178 research outputs found
A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data
Deducing the structure of neural circuits is one of the central problems of
modern neuroscience. Recently-introduced calcium fluorescent imaging methods
permit experimentalists to observe network activity in large populations of
neurons, but these techniques provide only indirect observations of neural
spike trains, with limited time resolution and signal quality. In this work we
present a Bayesian approach for inferring neural circuitry given this type of
imaging data. We model the network activity in terms of a collection of coupled
hidden Markov chains, with each chain corresponding to a single neuron in the
network and the coupling between the chains reflecting the network's
connectivity matrix. We derive a Monte Carlo Expectation--Maximization
algorithm for fitting the model parameters; to obtain the sufficient statistics
in a computationally-efficient manner, we introduce a specialized
blockwise-Gibbs algorithm for sampling from the joint activity of all observed
neurons given the observed fluorescence data. We perform large-scale
simulations of randomly connected neuronal networks with biophysically
realistic parameters and find that the proposed methods can accurately infer
the connectivity in these networks given reasonable experimental and
computational constraints. In addition, the estimation accuracy may be improved
significantly by incorporating prior knowledge about the sparseness of
connectivity in the network, via standard L penalization methods.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS303 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Covariate-assisted spectral clustering
Biological and social systems consist of myriad interacting units. The
interactions can be represented in the form of a graph or network. Measurements
of these graphs can reveal the underlying structure of these interactions,
which provides insight into the systems that generated the graphs. Moreover, in
applications such as connectomics, social networks, and genomics, graph data
are accompanied by contextualizing measures on each node. We utilize these node
covariates to help uncover latent communities in a graph, using a modification
of spectral clustering. Statistical guarantees are provided under a joint
mixture model that we call the node-contextualized stochastic blockmodel,
including a bound on the mis-clustering rate. The bound is used to derive
conditions for achieving perfect clustering. For most simulated cases,
covariate-assisted spectral clustering yields results superior to regularized
spectral clustering without node covariates and to an adaptation of canonical
correlation analysis. We apply our clustering method to large brain graphs
derived from diffusion MRI data, using the node locations or neurological
region membership as covariates. In both cases, covariate-assisted spectral
clustering yields clusters that are easier to interpret neurologically.Comment: 28 pages, 4 figures, includes substantial changes to theoretical
result
Nonparametric Bayes Modeling of Populations of Networks
Replicated network data are increasingly available in many research fields.
In connectomic applications, inter-connections among brain regions are
collected for each patient under study, motivating statistical models which can
flexibly characterize the probabilistic generative mechanism underlying these
network-valued data. Available models for a single network are not designed
specifically for inference on the entire probability mass function of a
network-valued random variable and therefore lack flexibility in characterizing
the distribution of relevant topological structures. We propose a flexible
Bayesian nonparametric approach for modeling the population distribution of
network-valued data. The joint distribution of the edges is defined via a
mixture model which reduces dimensionality and efficiently incorporates network
information within each mixture component by leveraging latent space
representations. The formulation leads to an efficient Gibbs sampler and
provides simple and coherent strategies for inference and goodness-of-fit
assessments. We provide theoretical results on the flexibility of our model and
illustrate improved performance --- compared to state-of-the-art models --- in
simulations and application to human brain networks
The Exact Equivalence of Distance and Kernel Methods for Hypothesis Testing
Distance-based tests, also called "energy statistics", are leading methods
for two-sample and independence tests from the statistics community.
Kernel-based tests, developed from "kernel mean embeddings", are leading
methods for two-sample and independence tests from the machine learning
community. A fixed-point transformation was previously proposed to connect the
distance methods and kernel methods for the population statistics. In this
paper, we propose a new bijective transformation between metrics and kernels.
It simplifies the fixed-point transformation, inherits similar theoretical
properties, allows distance methods to be exactly the same as kernel methods
for sample statistics and p-value, and better preserves the data structure upon
transformation. Our results further advance the understanding in distance and
kernel-based tests, streamline the code base for implementing these tests, and
enable a rich literature of distance-based and kernel-based methodologies to
directly communicate with each other.Comment: 24 pages main + 7 pages appendix, 3 figure
- …