Approximate Bayesian computation: Difference between revisions

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'''Approximate Bayesian computation (ABC)''' is a family of computational techniques in [[Bayesian statistics]]. 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 <ref name=Pritchard1999>{{cite journal|last = Pritchard|first = J. K.|coauthors = Seielstad, M. T., Perez-Lezaun, A., and Feldman, M. T.|title = Population Growth of Human Y Chromosomes: A Study of Y Chromosome Microsatellites|journal = Mol. Biol. Evol.|volume = 16|dateyear = 1999|pages = 1791–1798}}</ref><ref name=Beaumont>{{cite journal|last = Beaumont|first = M. A.|coauthors = Zhang, W. and [[David Balding|Balding, D. J.]]|title = Approximate Bayesian Computation in Population Genetics|journal = Genetics|volume = 162|date = Dec 2002|pages = 2025–2035|url = http://www.genetics.org/cgi/content/abstract/162/4/2025|pmid = 12524368|issue = 4|monthdate = Dec|day =December 1, 2002 01}}</ref> but have recently also been introduced to the analysis of complex and stochastic [[dynamical systems]] <ref name=Toni2009>{{cite journal |author = Toni, T.; Welch, D.; Strelkowa, N.; Ipsen, A.; Stumpf, M.P.H. |year = 2009 |title = Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems | journal = Journal of the Royal Society Interface |volume = 6 |issue = 31 |pages = 187&ndash;202 |doi = 10.1098/rsif.2008.0172 |url=http://rsif.royalsocietypublishing.org/content/6/31/187.abstract}}</ref>.

==Overview==

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:<math>P(\theta|D)\propto P(D|\theta) \pi(\theta)</math>

where <math>\theta</math> are the parameters of a probability model, <math>D</math> are the observed data, and <math>\pi(\theta)</math> is the [[prior distribution]] of the parameters <math>\theta</math>. <math>P(D|\theta)</math> is the [[likelihood]] of <math>\theta</math>, that is the probability of observing the data <math>D</math> given the model with parameter <math>\theta</math>.

The explicit evaluation of the likelihood <math>P(D|\theta)</math> is avoided in ABC approaches by considering distances between observed and data simulated from a model with parameter <math>\theta</math>. 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, <math>S(D)</math>, and use a distance <math>\Delta(S(D),S(X))</math> between the summary statistics of real and simulated data, <math>D</math> and <math>X</math>, respectively.

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For <math>\epsilon</math> sufficiently small the ABC procedure should deliver a good approximation to the true posterior, in particular if the summary statistic <math>S</math> 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]] such as [[Markov chain Monte Carlo]] <ref name=Marjoram>{{cite journal|last = Marjoram|first = P.|coauthors = Molitor, J., Plagnol, V. and Tavaré, S.|title = Markov chain Monte Carlo without likelihoods|journal = P Natl Acad Sci USA|volume = 100|number = 26|dateyear = 2003|pages = 15324–15328|doi = 10.1073/pnas.0306899100|pmid = 14663152}} </ref> <ref name=Plagnol>{{cite journal|last = Plagnol|first = V.|coauthors = Tavaré, S.|title = Approximate Bayesian computation and MCMC|journal = Monte Carlo and Quasi-Monte Carlo Methods 2002|year = 2004|url = http://www-gene.cimr.cam.ac.uk/vplagnol/papers/vpst-web.pdf|format=PDF}} (The link is to a preprint.)</ref> and [[Sequential Monte Carlo method]] <ref name=Toni2009> </ref> approaches. In these frameworks ABC can be used to tackle otherwise computationally intractable problems.

While ABC and related likelihood-free methods have overwhelmingly be employed for parameter estimation, they can also be used for [[model selection]], as the whole apparatus of Bayesian model selection can be adapted to the ABC framework <ref name= Toni2009b>{{cite journal |author = Toni, T.; Stumpf, M.P.H. |year = 2009 |title = Simulation-based model selection for dynamical systems in systems and population biology | journal = Bioinformatics |volume = (in press) |doi = doi:10.1093/bioinformatics/btp619 |url=http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp619}}</ref>.

An increasing number of software implementations of ABC approaches exist <ref name=Cornuet>{{cite journal|last = Cornuet|first = J-M.|coauthors = Santos, F., Beaumont, M. A., Robert, C. P., Marin, J-M., [[David Balding|Balding, D. J.]], Guillemaud, T. and Estoup, A.|title = Inferring population history with DIY ABC: a user-friendly approach to Approximate Bayesian Computation|journal = Bioinformatics|year = 2008|url = http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn514|pmid = 18842597|doi = 10.1093/bioinformatics/btn514|volume = 24|pages = 2713}} </ref>.

==See also==

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[http://abc-sysbio.sourceforge.net/ ABC SysBio] : A Tool for parameter inference and model selection in systems biology.

[[Category:Bayesian statistics]]