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Approximate Bayesian computation

Approximate Bayesian computation

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Approximate Bayesian computation (ABC) is a family of computational techniques in Bayesian statistics
Bayesian statistics
Bayesian statistics is that subset of the entire field of statistics in which the evidence about the true state of the world is expressed in terms of degrees of belief or, more specifically, Bayesian probabilities...

. These simulation techniques operate on summary data (such as population mean, or variance) to make broad inferences with less computation than might be required if all available data were analyzed in detail. They are especially useful in situations where evaluation of the likelihood is computationally prohibitive, or whenever suitable likelihoods are not available.

ABC methods originated in population and evolutionary genetics but have recently also been introduced to the analysis of complex and stochastic dynamical systems.

Overview


In standard Bayesian inference the posterior distribution is given by


where are the parameters of a probability model, are the observed data, and is the prior distribution of the parameters . is the likelihood
Likelihood
Likelihood is a measure of how likely an event is, and can be expressed in terms of, for example, probability or odds in favor.-Likelihood function:...

 of , that is the probability of observing the data given the model with parameter .

The explicit evaluation of the likelihood is avoided in ABC approaches by considering distances between observed and data simulated from a model with parameter . For sufficiently complex models and large data sets the probability of happening upon a simulation run that yields precisely the same dataset as the one observed will be very small, often unacceptably so. So rather than considering the data we consider a summary statistic of the data, , and use a distance between the summary statistics of real and simulated data, and , respectively.

The generic ABC approach to infer the posterior probability distribution of a parameter is as follows:
  1. Sample a candidate parameter vector from some proposal distribution .
  2. Simulate a dataset from the model with parameter .
  3. If then accept as a sample from the posterior.


For sufficiently small the ABC procedure should deliver a good approximation to the true posterior, in particular if the summary statistic is a sufficient statistic of the probability model. If sufficient statistics do not exist or are hard to come by, setting up a satisfying and efficient ABC approach can be challenging.

The generic procedure outlined above can be computationally inefficient but ABC and likelihood-free inferential procedures can be combined with the standard computational approaches used in Bayesian inference
Bayesian inference
In statistics, Bayesian inference is a method of statistical inference. It is often used in science and engineering to determine model parameters, make predictions about unknown variables, and to perform model selection...

 such as Markov chain Monte Carlo
Markov chain Monte Carlo
Markov chain Monte Carlo methods are a class of algorithms for sampling from probability distributions based on constructing a Markov chain that has the desired distribution as its equilibrium distribution. The state of the chain after a large number of steps is then used as a sample of the...

  and Sequential Monte Carlo method  approaches. In these frameworks ABC can be used to tackle otherwise computationally intractable problems.

While ABC and related likelihood-free methods have overwhelmingly been employed for parameter estimation, they can also be used for model selection
Model selection
Model selection is the task of selecting a statistical model from a set of candidate models, given data. In the simplest cases, a pre-existing set of data is considered...

, as the whole apparatus of Bayesian model selection can be adapted to the ABC framework.

An increasing number of software implementations of ABC approaches exist.

Recent advances in ABC methodology, computational implementations and applications are discussed at the ABC in ... meetings:

See also

  • Markov chain Monte Carlo
    Markov chain Monte Carlo
    Markov chain Monte Carlo methods are a class of algorithms for sampling from probability distributions based on constructing a Markov chain that has the desired distribution as its equilibrium distribution. The state of the chain after a large number of steps is then used as a sample of the...

  • Sequential Monte Carlo Method
  • Empirical Bayes

Software


DIYABC : "Do it yourself ABC".

ABC SysBio : A Tool for parameter inference and model selection in systems biology
Systems biology
Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...

 (see also Theoretical Background).

ABC Toolbox: Inference for Population Genetics
Population genetics
Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...

.

msBayes : Comparative phylogeographic inference