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  Model Selection for Mixtures of Mutagenetic Trees

Yin, J., Beerenwinkel, N., Rahnenführer, J., & Lengauer, T. (2006). Model Selection for Mixtures of Mutagenetic Trees. Statistical Applications in Genetics and Molecular Biology, 5: 17.

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... 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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 Urheber:
Yin, Junming1, Autor           
Beerenwinkel, Niko2, Autor           
Rahnenführer, Jörg2, Autor           
Lengauer, Thomas2, Autor           
Affiliations:
1International Max Planck Research School, MPI for Informatics, Max Planck Society, ou_1116551              
2Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society, ou_40046              

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 Zusammenfassung: 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.

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Sprache(n): eng - English
 Datum: 2007-04-022006
 Publikationsstatus: Erschienen
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 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: eDoc: 314620
Anderer: Local-ID: C125673F004B2D7B-7E0C9F42BD91FB39C12570500035F600-Yin05
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Titel: Statistical Applications in Genetics and Molecular Biology
Genre der Quelle: Zeitschrift
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Seiten: - Band / Heft: 5 Artikelnummer: 17 Start- / Endseite: - Identifikator: ISSN: 1544-6115