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New and Improved Algorithms for Unordered Tree Inclusion

Authors Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura

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ACM Subject Classification
  • Theory of computation → Graph algorithms analysis
Keywords
  • parameterized algorithms
  • tree inclusion
  • unordered trees
  • dynamic programming

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Abstract

The tree inclusion problem is, given two node-labeled trees P and T (the "pattern tree" and the "text tree"), to locate every minimal subtree in T (if any) that can be obtained by applying a sequence of node insertion operations to P. Although the ordered tree inclusion problem is solvable in polynomial time, the unordered tree inclusion problem is NP-hard. The currently fastest algorithm for the latter is from 1995 and runs in O(poly(m,n) * 2^{2d}) = O^*(2^{2d}) time, where m and n are the sizes of the pattern and text trees, respectively, and d is the maximum outdegree of the pattern tree. Here, we develop a new algorithm that improves the exponent 2d to d by considering a particular type of ancestor-descendant relationships and applying dynamic programming, thus reducing the time complexity to O^*(2^d). We then study restricted variants of the unordered tree inclusion problem where the number of occurrences of different node labels and/or the input trees' heights are bounded. We show that although the problem remains NP-hard in many such cases, it can be solved in polynomial time for c = 2 and in O^*(1.8^d) time for c = 3 if the leaves of P are distinctly labeled and each label occurs at most c times in T. We also present a randomized O^*(1.883^d)-time algorithm for the case that the heights of P and T are one and two, respectively.

Cite As Get BibTex

Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, and Takeyuki Tamura. New and Improved Algorithms for Unordered Tree Inclusion. In 29th International Symposium on Algorithms and Computation (ISAAC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 123, pp. 27:1-27:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018) https://doi.org/10.4230/LIPIcs.ISAAC.2018.27

Author Details

Tatsuya Akutsu
  • Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
Jesper Jansson
  • Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
Ruiming Li
  • Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
Atsuhiro Takasu
  • National Institute of Informatics, Chiyoda-ku, Tokyo, 101-8430, Japan
Takeyuki Tamura
  • Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan

Funding

  • Akutsu, Tatsuya: JSPS KAKENHI #18H04113
  • Tamura, Takeyuki: JSPS KAKENHI #25730005

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