Predicting Spiking Activities in DLS Neurons with Linear-Nonlinear-Poisson Model (original) (raw)
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Analysis of Neuronal Spike Trains, Deconstructed
Neuron, 2016
As information flows through the brain, neuronal firing progresses from encoding the world as sensed by the animal to driving the motor output of subsequent behavior. One of the more tractable goals of quantitative neuroscience is to develop predictive models that relate the sensory or motor streams with neuronal firing. Here we review and contrast analytical tools used to accomplish this task. We focus on classes of models in which the external variable is compared with one or more feature vectors to extract a low-dimensional representation, the history of spiking and other variables are potentially incorporated, and these factors are nonlinearly transformed to predict the occurrences of spikes. We illustrate these techniques in application to datasets of different degrees of complexity. In particular, we address the fitting of models in the presence of strong correlations in the external variable, as occurs in natural sensory stimuli and in movement. Spectral correlation between predicted and measured spike trains is introduced to contrast the relative success of different methods.
Neuronal Spike Train Analysis in Likelihood Space
PLoS ONE, 2011
Background: Conventional methods for spike train analysis are predominantly based on the rate function. Additionally, many experiments have utilized a temporal coding mechanism. Several techniques have been used for analyzing these two sources of information separately, but using both sources in a single framework remains a challenging problem. Here, an innovative technique is proposed for spike train analysis that considers both rate and temporal information. Methodology/Principal Findings: Point process modeling approach is used to estimate the stimulus conditional distribution, based on observation of repeated trials. The extended Kalman filter is applied for estimation of the parameters in a parametric model. The marked point process strategy is used in order to extend this model from a single neuron to an entire neuronal population. Each spike train is transformed into a binary vector and then projected from the observation space onto the likelihood space. This projection generates a newly structured space that integrates temporal and rate information, thus improving performance of distribution-based classifiers. In this space, the stimulus-specific information is used as a distance metric between two stimuli. To illustrate the advantages of the proposed technique, spiking activity of inferior temporal cortex neurons in the macaque monkey are analyzed in both the observation and likelihood spaces. Based on goodness-of-fit, performance of the estimation method is demonstrated and the results are subsequently compared with the firing rate-based framework. Conclusions/Significance: From both rate and temporal information integration and improvement in the neural discrimination of stimuli, it may be concluded that the likelihood space generates a more accurate representation of stimulus space. Further, an understanding of the neuronal mechanism devoted to visual object categorization may be addressed in this framework as well.
Parametric models to relate spike train and LFP dynamics with neural information processing
Frontiers in Computational Neuroscience, 2012
Spike trains and local field potentials (LFPs) resulting from extracellular current flows provide a substrate for neural information processing. Understanding the neural code from simultaneous spike-field recordings and subsequent decoding of information processing events will have widespread applications. One way to demonstrate an understanding of the neural code, with particular advantages for the development of applications, is to formulate a parametric statistical model of neural activity and its covariates. Here, we propose a set of parametric spike-field models (unified models) that can be used with existing decoding algorithms to reveal the timing of task or stimulus specific processing. Our proposed unified modeling framework captures the effects of two important features of information processing: time-varying stimulus-driven inputs and ongoing background activity that occurs even in the absence of environmental inputs. We have applied this framework for decoding neural latencies in simulated and experimentally recorded spike-field sessions obtained from the lateral intraparietal area (LIP) of awake, behaving monkeys performing cued look-and-reach movements to spatial targets. Using both simulated and experimental data, we find that estimates of trial-by-trial parameters are not significantly affected by the presence of ongoing background activity. However, including background activity in the unified model improves goodness of fit for predicting individual spiking events. Uncovering the relationship between the model parameters and the timing of movements offers new ways to test hypotheses about the relationship between neural activity and behavior. We obtained significant spike-field onset time correlations from single trials using a previously published data set where significantly strong correlation was only obtained through trial averaging. We also found that unified models extracted a stronger relationship between neural response latency and trial-by-trial behavioral performance than existing models of neural information processing. Our results highlight the utility of the unified modeling framework for characterizing spike-LFP recordings obtained during behavioral performance.
Neural Network Poisson Models for Behavioural and Neural Spike Train Data
One of the most important and challenging application areas for complex machine learning methods is to predict, characterize and model rich, multi-dimensional, neural data. Recent advances in neural recording techniques have made it possible to monitor the activities of a large number of neurons across different brain regions as animals perform behavioural tasks. This poses the critical challenge of establishing links between neural activity at a microscopic scale, which might for instance represent sensory input, and at a macroscopic scale, which then generates behaviour. Predominant modeling methods apply rather disjoint techniques to these scales; by contrast, we suggest an end-to-end model which exploits recent developments of flexible, but tractable, neural network point-process models to characterize dependencies between stimuli, actions, and neural data. We apply this model to a public dataset collected using Neuropixel probes in mice performing a visually-guided behavioural ...
