Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees

  • Authors:

  • Tatsuya Akutsu;Daiji Fukagawa;Magnús M. Halldórsson;Atsuhiro Takasu;Keisuke Tanaka

  • Affiliations:

  • Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan;Faculty of Culture and Information Science, Doshisha University, Kyoto 610-0394, Japan;ICE-TCS, School of Computer Science, Reykjavik University, 101 Reykjavik, Iceland;National Institute of Informatics, Tokyo 101-8430, Japan;Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Tokyo, Japan

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2013

Quantified Score

Hi-index 5.23

Visualization

Abstract

Given two rooted, labeled, unordered trees, the common subtree problem is to find a bijective matching between subsets of nodes of the trees of maximum cardinality which preserves labels and ancestry relationship. The tree edit distance problem is to determine the least cost sequence of insertions, deletions and substitutions that converts a tree into another given tree. Both problems are known to be hard to approximate within some constant factor in general. We tackle these problems from two perspectives: giving exact algorithms, either for special cases or in terms of some parameters; and approximation algorithms and hardness of approximation. We present a parameterized algorithm in terms of the number of branching nodes that solves both problems and yields polynomial algorithms for several special classes of trees. This is complemented with a tighter APX-hardness proof that holds when the trees are of height one and two, respectively. Furthermore, we present the first approximation algorithms for both problems. In particular, for the common subtree problem for t trees, we present an algorithm achieving a tlog"2(b"O"P"T+1) ratio, where b"O"P"T is the number of branching nodes in the optimal solution. We also present constant factor approximation algorithms for both problems in the case of bounded height trees.