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Author, Editor(s)

Author(s):

Yin, Junming
Beerenwinkel, Niko
Rahnenführer, Jörg
Lengauer, Thomas

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Not MPG Author(s):

Yin, Junming
Beerenwinkel, Niko

BibTeX cite key*:

Yin05

Title

Title*:

Model Selection for Mixtures of Mutagenetic Trees

Journal

Journal Title*:

Statistical Applications in Genetics and Molecular Biology

Journal's URL:

http://www.bepress.com/sagmb/

Download URL
for the article:


Language:

English

Publisher

Publisher's
Name:

Bepress

Publisher's URL:

http://www.bepress.com/

Publisher's
Address:

Berkeley, USA

ISSN:

1544-6115

Vol, No, pp, Date

Volume*:

5

Number:

1

Publishing Date:

2006

Pages*:

Article 17

Number of
VG Pages:


Page Start:


Page End:


Sequence Number:

17

DOI:


Note, Abstract, ©

Note:


(LaTeX) Abstract:

The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have been applied to infer the order and rate of occurrence of these mutations. Understanding and predicting this evolutionary process is an important prerequisite for the rational design of antiretroviral therapies. In practice, mixtures models of K mutagenetic trees provide more flexibility and are often more appropriate for modelling observed mutational patterns.

Here, we investigate the model selection problem for K-mutagenetic trees mixture models. We evaluate several classical model selection criteria including cross-validation, the Bayesian Information Criterion (BIC), and the Akaike Information Criterion. We also use the empirical Bayes method by constructing a prior probability distribution for the parameters of a mutagenetic trees mixture model and deriving the posterior probability of the model. In addition to the model dimension, we consider the redundancy of a mixture model, which is measured by comparing the topologies of trees within a mixture model. Based on the redundancy, we propose a new model selection criterion, which is a modification of the BIC.

Experimental results on simulated and on real HIV data show that the classical criteria tend to select models with far too many tree components. Only cross-validation and the modified BIC recover the correct number of trees and the tree topologies most of the time. At the same optimal performance, the runtime of the new BIC modification is about one order of magnitude lower. Thus, this model selection criterion can also be used for large data sets for which cross-validation becomes computationally infeasible.


URL for the Abstract:

http://www.bepress.com/sagmb/vol5/iss1/art17/

Categories,
Keywords:


HyperLinks / References / URLs:


Copyright Message:

... For 5 years from the date of initial publication in Statistical Applications in Genetics and Molecular Biology, the author (or copyright holder if different) grants bepress and exclusive right to distribution of the article in digital form...
Personal-use exceptions: The following uses are exempt from the exclusive 5-year period: ... a non-commercial open access repository, or publication site affiliated with the author's plase of employment ...

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Access Level:

Internal

Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

Appearance:

MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort


BibTeX Entry:

@ARTICLE{Yin05,
AUTHOR = {Yin, Junming and Beerenwinkel, Niko and Rahnenf{\"u}hrer, J{\"o}rg and Lengauer, Thomas},
TITLE = {Model Selection for Mixtures of Mutagenetic Trees},
JOURNAL = {Statistical Applications in Genetics and Molecular Biology},
PUBLISHER = {Bepress},
YEAR = {2006},
NUMBER = {1},
VOLUME = {5},
PAGES = {Article 17},
ADDRESS = {Berkeley, USA},
ISBN = {1544-6115},
}


Entry last modified by Uwe Brahm, 07/18/2007
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Editor(s)
Anja Becker
Created
08/01/2005 11:49:23 AM
Revisions
8.
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4.
Editor(s)
Uwe Brahm
Uwe Brahm
Uwe Brahm
Christine Kiesel
Christine Kiesel
Edit Dates
2007-07-18 17:58:12
2007-07-02 12:03:13
2007-04-30 14:56:24
02.04.2007 14:34:35
02.04.2007 14:31:44