Extracting conflict-free information from multi-labeled trees

Akshay Deepak, David Fernández-Baca, Michelle M Mcmahon

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain conflict-free information that is of interest and yet is not obvious. We define the information content of a MUL-tree T as the set of all conflict-free quartet topologies implied by T, and define the maximal reduced form of T as the smallest tree that can be obtained from T by pruning leaves and contracting edges while retaining the same information content. We show that any two MUL-trees with the same information content exhibit the same reduced form. This introduces an equivalence relation among MUL-trees with potential applications to comparing MUL-trees. We present an efficient algorithm to reduce a MUL-tree to its maximally reduced form and evaluate its performance on empirical datasets in terms of both quality of the reduced tree and the degree of data reduction achieved.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages81-92
Number of pages12
Volume7534 LNBI
DOIs
StatePublished - 2012
Event12th International Workshop on Algorithms in Bioinformatics, WABI 2012 - Ljubljana, Slovenia
Duration: Sep 10 2012Sep 12 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7534 LNBI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other12th International Workshop on Algorithms in Bioinformatics, WABI 2012
CountrySlovenia
CityLjubljana
Period9/10/129/12/12

Fingerprint

Labeled Trees
Labels
Data reduction
Topology
Information Content
Leaves
Conflict
Data Reduction
Phylogenetic Tree
Phylogenetics
Equivalence relation
Pruning
Efficient Algorithms
Imply
Evaluate

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Deepak, A., Fernández-Baca, D., & Mcmahon, M. M. (2012). Extracting conflict-free information from multi-labeled trees. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 7534 LNBI, pp. 81-92). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7534 LNBI). https://doi.org/10.1007/978-3-642-33122-0_7

Extracting conflict-free information from multi-labeled trees. / Deepak, Akshay; Fernández-Baca, David; Mcmahon, Michelle M.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7534 LNBI 2012. p. 81-92 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7534 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Deepak, A, Fernández-Baca, D & Mcmahon, MM 2012, Extracting conflict-free information from multi-labeled trees. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 7534 LNBI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7534 LNBI, pp. 81-92, 12th International Workshop on Algorithms in Bioinformatics, WABI 2012, Ljubljana, Slovenia, 9/10/12. https://doi.org/10.1007/978-3-642-33122-0_7
Deepak A, Fernández-Baca D, Mcmahon MM. Extracting conflict-free information from multi-labeled trees. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7534 LNBI. 2012. p. 81-92. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-33122-0_7
Deepak, Akshay ; Fernández-Baca, David ; Mcmahon, Michelle M. / Extracting conflict-free information from multi-labeled trees. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7534 LNBI 2012. pp. 81-92 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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