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—We design, implement, and evaluate algorithms for computing a matching of maximum cardinality in a bipartite graph on multicore and massively multithreaded computers. As computers with larger numbers of slower cores dominate the commodity processor market, the design of multithreaded algorithms to solve large matching problems becomes a necessity. Recent(More)
—In computing matchings in graphs on parallel processors , it is challenging to achieve high performance because these algorithms rely on searching for paths in the graph, and when these paths become long, there is little concurrency. We present a new algorithm and its shared-memory paral-lelization for computing maximum cardinality matchings in bipartite(More)
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the additivity of the fit of distances to tree when using flexi Weighted Least Squares. A variety of DNA and protein(More)
Sparse matrix-matrix multiplication (or SpGEMM) is a key primitive for many high-performance graph algorithms as well as for some linear solvers, such as algebraic multigrid. The scaling of existing parallel implementations of SpGEMM is heavily bound by communication. Even though 3D (or 2.5D) algorithms have been proposed and theoretically analyzed in the(More)
—Triangle counting and enumeration are important kernels that are used to characterize graphs. They are also used to compute important statistics such as clustering coefficients. We provide a simple exact algorithm that is based on operations on sparse adjacency matrices. By parallelizing the individual sparse matrix operations, we achieve a parallel(More)
When flow cytometric data on mixtures of cell populations are collected from samples under different experimental conditions, computational methods are needed (a) to classify the samples into similar groups, and (b) to characterize the changes within the corresponding populations due to the different conditions. Manual inspection has been used in the past(More)
Multi-channel, high throughput experimental methodologies for flow cytometry are transforming clinical immunology and hematol-ogy, and require the development of algorithms to analyze the high-dimensional, large-scale data. We describe the development of two combinatorial algorithms to identify rare cell populations in data from mice with acute(More)
In this article the results of Waddell and Azad (2009) are extended. In particular, the geometric percentage mean standard deviation measure of the fit of distances to a phylogenetic tree are adjusted for the number of parameters fitted on the tree. The formulae are also presented in their general form for any weight that is a function of the distance. The(More)