84,681 research outputs found
Bayesian Inference in Estimation of Distribution Algorithms
Metaheuristics such as Estimation of Distribution Algorithms and the Cross-Entropy method use probabilistic modelling and inference to generate candidate solutions in optimization problems. The model fitting task in this class of algorithms has largely been carried out to date based on maximum likelihood. An alternative approach that is prevalent in statistics and machine learning is to use Bayesian inference. In this paper, we provide a framework for the application of Bayesian inference techniques in probabilistic model-based optimization. Based on this framework, a simple continuous Bayesian Estimation of Distribution Algorithm is described. We evaluate and compare this algorithm experimentally with its maximum likelihood equivalent, UMDAG c
Practical bounds on the error of Bayesian posterior approximations: A nonasymptotic approach
Bayesian inference typically requires the computation of an approximation to
the posterior distribution. An important requirement for an approximate
Bayesian inference algorithm is to output high-accuracy posterior mean and
uncertainty estimates. Classical Monte Carlo methods, particularly Markov Chain
Monte Carlo, remain the gold standard for approximate Bayesian inference
because they have a robust finite-sample theory and reliable convergence
diagnostics. However, alternative methods, which are more scalable or apply to
problems where Markov Chain Monte Carlo cannot be used, lack the same
finite-data approximation theory and tools for evaluating their accuracy. In
this work, we develop a flexible new approach to bounding the error of mean and
uncertainty estimates of scalable inference algorithms. Our strategy is to
control the estimation errors in terms of Wasserstein distance, then bound the
Wasserstein distance via a generalized notion of Fisher distance. Unlike
computing the Wasserstein distance, which requires access to the normalized
posterior distribution, the Fisher distance is tractable to compute because it
requires access only to the gradient of the log posterior density. We
demonstrate the usefulness of our Fisher distance approach by deriving bounds
on the Wasserstein error of the Laplace approximation and Hilbert coresets. We
anticipate that our approach will be applicable to many other approximate
inference methods such as the integrated Laplace approximation, variational
inference, and approximate Bayesian computationComment: 22 pages, 2 figure
Computational statistics using the Bayesian Inference Engine
This paper introduces the Bayesian Inference Engine (BIE), a general
parallel, optimised software package for parameter inference and model
selection. This package is motivated by the analysis needs of modern
astronomical surveys and the need to organise and reuse expensive derived data.
The BIE is the first platform for computational statistics designed explicitly
to enable Bayesian update and model comparison for astronomical problems.
Bayesian update is based on the representation of high-dimensional posterior
distributions using metric-ball-tree based kernel density estimation. Among its
algorithmic offerings, the BIE emphasises hybrid tempered MCMC schemes that
robustly sample multimodal posterior distributions in high-dimensional
parameter spaces. Moreover, the BIE is implements a full persistence or
serialisation system that stores the full byte-level image of the running
inference and previously characterised posterior distributions for later use.
Two new algorithms to compute the marginal likelihood from the posterior
distribution, developed for and implemented in the BIE, enable model comparison
for complex models and data sets. Finally, the BIE was designed to be a
collaborative platform for applying Bayesian methodology to astronomy. It
includes an extensible object-oriented and easily extended framework that
implements every aspect of the Bayesian inference. By providing a variety of
statistical algorithms for all phases of the inference problem, a scientist may
explore a variety of approaches with a single model and data implementation.
Additional technical details and download details are available from
http://www.astro.umass.edu/bie. The BIE is distributed under the GNU GPL.Comment: Resubmitted version. Additional technical details and download
details are available from http://www.astro.umass.edu/bie. The BIE is
distributed under the GNU GP
Ensemble Kalman methods for high-dimensional hierarchical dynamic space-time models
We propose a new class of filtering and smoothing methods for inference in
high-dimensional, nonlinear, non-Gaussian, spatio-temporal state-space models.
The main idea is to combine the ensemble Kalman filter and smoother, developed
in the geophysics literature, with state-space algorithms from the statistics
literature. Our algorithms address a variety of estimation scenarios, including
on-line and off-line state and parameter estimation. We take a Bayesian
perspective, for which the goal is to generate samples from the joint posterior
distribution of states and parameters. The key benefit of our approach is the
use of ensemble Kalman methods for dimension reduction, which allows inference
for high-dimensional state vectors. We compare our methods to existing ones,
including ensemble Kalman filters, particle filters, and particle MCMC. Using a
real data example of cloud motion and data simulated under a number of
nonlinear and non-Gaussian scenarios, we show that our approaches outperform
these existing methods
Estimation and uncertainty of reversible Markov models
Reversibility is a key concept in Markov models and Master-equation models of
molecular kinetics. The analysis and interpretation of the transition matrix
encoding the kinetic properties of the model relies heavily on the
reversibility property. The estimation of a reversible transition matrix from
simulation data is therefore crucial to the successful application of the
previously developed theory. In this work we discuss methods for the maximum
likelihood estimation of transition matrices from finite simulation data and
present a new algorithm for the estimation if reversibility with respect to a
given stationary vector is desired. We also develop new methods for the
Bayesian posterior inference of reversible transition matrices with and without
given stationary vector taking into account the need for a suitable prior
distribution preserving the meta- stable features of the observed process
during posterior inference. All algorithms here are implemented in the PyEMMA
software - http://pyemma.org - as of version 2.0
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