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Engineering Zuffix Arrays

Authors Paolo Boldi , Stefano Marchini, Sebastiano Vigna

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Author Details

Paolo Boldi
  • Università degli Studi di Milano, Italy
Stefano Marchini
  • Università degli Studi di Milano, Italy
Sebastiano Vigna
  • Università degli Studi di Milano, Italy

Funding

This work was supported in part by project SERICS (PE00000014) under the NRRP MUR program funded by the EU - NGEU. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the Italian MUR. Neither the European Union nor the Italian MUR can be held responsible for them.

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Paolo Boldi, Stefano Marchini, and Sebastiano Vigna. Engineering Zuffix Arrays. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
https://doi.org/10.4230/LIPIcs.SEA.2024.2

Abstract

Searching patterns in long strings is a classical algorithmic problem with countless practical applications. Suffix trees and suffix arrays (and their variants) are a long-established solution that yields linear-time search (in the size of the pattern). In [Paolo Boldi and Sebastiano Vigna, 2018] it is shown that a z-map gadget can be attached to (enhanced) suffix arrays to improve their theoretical query time, obtaining a data structure called zuffix array. The main contribution of this paper is to show that a carefully engineered implementation of the z-map gadget does provide significant speedups with respect to enhanced suffix arrays on real-world datasets, albeit doubling the required space. In particular, for large alphabets we observe a sevenfold improvement in query time with respect to enhanced suffix arrays; even in the worst case (small alphabets), the query time is almost halved. Thus, zuffix arrays provide a very interesting new point in the space-time tradeoff spectrum.

Subject Classification

ACM Subject Classification
  • Theory of computation → Data structures design and analysis
Keywords
  • Suffix trees
  • suffix arrays
  • z-fast tries

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