Pseudo-marginal Bayesian inference for Gaussian process latent variable models

A Bayesian inference framework for supervised Gaussian process latent variable models is introduced. The framework overcomes the high correlations between latent variables and hyperparameters by collapsing the statistical model through approximate integration of the latent variables. Using an unbiased pseudo estimate for the marginal likelihood, the exact hyperparameter posterior can then be explored using collapsed Gibbs sampling and, conditional on these samples, the exact latent posterior can be explored through elliptical slice sampling. The framework is tested on both simulated and real examples. When compared with the standard approach based on variational inference, this approach leads to significant improvements in the predictive accuracy and quantification of uncertainty, as well as a deeper insight into the challenges of performing inference in this class of models.