Using semi-definite programming to enhance supertree resolvability

Shlomo Moran, Satish Rao, Sagi Snir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Supertree methods are used to construct a large tree over a large set of taxa, from a set of small trees over overlapping subsets of the complete taxa set. Since accurate reconstruction methods are currently limited to a maximum of few dozens of taxa, the use of a supertree method in order to construct the tree of life is inevitable. Supertree methods are broadly divided according to the input trees: When the input trees are unrooted, the basic reconstruction unit is a quartet tree. In this case, the basic decision problem of whether there exists a tree that agrees with all quartets is NP-complete. On the other hand, when the input trees are rooted, the basic reconstruction unit is a rooted triplet, and the above decision problem has a polynomial time algorithm. However, when there is no tree which agrees with all triplets, it would be desirable to find the tree that agrees with the maximum number of triplets. However, this optimization problem was shown to be NP-hard. Current heuristic approaches perform mincut on a graph representing the triplets inconsistency and return a tree that is guaranteed to satisfy some required properties. In this work we present a different heuristic approach that guarantees the properties provided by the current methods and give experimental evidence that it significantly outperforms currently used methods. This method is based on divide and conquer where we use a semi-definite programming approach in the divide step.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages89-103
Number of pages15
DOIs
StatePublished - 2005
Externally publishedYes
Event5th International Workshop on Algorithms in Bioinformatics, WABI 2005 - Mallorca, Spain
Duration: 3 Oct 20056 Oct 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3692 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference5th International Workshop on Algorithms in Bioinformatics, WABI 2005
Country/TerritorySpain
CityMallorca
Period3/10/056/10/05

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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