2,532 research outputs found
A Nonparametric Bayesian Approach to Uncovering Rat Hippocampal Population Codes During Spatial Navigation
Rodent hippocampal population codes represent important spatial information
about the environment during navigation. Several computational methods have
been developed to uncover the neural representation of spatial topology
embedded in rodent hippocampal ensemble spike activity. Here we extend our
previous work and propose a nonparametric Bayesian approach to infer rat
hippocampal population codes during spatial navigation. To tackle the model
selection problem, we leverage a nonparametric Bayesian model. Specifically, to
analyze rat hippocampal ensemble spiking activity, we apply a hierarchical
Dirichlet process-hidden Markov model (HDP-HMM) using two Bayesian inference
methods, one based on Markov chain Monte Carlo (MCMC) and the other based on
variational Bayes (VB). We demonstrate the effectiveness of our Bayesian
approaches on recordings from a freely-behaving rat navigating in an open field
environment. We find that MCMC-based inference with Hamiltonian Monte Carlo
(HMC) hyperparameter sampling is flexible and efficient, and outperforms VB and
MCMC approaches with hyperparameters set by empirical Bayes
DPO - Denoising, Deconvolving, and Decomposing Photon Observations
The analysis of astronomical images is a non-trivial task. The D3PO algorithm
addresses the inference problem of denoising, deconvolving, and decomposing
photon observations. Its primary goal is the simultaneous but individual
reconstruction of the diffuse and point-like photon flux given a single photon
count image, where the fluxes are superimposed. In order to discriminate
between these morphologically different signal components, a probabilistic
algorithm is derived in the language of information field theory based on a
hierarchical Bayesian parameter model. The signal inference exploits prior
information on the spatial correlation structure of the diffuse component and
the brightness distribution of the spatially uncorrelated point-like sources. A
maximum a posteriori solution and a solution minimizing the Gibbs free energy
of the inference problem using variational Bayesian methods are discussed.
Since the derivation of the solution is not dependent on the underlying
position space, the implementation of the D3PO algorithm uses the NIFTY package
to ensure applicability to various spatial grids and at any resolution. The
fidelity of the algorithm is validated by the analysis of simulated data,
including a realistic high energy photon count image showing a 32 x 32 arcmin^2
observation with a spatial resolution of 0.1 arcmin. In all tests the D3PO
algorithm successfully denoised, deconvolved, and decomposed the data into a
diffuse and a point-like signal estimate for the respective photon flux
components.Comment: 22 pages, 8 figures, 2 tables, accepted by Astronomy & Astrophysics;
refereed version, 1 figure added, results unchanged, software available at
http://www.mpa-garching.mpg.de/ift/d3po
Fast and scalable non-parametric Bayesian inference for Poisson point processes
We study the problem of non-parametric Bayesian estimation of the intensity
function of a Poisson point process. The observations are independent
realisations of a Poisson point process on the interval . We propose two
related approaches. In both approaches we model the intensity function as
piecewise constant on bins forming a partition of the interval . In
the first approach the coefficients of the intensity function are assigned
independent gamma priors, leading to a closed form posterior distribution. On
the theoretical side, we prove that as the posterior
asymptotically concentrates around the "true", data-generating intensity
function at an optimal rate for -H\"older regular intensity functions (). In the second approach we employ a gamma Markov chain prior on the
coefficients of the intensity function. The posterior distribution is no longer
available in closed form, but inference can be performed using a
straightforward version of the Gibbs sampler. Both approaches scale well with
sample size, but the second is much less sensitive to the choice of .
Practical performance of our methods is first demonstrated via synthetic data
examples. We compare our second method with other existing approaches on the UK
coal mining disasters data. Furthermore, we apply it to the US mass shootings
data and Donald Trump's Twitter data.Comment: 45 pages, 22 figure
Mixed membership stochastic blockmodels
Observations consisting of measurements on relationships for pairs of objects
arise in many settings, such as protein interaction and gene regulatory
networks, collections of author-recipient email, and social networks. Analyzing
such data with probabilisic models can be delicate because the simple
exchangeability assumptions underlying many boilerplate models no longer hold.
In this paper, we describe a latent variable model of such data called the
mixed membership stochastic blockmodel. This model extends blockmodels for
relational data to ones which capture mixed membership latent relational
structure, thus providing an object-specific low-dimensional representation. We
develop a general variational inference algorithm for fast approximate
posterior inference. We explore applications to social and protein interaction
networks.Comment: 46 pages, 14 figures, 3 table
- …