arXiv subjects

Matevž Jekovec

Publications and source records attributed to Matevž Jekovec.

3 recordsLinked to original sources

arXiv2018

Sliding Suffix Tree using LCA

We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We present an indexed version of the sliding window using the suffix tree, the link tree and the lowest common ancestor. The data structure of size $Θ(|W|)$ has optimal time queries $Θ(m+occ)$ and amortized constant time updates, where $m$ is the length of the query string and $occ$ is the number of its occurrences.

cs.DS↗

arXiv2016

ERA Revisited: Theoretical and Experimental Evaluation

Efficient construction of the suffix tree given an input text is an active area of research from the time it was first introduced. Both theoretical computer scientists and engineers tackled the problem. In this paper we focus on the fastest practical suffix tree construction algorithm to date, ERA. We first provide a theoretical analysis of the algorithm assuming the uniformly random text as an input and using the PEM model of computation with respect to the lower bounds. Secondly, we empirically confirm the theoretical results in different test scenarios exposing the critical terms. Thirdly, we discuss the fundamental characteristics of the input text where the fastest suffix tree construction algorithms in practice fail. This paper serves as a foundation for further research in the parallel text indexing area.

cs.DC↗

arXiv2015

Parallel Query in the Suffix Tree

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. The parallel query in the suffix trie requires $O(m + p)$ work, $O(m/p + \lg p)$ time and $O(n^2)$ space in the worst case. We extend the same technique to the suffix tree where we show it is, by design, inherently sequential in the worst case. Finally we perform the parallel query using an interleaved approach and achieve $O(m \lg p)$ work, $O(\frac{m}{p} \lg p)$ time and $O(n \lg p)$ space in the worst case.

cs.DS↗