10,519 research outputs found
Joint estimation of multiple related biological networks
Graphical models are widely used to make inferences concerning interplay in
multivariate systems. In many applications, data are collected from multiple
related but nonidentical units whose underlying networks may differ but are
likely to share features. Here we present a hierarchical Bayesian formulation
for joint estimation of multiple networks in this nonidentically distributed
setting. The approach is general: given a suitable class of graphical models,
it uses an exchangeability assumption on networks to provide a corresponding
joint formulation. Motivated by emerging experimental designs in molecular
biology, we focus on time-course data with interventions, using dynamic
Bayesian networks as the graphical models. We introduce a computationally
efficient, deterministic algorithm for exact joint inference in this setting.
We provide an upper bound on the gains that joint estimation offers relative to
separate estimation for each network and empirical results that support and
extend the theory, including an extensive simulation study and an application
to proteomic data from human cancer cell lines. Finally, we describe
approximations that are still more computationally efficient than the exact
algorithm and that also demonstrate good empirical performance.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS761 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
A Bayesian alternative to mutual information for the hierarchical clustering of dependent random variables
The use of mutual information as a similarity measure in agglomerative
hierarchical clustering (AHC) raises an important issue: some correction needs
to be applied for the dimensionality of variables. In this work, we formulate
the decision of merging dependent multivariate normal variables in an AHC
procedure as a Bayesian model comparison. We found that the Bayesian
formulation naturally shrinks the empirical covariance matrix towards a matrix
set a priori (e.g., the identity), provides an automated stopping rule, and
corrects for dimensionality using a term that scales up the measure as a
function of the dimensionality of the variables. Also, the resulting log Bayes
factor is asymptotically proportional to the plug-in estimate of mutual
information, with an additive correction for dimensionality in agreement with
the Bayesian information criterion. We investigated the behavior of these
Bayesian alternatives (in exact and asymptotic forms) to mutual information on
simulated and real data. An encouraging result was first derived on
simulations: the hierarchical clustering based on the log Bayes factor
outperformed off-the-shelf clustering techniques as well as raw and normalized
mutual information in terms of classification accuracy. On a toy example, we
found that the Bayesian approaches led to results that were similar to those of
mutual information clustering techniques, with the advantage of an automated
thresholding. On real functional magnetic resonance imaging (fMRI) datasets
measuring brain activity, it identified clusters consistent with the
established outcome of standard procedures. On this application, normalized
mutual information had a highly atypical behavior, in the sense that it
systematically favored very large clusters. These initial experiments suggest
that the proposed Bayesian alternatives to mutual information are a useful new
tool for hierarchical clustering
Spike Clustering and Neuron Tracking over Successive Time Windows
This paper introduces a new methodology for tracking signals from individual neurons over time in multiunit extracellular recordings. The core of our strategy relies upon an extension of a traditional mixture model approach, with parameter optimization via expectation-maximimization (EM), to incorporate clustering results from the preceding time period in a Bayesian manner. EM initialization is also achieved by utilizing these prior clustering results. After clustering, we match the current and prior clusters to track persisting neurons. Applications of this spike sorting method to recordings from macaque parietal cortex show that it provides significantly more consistent clustering and tracking results
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