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Using long fragments to reconstruct RNA backbones

Using long fragments to reconstruct RNA backbones

引用

7th IEEE international conference on Bioinformatics and Bioengineering, BIBE

作者： Utriainen, Tapani Kemp, Graham J. L. Department of Computer Science and Engineering Chalmers University of Technology SE-412 96 Göteborg Sweden

ISBN: (纸本)1424415098

this study addresses to what extent RNA backbones consist of long, recurring fragments. A dynamic programming algorithm is presented that finds the smallest set of fragments that are required to reconstruct the backbone of a known macromolecule within a given root mean square bound. this algorithm is guaranteed to find a global minimum. the program has been used for reconstructing the backbones of several known RNA structures, using fragments taken from ribosomal RNA. Each of these target structures could be approximated within a root mean square deviation of 1.0Å using fragments with an average length of more than eight nucleotides. ©2007 IEEE.

关键词： RNA

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Self-optimizing parallel algorithms for haplotype reconstruction and their evaluation on the JPT and CHB genotype data

Self-optimizing parallel algorithms for haplotype reconstruc...

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7th IEEE international conference on Bioinformatics and Bioengineering, BIBE

作者： Trinca, Dragos Rajasekaran, Sanguthevar Department of Computer Science and Engineering University of Connecticut Storrs CT 06269 United States

ISBN: (纸本)1424415098

the haplotype reconstruction problem has received a great deal of attention in the bioinformatics literature. the algorithms proposed thus far for this problem can be grouped into two main categories: statistical and combinatorial. In this paper, we focus on combinatorial algorithms for haplotype reconstruction based on Clark's method. Specifically, we propose several self-optimizing parallel algorithms for haplotype reconstruction based on Clark's method. Experimental results show that the proposed self-optimizing parallel algorithms can be viewed as an efficient alternative not only to Clark's algorithm, but also to some previously proposed (integer) linear programming formulations. ©2007 IEEE.

关键词： Parallel algorithms

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Visualization of message races in MPI parallel programs

Visualization of message races in MPI parallel programs

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CIT 2007: 7th IEEE international conference on Computer and Information Technology

作者： Park, Mi-Young Hai, Nguyen Cao Truong Jun, Yong-Kee Park, Hyuk-Ro School of Electronics and Computer Engineering Chonnam National University Korea Republic of Dept. of Information Science GyeongSang National University Korea Republic of

ISBN: (纸本)0769529836

As parallel programs become larger and more complex, it is harder to understand and debug parallel programs. If those programs have race conditions, intended or otherwise, it is more difficult to understand and debug. Visualization is widely accepted as a powerful technique to understand and manage the complexity of parallel programs as well as to detect race conditions. this paper presents a new visualization tool for debugging race conditions in message-passing programs. Our visualization aims to provide effective and useful visualization for programmers to understand complex phenomena such as the interaction of concurrent processes, to handle enormous visual information, and to debug message races in MPI parallel programs. © 2007 IEEE.

关键词： Parallel programming

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From mathematics to software engineering: Introducing category theory into the computer science curriculum

From mathematics to software engineering: Introducing catego...

引用

7th international conference on Computational science (ICCS 2007)

作者： Zheng, Yujun Shi, Haihe Xue, Jinyun Chinese Acad Sci Inst Software Beijing 100080 Peoples R China Jiangxi Normal Univ Coll Comp Inf & Engn Nanchang 330027 Peoples R China Grad Univ Chinese Acad Sci Beijing 100080 Peoples R China

ISBN: (纸本)9783540725879

Category theory, with its increasing role in computer science, has proved useful in the investigation of programming languages and other theoretical aspects of software engineering. As a bridge-building exercise, we introduce the category theory course into the computer science curriculum, the purpose of which includes building a unified framework to generalize the discrete structures of mathematical courses and providing an environment for formulating concepts of other software engineering courses. We develop a teaching schema, summarize our experiences, and give some suggestions for pedagogical techniques for the course.

