Faster Prefix-Sorting Algorithms for Deterministic Finite Automata

Authors Sung-Hwan Kim , Francisco Olivares , Nicola Prezza

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Author Details

Sung-Hwan Kim
  • DAIS, Ca' Foscari University of Venice, Italy
Francisco Olivares
  • CeBiB - Centre for Biotechnology and Bioengineering, Santiago, Chile
  • Department of Computer Science, University of Chile, Santiago, Chile
Nicola Prezza
  • DAIS, Ca' Foscari University of Venice, Italy

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Sung-Hwan Kim, Francisco Olivares, and Nicola Prezza. Faster Prefix-Sorting Algorithms for Deterministic Finite Automata. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 16:1-16:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)


Sorting is a fundamental algorithmic pre-processing technique which often allows to represent data more compactly and, at the same time, speeds up search queries on it. In this paper, we focus on the well-studied problem of sorting and indexing string sets. Since the introduction of suffix trees in 1973, dozens of suffix sorting algorithms have been described in the literature. In 2017, these techniques were extended to sets of strings described by means of finite automata: the theory of Wheeler graphs [Gagie et al., TCS'17] introduced automata whose states can be totally-sorted according to the co-lexicographic (co-lex in the following) order of the prefixes of words accepted by the automaton. More recently, in [Cotumaccio, Prezza, SODA'21] it was shown how to extend these ideas to arbitrary automata by means of partial co-lex orders. This work showed that a co-lex order of minimum width (thus optimizing search query times) on deterministic finite automata (DFAs) can be computed in O(m² + n^{5/2}) time, m being the number of transitions and n the number of states of the input DFA. In this paper, we exhibit new combinatorial properties of the minimum-width co-lex order of DFAs and exploit them to design faster prefix sorting algorithms. In particular, we describe two algorithms sorting arbitrary DFAs in O(mn) and O(n² log n) time, respectively, and an algorithm sorting acyclic DFAs in O(m log n) time. Within these running times, all algorithms compute also a smallest chain partition of the partial order (required to index the DFA). We present an experiment result to show that an optimized implementation of the O(n² log n)-time algorithm exhibits a nearly-linear behaviour on large deterministic pan-genomic graphs and is thus also of practical interest.

Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
  • Theory of computation → Formal languages and automata theory
  • String Matching
  • Deterministic Finite Automata
  • Graph Indexing
  • Co-lexicographical Sorting


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