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.

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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., ...
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What sort of data would be appropriate to analyze under an MCMC method?

MCMC methods describe stochastic sampling but I'm not entirely sure the contexts in real datasets one would wish to apply MCMC methods. What kind of data could I gain insight into with MCMC methods?
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Comparison of MCMC methods? [closed]

Where can I find a good comparison of Gibbs, Metropolis, and Hybrid MCMC in R or Python? I have thus far found this ...
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Need help deriving a gibbs sampler for a normal mixture model with two components

Let $\theta_i$ be an indicator that the i-th eruption is a long eruption. (i.e. $\theta_i = 1$ if the i-th eruption is long and $\theta_i = 0$ otherwise.) Assume the following model and derive a ...
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Gibbs Sampling with given Posterior Distribution

I'm trying to implement an algorithm from a paper which assigns three types of labels $m_i, m_d$ and $m_s$. Here $m_i$ labels a collection of documents $G_i , m_d$ a subcollection of them and $m_s$ ...
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Sampling from a portion of the normal distribution?

I have a a conditional distribution $p(X_1 | \theta) \propto MVN(\mu, \Omega) \pi(X_1)$ where $X_1=[x_1, x_2, \dots, x_n]'$ and $\pi(X_1)=1$ when all $x_i \in [0,a)$ and $0$ otherwise. Is there any ...
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Gibbs Sampling and Probability Notation

Problem 1 I am trying to implement Gibbs Sampling for the following problem: There is a grid measuring 3 x 3 sites, each "site" can be designated in a state, $X$, of 1 or -1. The sites are numbered ...
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Gibbs within Metropolis

Consider a model with two parameters, $\alpha$ and $\beta$. We want to sample these two parameters conditioning on two data points, $d_1$ and $d_2$. Is it possible to use an algorithm like this: 1) ...
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Methods of fitting a dynamic linear model

I'm taking a time series course and am learning about exchangeable time series form of dynamic linear models (DLMs). This is given by: \begin{align*} \mathbf{y}_t' &= ...
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Gibbs Sampling form Non-standard distribution in R

Gibbs sampling examples in R has involved initializing and updating iteratively from conditional that are in standard form. Has anyone performed on a gibbs sampling when the conditionals are in ...
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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 ...
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Is my OpenBUGS / WinBUGS model well specified?

I've just started trying to use OpenBUGS for Bayesian analysis of stochastic volatility models. In particular, I'm trying to calculate stochastic covariance, similar to the DC-MSV model specified by ...
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Posterior parameter distribution

I am considering the following non-linear state space model: $X_t=\frac{X_{t-1}}{2}+25\frac{X_{t-1}}{1+X_{t-1}^2}+8\cos{1.2t}+\epsilon_t, \epsilon_t\sim N(0,\sigma_x^2 ) $ ...
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Understanding a measure of convergence of MCMC simulations

I am trying to better understand better the Gelman/Rubin measure of convergence of MCMCs. The method starts off by defining two quantities: $B$ and $W$. $B$ is said to be the between chain variance ...
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STEP BY STEP approach to learn LDA (Latent Dirchlet Allocation)

I have an urgent need to understand Latent Dirchlet Allocation (LDA) for Topic Modeling. I tried several sources, but it seems I do not have required knowledge to learn this. My statistics knowledge ...
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1answer
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Is Slice Sampling a special case of Gibbs Sampling?

