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Model building; Conjugate prior; Linear regression; Empirical Bayes; Hierarchical model; Posterior approximation; Markov chain Monte Carlo; Laplace's approximation; Integrated nested Laplace approximations; Variational inference; Approximate Bayesian computation; Estimators; Bayesian estimator; Credible interval; Maximum a posteriori estimation ...
The reparameterization trick (aka "reparameterization gradient estimator") is a technique used in statistical machine learning, particularly in variational inference, variational autoencoders, and stochastic optimization.
Variational Bayesian methods are a family of techniques for approximating intractable integrals arising in Bayesian inference and machine learning.They are typically used in complex statistical models consisting of observed variables (usually termed "data") as well as unknown parameters and latent variables, with various sorts of relationships among the three types of random variables, as ...
Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model.
Stan is a probabilistic programming language for statistical inference written in C++; ArviZ a Python library for exploratory analysis of Bayesian models; Bambi is a high-level Bayesian model-building interface based on PyMC
The KL-D from the free energy expression maximizes the probability mass of the q-distribution that overlaps with the p-distribution, which unfortunately can result in mode-seeking behaviour. The "reconstruction" term is the remainder of the free energy expression, and requires a sampling approximation to compute its expectation value. [8]
The likelihood estimate needs to be as large as possible; because it's a lower bound, getting closer improves the approximation of the log likelihood. By substituting in the factorized version of , (), parameterized over the hidden nodes as above, is simply the negative relative entropy between and plus other terms independent of if is defined as
Bayesian inference, demographic history, population splits: I. J. Wilson, Weale, D.Balding BayesPhylogenies [8] Bayesian inference of trees using Markov chain Monte Carlo methods: Bayesian inference, multiple models, mixture model (auto-partitioning) M. Pagel, A. Meade BayesTraits [9]