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Author Chor, Benny ♦ Tuller, Tamir
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2006
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Maximum likelihood ♦ Approximate vertex cover ♦ Intractability ♦ Maximum parsimony ♦ Tree reconstruction
Abstract Maximum likelihood (ML) is an increasingly popular optimality criterion for selecting evolutionary trees [Felsenstein 1981]. Finding optimal ML trees appears to be a very hard computational task, but for tractable cases, ML is the method of choice. In particular, algorithms and heuristics for ML take longer to run than algorithms and heuristics for the second major character based criterion, maximum parsimony (MP). However, while MP has been known to be NP-complete for over 20 years [Foulds and Graham, 1982; Day et al. 1986], such a hardness result for ML has so far eluded researchers in the field.An important work by Tuffley and Steel [1997] proves quantitative relations between the parsimony values of given sequences and the corresponding log likelihood values. However, a direct application of their work would only give an exponential time reduction from MP to ML. Another step in this direction has recently been made by Addario-Berry et al. [2004], who proved that ancestral maximum likelihood (AML) is NP-complete. AML “lies in between” the two problems, having some properties of MP and some properties of ML. Still, the AML proof is not directly applicable to the ML problem.We resolve the question, showing that “regular” ML on phylogenetic trees is indeed intractable. Our reduction follows the vertex cover reductions for MP [Day et al. 1986] and AML [Addario-Berry et al. 2004], but its starting point is an approximation version of vertex cover, known as gap vc. The crux of our work is not the reduction, but its correctness proof. The proof goes through a series of tree modifications, while controlling the likelihood losses at each step, using the bounds of Tuffley and Steel [1997]. The proof can be viewed as correlating the value of any ML solution to an arbitrarily close approximation to vertex cover.
ISSN 00045411
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2006-09-01
Publisher Place New York
e-ISSN 1557735X
Journal Journal of the ACM (JACM)
Volume Number 53
Issue Number 5
Page Count 23
Starting Page 722
Ending Page 744


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Source: ACM Digital Library