide and assist the user to formulate an initial query and can be exploited in the process of retrieving relevant information. The different kinds of knowledge are organized in different points of view. This may be considered an enrichment of the exploration level which is coherent with the concept of document/query structure.

Keywords: Information Retrieval Systems, machine learning, classification, Galois lattices, Self Organizing Map.

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

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

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

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

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

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

Keywords: Barley, crossbreed, genetic similarity, ISSR.

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Authors: 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

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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: Hsing-Kuo Pao, John Case

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

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

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Authors: C. Lodato, S. Lopes

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This paper describes a segmentation algorithm based on the cooperation of an optical flow estimation method with edge detection and region growing procedures. The proposed method has been developed as a pre-processing stage to be used in methodologies and tools for video/image indexing and retrieval by content. The addressed problem consists in extracting whole objects from background for producing images of single complete objects from videos or photos. The extracted images are used for calculating the object visual features necessary for both indexing and retrieval processes. The first task of the algorithm exploits the cues from motion analysis for moving area detection. Objects and background are then refined using respectively edge detection and region growing procedures. These tasks are iteratively performed until objects and background are completely resolved. The developed method has been applied to a variety of indoor and outdoor scenes where objects of different type and shape are represented on variously textured background.

Keywords: Motion Detection, Object Extraction, Optical Flow, Segmentation.

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Authors: Sanaa Chafik, ImaneDaoudi, Mounim A. El Yacoubi, Hamid El Ouardi

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Locality Sensitive Hashing (LSH) is one of the most promising techniques for solving nearest neighbour search problem in high dimensional space. Euclidean LSH is the most popular variation of LSH that has been successfully applied in many multimedia applications. However, the Euclidean LSH presents limitations that affect structure and query performances. The main limitation of the Euclidean LSH is the large memory consumption. In order to achieve a good accuracy, a large number of hash tables is required. In this paper, we propose a new hashing algorithm to overcome the storage space problem and improve query time, while keeping a good accuracy as similar to that achieved by the original Euclidean LSH. The Experimental results on a real large-scale dataset show that the proposed approach achieves good performances and consumes less memory than the Euclidean LSH.

Keywords: Approximate Nearest Neighbor Search, Content based image retrieval (CBIR), Curse of dimensionality, Locality sensitive hashing, Multidimensional indexing, Scalability.

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Authors: P. Shunmugapriya, S. Kanmani, P. Jude Fredieric, U. Vignesh, J. Reman Justin, K. Vivek

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Vehicle Routing Problem (VRP) is a complex combinatorial optimization problem and it is quite difficult to find an optimal solution consisting of a set of routes for vehicles whose total cost is minimum. Evolutionary and swarm intelligent (SI) algorithms play a vital role in solving optimization problems. While the SI algorithms perform search, the diversity between the solutions they exploit is very important. This is because of the need to avoid early convergence and to get an appropriate balance between the exploration and exploitation. Therefore, it is important to check how far the solutions are diverse. In this paper, we measure the similarity between solutions, which ABC exploits while optimizing VRP. The similar solutions found are discarded at the end of the iteration and only unique solutions are passed on to the next iteration. The bees of discarded solutions become scouts and they start searching for new solutions. This process is continued and results show that the solution is optimized at lesser number of iterations but with the overhead of computing similarity in all the iterations. The problem instance from Solomon benchmarked dataset has been used for evaluating the presented methodology.

Keywords: ABC algorithm, vehicle routing problem, optimization, Jaccard’s similarity measure.

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Authors: Lenka Krulikovská, Jaroslav Polec

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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: B. J. Sandesh, Saurabha Jirgi, S. Vidya, Prakash Eljer, Gowri Srinivasa

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In this paper, we propose a framework to help users to search and retrieve the portions in the lecture video of their interest. This is achieved by temporally segmenting and indexing the lecture video using the topic keywords. We use transcribed text from the video and documents relevant to the video topic extracted from the web for this purpose. The keywords for indexing are found by applying the non-negative matrix factorization (NMF) topic modeling techniques on the web documents. Our proposed technique first creates indices on the transcribed documents using the topic keywords, and these are mapped to the video to find the start and end time of the portions of the video for a particular topic. This time information is stored in the index table along with the topic keyword which is used to retrieve the specific portions of the video for the query provided by the users.

