48,108 research outputs found
Connecting the Dots: Towards Continuous Time Hamiltonian Monte Carlo
Continuous time Hamiltonian Monte Carlo is introduced, as a powerful
alternative to Markov chain Monte Carlo methods for continuous target
distributions. The method is constructed in two steps: First Hamiltonian
dynamics are chosen as the deterministic dynamics in a continuous time
piecewise deterministic Markov process. Under very mild restrictions, such a
process will have the desired target distribution as an invariant distribution.
Secondly, the numerical implementation of such processes, based on adaptive
numerical integration of second order ordinary differential equations is
considered. The numerical implementation yields an approximate, yet highly
robust algorithm that, unlike conventional Hamiltonian Monte Carlo, enables the
exploitation of the complete Hamiltonian trajectories (hence the title). The
proposed algorithm may yield large speedups and improvements in stability
relative to relevant benchmarks, while incurring numerical errors that are
negligible relative to the overall Monte Carlo errors
Hamiltonian Monte Carlo Acceleration Using Surrogate Functions with Random Bases
For big data analysis, high computational cost for Bayesian methods often
limits their applications in practice. In recent years, there have been many
attempts to improve computational efficiency of Bayesian inference. Here we
propose an efficient and scalable computational technique for a
state-of-the-art Markov Chain Monte Carlo (MCMC) methods, namely, Hamiltonian
Monte Carlo (HMC). The key idea is to explore and exploit the structure and
regularity in parameter space for the underlying probabilistic model to
construct an effective approximation of its geometric properties. To this end,
we build a surrogate function to approximate the target distribution using
properly chosen random bases and an efficient optimization process. The
resulting method provides a flexible, scalable, and efficient sampling
algorithm, which converges to the correct target distribution. We show that by
choosing the basis functions and optimization process differently, our method
can be related to other approaches for the construction of surrogate functions
such as generalized additive models or Gaussian process models. Experiments
based on simulated and real data show that our approach leads to substantially
more efficient sampling algorithms compared to existing state-of-the art
methods
Polynomial Chaos Expansion of random coefficients and the solution of stochastic partial differential equations in the Tensor Train format
We apply the Tensor Train (TT) decomposition to construct the tensor product
Polynomial Chaos Expansion (PCE) of a random field, to solve the stochastic
elliptic diffusion PDE with the stochastic Galerkin discretization, and to
compute some quantities of interest (mean, variance, exceedance probabilities).
We assume that the random diffusion coefficient is given as a smooth
transformation of a Gaussian random field. In this case, the PCE is delivered
by a complicated formula, which lacks an analytic TT representation. To
construct its TT approximation numerically, we develop the new block TT cross
algorithm, a method that computes the whole TT decomposition from a few
evaluations of the PCE formula. The new method is conceptually similar to the
adaptive cross approximation in the TT format, but is more efficient when
several tensors must be stored in the same TT representation, which is the case
for the PCE. Besides, we demonstrate how to assemble the stochastic Galerkin
matrix and to compute the solution of the elliptic equation and its
post-processing, staying in the TT format.
We compare our technique with the traditional sparse polynomial chaos and the
Monte Carlo approaches. In the tensor product polynomial chaos, the polynomial
degree is bounded for each random variable independently. This provides higher
accuracy than the sparse polynomial set or the Monte Carlo method, but the
cardinality of the tensor product set grows exponentially with the number of
random variables. However, when the PCE coefficients are implicitly
approximated in the TT format, the computations with the full tensor product
polynomial set become possible. In the numerical experiments, we confirm that
the new methodology is competitive in a wide range of parameters, especially
where high accuracy and high polynomial degrees are required.Comment: This is a major revision of the manuscript arXiv:1406.2816 with
significantly extended numerical experiments. Some unused material is remove
On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo
Approximate Bayesian computation (ABC) has gained popularity over the past few years for the analysis of complex models arising in population genetics, epidemiology and system biology. Sequential Monte Carlo (SMC) approaches have become work-horses in ABC. Here we discuss how to construct the perturbation kernels that are required in ABC SMC approaches, in order to construct a sequence of distributions that start out from a suitably defined prior and converge towards the unknown posterior. We derive optimality criteria for different kernels, which are based on the Kullback-Leibler divergence between a distribution and the distribution of the perturbed particles. We will show that for many complicated posterior distributions, locally adapted kernels tend to show the best performance. We find that the added moderate cost of adapting kernel functions is easily regained in terms of the higher acceptance rate. We demonstrate the computational efficiency gains in a range of toy examples which illustrate some of the challenges faced in real-world applications of ABC, before turning to two demanding parameter inference problems in molecular biology, which highlight the huge increases in efficiency that can be gained from choice of optimal kernels. We conclude with a general discussion of the rational choice of perturbation kernels in ABC SMC settings
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