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On Computing Minimum Wheeler DFA from Their Language

Authors: Ruben Becker, Davide Cenzato, Nicola Prezza, and Daniel Puttini

Published in: LIPIcs, Volume 388, 34th Annual European Symposium on Algorithms (ESA 2026)


Abstract
Wheeler automata have recently emerged as a powerful generalization of the Burrows-Wheeler Transform, enabling optimal linear-time pattern matching on compressed labeled graphs - a task that is otherwise computationally hard. Consequently, when an automaton recognizes a Wheeler language (i.e., it is equivalent to some Wheeler automaton), computing its minimum equivalent Wheeler DFA is a powerful indexing strategy. This problem is particularly relevant in computational pangenomics, where pangenome graphs frequently recognize Wheeler languages. However, constructing the minimum Wheeler DFA for a Wheeler language has remained a computational bottleneck. The problem is known to be PSPACE-hard for nondeterministic inputs. When the input is a DFA, state-of-the-art solutions forced a compromise: they were either fast but limited to acyclic DFAs (Alanko et al., SODA 2020) or capable of handling general topologies but prohibitively slow (D'Agostino et al., TCS 2023). In this work, we bridge this gap with the first algorithm solving the problem for general DFAs in near-optimal, linearithmic output-sensitive time. By matching the efficiency of acyclic-only solutions while retaining full generality, our approach improves upon the previous general solution by at least a quadratic factor. We demonstrate the practical impact of our algorithm on real-world pangenome graphs; our tool achieves a processing throughput of over 10⁵ transitions per second on a standard workstation, enabling the construction of a provably optimal pattern matching data structure in such applications.

Cite as

Ruben Becker, Davide Cenzato, Nicola Prezza, and Daniel Puttini. On Computing Minimum Wheeler DFA from Their Language. In 34th Annual European Symposium on Algorithms (ESA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 388, pp. 132:1-132:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{becker_et_al:LIPIcs.ESA.2026.132,
  author =	{Becker, Ruben and Cenzato, Davide and Prezza, Nicola and Puttini, Daniel},
  title =	{{On Computing Minimum Wheeler DFA from Their Language}},
  booktitle =	{34th Annual European Symposium on Algorithms (ESA 2026)},
  pages =	{132:1--132:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-445-1},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{388},
  editor =	{Bille, Philip and Pettie, Seth and Storandt, Sabine},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2026.132},
  URN =		{urn:nbn:de:0030-drops-272685},
  doi =		{10.4230/LIPIcs.ESA.2026.132},
  annote =	{Keywords: Wheeler Automata, Minimum DFA, Pangenomics, Pattern Matching}
}
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