Keywords: Video indexing and retrieval, lecture videos, content based video search, multimodal indexing.

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Authors: Ahmet Güven, Ö. Özgür Bozkurt, Oya Kalıpsız

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Number of documents being created increases at an increasing pace while most of them being in already known topics and little of them introducing new concepts. This fact has started a new era in information retrieval discipline where the requirements have their own specialties. That is digging into topics and concepts and finding out subtopics or relations between topics. Up to now IR researches were interested in retrieving documents about a general topic or clustering documents under generic subjects. However these conventional approaches can-t go deep into content of documents which makes it difficult for people to reach to right documents they were searching. So we need new ways of mining document sets where the critic point is to know much about the contents of the documents. As a solution we are proposing to enhance LSI, one of the proven IR techniques by supporting its vector space with n-gram forms of words. Positive results we have obtained are shown in two different application area of IR domain; querying a document database, clustering documents in the document database.

Keywords: Document clustering, Information Extraction, Information Retrieval, LSI, n-gram.

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Authors: Shamim Ahmed Koichi Nishigaki

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

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

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Authors: Jincheol Han, Hyunsun Ju, Jonghoon Chun

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Sharing consistent and correct master data among disparate applications in a reverse-logistics chain has long been recognized as an intricate problem. Although a master data management (MDM) system can surely assume that responsibility, applications that need to co-operate with it must comply with proprietary query interfaces provided by the specific MDM system. In this paper, we present a RFID-ready MDM system which makes master data readily available for any participating applications in a reverse-logistics chain. We propose a RFID-wrapper as a part of our MDM. It acts as a gateway between any data retrieval request and query interfaces that process it. With the RFID-wrapper, any participating applications in a reverse-logistics chain can easily retrieve master data in a way that is analogous to retrieval of any other RFID-based logistics transactional data.

Keywords: Reverse Logistics, Master Data Management, RFID.

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Authors: Rajeev, N. K. Raigar

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

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

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Authors: Ashutosh Kumar Singh, Ravi Kumar P

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This paper gives an introduction to Web mining, then describes Web Structure mining in detail, and explores the data structure used by the Web. This paper also explores different Page Rank algorithms and compare those algorithms used for Information Retrieval. In Web Mining, the basics of Web mining and the Web mining categories are explained. Different Page Rank based algorithms like PageRank (PR), WPR (Weighted PageRank), HITS (Hyperlink-Induced Topic Search), DistanceRank and DirichletRank algorithms are discussed and compared. PageRanks are calculated for PageRank and Weighted PageRank algorithms for a given hyperlink structure. Simulation Program is developed for PageRank algorithm because PageRank is the only ranking algorithm implemented in the search engine (Google). The outputs are shown in a table and chart format.

Keywords: Web Mining, Web Structure, Web Graph, LinkAnalysis, PageRank, Weighted PageRank, HITS, DistanceRank, DirichletRank,

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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: Konstantinos C. Kartsakalis, Angeliki Skoura, Vasileios Megalooikonomou

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The fuzzy composition of objects depicted in images acquired through MR imaging or the use of bio-scanners has often been a point of controversy for field experts attempting to effectively delineate between the visualized objects. Modern approaches in medical image segmentation tend to consider fuzziness as a characteristic and inherent feature of the depicted object, instead of an undesirable trait. In this paper, a novel technique for efficient image retrieval in the context of images in which segmented objects are either crisp or fuzzily bounded is presented. Moreover, the proposed method is applied in the case of multiple, even conflicting, segmentations from field experts. Experimental results demonstrate the efficiency of the suggested method in retrieving similar objects from the aforementioned categories while taking into account the fuzzy nature of the depicted data.

Keywords: Fuzzy Object, Fuzzy Image Segmentation, Motion Descriptors, MRI Imaging, Object-Based Image Retrieval.

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Authors: Yifan Fan, Xudong Luo, Pingping Lin

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An essential task in the field of artificial intelligence is to allow computers to interact with people through natural language. Therefore, researches such as virtual assistants and dialogue systems have received widespread attention from industry and academia. The response generation plays a crucial role in dialogue systems, so to push forward the research on this topic, this paper surveys various methods for response generation. We sort out these methods into three categories. First one includes finite state machine methods, framework methods, and instance methods. The second contains full-text indexing methods, ontology methods, vast knowledge base method, and some other methods. The third covers retrieval methods and generative methods. We also discuss some hybrid methods based knowledge and deep learning. We compare their disadvantages and advantages and point out in which ways these studies can be improved further. Our discussion covers some studies published in leading conferences such as IJCAI and AAAI in recent years.

