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algorithms in Bioinformatics - 10th international workshop, WABI 2010, Proceedings

10th international workshop on algorithms in Bioinformatics, WABI 2010

ISBN: (纸本)3642152937

the proceedings contain 30 papers. the topics discussed include: a worst-case and practical speedup for the RNA co-folding problem using the four-Russians idea;sparse estimation for structural variability;data structures for accelerating Tanimoto queries on real valued vectors;sparsification of RNA structure prediction including pseudoknots;reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss;listing all sorting reversals in quadratic time;discovering kinship through small subsets;fixed-parameter algorithm for haplotype inferences on general pedigrees with small number of sites;haplotypes versus genotypes on pedigrees;haplotype inference on pedigrees with recombinations and mutations;identifying rare cell populations in comparative flow cytometry;design of an efficient out-of-core read alignment algorithm;and enumerating chemical organizations in consistent metabolic networks: complexity and algorithms.

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data structures for Accelerating Tanimoto Queries on Real Valued Vectors

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10th workshop on algorithms in Bioinformatics

作者： Kristensen, thomas G. Pedersen, Christian N. S. Aarhus Univ Bioinformat Res Ctr DK-8000 Aarhus C Denmark

ISBN: (纸本)9783642152931

Previous methods for accelerating Tanimoto queries have been based on using bit strings for representing molecules. No work has gone into examining accelerating Tanimoto queries on real valued descriptors, even though these offer a much more fine grained measure of similarity between molecules. this study utilises a recently discovered reduction from Tanimoto queries to distance queries in Euclidean space to accelerate Tanimoto queries using standard metric data structures. the presented experiments show that it is possible to gain a significant speedup and that general metric data structures are better suited than a data structure tailored for Euclidean space on vectors generated from molecular data.

关键词： data structures

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10th international workshop on algorithms in Bioinformatics, WABI 2010

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10th international workshop on algorithms in Bioinformatics, WABI 2010

ISBN: (纸本)9783642152931

the proceedings contain 30 papers. the special focus in this conference is on algorithms in Bioinformatics. the topics include: Fixed-parameter algorithm for haplotype inferences on general pedigrees with small number of sites;haplotypes versus genotypes on pedigrees;haplotype inference on pedigrees with recombinations and mutations;identifying rare cell populations in comparative flow cytometry;Fast mapping and precise alignment of AB SOLiD color reads to reference DNA;design of an efficient out-of-core read alignment algorithm;Estimation of alternative splicing isoform frequencies from RNA-seq data;improved orientations of physical networks;enumerating chemical organisations in consistent metabolic networks: Complexity and algorithms;sparse estimation for structural variability;efficient subgraph frequency estimation with G-Tries;accuracy guarantees for phylogeny reconstruction algorithms based on balanced minimum evolution;the complexity of inferring a minimally resolved phylogenetic supertree;reducing multi-state to binary perfect phylogeny with applications to missing, removable, inserted, and deleted data;an experimental study of quartets MaxCut and other supertree methods;An efficient method for DNA-based species assignment via gene tree and species tree reconciliation;effective algorithms for fusion gene detection;swiftly computing center strings;speeding up exact motif discovery by bounding the expected clump size;Pair HMM based gap statistics for re-evaluation of indels in alignments with affine gap penalties;data structures for accelerating tanimoto queries on real valued vectors;quantifying the strength of natural selection of a motif sequence;Sparsification of RNA structure prediction including pseudoknots;Prediction of RNA secondary structure including kissing hairpin motifs;Genomic distance with DCJ and indels.

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A rectangle-intersection algorithm with limited resource requirements

A rectangle-intersection algorithm with limited resource req...

