34,772 research outputs found
False discovery rate regression: an application to neural synchrony detection in primary visual cortex
Many approaches for multiple testing begin with the assumption that all tests
in a given study should be combined into a global false-discovery-rate
analysis. But this may be inappropriate for many of today's large-scale
screening problems, where auxiliary information about each test is often
available, and where a combined analysis can lead to poorly calibrated error
rates within different subsets of the experiment. To address this issue, we
introduce an approach called false-discovery-rate regression that directly uses
this auxiliary information to inform the outcome of each test. The method can
be motivated by a two-groups model in which covariates are allowed to influence
the local false discovery rate, or equivalently, the posterior probability that
a given observation is a signal. This poses many subtle issues at the interface
between inference and computation, and we investigate several variations of the
overall approach. Simulation evidence suggests that: (1) when covariate effects
are present, FDR regression improves power for a fixed false-discovery rate;
and (2) when covariate effects are absent, the method is robust, in the sense
that it does not lead to inflated error rates. We apply the method to neural
recordings from primary visual cortex. The goal is to detect pairs of neurons
that exhibit fine-time-scale interactions, in the sense that they fire together
more often than expected due to chance. Our method detects roughly 50% more
synchronous pairs versus a standard FDR-controlling analysis. The companion R
package FDRreg implements all methods described in the paper
Bayesian Synthesis: Combining subjective analyses, with an application to ozone data
Bayesian model averaging enables one to combine the disparate predictions of
a number of models in a coherent fashion, leading to superior predictive
performance. The improvement in performance arises from averaging models that
make different predictions. In this work, we tap into perhaps the biggest
driver of different predictions---different analysts---in order to gain the
full benefits of model averaging. In a standard implementation of our method,
several data analysts work independently on portions of a data set, eliciting
separate models which are eventually updated and combined through a specific
weighting method. We call this modeling procedure Bayesian Synthesis. The
methodology helps to alleviate concerns about the sizable gap between the
foundational underpinnings of the Bayesian paradigm and the practice of
Bayesian statistics. In experimental work we show that human modeling has
predictive performance superior to that of many automatic modeling techniques,
including AIC, BIC, Smoothing Splines, CART, Bagged CART, Bayes CART, BMA and
LARS, and only slightly inferior to that of BART. We also show that Bayesian
Synthesis further improves predictive performance. Additionally, we examine the
predictive performance of a simple average across analysts, which we dub Convex
Synthesis, and find that it also produces an improvement.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS444 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Bayesian semiparametric analysis for two-phase studies of gene-environment interaction
The two-phase sampling design is a cost-efficient way of collecting expensive
covariate information on a judiciously selected subsample. It is natural to
apply such a strategy for collecting genetic data in a subsample enriched for
exposure to environmental factors for gene-environment interaction (G x E)
analysis. In this paper, we consider two-phase studies of G x E interaction
where phase I data are available on exposure, covariates and disease status.
Stratified sampling is done to prioritize individuals for genotyping at phase
II conditional on disease and exposure. We consider a Bayesian analysis based
on the joint retrospective likelihood of phases I and II data. We address
several important statistical issues: (i) we consider a model with multiple
genes, environmental factors and their pairwise interactions. We employ a
Bayesian variable selection algorithm to reduce the dimensionality of this
potentially high-dimensional model; (ii) we use the assumption of gene-gene and
gene-environment independence to trade off between bias and efficiency for
estimating the interaction parameters through use of hierarchical priors
reflecting this assumption; (iii) we posit a flexible model for the joint
distribution of the phase I categorical variables using the nonparametric Bayes
construction of Dunson and Xing [J. Amer. Statist. Assoc. 104 (2009)
1042-1051].Comment: Published in at http://dx.doi.org/10.1214/12-AOAS599 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Bayesian Dropout
Dropout has recently emerged as a powerful and simple method for training
neural networks preventing co-adaptation by stochastically omitting neurons.
Dropout is currently not grounded in explicit modelling assumptions which so
far has precluded its adoption in Bayesian modelling. Using Bayesian entropic
reasoning we show that dropout can be interpreted as optimal inference under
constraints. We demonstrate this on an analytically tractable regression model
providing a Bayesian interpretation of its mechanism for regularizing and
preventing co-adaptation as well as its connection to other Bayesian
techniques. We also discuss two general approximate techniques for applying
Bayesian dropout for general models, one based on an analytical approximation
and the other on stochastic variational techniques. These techniques are then
applied to a Baysian logistic regression problem and are shown to improve
performance as the model become more misspecified. Our framework roots dropout
as a theoretically justified and practical tool for statistical modelling
allowing Bayesians to tap into the benefits of dropout training.Comment: 21 pages, 3 figures. Manuscript prepared 2014 and awaiting submissio
Targeting Bayes factors with direct-path non-equilibrium thermodynamic integration
Thermodynamic integration (TI) for computing marginal likelihoods is based on an inverse annealing path from the prior to the posterior distribution. In many cases, the resulting estimator suffers from high variability, which particularly stems from the prior regime. When comparing complex models with differences in a comparatively small number of parameters, intrinsic errors from sampling fluctuations may outweigh the differences in the log marginal likelihood estimates. In the present article, we propose a thermodynamic integration scheme that directly targets the log Bayes factor. The method is based on a modified annealing path between the posterior distributions of the two models compared, which systematically avoids the high variance prior regime. We combine this scheme with the concept of non-equilibrium TI to minimise discretisation errors from numerical integration. Results obtained on Bayesian regression models applied to standard benchmark data, and a complex hierarchical model applied to biopathway inference, demonstrate a significant reduction in estimator variance over state-of-the-art TI methods
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