关键词： Software engineering

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QOMA2: Optimizing the alignment of many sequences

QOMA2: Optimizing the alignment of many sequences

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7th IEEE international conference on Bioinformatics and Bioengineering, BIBE

作者： Zhang, Xu Kahveci, Tamer Computer and Information Science and Engineering University of Florida Gainesville FL 32611 United States

ISBN: (纸本)1424415098

We consider the problem of aligning multiple protein sequences with the goal of maximizing the SP (Sum-of-Pairs) score, when the number of sequences is large. the QOMA (Quasi-Optimal Multiple Alignment) algorithm addressed this problem when the number of sequences is small. However, as the number of sequences increases, QOMA becomes impractical. this paper develops a new algorithm, QOMA2, which optimizes the SP score of the alignment of arbitrarily large number of sequences. Given an initial (potentially sub-optimal) alignment, QOMA2 selects short subsequences from this alignment by placing a window on it. It quickly estimates the amount of improvement that can be obtained by optimizing the alignment of the subsequences in short windows on this alignment. this estimate is called the SW (Sum of Weights) score. It employs a dynamic programming algorithm that selects the set of window positions with the largest total expected improvement. It partitions the subsequences within each window into clusters such that the number of subsequences in each cluster is small enough to be optimally aligned within a given time. Also, it aims to select these clusters so that the optimal alignment of the subsequences in these clusters produces the highest expected SP score. the experimental results show that QOMA2 produces high SP scores quickly even for large number of sequences. they also show that the SW score and the resulting SP score are highly correlated. this implies that it is promising to aim for optimizing the SW score since it is much cheaper than aligning multiple sequences optimally. the software and the benchmark data set are available from the authors on request. ©2007 IEEE.

关键词： Dynamic programming

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A new hybrid technique for dermatological image registration

A new hybrid technique for dermatological image registration

引用

7th IEEE international conference on Bioinformatics and Bioengineering, BIBE

作者： Huang, Heng Bergstresser, Paul Computer Science and Engineering Univ. of Texas Arlington TX United States Department of Dermatology Univ. of Texas Southwestern Medical Center

ISBN: (纸本)1424415098

Malignant melanoma is nowadays one of the most malignant tumors among white-skinned populations around the world. the key element in malignant melanoma treatment is the detection of melanomas and their changes at an early stage, before they develop irreversible clinically significant and potentially fatal damage to the patients. Computer automatic diagnosis of skin lesions using early symptoms would be particularly useful as an aid in primary care. During such computer systems, there is a significant clinical demand for accurate dermatological image registration. In this paper, we introduce a new algorithm for the registration of melanomas in successive dermatological image. We reduce the melanoma registration problem to a bipartite graph matching problem. the Voronoi cells are used to measure the similarity between melanomas and build the weighted bipartite graph. A minimum weight maximum cardinality matching is employed to find the global correspondences between dermatological images. Distances order and dynamic programming method are applied into the bipartite graph matching to preserve topology of melanoma distribution. the dermatoscopy images are used to validate the effectiveness of our approach. Since our method is a general registration method for melanomas, it can also be used in other dermatological images. ©2007 IEEE.

关键词： Image registration

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Word sense disambiguation using inductive logic programming

Word sense disambiguation using inductive logic programming

引用

16th international conference of Inductive Logic programming, ILP 2006

作者： Specia, Lucia Srinivasan, Ashwin Ramakrishnan, Ganesh Das Graças Volpe Nunes, Maria ICMC University of São Paulo Trabalhador São-Carlense 400 São Carlos 13560-970 Brazil IBM India Research Laboratory Indian Institute of Technology Block 1 New Delhi 110016 India Dept. of Computer Science and Engineering Centre for Health Informatics University of New South Wales Sydney Australia

