Questions tagged [bayesian]

Bayesian (after Thomas Bayes) refers to methods in probability and statistics that involve quantifying uncertainty about parameter or latent variable estimates by incorporating both prior and observed information. Bayesian modeling, inference, optimization, and model comparison techniques are on topic. A programming element is expected; theoretical/methodological questions should go to https://stats.stackexchange.com.

Overview

Bayesian inference is a method of statistical inference which uses Bayes' theorem - named after Thomas Bayes (1702-1761) - to quantify the uncertainty of parameters or latent variables. The statement of Bayes' theorem in Bayesian inference is

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Here θ represents the parameters to be inferred and d the data. P(θ|d) is the posterior probability and P(d|θ) is the likelihood function. P(θ) is the prior: a function encoding previous beliefs about θ within a model appropriate for the data. P(d) is a normalization factor.

The formula is used as an updating procedure: as more data become available, the posterior can be updated successively. In the first instance, the prior must be specified by the user. In later updates, the prior is usually chosen to be the posterior from a previous updating procedure.

References

The following threads contain lists of references:

The following journals are dedicated to research in Bayesian statistics:

Tag usage

Questions on tag should be about implementation and programming problems, not about the statistical or theoretical properties of the technique. Consider whether your question might be better suited to Cross Validated, the StackExchange site for statistics, machine learning and data analysis.

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BayesServer: InvalidNetworkException: Node [Knowledge] has a null distribution

I am trying to build a Dynamic Bayesian Network using the BayesServer library in C# for my Unity3D game. I have the following method which implements the network // numberOfDistractors and levelId will be used later for added complexity in…
Vipin Verma
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simulating what if scenarios using Bayesian model - rstanarm

I am fitting a model (very much simplified for reproducible) like so: library(datasets) library(rstanarm) set.seed(42) rm(list = ls(all = TRUE)) prediction_data1 <- data.frame( Petal.Length = 1.4 ) prediction_data2 <- data.frame( …
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Does the GaussianProcessRegressor class in scikit-learn do the operations in a parallelized manner?

I do not notice any performance improvements when using GaussianProcessRegressor on a machine which has 8 cores (16 threads) available or a machine which has 4 cores (8 threads). So I wonder, is the GaussianProcessRegressor class in…
Amir
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Implement Dynamic Bayesian Network in Unity3d using Bayes server c# library

I am trying to create a dynamic Bayesian network for parameter learning using the Bayes server in C# in my Unity game. The implementation is based on this article. A brief explanation of the model shown in the figure below: When a player starts…
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PRML: how to plot the minimum misclassification-rate decision boundary?

This is the synthetic classification data set with data from the two classes shown in red and blue. The blue class is generated from a single Gaussian while the red class comes from a mixture of two Gaussians. Since we have the prior probabilities…
Charles
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How to deal with panel data using the brms package in r

I have a panel data set (several observations of different individuals over time) for which I want to construct a simple bayesian multilevel model. Therefore, I want to use the brms package. Does anyone know how to deal with the panel data structure…
Activation
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ArgumentException: The Assembly Microsoft.Msagl is referenced by BayesServer.Layout

I need help with implementing the bayes network in Unity. I downloaded the bayes server developer API from here as zip and extracted it in my Unity assets folder. When I try to build the game, I get the following error. Could you please help me with…
Vipin Verma
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Coverage probability estimation for Bayesian Credible interval (Normal Distribution)

Bayesian Inference for the Normal Distribution, I use the following r code to obtain the posterior distribution. install.packages(c("mvtnorm","loo","coda"), repos="https://cloud.r-project.org/",dependencies=TRUE) options(repos=c(getOption('repos'),…
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How to control the figure which appears in bayesopt function?

bayesopt draws figures like this: How to access such figures in order to modify title or something? If I use gcf it is not guaranteed I get the correct figure because I could change focus to another figure window during execution.
Dims
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bayesian survival analysis wth rstan

I want to construct stan(rstan) code for survival analysis using weibull distribution. But my stan code always can't work. If Anyone knows how to deal with my problem, please teach me. My data is like that Movement:(time that took oranisum…
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Dirichlet Multinomial model in JAGS with categorical X

Can someone help with JAGS code for a Bayesian multinomial logistic model with one categorical X variable (Dirichlet prior)? My representative sample is the matrix "z" in the code below that represents the 3 outcomes and "site", in the bottom line…
user40950
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Python code to enumerate over all acyclic digraphs with 5 nodes

So I was recently studying this course on Probabilistic Graphical Models and I wanted to try a hands-on example. In the example, I want to loop over all possible combinations (29,281) acyclic digraphs (or DAGs) and see how they fit the data. I know…
Sahil Puri
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Problems with Naive Bayes implemented on Amazon fine food reviews dataset

cv accuracy cv accuracy graph test accuracy I am trying to implement Naive bayes on fine food reviews dataset of amazon. Can you review the code and tell why there is such a big difference between cross validation accuracy and test…
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BAYESAB testing for normal distributions

In the BAYESAB package, the below example is provided: A_norm <- rnorm(100, 6, 1.5) B_norm <- rnorm(100, 5, 2.5) AB2 <- bayesTest(A_norm, B_norm, priors = c('mu' = 5, 'lambda' = 1, 'alpha' = 3, 'beta' = 1), distribution =…
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Why does Dynesty multiprocessing with ThreadPoolExecutor not use all cores?

I am trying to run a simple example with nested sampling and dynesty. I installed dynesty from github: https://github.com/joshspeagle/dynesty Computer Setup OS: Mac OSX El Capitan (10.11.6) CPU: 8 cores RAM: 16.0 GB gcc: 4.8.5 via conda install…
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