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 structu...
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;datastructures 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.
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...
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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 datastructures. the presented experiments show that it is possible to gain a significant speedup and that general metric datastructures are better suited than a data structure tailored for Euclidean space on vectors generated from molecular data.
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...
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;datastructures 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.
It is demonstrated that power-efficient software also requires simplicity and the use of elementary datastructures in addition to asymptotically optimal CPU and memory requirements. though in the past few decades muc...
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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 ...
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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 algorithmsthat overcome that bottleneck by keeping the frequent itemsets in compact datastructures, 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-Growthalgorithms. Two case studies analyzing the algorithms are carried out phase by phase using two synthetic datasets generated in order i) to see their performance withdatasets 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.
Safe is a first-order eager language with facilities for programmer controlled destruction and copying of datastructures. It provides also regions, i.e. disjoint parts of the heap, where the program allocates data st...
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ISBN:
(纸本)9783642119989
Safe is a first-order eager language with facilities for programmer controlled destruction and copying of datastructures. It provides also regions, i.e. disjoint parts of the heap, where the program allocates datastructures. 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.
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 s...
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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 n...
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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 ro...
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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.
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 crystalliz...
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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) 2010international Centre for Diffraction data. [DOI: 10.1154/1.3478418]
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