24,146 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
Matching matched filtering with deep networks in gravitational-wave astronomy
We report on the construction of a deep convolutional neural network that can
reproduce the sensitivity of a matched-filtering search for binary black hole
gravitational-wave signals. The standard method for the detection of well
modeled transient gravitational-wave signals is matched filtering. However, the
computational cost of such searches in low latency will grow dramatically as
the low frequency sensitivity of gravitational-wave detectors improves.
Convolutional neural networks provide a highly computationally efficient method
for signal identification in which the majority of calculations are performed
prior to data taking during a training process. We use only whitened time
series of measured gravitational-wave strain as an input, and we train and test
on simulated binary black hole signals in synthetic Gaussian noise
representative of Advanced LIGO sensitivity. We show that our network can
classify signal from noise with a performance that emulates that of match
filtering applied to the same datasets when considering the sensitivity defined
by Reciever-Operator characteristics.Comment: 5 pages, 3 figures, submitted to PR
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
A point process framework for modeling electrical stimulation of the auditory nerve
Model-based studies of auditory nerve responses to electrical stimulation can
provide insight into the functioning of cochlear implants. Ideally, these
studies can identify limitations in sound processing strategies and lead to
improved methods for providing sound information to cochlear implant users. To
accomplish this, models must accurately describe auditory nerve spiking while
avoiding excessive complexity that would preclude large-scale simulations of
populations of auditory nerve fibers and obscure insight into the mechanisms
that influence neural encoding of sound information. In this spirit, we develop
a point process model of the auditory nerve that provides a compact and
accurate description of neural responses to electric stimulation. Inspired by
the framework of generalized linear models, the proposed model consists of a
cascade of linear and nonlinear stages. We show how each of these stages can be
associated with biophysical mechanisms and related to models of neuronal
dynamics. Moreover, we derive a semi-analytical procedure that uniquely
determines each parameter in the model on the basis of fundamental statistics
from recordings of single fiber responses to electric stimulation, including
threshold, relative spread, jitter, and chronaxie. The model also accounts for
refractory and summation effects that influence the responses of auditory nerve
fibers to high pulse rate stimulation. Throughout, we compare model predictions
to published physiological data and explain differences in auditory nerve
responses to high and low pulse rate stimulation. We close by performing an
ideal observer analysis of simulated spike trains in response to sinusoidally
amplitude modulated stimuli and find that carrier pulse rate does not affect
modulation detection thresholds.Comment: 1 title page, 27 manuscript pages, 14 figures, 1 table, 1 appendi
Classification-based prediction of effective connectivity between timeseries with a realistic cortical network model
Effective connectivity measures the pattern of causal interactions between brain regions. Traditionally, these patterns of causality are inferred from brain recordings using either non-parametric, i.e., model-free, or parametric, i.e., model-based, approaches. The latter approaches, when based on biophysically plausible models, have the advantage that they may facilitate the interpretation of causality in terms of underlying neural mechanisms. Recent biophysically plausible neural network models of recurrent microcircuits have shown the ability to reproduce well the characteristics of real neural activity and can be applied to model interacting cortical circuits. Unfortunately, however, it is challenging to invert these models in order to estimate effective connectivity from observed data. Here, we propose to use a classification-based method to approximate the result of such complex model inversion. The classifier predicts the pattern of causal interactions given a multivariate timeseries as input. The classifier is trained on a large number of pairs of multivariate timeseries and the respective pattern of causal interactions, which are generated by simulation from the neural network model. In simulated experiments, we show that the proposed method is much more accurate in detecting the causal structure of timeseries than current best practice methods. Additionally, we present further results to characterize the validity of the neural network model and the ability of the classifier to adapt to the generative model of the data
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