ISBN: (纸本)9783540738466

the identification of the correct sense of a word is necessary for many tasks in automatic natural language processing like machine translation, information retrieval, speech and text processing. Automatic Word Sense Disambiguation (WSD) is difficult and accuracies with state-of-the art methods are substantially lower than in other areas of text understanding like part-of-speech tagging. One shortcoming of these methods is that they do not utilize substantial sources of background knowledge, such as semantic taxonomies and dictionaries, which are now available in electronic form (the methods largely use shallow syntactic features). Empirical results from the use of Inductive Logic programming (ILP) have repeatedly shown the ability of ILP systems to use diverse sources of background knowledge. In this paper we investigate the use of ILP for WSD in two different ways: (a) as a stand-alone constructor of models for WSD;and (b) to build interesting features, which can then be used by standard model-builders such as SVM. In our experiments we examine a monolingual WSD task using the 32 English verbs contained in the SENSEVAL-3 benchmark data;and a bilingual WSD task using 7 highly ambiguous verbs in machine translation from English to Portuguese. Background knowledge available is from eight sources that provide a wide range of syntactic and semantic information. For both WSD tasks, experimental results show that ILP-constructed models and models built using ILP-generated features have higher accuracies than those obtained using a state-of-the art feature-based technique equipped with shallow syntactic features. this suggests that the use of ILP with diverse sources of background knowledge can provide one way for making substantial progress in the field of automatic WSD. © Springer-Verlag Berlin Heidelberg 2007.

关键词： Logic programming

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Evolutionary design of resilient substitution boxes: From coding to hardware implementation

引用

7th international conference on Evolvable Systems: From Biology to Hardware, ICES 2007

作者： Nedjah, Nadia De Macedo Mourelle, Luiza Department of Electronics Engineering and Telecommunications Engineering Faculty State University of Rio de Janeiro Brazil Department of System Engineering and Computation Engineering Faculty State University of Rio de Janeiro Brazil

ISBN: (纸本)9783540746256

S-boxes constitute a cornerstone component in symmetric-key cryptographic algorithms, such as DES and AES encryption systems. In block ciphers, they are typically used to obscure the relationship between the plaintext and the ciphertext. Non-linear and non-correlated S-boxes are the most secure against linear and differential cryptanalysis. In this paper, we focus on a two-fold objective: first, we evolve regular an S-box with high non-linearity and low auto-correlation properties using evolutionary computation;then automatically generate evolvable hardware for the obtained S-box. Targeting the former, we use the Nash equilibrium-based multi-objective evolutionary algorithm to optimise regularity, non-linearity and auto- correlation, which constitute the three main desired properties in resilient S-boxes. Pursuing the latter, we exploit genetic programming to automatically generate the evolvable hardware designs of substitution boxes that minimise hardware space, encryption/decryption time and dissipated power, which form the three main hardware characteristics. We compare our results against existing and well-known designs, which were produced by using conventional methods as well as through evolution. © Springer-Verlag Berlin Heidelberg 2007.

关键词： Computer hardware

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Extreme programming and Agile Processes in Software engineering - 7th international conference, XP 2006, Proceedings

引用

7th international conference on Extreme programming and Agile Processes in Software engineering, XP 2006

ISBN: (纸本)3540350942

the proceedings contain 30 papers. the topics discussed include: a distributed cognition account of mature XP teams;foundations of agile decision making from agile mentors and developers;software development as a collaborative writing project;comparative analysis of job satisfaction in agile and non-agile software development teams;the collaborative nature of pair programming;leveraging code smell detection with inter-smell relations;studying the evolution of quality metrics in an agile/distributed project;the effect of test-driven development on program code;configuring hybrid agile-tradition software processes;agility in the avionics software world;security planning and refactoring in extreme programming;augmenting the agile planning toolbox;and storytelling in interaction: agility in practice.

关键词： Software engineering

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Report of the 7th international Workshop on Aspect-Oriented Modeling

引用

international MoDELS 2005

作者： Kienzle, J Gray, J Stein, D McGill Univ Sch Comp Sci Montreal PQ Canada Univ Alabama Dept Comp & Informat Sci Birmingham AL 35294 USA Univ Duisburg Essen Inst Comp Sci & Business Informat Syst Essen Germany

ISBN: (纸本)3540317805

this report summarizes the outcome of the 7th Workshop on Aspect-Oriented Modeling (AOM) held in conjunction with the 8th international conference on Model Driven engineering Languages and Systems - MODELS 2005 - in Montego Bay, Jamaica, on the 2nd of October 2005. the workshop brought together researchers and practitioners from two communities: aspect-oriented software development (AOSD) and software model engineering. It provided a forum for discussing the state of the art in modeling crosscutting concerns at different stages of the software development process: requirements elicitation and analysis, software architecture, detailed design, and mapping to aspect-oriented programming constructs. this paper gives an overview of the accepted submissions, and summarizes the results of the different discussion groups.

关键词： Object oriented programming

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