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On the Complexity of the (𝓁, k)-Median Problems

Authors: Luís Cunha, Thiago Nascimento, Marilia D. V. Braga, and Jens Stoye

Published in: LIPIcs, Volume 390, 26th International Conference on Algorithms for Bioinformatics (WABI 2026)


Abstract
The genome median problem is a central computational problem in comparative genomics, as it models the reconstruction of an ancestral genome from a set of related genomes. Given 𝓁 genomes and a distance measure, the problem asks for a genome that minimizes the sum of the distances to the input genomes. Two classical distances are the breakpoint distance and the double-cut-and-join (DCJ) distance. For multichromosomal circular genomes, the median problem is polynomial-time solvable under the breakpoint distance, whereas it is NP-hard under the DCJ distance. For even integer k ≥ 2, the σ_k distance interpolates between these two extremes: σ₂ corresponds to the breakpoint distance, while σ_∞ corresponds to the DCJ distance. A central open problem in this setting is the (3,4)-Median problem, which asks for a median of three genomes under the σ₄ distance, the first intermediate distance after the breakpoint distance. Motivated by this question, we study the more general (𝓁,k)-Median problem, in which 𝓁 is the number of input genomes and k determines the σ_k distance. We prove that (𝓁,6)-Median for every 𝓁 ≥ 4 and (3,12)-Median are NP-complete. We then extend the hardness of (𝓁,6)-Median to (𝓁,k)-Median for all even k ≥ 6, and the hardness of (3,12)-Median to (3,k)-Median for all even k ≥ 12. These results identify broad hardness regions in the (𝓁,k) parameter space and delimit the remaining open cases around the fundamental (3,4)-Median problem.

Cite as

Luís Cunha, Thiago Nascimento, Marilia D. V. Braga, and Jens Stoye. On the Complexity of the (𝓁, k)-Median Problems. In 26th International Conference on Algorithms for Bioinformatics (WABI 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 390, pp. 19:1-19:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{cunha_et_al:LIPIcs.WABI.2026.19,
  author =	{Cunha, Lu{\'\i}s and Nascimento, Thiago and Braga, Marilia D. V. and Stoye, Jens},
  title =	{{On the Complexity of the (𝓁, k)-Median Problems}},
  booktitle =	{26th International Conference on Algorithms for Bioinformatics (WABI 2026)},
  pages =	{19:1--19:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-446-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{390},
  editor =	{El-Mabrouk, Nadia and Vandin, Fabio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2026.19},
  URN =		{urn:nbn:de:0030-drops-275231},
  doi =		{10.4230/LIPIcs.WABI.2026.19},
  annote =	{Keywords: Genome rearrangement, median problem, sigma-k distance}
}

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