29,735 research outputs found
Scalable Inference for Markov Processes with Intractable Likelihoods
Bayesian inference for Markov processes has become increasingly relevant in
recent years. Problems of this type often have intractable likelihoods and
prior knowledge about model rate parameters is often poor. Markov Chain Monte
Carlo (MCMC) techniques can lead to exact inference in such models but in
practice can suffer performance issues including long burn-in periods and poor
mixing. On the other hand approximate Bayesian computation techniques can allow
rapid exploration of a large parameter space but yield only approximate
posterior distributions. Here we consider the combined use of approximate
Bayesian computation (ABC) and MCMC techniques for improved computational
efficiency while retaining exact inference on parallel hardware
The iterated auxiliary particle filter
We present an offline, iterated particle filter to facilitate statistical
inference in general state space hidden Markov models. Given a model and a
sequence of observations, the associated marginal likelihood L is central to
likelihood-based inference for unknown statistical parameters. We define a
class of "twisted" models: each member is specified by a sequence of positive
functions psi and has an associated psi-auxiliary particle filter that provides
unbiased estimates of L. We identify a sequence psi* that is optimal in the
sense that the psi*-auxiliary particle filter's estimate of L has zero
variance. In practical applications, psi* is unknown so the psi*-auxiliary
particle filter cannot straightforwardly be implemented. We use an iterative
scheme to approximate psi*, and demonstrate empirically that the resulting
iterated auxiliary particle filter significantly outperforms the bootstrap
particle filter in challenging settings. Applications include parameter
estimation using a particle Markov chain Monte Carlo algorithm
Efficient Sequential Monte-Carlo Samplers for Bayesian Inference
In many problems, complex non-Gaussian and/or nonlinear models are required
to accurately describe a physical system of interest. In such cases, Monte
Carlo algorithms are remarkably flexible and extremely powerful approaches to
solve such inference problems. However, in the presence of a high-dimensional
and/or multimodal posterior distribution, it is widely documented that standard
Monte-Carlo techniques could lead to poor performance. In this paper, the study
is focused on a Sequential Monte-Carlo (SMC) sampler framework, a more robust
and efficient Monte Carlo algorithm. Although this approach presents many
advantages over traditional Monte-Carlo methods, the potential of this emergent
technique is however largely underexploited in signal processing. In this work,
we aim at proposing some novel strategies that will improve the efficiency and
facilitate practical implementation of the SMC sampler specifically for signal
processing applications. Firstly, we propose an automatic and adaptive strategy
that selects the sequence of distributions within the SMC sampler that
minimizes the asymptotic variance of the estimator of the posterior
normalization constant. This is critical for performing model selection in
modelling applications in Bayesian signal processing. The second original
contribution we present improves the global efficiency of the SMC sampler by
introducing a novel correction mechanism that allows the use of the particles
generated through all the iterations of the algorithm (instead of only
particles from the last iteration). This is a significant contribution as it
removes the need to discard a large portion of the samples obtained, as is
standard in standard SMC methods. This will improve estimation performance in
practical settings where computational budget is important to consider.Comment: arXiv admin note: text overlap with arXiv:1303.3123 by other author
Scalable Planning and Learning for Multiagent POMDPs: Extended Version
Online, sample-based planning algorithms for POMDPs have shown great promise
in scaling to problems with large state spaces, but they become intractable for
large action and observation spaces. This is particularly problematic in
multiagent POMDPs where the action and observation space grows exponentially
with the number of agents. To combat this intractability, we propose a novel
scalable approach based on sample-based planning and factored value functions
that exploits structure present in many multiagent settings. This approach
applies not only in the planning case, but also in the Bayesian reinforcement
learning setting. Experimental results show that we are able to provide high
quality solutions to large multiagent planning and learning problems
OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects
Counting circular objects such as cell colonies is an important source of
information for biologists. Although this task is often time-consuming and
subjective, it is still predominantly performed manually. The aim of the
present work is to provide a new tool to enumerate circular objects from
digital pictures and video streams. Here, I demonstrate that the created
program, OpenCFU, is very robust, accurate and fast. In addition, it provides
control over the processing parameters and is implemented in an in- tuitive and
modern interface. OpenCFU is a cross-platform and open-source software freely
available at http://opencfu.sourceforge.net
- …