Keywords: Retrieval, generative, deep learning, response generation, knowledge.

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Authors: G. Poonkuzhali, K.Thiagarajan, K.Sarukesi, G.V.Uma

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The emergence of the Internet has brewed the revolution of information storage and retrieval. As most of the data in the web is unstructured, and contains a mix of text, video, audio etc, there is a need to mine information to cater to the specific needs of the users without loss of important hidden information. Thus developing user friendly and automated tools for providing relevant information quickly becomes a major challenge in web mining research. Most of the existing web mining algorithms have concentrated on finding frequent patterns while neglecting the less frequent ones that are likely to contain outlying data such as noise, irrelevant and redundant data. This paper mainly focuses on Signed approach and full word matching on the organized domain dictionary for mining web content outliers. This Signed approach gives the relevant web documents as well as outlying web documents. As the dictionary is organized based on the number of characters in a word, searching and retrieval of documents takes less time and less space.

Keywords: Outliers, Relevant document, , Signed Approach, Web content mining, Web documents..

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Authors: Radhwan Yousif Sedik Al-Jawadi

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Optimization is necessary for finding appropriate solutions to a range of real-life problems. In particular, genetic (or more generally, evolutionary) algorithms have proved very useful in solving many problems for which analytical solutions are not available. In this paper, we present an optimization algorithm called Dynamic Schema with Dissimilarity and Similarity of Chromosomes (DSDSC) which is a variant of the classical genetic algorithm. This approach constructs new chromosomes from a schema and pairs of existing ones by exploring their dissimilarities and similarities. To show the effectiveness of the algorithm, it is tested and compared with the classical GA, on 15 two-dimensional optimization problems taken from literature. We have found that, in most cases, our method is better than the classical genetic algorithm.

Keywords: Genetic algorithm, similarity and dissimilarity, chromosome injection, dynamic schema.

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Authors: K. Oh, J. P. Hwang, E. Kim, H. Lee

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This paper presents an algorithm which extends the rapidly-exploring random tree (RRT) framework to deal with change of the task environments. This algorithm called the Retrieval RRT Strategy (RRS) combines a support vector machine (SVM) and RRT and plans the robot motion in the presence of the change of the surrounding environment. This algorithm consists of two levels. At the first level, the SVM is built and selects a proper path from the bank of RRTs for a given environment. At the second level, a real path is planned by the RRT planners for the given environment. The suggested method is applied to the control of KUKA™,, a commercial 6 DOF robot manipulator, and its feasibility and efficiency are demonstrated via the cosimulatation of MatLab™, and RecurDyn™,.

Keywords: Path planning, RRT, 6 DOF manipulator, SVM.

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Authors: R. Saraçoğlu, N. Allahverdi

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

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

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Authors: Mohammed Salahat, Steve Wade

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This paper presents an application of a “Systematic Soft Domain Driven Design Framework” as a soft systems approach to domain-driven design of information systems development. The framework use SSM as a guiding methodology within which we have embedded a sequence of design tasks based on the UML leading to the implementation of a software system using the Naked Objects framework. This framework have been used in action research projects that have involved the investigation and modelling of business processes using object-oriented domain models and the implementation of software systems based on those domain models. Within this framework, Soft Systems Methodology (SSM) is used as a guiding methodology to explore the problem situation and to develop the domain model using UML for the given business domain. The framework is proposed and evaluated in our previous works, and a real case study “Information Retrieval System for academic research” is used, in this paper, to show further practice and evaluation of the framework in different business domain. We argue that there are advantages from combining and using techniques from different methodologies in this way for business domain modelling. The framework is overviewed and justified as multimethodology using Mingers multimethodology ideas.

Keywords: SSM, UML, domain-driven design, soft domaindriven design, naked objects, soft language, information retrieval, multimethodology.