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10th IEEE international Conference on Computer and Information Technology, CIT-2010, 7th IEEE international Conference on Embedded Software and Systems, ICESS-2010, 10th IEEE Int. Conf. Scalable Computing and Communications, ScalCom-2010

作者： Dévai, Frank Neumann, László Department of Informatics London South Bank University London United Kingdom ICREA Computer Vision and Robotics Group University of Girona Spain

ISBN: (纸本)9780769541082

It is demonstrated that power-efficient software also requires simplicity and the use of elementary data structures in addition to asymptotically optimal CPU and memory requirements. though in the past few decades much effort has been devoted to reporting all k intersecting pairs in a planar set of n iso-oriented rectangles, all the known algorithms using elementary data structures, such as linked lists, are either not optimal, report some intersections repeatedly or fail to report some altogether. A simpler algorithm is proposed that uses only linear arrays and that takes O(n log n + k) time and O(n) space, which are the best possible under the algebraic RAM model of computation. the algorithm is designed for systems with limited resources, such as mobile 3D graphics, and can be implemented in less than 100 lines of Java code. © 2010 Crown Copyright.

关键词： data structures

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Comparison of two association rule mining algorithms without candidate generation

Comparison of two association rule mining algorithms without...

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10th IASTED international Conference on Artificial Intelligence and Applications, AIA 2010

作者： Yildiz, Bariş Ergenç, Belgin Department of Computer Engineering Izmir Institute of Technology Gulbahce Koyu 35430 Urla Izmir Turkey

ISBN: (纸本)9780889868182

Association rule mining techniques play an important role in data mining research where the aim is to find interesting correlations among sets of items in databases. Although the Apriori algorithm of association rule mining is the one that boosted data mining research, it has a bottleneck in its candidate generation phase that requires multiple passes over the source data. FP-Growth and Matrix Apriori are two algorithms that overcome that bottleneck by keeping the frequent itemsets in compact data structures, eliminating the need of candidate generation. To our knowledge, there is no work to compare those two similar algorithms focusing on their performances in different phases of execution. In this study, we compare Matrix Apriori and FP-Growth algorithms. Two case studies analyzing the algorithms are carried out phase by phase using two synthetic datasets generated in order i) to see their performance with datasets having different characteristics, ii) to understand the causes of performance differences in different phases. Our findings are i) performances of algorithms are related to the characteristics of the given dataset and threshold value, ii) Matrix Apriori outperforms FP-Growth in total performance for threshold values below 10%, iii) although building matrix data structure has higher cost, finding itemsets is faster.

关键词： data mining

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A Simple Region Inference Algorithm for a First-Order Functional Language

A Simple Region Inference Algorithm for a First-Order Functi...

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18th international workshop on Functional and Constraint Logic Programming

作者： Montenegro, Manuel Pena, Ricardo Segura, Clara Univ Complutense Madrid Dept Sistemas Informat & Computac E-28040 Madrid Spain

ISBN: (纸本)9783642119989

Safe is a first-order eager language with facilities for programmer controlled destruction and copying of data structures. It provides also regions, i.e. disjoint parts of the heap, where the program allocates data structures. the runtime system does not need a garbage collector and all allocation/deallocation actions are done in constant time. the language is aimed at inferring and certifying upper bounds for memory consumption in a Proof Carrying Code environment. Some of its analyses have been presented elsewhere [7,8]. In this paper we present an inference algorithm for annotating programs with regions which is both simpler to understand and more efficient than other related algorithms. Programmers are assumed to write programs and to declare datatypes without any reference to regions. the algorithm decides the regions needed by every function. It also allows polymorphic recursion with respect to regions. We show convincing examples of programs before and after region annotation, prove the correctness and optimality of the algorithm, and give its asymptotic cost.

关键词： data structures

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An interactive, multi-modal approach to analysing high-resolution image mass spectrometry data

An interactive, multi-modal approach to analysing high-resol...

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15th international workshop on Vision, Modeling and Visualization, VMV 2010

作者： Smit, F.A. Van Liere, R. Fornai, L. Heeren, R. CWI Amsterdam Netherlands AMOLF Amsterdam Netherlands