I read on this thread the following: If you can use both the gibbs sampler and slice sampling to sample from a posterior I would use the Gibbs sampler as the slice sampler seems unnecessary to ...
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123 views

Gibbs Sampling Detecting Change point in time series

I was reading through this one page paper on using Gibbs sampling for detecting a change point in a time series like data. While I understand the part where the $\lambda$ and $\phi$ are chosen from a ...
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References on deterministc augmented variable for Gibbs sampling

According to Wikipedia, It is also possible to extend Gibbs sampling in various ways. ... It is ... possible to incorporate variables that are not random variables, but whose value is ...
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Gibbs sample from AR(1) of exogenous input

I am trying to fit a model where there is a sequence of exogenous "shocks", $X_1, X_2, ..., X_T$, and a AR(1) of these shocks explain $Y_1, Y_2, ..., Y_T$. Specifically, Data (known): $X_1, X_2, ...
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Mixture of probits: understanding truncated-based likelihoods

I am trying to implement a mixture model of probits to infer the best decision boundary for every latent subpopulation. When doing Gibbs sampling, we eventually have to compute $P(y^* | w_c)$ where ...
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53 views

Gibbs Sampling Inserting Some Known Predictors

Imagine you would like to use a simple Gibbs sampling to resample from a joint probability distribution which is difficult to model (but you know all the conditionals ...
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MCMC for Bayesian Inference (Gibbs Sampling) Varying Observed Data

At every step $k$, a Markov chain Monte Carlo algorithm for Bayesian inference with Gibbs sampling draws a parameter of the model to fit, $\beta_i^{(k)}$, from the conditional ...
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Gibbs sampling for correlated random variables

Short summary Suppose two latent variables of a hierarchical model are correlated. Let $1-\epsilon$ be the degree of correlation. As $\epsilon\rightarrow 0$ the variables become perfectly correlated ...
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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 ...
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How to implement a metropolis hastings algorithm to find the posterior pdf of a time-dependent parameter?

Assume that I have a time series observations denoted by Yi where i is from 1-5000. yi=β1 x1i + β2 x2i + β3 x3i + Ci; Here x is the input. I have to find the values of Betas. But, I'm taking all ...
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What methodology should I choose? If hiearchical, what model design?

I am working on a problem that has can beyond my level of understanding. I am quite familiar with R, so that would be my preferred choice but I also have access to SAS. Data I have created a fake ...
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Practical Implementation of Gibbs Sampling in Latent Diriclet Allocation

In the collapsed Gibbs sampling version of LDA, the posterior distribution of topic assignments for each word is sampled. From what I have read (e.g. ...
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72 views

Kalman filter conceptual question

I'm using the function dlmGibbsDIG (Gibbs sampler) in the dlmpackage from R to estimate the unknown variances. The output are ...
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1answer
119 views

Can I subsample a large dataset at every MCMC iteration?

I have a large dataset from which I want to perform a bayesian probit regression using Gibbs sampling 1. Since the dataset has one milion rows, and variables from a truncated normal must be sampled ...
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What will happen if we sample the most probable value in the Gibbs sampling?

I am now working with the Gibbs sampling. One problem that puzzled me is that when we use the Gibbs sampling, we always sample randomly from the conditional probability. What will happen if we sample ...
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55 views

Gibbs sampling with Log-Normal observations

I am writing a Gibbs sampler for data that is Log-Normal (LN) distributed, with unknown mean and variance. There is a wealth of information on inference for LN models when either the mean or variance ...
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Posterior distribution of precision for multivariate normal with normal-wishart prior

I'm trying to derive the posterior distribution for the precision matrix for the multivariate normal with normal-wishart prior. According to wikipedia and other sources the answer is as follows: ...
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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 ...
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Gibbs sampling how to sample from the conditional probability? Bayesian model

I want to learn Gibbs sampling for a Bayesian model. How can I sample the variable from the conditional distribution? In this example, arrow means dependent; for example, ...
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Proper likelihood function in acceptance probability of Gibbs Sampler

I have a question about the acceptance ratio used when implementing a random walk M-H in a gibbs sampler to generate sample paths of an unobservable process. When computing the likelihood of a set of ...
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1answer
119 views

Gibbs sampling with Dirichlet Likelihood

I have a sequence of observations that I am representing as proportions: X1 X2 X3 X4 X5 0.10 0.20 0.50 0.12 0.08 0.07 0.24 0.55 0.04 0.10 ... ...
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how to predict Yn value in this formula with Metropolis Hastings or Gibbs?

