Hierarchical Bayesian models based on Gaussian processes a re considered useful for describing complex nonlinear statistical dependen cies among variables in real-world data. However, effective Monte Carlo algorithm s for inference with these models have not yet been established, except for sever al simple cases. In this study, we show that, compared with the slow inference ac hieved with existing program libraries, the performance of Riemannian-m anifold Hamiltonian Monte Carlo (RMHMC) can be drastically improved by optimisi ng the computation order according to the model structure and dynamical ly programming the eigendecomposition. This improvement cannot be achieved w hen using an existing library based on a naive automatic differentiator. W e nu merically demonstrate that RMHMC effectively samples from the posterior, allowin g the calculation of model evidence, in a Bayesian logistic regression on simula ted data and in the estimation of propensity functions for the American nation al medical expenditure data using several Bayesian multiple-kernel models. These results lay a foundation for implementing effective Monte Carlo algorithms for analysing real-world data with Gaussian processes, and highlight the need to deve lop a customisable library set that allows users to incorporate dynamically pr ogrammed objects and finely optimises the mode of automatic differentiation depe nding on the model structure.

First provide a summary of the paper, and then address the following criteria: Quality, clarity, originality and significance. The authors introduce a novel RMHMC type method based on a semi-separable Hamiltonian for use in hierarchical models. The aim of the paper is to enable computationally efficient sampling from hierarchical models where there is strong correlation structure between the parameters and the hyperparameters. The authors give a clear introduction to hierarchical models and RMHMC before describing the proposed semi-separable integrator. The "trick" used in this paper is to define metric tensors independently over the parameters and hyperparameters, which allows both sets of parameters to be updated iteratively based on a single Hamiltonian that combines both quantities.

Sampling from hierarchical Bayesian models is often difficult for MCMC methods, because of the strong correlations between the model parameters and the hyperparameters. Recent Riemannian manifold Hamiltonian Monte Carlo (RMHMC) methods have significant potential advantages in this setting, but are computationally expensive. We introduce a new RMHMC method, which we call semi-separable Hamiltonian Monte Carlo, which uses a specially designed mass matrix that allows the joint Hamiltonian over model parameters and hyperparameters to decompose into two simpler Hamiltonians. This structure is exploited by a new integrator which we call the alternating blockwise leapfrog algorithm. The resulting method can mix faster than simpler Gibbs sampling while being simpler and more efficient than previous instances of RMHMC.

Sampling from hierarchical Bayesian models is often difficult for MCMC methods, because of the strong correlations between the model parameters and the hyperparameters. Recent Riemannian manifold Hamiltonian Monte Carlo (RMHMC) methods have significant potential advantages in this setting, but are computationally expensive. We introduce a new RMHMC method, which we call semi-separable Hamiltonian Monte Carlo, which uses a specially designed mass matrix that allows the joint Hamiltonian over model parameters and hyperparameters to decompose into two simpler Hamiltonians. This structure is exploited by a new integrator which we call the alternating blockwise leapfrog algorithm. The resulting method can mix faster than simpler Gibbs sampling while being simpler and more efficient than previous instances of RMHMC.

The performance of Markov chain Monte Carlo methods is often sensitive to the scaling and correlations between the random variables of interest. An important source of information about the local correlation and scale is given by the Hessian matrix of the target distribution, but this is often either computationally expensive or infeasible. In this paper we propose MCMC samplers that make use of quasi-Newton approximations, which approximate the Hessian of the target distribution from previous samples and gradients generated by the sampler. A key issue is that MCMC samplers that depend on the history of previous states are in general not valid. We address this problem by using limited memory quasi-Newton methods, which depend only on a fixed window of previous samples. On several real world datasets, we show that the quasi-Newton sampler is more effective than standard Hamiltonian Monte Carlo at a fraction of the cost of MCMC methods that require higher-order derivatives.

Sampling from hierarchical Bayesian models is often difficult for MCMC methods, because of the strong correlations between the model parameters and the hyperparameters. Recent Riemannian manifold Hamiltonian Monte Carlo (RMHMC) methods have significant potential advantages in this setting, but are computationally expensive. We introduce a new RMHMC method, which we call semi-separable Hamiltonian Monte Carlo, which uses a specially designed mass matrix that allows the joint Hamiltonian over model parameters and hyperparameters to decompose into two simpler Hamiltonians. This structure is exploited by a new integrator which we call the alternating blockwise leapfrog algorithm. The resulting method can mix faster than simpler Gibbs sampling while being simpler and more efficient than previous instances of RMHMC.

Sampling from hierarchical Bayesian models is often difficult for MCMC methods, because of the strong correlations between the model parameters and the hyperparameters. Recent Riemannian manifold Hamiltonian Monte Carlo (RMHMC) methods have significant potential advantages in this setting, but are computationally expensive. We introduce a new RMHMC method, which we call semi-separable Hamiltonian Monte Carlo, which uses a specially designed mass matrix that allows the joint Hamiltonian over model parameters and hyperparameters to decompose into two simpler Hamiltonians. This structure is exploited by a new integrator which we call the alternating blockwise leapfrog algorithm. The resulting method can mix faster than simpler Gibbs sampling while being simpler and more efficient than previous instances of RMHMC.

We introduce a recent symplectic integration scheme derived for solving physically motivated systems with non-separable Hamiltonians. We show its relevance to Riemannian manifold Hamiltonian Monte Carlo (RMHMC) and provide an alternative to the currently used generalised leapfrog symplectic integrator, which relies on solving multiple fixed point iterations to convergence. Via this approach, we are able to reduce the number of higher-order derivative calculations per leapfrog step. We explore the implications of this integrator and demonstrate its efficacy in reducing the computational burden of RMHMC. Our code is provided in a new open-source Python package, hamiltorch.

Sampling from hierarchical Bayesian models is often difficult for MCMC methods, because of the strong correlations between the model parameters and the hyperparameters. Recent Riemannian manifold Hamiltonian Monte Carlo (RMHMC) methods have significant potential advantages in this setting, but are computationally expensive. We introduce a new RMHMC method, which we call semi-separable Hamiltonian Monte Carlo, which uses a specially designed mass matrix that allows the joint Hamiltonian over model parameters and hyperparameters to decompose into two simpler Hamiltonians. This structure is exploited by a new integrator which we call the alternating blockwise leapfrog algorithm. The resulting method can mix faster than simpler Gibbs sampling while being simpler and more efficient than previous instances of RMHMC.

The performance of Markov chain Monte Carlo methods is often sensitive to the scaling and correlations between the random variables of interest. An important source of information about the local correlation and scale is given by the Hessian matrix of the target distribution, but this is often either computationally expensive or infeasible. In this paper we propose MCMC samplers that make use of quasi-Newton approximations from the optimization literature, that approximate the Hessian of the target distribution from previous samples and gradients generated by the sampler. A key issue is that MCMC samplers that depend on the history of previous states are in general not valid. We address this problem by using limited memory quasi-Newton methods, which depend only on a fixed window of previous samples. On several real world datasets, we show that the quasi-Newton sampler is a more effective sampler than standard Hamiltonian Monte Carlo at a fraction of the cost of MCMC methods that require higher-order derivatives.