The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
Open accessAbstract
The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, steppingstone sampling (SS), which uses importance sampling to estimate each ratio in a series (the "stepping stones") bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed.
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Cites
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A general comparison of relaxed molecular clock models
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“This approach generalizes the method suggested by Friel and Pettitt (2008), which corresponds to the special case α = 0.25, and is analogous to the sigmoidal function proposed by Lepage et al. (2007) in a model-switch TI framework.”
MethodInfluential
Cited by
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., & Rasnitsyn, A. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys058 · Cited by 930
Total-Evidence Dating under the Fossilized Birth–Death Process
Zhang, C., Stadler, T., Klopfstein, S., Heath, T. A., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syv080 · Cited by 419
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., et al. (2017) · Nature · doi:10.1038/nature22400 · Cited by 353
Slater, G. J., Harmon, L. J., & Alfaro, M. E. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01723.x · Cited by 334
Metadata
- Authors
- Xie, W., Lewis, P. O., Fan, Y., Kuo, L., & Chen, M.-H.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-12-27
- Volume
- 60
- Issue
- 2
- Pages
- 150-160
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2118048521
- Cited by
- 1,050
- References
- 4
- FWCI
- 18.58
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Xie, W., Lewis, P. O., Fan, Y., Kuo, L., & Chen, M.-H. (2011). Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection. Systematic Biology. https://doi.org/10.1093/sysbio/syq085
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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