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Register a new userReliable ABC model choice via random forests
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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. We propose a novel approach based on a machine learning tool named random forests 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 random forests and postponing the approximation of the posterior probability of the predicted MAP for a second stage also relying on random forests. Compared with earlier implementations of ABC model choice, the ABC random forest 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 fifty), and (iv) it includes an approximation of the posterior probability of the selected model. The call to random forests 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. The proposed methodologies are implemented in the R package abcrf available on the CRAN.
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The choice of the summary statistics used in Bayesian inference and in particular in ABC algorithms has bearings on the validation of the resulting inference. Those statistics are nonetheless customarily used in ABC algorithms without consistency checks. We derive necessary and sufficient conditions on summary statistics for the corresponding Bayes factor to be convergent, namely to asymptotically select the true model. Those conditions, which amount to the expectations of the summary statistics to asymptotically differ under both models, are quite natural and can be exploited in ABC settings to infer whether or not a choice of summary statistics is appropriate, via a Monte Carlo validation.
This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100036). Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian inference for models associated with intractable likelihood functions. Most ABC implementations require the preliminary selection of a vector of informative statistics summarizing raw data. Furthermore, in almost all existing implementations, the tolerance level that separates acceptance from rejection of simulated parameter values needs to be calibrated. We propose to conduct likelihood-free Bayesian inferences about parameters with no prior selection of the relevant components of the summary statistics and bypassing the derivation of the associated tolerance level. The approach relies on the random forest methodology of Breiman (2001) applied in a (non parametric) regression setting. We advocate the derivation of a new random forest for each component of the parameter vector of interest. When compared with earlier ABC solutions, this method offers significant gains in terms of robustness to the choice of the summary statistics, does not depend on any type of tolerance level, and is a good trade-off in term of quality of point estimator precision and credible interval estimations for a given computing time. We illustrate the performance of our methodological proposal and compare it with earlier ABC methods on a Normal toy example and a population genetics example dealing with human population evolution. All methods designed here have been incorporated in the R package abcrf (version 1.7) available on CRAN.
Random forest (RF) methodology is one of the most popular machine learning techniques for prediction problems. In this article, we discuss some cases where random forests may suffer and propose a novel generalized RF method, namely regression-enhanced random forests (RERFs), that can improve on RFs by borrowing the strength of penalized parametric regression. The algorithm for constructing RERFs and selecting its tuning parameters is described. Both simulation study and real data examples show that RERFs have better predictive performance than RFs in important situations often encountered in practice. Moreover, RERFs may incorporate known relationships between the response and the predictors, and may give reliable predictions in extrapolation problems where predictions are required at points out of the domain of the training dataset. Strategies analogous to those described here can be used to improve other machine learning methods via combination with penalized parametric regression techniques.
As a testament to their success, the theory of random forests has long been outpaced by their application in practice. In this paper, we take a step towards narrowing this gap by providing a consistency result for online random forests.
Big Data is one of the major challenges of statistical science and has numerous consequences from algorithmic and theoretical viewpoints. Big Data always involve massive data but they also often include online data and data heterogeneity. Recently some statistical methods have been adapted to process Big Data, like linear regression models, clustering methods and bootstrapping schemes. Based on decision trees combined with aggregation and bootstrap ideas, random forests were introduced by Breiman in 2001. They are a powerful nonparametric statistical method allowing to consider in a single and versatile framework regression problems, as well as two-class and multi-class classification problems. Focusing on classification problems, this paper proposes a selective review of available proposals that deal with scaling random forests to Big Data problems. These proposals rely on parallel environments or on online adaptations of random forests. We also describe how related quantities -- such as out-of-bag error and variable importance -- are addressed in these methods. Then, we formulate various remarks for random forests in the Big Data context. Finally, we experiment five variants on two massive datasets (15 and 120 millions of observations), a simulated one as well as real world data. One variant relies on subsampling while three others are related to parallel implementations of random forests and involve either various adaptations of bootstrap to Big Data or to divide-and-conquer approaches. The fifth variant relates on online learning of random forests. These numerical experiments lead to highlight the relative performance of the different variants, as well as some of their limitations.
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