On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$ in $O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n)$ time for $p \le m$. For approximate pattern matching with $k$ differences or mismatches, we show how to compute all occurrences of a given pattern in $O(\frac{m^k\sigma^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ})$ time, where $\sigma$ is the size of the alphabet and $p \le \sigma^k m^k$. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns $P$ and $P'$, we present a data structure for computing the interval of $PP'$ in $O(\lg\lg n)$ sequential time, or in $O(1+\lg_p\lg n)$ parallel time. All our data structures are of size $O(n)$ bits (in addition to the suffix array)

Computationally efficient algorithms for the two-dimensional Kolmogorov-Smirnov test

Goodness-of-fit statistics measure the compatibility of random samples against some theoretical or reference probability distribution function. The classical one-dimensional Kolmogorov-Smirnov test is a non-parametric statistic for comparing two empirical distributions which defines the largest absolute difference between the two cumulative distribution functions as a measure of disagreement. Adapting this test to more than one dimension is a challenge because there are 2^d-1 independent ways of ordering a cumulative distribution function in d dimensions. We discuss Peacock's version of the Kolmogorov-Smirnov test for two-dimensional data sets which computes the differences between cumulative distribution functions in 4n^2 quadrants. We also examine Fasano and Franceschini's variation of Peacock's test, Cooke's algorithm for Peacock's test, and ROOT's version of the two-dimensional Kolmogorov-Smirnov test. We establish a lower-bound limit on the work for computing Peacock's test of Omega(n^2.lg(n)), introducing optimal algorithms for both this and Fasano and Franceschini's test, and show that Cooke's algorithm is not a faithful implementation of Peacock's test. We also discuss and evaluate parallel algorithms for Peacock's test

Parallel Construction of Wavelet Trees on Multicore Architectures

The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their construction time. In this paper, we introduce two algorithms that reduce the time complexity of a wavelet tree's construction by taking advantage of nowadays ubiquitous multicore machines. Our first algorithm constructs all the levels of the wavelet in parallel in $O(n)$ time and $O(n\lg\sigma + \sigma\lg n)$ bits of working space, where $n$ is the size of the input sequence and $\sigma$ is the size of the alphabet. Our second algorithm constructs the wavelet tree in a domain-decomposition fashion, using our first algorithm in each segment, reaching $O(\lg n)$ time and $O(n\lg\sigma + p\sigma\lg n/\lg\sigma)$ bits of extra space, where $p$ is the number of available cores. Both algorithms are practical and report good speedup for large real datasets.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094

A GPU-accelerated Branch-and-Bound Algorithm for the Flow-Shop Scheduling Problem

Branch-and-Bound (B&B) algorithms are time intensive tree-based exploration methods for solving to optimality combinatorial optimization problems. In this paper, we investigate the use of GPU computing as a major complementary way to speed up those methods. The focus is put on the bounding mechanism of B&B algorithms, which is the most time consuming part of their exploration process. We propose a parallel B&B algorithm based on a GPU-accelerated bounding model. The proposed approach concentrate on optimizing data access management to further improve the performance of the bounding mechanism which uses large and intermediate data sets that do not completely fit in GPU memory. Extensive experiments of the contribution have been carried out on well known FSP benchmarks using an Nvidia Tesla C2050 GPU card. We compared the obtained performances to a single and a multithreaded CPU-based execution. Accelerations up to x100 are achieved for large problem instances