An Empirical Model for Reliable Spiking Activity
Neural computation, 2015
Understanding a neuron's transfer function, which relates a neuron's inputs to its outputs, is essential for understanding the computational role of single neurons. Recently, statistical models, based on point processes and using generalized linear model (GLM) technology, have been widely applied to predict dynamic neuronal transfer functions. However, the standard version of these models fails to capture important features of neural activity, such as responses to stimuli that elicit highly reliable trial-to-trial spiking. Here, we consider a generalization of the usual GLM that incorporates nonlinearity by modeling reliable and nonreliable spikes as being generated by distinct stimulus features. We develop and apply these models to spike trains from olfactory bulb mitral cells recorded in vitro. We find that spike generation in these neurons is better modeled when reliable and unreliable spikes are considered separately and that this effect is most pronounced for neurons wi...
Fitting neuron models to spike trains
Frontiers in …, 2011
Computational modeling is increasingly used to understand the function of neural circuits in systems neuroscience. These studies require models of individual neurons with realistic input–output properties. Recently, it was found that spiking models can accurately predict the precisely timed spike trains produced by cortical neurons in response to somatically injected currents, if properly fitted. This requires fitting techniques that are efficient and flexible enough to easily test different candidate models. We present a generic solution, based on the Brian simulator (a neural network simulator in Python), which allows the user to define and fit arbitrary neuron models to electrophysiological recordings. It relies on vectorization and parallel computing techniques to achieve efficiency. We demonstrate its use on neural recordings in the barrel cortex and in the auditory brainstem, and confirm that simple adaptive spiking models can accurately predict the response of cortical neurons. Finally, we show how a complex multicompartmental model can be reduced to a simple effective spiking model.
Journal of Neuroscience Methods, 1999
We present a method to estimate the neuronal firing rate from single-trial spike trains. The method, based on convolution of the spike train with a fixed kernel function, is calibrated by means of simulated spike trains for a representative selection of realistic dynamic rate functions. We derive rules for the optimized use and performance of the kernel method, specifically with respect to an effective choice of the shape and width of the kernel functions. An application of our technique to the on-line, single-trial reconstruction of arm movement trajectories from multiple single-unit spike trains using dynamic population vectors illustrates a possible use of the proposed method.
Building a Dynamical Network Model from Neural Spiking Data Application of Poisson Likelihood
Research showed that, the information transmitted in biological neurons is encoded in the instants of successive action potentials or their firing rate. In addition to that, in-vivo operation of the neuron makes measurement difficult and thus continuous data collection is restricted. Due to those reasons, classical mean square estimation techniques that are frequently used in neural network training is very difficult to apply. In such situations, point processes and related likelihood methods may be beneficial. In this study, we will present how one can apply certain methods to use the stimulus-response data obtained from a neural process in the mathematical modeling of a neuron. The study is theoretical in nature and it will be supported by simulations. In addition it will be compared to a similar study.
Predicting Spike Occurrence and Neuronal Responsiveness from LFPs in Primary Somatosensory Cortex
Local Field Potentials (LFPs) integrate multiple neuronal events like synaptic inputs and intracellular potentials. LFP spatiotemporal features are particularly relevant in view of their applications both in research (e.g. for understanding brain rhythms, inter-areal neural communication and neronal coding) and in the clinics (e.g. for improving invasive Brain-Machine Interface devices). However the relation between LFPs and spikes is complex and not fully understood. As spikes represent the fundamental currency of neuronal communication this gap in knowledge strongly limits our comprehension of neuronal phenomena underlying LFPs. We investigated the LFP-spike relation during tactile stimulation in primary somatosensory (S-I) cortex in the rat. First we quantified how reliably LFPs and spikes code for a stimulus occurrence. Then we used the information obtained from our analyses to design a predictive model for spike occurrence based on LFP inputs. The model was endowed with a flexible meta-structure whose exact form, both in parameters and structure, was estimated by using a multi-objective optimization strategy. Our method provided a set of nonlinear simple equations that maximized the match between models and true neurons in terms of spike timings and Peri Stimulus Time Histograms. We found that both LFPs and spikes can code for stimulus occurrence with millisecond precision, showing, however, high variability. Spike patterns were predicted significantly above chance for 75% of the neurons analysed. Crucially, the level of prediction accuracy depended on the reliability in coding for the stimulus occurrence. The best predictions were obtained when both spikes and LFPs were highly responsive to the stimuli. Spike reliability is known to depend on neuron intrinsic properties (i.e. on channel noise) and on spontaneous local network fluctuations. Our results suggest that the latter, measured through the LFP response variability, play a dominant role.