Related papers: Designing a parallel suffix sort
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
We introduce and study a generalized Parikh matrix mapping based on tracking the occurrence counts of special types of subsequences. These matrices retain more information about a word than the original Parikh matrix mapping while…
Multiresolution Matrix Factorization (MMF) was recently introduced as a method for finding multiscale structure and defining wavelets on graphs/matrices. In this paper we derive pMMF, a parallel algorithm for computing the MMF…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
We find a succinct expression for computing the sequence $x_t = a_t x_{t-1} + b_t$ in parallel with two prefix sums, given $t = (1, 2, \dots, n)$, $a_t \in \mathbb{R}^n$, $b_t \in \mathbb{R}^n$, and initial value $x_0 \in \mathbb{R}$. On…
We give the first concise description of the fastest known suffix sorting algorithm in main memory, the DivSufSort by Yuta Mori. We then present an extension that also computes the LCP-array, which is competitive with the fastest known…
The aim of the paper is to introduce general techniques in order to optimize the parallel execution time of sorting on a distributed architectures with processors of various speeds. Such an application requires a partitioning step. For…
A wide variety of problems in machine learning, including exemplar clustering, document summarization, and sensor placement, can be cast as constrained submodular maximization problems. Unfortunately, the resulting submodular optimization…
A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not…
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
In this paper we develop optimal algorithms in the binary-forking model for a variety of fundamental problems, including sorting, semisorting, list ranking, tree contraction, range minima, and ordered set union, intersection and difference.…
The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show…
This work presents a comparison for the performance of sequential sorting algorithms under four different modes of execution, the sequential processing mode, a conventional multi-threading implementation, multi-threading with OpenMP Library…
A fundamental algorithm for selecting ranks from a finite subset of an ordered set is Radix Selection. This algorithm requires the data to be given as strings of symbols over an ordered alphabet, e.g., binary expansions of real numbers. Its…
Previous work identifying depth-optimal $n$-channel sorting networks for $9\leq n \leq 16$ is based on exploiting symmetries of the first two layers. However, the naive generate-and-test approach typically applied does not scale. This paper…
Parametric search has been widely used in geometric algorithms. Cole's improvement provides a way of saving a logarithmic factor in the running time over what is achievable using the standard method. Unfortunately, this improvement comes at…
Given the query string of length $m$, we explore a parallel query in a static suffix tree based data structure for $p \ll n$, where $p$ is the number of processors and $n$ is the length of the text. We present three results on CREW PRAM.…
Preferential attachment lies at the heart of many network models aiming to replicate features of real world networks. To simulate the attachment process, conduct statistical tests, or obtain input data for benchmarks, efficient algorithms…