I have a model with this formula: $$ Y_n=aX_n^b + e_n $$ $$ X_n \in [0,2] \quad\quad a = 1.5 \quad\quad b = 0.5 \quad \quad e_n = N(μ = 0, σ^2 = 1) $$ I want to predict "$Y_n$" value with using ...
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EM on product of multinomials

I have the following conditional density: $$ P(x | \theta, \pi) = \prod_{i=1}^I \prod_{j=1}^J t_{ij}! \prod_{k=1}^K \frac{1}{x_{ijk}!}(\sum_{l=1}^L \theta_{il} \pi_{jkl})^{x_{ijk}} $$ Here, $x$ is ...
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Gibbs measure and normal distribution

On Wikipedia, the Gibbs measure defines the probability as: $$ P(X=x) = \frac{1}{Z(\beta)}\exp(-\beta E(x)) $$ Now, the familiar form of the normal distribution is: $$ P(x) = ...
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Conditionals for Gibbs sampling of relational clusters

I'm trying to implement a Gibbs sampler, but I'm having trouble to find some of the conditionals of this model. Model We have $A$ actors, $K$ classes or clusters, and a matrix $\phi$ that determines ...
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Gibbs sampler for conditionals that are exponential: Example from Casella & George paper

I am trying to work out Example 2 from Casella and George's paper "Explaining the Gibbs Sampler" in R. The example is: ...
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Joint and Conditional probability

I'm trying to prove a result for Gibbs Sampling with multiple latent variables. I am not sure what the expansion of both the joint and conditional probability would be. In particular, let's say that ...
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Gibbs sampling for LDA — does a small Dirichlet concentration parameter make a difference?

I'm using a Gibbs sampler for Latent Dirichlet allocation as described by Griffiths and Steyvers (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387300/). The sampling of a new topic $j$ for word $i$ is ...
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187 views

How can I estimate the precision of a normal using a Gibbs sampler?

I am trying to estimate the precision $\tau$ of a normal distribution with either WinBUGS or OpenBUGS: $c \sim \text{normal}(\mu,\tau)$ $\mu \rightarrow \lambda \cdot t^{-\beta}$ $\tau \sim ...
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What are the main differences between classical and Gibbs sampling Latent Dirichlet Allocations?

In these weeks I have been studying the classical Latent Dirichlet Allocation (LDA) algorithm by David Blei and colleagues (2003), and the LDA variant based on Gibbs sampling introduced by Tom ...
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Sampling from truncated distribution

I want to sample from a truncated distribution that appears in a Gibbs sampling scheme. The full conditional of the distribution is given by $p(X = k | \ldots) \propto (1 - p)^{k - 1} \mathbb{1} ( s ...
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Gibbs sampler for local linear trend model

Question: Consider the local linear trend model given by: \begin{align*} y_t = \mu_t + \tau \varepsilon_t \ \cdots \ \text{Observation equation} \\ \mu_{t+1} = \phi \mu_t + \eta_t \ \cdots \ ...
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Convergence theorem for Gibbs sampling

The convergence theorem for Gibbs sampling states: Given a random Vektor $X$ with $X_1,X_2,...X_K$ and the knowlegde about the conditional distribution of $X_k$ we can find the actual distribution ...
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154 views

Unsupervised Bayesian naive Bayes

I'm reading a paper Gibbs sampling for the uninitiated. In this paper, the authors try to use Gibbs sampling for a bayesian naive bayes model. They formalize the model as a graphical model in page 8. ...
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Implementing Latent Dirichlet Allocation - notation confusion

I am trying to implement LDA using the collapsed Gibbs sampler from http://www.uoguelph.ca/~wdarling/research/papers/TM.pdf the main algorithm is shown below I'm a bit confused about the notation ...