Reliable ABC model choice via random forests

Bioinformatics. 2016 Mar 15;32(6):859-66. doi: 10.1093/bioinformatics/btv684. Epub 2015 Nov 20.


Motivation: Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques.

Results: We propose a novel approach based on a machine learning tool named random forests (RF) to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with RF and postponing the approximation of the posterior probability of the selected model for a second stage also relying on RF. Compared with earlier implementations of ABC model choice, the ABC RF approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least 50) and (iv) it includes an approximation of the posterior probability of the selected model. The call to RF will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets.

Availability and implementation: The proposed methodology is implemented in the R package abcrf available on the CRAN.


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms
  • Bayes Theorem
  • Computer Simulation
  • Genetics, Population*
  • Models, Genetic