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Authors: Lin Yang, Zhian Mi, Jiacheng Xiao, Rong Li

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Swimming with the tide of deep learning, the field of music information retrieval (MIR) experiences parallel development and a sheer variety of feature-learning models has been applied to music classification and tagging tasks. Among those learning techniques, the deep convolutional neural networks (CNNs) have been widespreadly used with better performance than the traditional approach especially in music genre classification and prediction. However, regarding the music recommendation, there is a large semantic gap between the corresponding audio genres and the various aspects of a song that influence user preference. In our study, aiming to bridge the gap, we strive to construct an automatic music aesthetic annotation model with MIDI format for better comparison and measurement of the similarity between music pieces in the way of harmonic analysis. We use the matrix of qualification converted from MIDI files as input to train two different classifiers, support vector machine (SVM) and Decision Tree (DT). Experimental results in performance of a tag prediction task have shown that both learning algorithms are capable of extracting high-level properties in an end-to end manner from music information. The proposed model is helpful to learn the audience taste and then the resulting recommendations are likely to appeal to a niche consumer.

Keywords: Harmonic analysis, machine learning, music classification and tagging, MIDI.

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Authors: Alan C. Lin, Ricky N. Joevan

Abstract:

This paper focuses on developing a system to transfer mold base plates and standard parts faster during the stage of injection mold design. This system not only provides a way to compare the file version, but also it utilizes Siemens NX 10 to isolate the updated information into a single executable file (.dll), and then, the file can be transferred without the need of transferring the whole file. By this way, the system can help the user to download only necessary mold base plates and standard parts, and those parts downloaded are only the updated portions.

Keywords: CAD, injection molding, mold base, data retrieval.

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Authors: Ágnes Vathy-Fogarassy, Balázs Feil, János Abonyi

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Most of fuzzy clustering algorithms have some discrepancies, e.g. they are not able to detect clusters with convex shapes, the number of the clusters should be a priori known, they suffer from numerical problems, like sensitiveness to the initialization, etc. This paper studies the synergistic combination of the hierarchical and graph theoretic minimal spanning tree based clustering algorithm with the partitional Gath-Geva fuzzy clustering algorithm. The aim of this hybridization is to increase the robustness and consistency of the clustering results and to decrease the number of the heuristically defined parameters of these algorithms to decrease the influence of the user on the clustering results. For the analysis of the resulted fuzzy clusters a new fuzzy similarity measure based tool has been presented. The calculated similarities of the clusters can be used for the hierarchical clustering of the resulted fuzzy clusters, which information is useful for cluster merging and for the visualization of the clustering results. As the examples used for the illustration of the operation of the new algorithm will show, the proposed algorithm can detect clusters from data with arbitrary shape and does not suffer from the numerical problems of the classical Gath-Geva fuzzy clustering algorithm.

Keywords: Clustering, fuzzy clustering, minimal spanning tree, cluster validity, fuzzy similarity.

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Authors: Permphan Dharmasaroja

Abstract:

Acute disseminated encephalomyelitis (ADEM) has been reported to develop after a hymenoptera sting, but its pathogenesis is not known in detail. Myelin basic protein (MBP)- specific T cells have been detected in the blood of patients with ADEM, and a proportion of these patients develop multiple sclerosis (MS). In an attempt to understand the mechanisms underlying ADEM, molecular mimicry between hymenoptera venom peptides and the human immunodominant MBP peptide was scrutinized, based on the sequence and structural similarities, whether it was the root of the disease. The results suggest that the three wasp venom peptides have low sequence homology with the human immunodominant MBP residues 85-99. Structural similarity analysis among the three venom peptides and the MS-related HLA-DR2b (DRA, DRB1*1501)-associated immunodominant MHC binding/TCR contact residues 88-93, VVHFFK showed that hyaluronidase residues 7-12, phospholipase A1 residues 98-103, and antigen 5 residues 109-114 showed a high degree of similarity 83.3%, 100%, and 83.3% respectively. In conclusion, some wasp venom peptides, particularly phospholipase A1, may potentially act as the molecular motifs of the human 3HLA-DR2b-associated immunodominant MBP88-93, and possibly present a mechanism for induction of wasp sting-associated ADEM.

Keywords: central nervous system, Hymenoptera, myelin basicprotein, molecular mimicry.

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

Abstract:

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

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

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