Questions tagged [gibbs]

The Gibbs sampler is a simple form of Markov Chain Monte Carlo simulation, widely used in Bayesian statistics, based on sampling from full conditional distributions for each variable or group of variables. The name comes from the method being first used on Gibbs random fields modeling of images by Geman and Geman (1984).

The Gibbs sampler is a type of Markov Chain Monte Carlo (MCMC) simulation that produces a Markov chain guaranteed to converge to a target distribution $\pi$ of interest.

Assuming this target $\pi$ is defined on a space of dimension larger than one, the sampler is based on iterated simulations from the full conditional distributions associated with $\pi$ for each variable, though variants exist, such as sampling from blocks of variables conditional on all other variables. There also exist versions for univariate targets $\pi$ based on completion schemes like slice sampling.

On convergence, each full iteration across all variables yields samples from the joint multivariate distribution. As with most MCMC schemes, successive iterates are generally dependent.

It is widely used in Bayesian inference, though it's not limited to Bayesian approaches. For instance, the popular BUGS software takes its acronym from Gibbs sampling, as it stands for Bayes Using Gibbs Sampling.

Reference: http://en.wikipedia.org/wiki/Gibbs_sampling

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Can someone explain Gibbs sampling in very simple words?

I'm doing some reading on topic modeling (with Latent Dirichlet Allocation) which makes use of Gibbs sampling. As a newbie in statistics―well, I know things like binomials, multinomials, priors, etc.―,I find it difficult to grasp how Gibbs sampling…
Thea
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What is the difference between Metropolis-Hastings, Gibbs, Importance, and Rejection sampling?

I have been trying to learn MCMC methods and have come across Metropolis-Hastings, Gibbs, Importance, and Rejection sampling. While some of these differences are obvious, i.e., how Gibbs is a special case of Metropolis-Hastings when we have the full…
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OpenBugs vs. JAGS

I am about to try out a BUGS style environment for estimating Bayesian models. Are there any important advantages to consider in choosing between OpenBugs or JAGS? Is one likely to replace the other in the foreseeable future? I will be using the…
DanB
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A good Gibbs sampling tutorials and references

I want to learn how Gibbs Sampling works and I am looking for a good basic to intermediate paper. I have a computer science background and basic statistic knowledge. Anyone has read good material around? where did you learn it?
fabrizioM
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When would one use Gibbs sampling instead of Metropolis-Hastings?

There are different kinds of MCMC algorithms: Metropolis-Hastings Gibbs Importance/rejection sampling (related). Why would one use Gibbs sampling instead of Metropolis-Hastings? I suspect there are cases when inference is more tractable with…
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Gibbs sampling versus general MH-MCMC

I have just been doing some reading on Gibbs sampling and Metropolis Hastings algorithm and have a couple of questions. As I understand it, in the case of Gibbs sampling, if we have a large multivariate problem, we sample from the conditional…
Luca
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Does the Gibbs Sampling algorithm guarantee detailed balance?

I have it on supreme authority1 that Gibbs Sampling is a special case of the Metropolis-Hastings algorithm for Markov Chain Monte Carlo sampling. The MH algorithm always gives a transition probability with the detailed balance property; I expect…
Ian
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What are some well known improvements over textbook MCMC algorithms that people use for bayesian inference?

When I'm coding a Monte Carlo simulation for some problem, and the model is simple enough, I use a very basic textbook Gibbs sampling. When it's not possible to use Gibbs sampling, I code the textbook Metropolis-Hastings I've learned years ago. The…
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Stan $\hat{R}$ versus Gelman-Rubin $\hat{R}$ definition

I was going through the Stan documentation which can be downloaded from here. I was particularly interested in their implementation of the Gelman-Rubin diagnostic. The original paper Gelman & Rubin (1992) define the the potential scale reduction…
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Where do the full conditionals come from in Gibbs sampling?

MCMC algorithms like Metropolis-Hastings and Gibbs sampling are ways of sampling from the joint posterior distributions. I think I understand and can implement metropolis-hasting pretty easily--you simply choose starting points somehow, and 'walk…
cespinoza
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How to derive Gibbs sampling?

I'm actually hesitating to ask this, because I'm afraid I will be referred to other questions or Wikipedia on Gibbs sampling, but I don't have the feeling that they describe what's at hand. Given a conditional probability…
Anne van Rossum
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Marginal Likelihood from the Gibbs Output

I'm reproducing from scratch the results in Section 4.2.1 of Marginal Likelihood from the Gibbs Output Siddhartha Chib Journal of the American Statistical Association, Vol. 90, No. 432. (Dec., 1995), pp. 1313-1321. It's a mixture of normals model…
Zen
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Gibbs sampling for Ising model

Homework question: Consider the 1-d Ising model. Let $x = (x_1,...x_d)$. $x_i$ is either -1 or +1 $\pi(x) \propto e^{\sum_{i=1}^{39}x_ix_{i+1}}$ Design a gibbs sampling algorithm to generate samples approximately from target distribution $\pi(x)$.…
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How do programs like BUGS/JAGS automatically determine conditional distributions for Gibbs sampling?

Seems like full conditionals are often quite difficult to derive, yet programs like JAGS and BUGS derive them automatically. Can someone explain how they algorithmically generate full conditionals for any arbitrary model specification?
user4733
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Is Gibbs sampling an MCMC method?

As far as I understand it, it is (at least, that is how Wikipedia defines it). But I've found this statement by Efron* (emphasis added): Markov chain Monte Carlo (MCMC) is the great success story of modern-day Bayesian statistics. MCMC, and its…
Gabriel
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