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Genetic Programming with Primitive Recursion
Genetic Programming with Primitive Recursion

Chapter 2 SEQUENCE ALIGNMENT
Chapter 2 SEQUENCE ALIGNMENT

WAVELET-BASED DENOISING USING HIDDEN MARKOV MODELS ECE Department, MS-366 Rice University
WAVELET-BASED DENOISING USING HIDDEN MARKOV MODELS ECE Department, MS-366 Rice University

... previous section, it can be easily shown that the (state-)conditional probability density functions for the noisy wavelet coefficient at node are given as follows:  ?I   N  ...
Literature Review ()
Literature Review ()

... recognition, databases, data mining, artificial intelligence and bioinformatics [10]. The range query problem itself is to find all points p within a given radius r of another point q. Other variants of this problem include nearest neighbour query, k-nearest neighbour query, spatial join, and approx ...
An Improved Ant Colony Optimisation Algorithm for the 2D HP
An Improved Ant Colony Optimisation Algorithm for the 2D HP

User-Driven Narrative Variation in Large Story Domains using
User-Driven Narrative Variation in Large Story Domains using

An Efficient Algorithm for Discovering Motifs in Large DNA
An Efficient Algorithm for Discovering Motifs in Large DNA

Likelihood inference for generalized Pareto distribution
Likelihood inference for generalized Pareto distribution

... Davison, A. C.; Smith, R. L. (1990). Models for exceedances over high thresholds. With discussion and a reply by the authors. JRSS-B Embrechts, P. Klüppelberg, C. and Mikosch, T. (1997). Modelling Extremal Events for Insurance and Finance. Springer-Verlag, Berlin. McNeil, A. J., Frey, R. and Embrec ...
Taxonomic evaluation of the Streptomyces griseus clade using
Taxonomic evaluation of the Streptomyces griseus clade using

... informative, also showing a relatively high degree of conservation (Zeigler, 2003). In comparison with the fulllength 16S rRNA gene sequence, each individual proteincoding locus contained more variation, to different degrees. The proportion of variable sites in the alleles varied from 24.0 % (atpD) ...
Locality Preserving Hashing Kang Zhao, Hongtao Lu and Jincheng Mei
Locality Preserving Hashing Kang Zhao, Hongtao Lu and Jincheng Mei

... where bk is a bias, f (·) is an arbitrary function and sgn(·) is the sign function. Then the corresponding {0, 1} code can be given by 12 (1 + yik ). Broadly, hashing methods can be roughly divided into two main categories (Gong and Lazebnik 2011; Liu et al. 2011): data-independent methods and data- ...
Rapid Diversification of RNase A Superfamily Ribonucleases from
Rapid Diversification of RNase A Superfamily Ribonucleases from

... gene sequences, but it is interesting that the rate of radical nonsynonymous substitution is high, given that the isoelectric points of the various Rana ribonucleases do not differ markedly from one another. As there are no mammalian genes that are clearly orthologous to the Rana ribonucleases, we h ...
Predictive Subspace Clustering - ETH
Predictive Subspace Clustering - ETH

... is dependent on recovering the true clusters and vice-versa; (b) subspaces can intersect at several locations which causes difficulties when attempting to assign points to subspaces at these intersections, and standard clustering techniques such as K-means may not be suitable; (c) the subspace param ...
Constant-Time LCA Retrieval
Constant-Time LCA Retrieval

... First, we reduce the LCA problem to the Restricted Range Minima {RRM} (simple case of Range Minimum Query {RMQ}) problem. Problem of finding the smallest number in an interval of a fixed list of numbers, where the difference between two successive numbers in the list is exactly one. We’ll solve the ...
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MULTICAST RECIPIENT MAXIMIZATION PROBLEM IN 802 16



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Lecture Notes for Algorithm Analysis and Design

... Although there are a few thousand variations of the computer with different architectures and internal organization, it is best to think about them at the level of the assembly language. Despite architectural variations, the assembly level language support is very similar - the major difference bein ...
Incremental Mining of Frequent Query Patterns
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... There have been many studies on efficient discovery of frequent patterns for XML queries. Traditional frequent pattern mining approaches typically follow a straightforward candidate generate-and-test strategy, which includes two phases of frequent pattern generation and containment testing. The rece ...
isBF: Scalable In-Packet Bloom Filter Based Multicast
isBF: Scalable In-Packet Bloom Filter Based Multicast

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A Nonlinear Programming Algorithm for Solving Semidefinite

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Induction and Recursion 093 ICS 253: Discrete

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Analysis of expressed sequence tags from the Huperzia serrata leaf

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Binary Integer Programming in associative data models

High diversity of the `Spumella-like` flagellates: an investigation
High diversity of the `Spumella-like` flagellates: an investigation

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Computational phylogenetics

Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species.Producing a phylogenetic tree requires a measure of homology among the characteristics shared by the taxa being compared. In morphological studies, this requires explicit decisions about which physical characteristics to measure and how to use them to encode distinct states corresponding to the input taxa. In molecular studies, a primary problem is in producing a multiple sequence alignment (MSA) between the genes or amino acid sequences of interest. Progressive sequence alignment methods produce a phylogenetic tree by necessity because they incorporate new sequences into the calculated alignment in order of genetic distance.
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