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A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Authors: Sangsoo Park, Sung Gwan Park, Bastien Cazaux, Kunsoo Park, and Eric Rivals

Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)


Abstract
The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of lengths of the strings in P. In this paper we present a new algorithm to construct HOG in O(||P||) time and space. Hence, the construction time and space of HOG are better than those of the overlap graph, which are O(||P|| + n²).

Cite as

Sangsoo Park, Sung Gwan Park, Bastien Cazaux, Kunsoo Park, and Eric Rivals. A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 22:1-22:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{park_et_al:LIPIcs.CPM.2021.22,
  author =	{Park, Sangsoo and Park, Sung Gwan and Cazaux, Bastien and Park, Kunsoo and Rivals, Eric},
  title =	{{A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{22:1--22:9},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-186-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{191},
  editor =	{Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.22},
  URN =		{urn:nbn:de:0030-drops-139736},
  doi =		{10.4230/LIPIcs.CPM.2021.22},
  annote =	{Keywords: overlap graph, hierarchical overlap graph, shortest superstring problem, border array}
}
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