26 research outputs found
Semiparametric inference in mixture models with predictive recursion marginal likelihood
Predictive recursion is an accurate and computationally efficient algorithm
for nonparametric estimation of mixing densities in mixture models. In
semiparametric mixture models, however, the algorithm fails to account for any
uncertainty in the additional unknown structural parameter. As an alternative
to existing profile likelihood methods, we treat predictive recursion as a
filter approximation to fitting a fully Bayes model, whereby an approximate
marginal likelihood of the structural parameter emerges and can be used for
inference. We call this the predictive recursion marginal likelihood.
Convergence properties of predictive recursion under model mis-specification
also lead to an attractive construction of this new procedure. We show
pointwise convergence of a normalized version of this marginal likelihood
function. Simulations compare the performance of this new marginal likelihood
approach that of existing profile likelihood methods as well as Dirichlet
process mixtures in density estimation. Mixed-effects models and an empirical
Bayes multiple testing application in time series analysis are also considered
A nonparametric empirical Bayes framework for large-scale multiple testing
We propose a flexible and identifiable version of the two-groups model,
motivated by hierarchical Bayes considerations, that features an empirical null
and a semiparametric mixture model for the non-null cases. We use a
computationally efficient predictive recursion marginal likelihood procedure to
estimate the model parameters, even the nonparametric mixing distribution. This
leads to a nonparametric empirical Bayes testing procedure, which we call
PRtest, based on thresholding the estimated local false discovery rates.
Simulations and real-data examples demonstrate that, compared to existing
approaches, PRtest's careful handling of the non-null density can give a much
better fit in the tails of the mixture distribution which, in turn, can lead to
more realistic conclusions.Comment: 18 pages, 4 figures, 3 table
MCMC implementation for Bayesian hidden semi-Markov models with illustrative applications
Copyright © Springer 2013. The final publication is available at Springer via http://dx.doi.org/10.1007/s11222-013-9399-zHidden Markov models (HMMs) are flexible, well established models useful in a diverse range of applications.
However, one potential limitation of such models lies in their inability to explicitly structure the holding times of each hidden state. Hidden semi-Markov models (HSMMs) are more useful in the latter respect as they incorporate additional temporal structure by explicit modelling of the holding times. However, HSMMs have generally received less attention in the literature, mainly due to their intensive computational requirements. Here a Bayesian implementation of HSMMs is presented. Recursive algorithms are proposed in conjunction with Metropolis-Hastings in such a way as to avoid sampling from the distribution of the hidden state sequence in the MCMC sampler. This provides a computationally tractable estimation framework for HSMMs avoiding the limitations associated with the conventional EM algorithm regarding model flexibility. Performance of the proposed implementation is demonstrated through simulation experiments as well as an illustrative application relating to recurrent failures in a network of underground water pipes where random effects are also included into the HSMM to allow for pipe heterogeneity
Explicit-Duration Hidden Markov Model Inference of UP-DOWN States from Continuous Signals
Neocortical neurons show UP-DOWN state (UDS) oscillations under a variety of conditions. These UDS have been extensively studied because of the insight they can yield into the functioning of cortical networks, and their proposed role in putative memory formation. A key element in these studies is determining the precise duration and timing of the UDS. These states are typically determined from the membrane potential of one or a small number of cells, which is often not sufficient to reliably estimate the state of an ensemble of neocortical neurons. The local field potential (LFP) provides an attractive method for determining the state of a patch of cortex with high spatio-temporal resolution; however current methods for inferring UDS from LFP signals lack the robustness and flexibility to be applicable when UDS properties may vary substantially within and across experiments. Here we present an explicit-duration hidden Markov model (EDHMM) framework that is sufficiently general to allow statistically principled inference of UDS from different types of signals (membrane potential, LFP, EEG), combinations of signals (e.g., multichannel LFP recordings) and signal features over long recordings where substantial non-stationarities are present. Using cortical LFPs recorded from urethane-anesthetized mice, we demonstrate that the proposed method allows robust inference of UDS. To illustrate the flexibility of the algorithm we show that it performs well on EEG recordings as well. We then validate these results using simultaneous recordings of the LFP and membrane potential (MP) of nearby cortical neurons, showing that our method offers significant improvements over standard methods. These results could be useful for determining functional connectivity of different brain regions, as well as understanding network dynamics