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DOI: 10.4230/LIPIcs.CPM.2024.9

Tight Bounds for Compressing Substring Samples

Authors: Philip Bille, Christian Mikkelsen Fuglsang, and Inge Li Gørtz

Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)

Abstract

We consider the problem of compressing a set of substrings sampled from a string and analyzing the size of the compression. Given a string S of length n, and integers d and m where n ≥ m ≥ 2d > 0, let SCS(S, m, d) be the string obtained by sequentially concatenating substrings of length m sampled regularly at intervals of d starting at position 1 in S. We consider the size of the LZ77 parsing of SCS(S, m, d), in relation to the size of the LZ77 parsing of S. This is motivated by genome sequencing, where the mentioned sampling process is an idealization of the short-read DNA sequencing. We show the following upper bound: |LZ77(SCS(S, m, d))| ≤ |LZ77(S)| + 2(n-m)/d. We also give a lower bound showing that this is tight. This improves previous results by Badkobeh et al. [ICTCS 2022], and closes the open problem of whether their bound can be improved. Another natural question is whether assuming that all letters in S are part of a sample, it is always the case that |LZ77(S)| ≤ |LZ77(SCS(S, m, d))|. Surprisingly, we show that there is a family of strings such that |LZ77(SCS(S, m, d))| = |LZ77(S)| - 1.

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Philip Bille, Christian Mikkelsen Fuglsang, and Inge Li Gørtz. Tight Bounds for Compressing Substring Samples. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 9:1-9:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bille_et_al:LIPIcs.CPM.2024.9,
  author =	{Bille, Philip and Fuglsang, Christian Mikkelsen and G{\o}rtz, Inge Li},
  title =	{{Tight Bounds for Compressing Substring Samples}},
  booktitle =	{35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)},
  pages =	{9:1--9:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-326-3},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{296},
  editor =	{Inenaga, Shunsuke and Puglisi, Simon J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.9},
  URN =		{urn:nbn:de:0030-drops-201192},
  doi =		{10.4230/LIPIcs.CPM.2024.9},
  annote =	{Keywords: Compression, Algorithms, Lempel-Ziv}
}

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Tight Bounds for Compressing Substring Samples

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