20,809 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
Respondent-Driven Sampling: An Assessment of Current Methodology
Respondent-Driven Sampling (RDS) employs a variant of a link-tracing network
sampling strategy to collect data from hard-to-reach populations. By tracing
the links in the underlying social network, the process exploits the social
structure to expand the sample and reduce its dependence on the initial
(convenience) sample.
The primary goal of RDS is typically to estimate population averages in the
hard-to-reach population. The current estimates make strong assumptions in
order to treat the data as a probability sample. In particular, we evaluate
three critical sensitivities of the estimators: to bias induced by the initial
sample, to uncontrollable features of respondent behavior, and to the
without-replacement structure of sampling.
This paper sounds a cautionary note for the users of RDS. While current RDS
methodology is powerful and clever, the favorable statistical properties
claimed for the current estimates are shown to be heavily dependent on often
unrealistic assumptions.Comment: 35 pages, 29 figures, under revie
Activity Recognition using Hierarchical Hidden Markov Models on Streaming Sensor Data
Activity recognition from sensor data deals with various challenges, such as
overlapping activities, activity labeling, and activity detection. Although
each challenge in the field of recognition has great importance, the most
important one refers to online activity recognition. The present study tries to
use online hierarchical hidden Markov model to detect an activity on the stream
of sensor data which can predict the activity in the environment with any
sensor event. The activity recognition samples were labeled by the statistical
features such as the duration of activity. The results of our proposed method
test on two different datasets of smart homes in the real world showed that one
dataset has improved 4% and reached (59%) while the results reached 64.6% for
the other data by using the best methods
Hidden Markov models for the activity profile of terrorist groups
The main focus of this work is on developing models for the activity profile
of a terrorist group, detecting sudden spurts and downfalls in this profile,
and, in general, tracking it over a period of time. Toward this goal, a
-state hidden Markov model (HMM) that captures the latent states underlying
the dynamics of the group and thus its activity profile is developed. The
simplest setting of corresponds to the case where the dynamics are
coarsely quantized as Active and Inactive, respectively. A state estimation
strategy that exploits the underlying HMM structure is then developed for spurt
detection and tracking. This strategy is shown to track even nonpersistent
changes that last only for a short duration at the cost of learning the
underlying model. Case studies with real terrorism data from open-source
databases are provided to illustrate the performance of the proposed
methodology.Comment: Published in at http://dx.doi.org/10.1214/13-AOAS682 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Hyper-Spectral Image Analysis with Partially-Latent Regression and Spatial Markov Dependencies
Hyper-spectral data can be analyzed to recover physical properties at large
planetary scales. This involves resolving inverse problems which can be
addressed within machine learning, with the advantage that, once a relationship
between physical parameters and spectra has been established in a data-driven
fashion, the learned relationship can be used to estimate physical parameters
for new hyper-spectral observations. Within this framework, we propose a
spatially-constrained and partially-latent regression method which maps
high-dimensional inputs (hyper-spectral images) onto low-dimensional responses
(physical parameters such as the local chemical composition of the soil). The
proposed regression model comprises two key features. Firstly, it combines a
Gaussian mixture of locally-linear mappings (GLLiM) with a partially-latent
response model. While the former makes high-dimensional regression tractable,
the latter enables to deal with physical parameters that cannot be observed or,
more generally, with data contaminated by experimental artifacts that cannot be
explained with noise models. Secondly, spatial constraints are introduced in
the model through a Markov random field (MRF) prior which provides a spatial
structure to the Gaussian-mixture hidden variables. Experiments conducted on a
database composed of remotely sensed observations collected from the Mars
planet by the Mars Express orbiter demonstrate the effectiveness of the
proposed model.Comment: 12 pages, 4 figures, 3 table
The Computational Structure of Spike Trains
Neurons perform computations, and convey the results of those computations
through the statistical structure of their output spike trains. Here we present
a practical method, grounded in the information-theoretic analysis of
prediction, for inferring a minimal representation of that structure and for
characterizing its complexity. Starting from spike trains, our approach finds
their causal state models (CSMs), the minimal hidden Markov models or
stochastic automata capable of generating statistically identical time series.
We then use these CSMs to objectively quantify both the generalizable structure
and the idiosyncratic randomness of the spike train. Specifically, we show that
the expected algorithmic information content (the information needed to
describe the spike train exactly) can be split into three parts describing (1)
the time-invariant structure (complexity) of the minimal spike-generating
process, which describes the spike train statistically; (2) the randomness
(internal entropy rate) of the minimal spike-generating process; and (3) a
residual pure noise term not described by the minimal spike-generating process.
We use CSMs to approximate each of these quantities. The CSMs are inferred
nonparametrically from the data, making only mild regularity assumptions, via
the causal state splitting reconstruction algorithm. The methods presented here
complement more traditional spike train analyses by describing not only spiking
probability and spike train entropy, but also the complexity of a spike train's
structure. We demonstrate our approach using both simulated spike trains and
experimental data recorded in rat barrel cortex during vibrissa stimulation.Comment: Somewhat different format from journal version but same conten
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