ISBN: (纸本)9783905673791

the output resolution of imaging mass spectrometers is increasing rapidly due to advances in engineering and the use of tiling. Imaging-MS data is often displayed as a total-ion-count (TIC) image;however, anatomical structures are not easily identifiable from TIC images. For this purpose, additional high-resolution images that originate from different imaging modalities, such as stained histological data, are preferred. these modalities are most useful when fused;i.e., when the corresponding images are spatially aligned with respect to each other. the viewing and analysis of such data is ideally performed in real-time and at the highest possible resolution, allowing users to interactively query the combination of all fused data at the highest detail. However, proper alignment between modalities and interactively presenting large volumes of data is as of yet a challenge. We present a system for the simultaneous viewing and analysis of high-resolution data from different imaging modalities. Fusion is provided in such a way that interaction in one modality can be mapped to different modalities. For example, anatomical structures can be identified from histological data and their spatial extent mapped to a corresponding region-of-interest in the image MS data, allowing the analysis of its chemical compounds. In turn, the MS data can be analysed and filtered, for example using multi-variate analysis such as PCA, and the result mapped back to structures in other modalities. Level-of-detail, region-of-interest and asynchronous data processing algorithms ensure that the system can be operated interactively at the highest resolution. © the Eurographics Association 2010.

关键词： Chemical analysis

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Non-myopic innovations dual controller

Non-myopic innovations dual controller

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10th IFAC international workshop on Adaptation and Learning in Control and Signal Processing, ALCOSP 2010

作者： Flídr, Miroslav Šimandl, Miroslav Research Centre Data - Algorithms - Decision Making University of West Bohemia Univerzitní 8 30614 Plzeň Czech Republic Department of Cybernetics Faculty of Applied Sciences University of West Bohemia Univerzitní 8 30614 Plzeň Czech Republic

ISBN: (纸本)9783902661852

Optimal control of a linear discrete stochastic state space system with uncertain parameters is treated. the problem statement leads to design of a dual controllers. Unfortunately, except for few special cases it is not possible to obtain closed-form solution for such controller. Many suboptimal approaches were proposed to overcome this obstacle, however, mostly they restrict the control horizon only to one step ahead and thus suffer from myopic behaviour. this paper presents technique that makes it possible to derive suboptimal dual controller in closed-form for arbitrarily long control horizon. the design of the presented controller is based on the innovations dual controller and use of the partial certainty equivalence principle. the proposed dual controller is compared to other non-dual controllers in a numerical example. © 2010 IFAC.

关键词： Controllers

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Optimization of CdxHg1−xTe laser structures and stimulated emission at room temperature under optical excitation

Optimization of CdxHg1−xTe laser structures and stimulated ...

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international Conference/workshop on Laser and Fiber-Optical Networks Modeling (LFNM)

作者： A. A. Andronov Yu. N. Nozdrin A. V. Okomel'kov N. N. Mikhailov G. Yu. Sidorov V. S. Varavin Institute for Physics of Microstructures Russian Academy of Sciences Nizhny Novgorod Russia Siberian Branch Institute of Semiconductor Physics Russian Academy of Science Novosibirsk Russia Institute of Semiconductor Physics Siberian Branch Russian Academy of Sciemces Novosibirsk Russia

the main requirements for the MCT (Cd x Hg 1-x Te) structures optimization for increase of the stimulated emission wavelength under optical pumping are discussed. the stimulated emission at wavelengths 2-2.5 μm at room temperature from optimized MCT structures is observed experimentally. the obtained experimental data are the first observation of stimulated emission from the MCT structures at these wavelengths at room temperature.

关键词： Stimulated emission Optical pumping Strips Annealing Optical fiber amplifiers Films Laser modes

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Crystal structure and diffraction data for a polymorph of voglibose (C₁₀H₂₁NO₇)

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POWDER DIFFRACTION 2010年第3期25卷 S28-S30页

作者： Zhang, G. Q. Lv, G. L. Zhejiang Sci Tech Univ Key Lab Adv Text Mat & Mfg Technol Hangzhou 310018 Zhejiang Peoples R China

X-ray powder diffraction data of voglibose are reported, and its crystal and molecular structures were determined by simulated annealing and rigid-body Rietveld refinement methods. Voglibose was found to be crystallized in triclinic symmetry with space group P-1. the lattice parameters were determined to be a=6.1974(6) angstrom, b=6.9918(5) angstrom, c=7.3955(9) angstrom, alpha=70.8628(3), beta=103.5312(4), gamma=94.3867(5), V=294.2(2) angstrom(3), and rho(cal)=1.495 g/cm(3). the crystal structure contains isolated C10H21NO7 molecular. (C) 2010 international Centre for Diffraction data. [DOI: 10.1154/1.3478418]

关键词： voglibose X-ray powder diffraction crystal structure

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