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Journal of Computational Neuroscience

Yu Chen, Qi Xin, Valérie Ventura, Robert E Kass
Point process regression models, based on generalized linear model (GLM) technology, have been widely used for spike train analysis, but a recent paper by Gerhard et al. described a kind of instability, in which fitted models can generate simulated spike trains with explosive firing rates. We analyze the problem by extending the methods of Gerhard et al. First, we improve their instability diagnostic and extend it to a wider class of models. Next, we point out some common situations in which instability can be traced to model lack of fit...
September 15, 2018: Journal of Computational Neuroscience
Zhengdong Xiao, Sile Hu, Qiaosheng Zhang, Xiang Tian, Yaowu Chen, Jing Wang, Zhe Chen
Brain-machine interfaces (BMIs) have been widely used to study basic and translational neuroscience questions. In real-time closed-loop neuroscience experiments, many practical issues arise, such as trial-by-trial variability, and spike sorting noise or multi-unit activity. In this paper, we propose a new framework for change-point detection based on ensembles of independent detectors in the context of BMI application for detecting acute pain signals. Motivated from ensemble learning, our proposed "ensembles of change-point detectors" (ECPDs) integrate multiple decisions from independent detectors, which may be derived based on data recorded from different trials, data recorded from different brain regions, data of different modalities, or models derived from different learning methods...
September 12, 2018: Journal of Computational Neuroscience
Giuseppe Vinci, Valérie Ventura, Matthew A Smith, Robert E Kass
It is now common to record dozens to hundreds or more neurons simultaneously, and to ask how the network activity changes across experimental conditions. A natural framework for addressing questions of functional connectivity is to apply Gaussian graphical modeling to neural data, where each edge in the graph corresponds to a non-zero partial correlation between neurons. Because the number of possible edges is large, one strategy for estimating the graph has been to apply methods that aim to identify large sparse effects using an [Formula: see text] penalty...
September 6, 2018: Journal of Computational Neuroscience
Thomas Heiberg, Birgit Kriener, Tom Tetzlaff, Gaute T Einevoll, Hans E Plesser
Capturing the response behavior of spiking neuron models with rate-based models facilitates the investigation of neuronal networks using powerful methods for rate-based network dynamics. To this end, we investigate the responses of two widely used neuron model types, the Izhikevich and augmented multi-adapative threshold (AMAT) models, to a range of spiking inputs ranging from step responses to natural spike data. We find (i) that linear-nonlinear firing rate models fitted to test data can be used to describe the firing-rate responses of AMAT and Izhikevich spiking neuron models in many cases; (ii) that firing-rate responses are generally too complex to be captured by first-order low-pass filters but require bandpass filters instead; (iii) that linear-nonlinear models capture the response of AMAT models better than of Izhikevich models; (iv) that the wide range of response types evoked by current-injection experiments collapses to few response types when neurons are driven by stationary or sinusoidally modulated Poisson input; and (v) that AMAT and Izhikevich models show different responses to spike input despite identical responses to current injections...
August 27, 2018: Journal of Computational Neuroscience
Jonathan D Drover, Nicholas D Schiff
We propose a method - Frequency extracted hierarchical decomposition (FEHD) - for studying multivariate time series that identifies linear combinations of its components that possess a causally hierarchical structure - the method orders the components so that those at the "top" of the hierarchy drive those below. The method shares many of the features of the "hierarchical decomposition" method of Repucci et al. (Annals of Biomedical Engineering, 29, 1135-1149, 2001) but makes a crucial advance - the proposed method is capable of determining this causal hierarchy over arbitrarily specified frequency bands...
July 30, 2018: Journal of Computational Neuroscience
Jessica L Gaines, Kathleen E Finn, Julia P Slopsema, Lane A Heyboer, Katharine H Polasek
Surface electrical stimulation has the potential to be a powerful and non-invasive treatment for a variety of medical conditions but currently it is difficult to obtain consistent evoked responses. A viable clinical system must be able to adapt to variations in individuals to produce repeatable results. To more fully study the effect of these variations without performing exhaustive testing on human subjects, a system of computer models was created to predict motor and sensory axon activation in the median nerve due to surface electrical stimulation at the elbow...
August 2018: Journal of Computational Neuroscience
Rodrigo F O Pena, Michael A Zaks, Antonio C Roque
Spontaneous cortical population activity exhibits a multitude of oscillatory patterns, which often display synchrony during slow-wave sleep or under certain anesthetics and stay asynchronous during quiet wakefulness. The mechanisms behind these cortical states and transitions among them are not completely understood. Here we study spontaneous population activity patterns in random networks of spiking neurons of mixed types modeled by Izhikevich equations. Neurons are coupled by conductance-based synapses subject to synaptic noise...
June 19, 2018: Journal of Computational Neuroscience
Shigeru Kubota, Jonathan E Rubin
Excessive synchronization in neural activity is a hallmark of Parkinson's disease (PD). A promising technique for treating PD is coordinated reset (CR) neuromodulation in which a neural population is desynchronized by the delivery of spatially-distributed current stimuli using multiple electrodes. In this study, we perform numerical optimization to find the energy-optimal current waveform for desynchronizing neuronal network with CR stimulation, by proposing and applying a new optimization method based on the direct search algorithm...
June 7, 2018: Journal of Computational Neuroscience
Yimeng Zhang, Tai Sing Lee, Ming Li, Fang Liu, Shiming Tang
In this study, we evaluated the convolutional neural network (CNN) method for modeling V1 neurons of awake macaque monkeys in response to a large set of complex pattern stimuli. CNN models outperformed all the other baseline models, such as Gabor-based standard models for V1 cells and various variants of generalized linear models. We then systematically dissected different components of the CNN and found two key factors that made CNNs outperform other models: thresholding nonlinearity and convolution. In addition, we fitted our data using a pre-trained deep CNN via transfer learning...
June 5, 2018: Journal of Computational Neuroscience
L R González-Ramírez, M A Kramer
In this paper we study the influence of inhibition on an activity-based neural field model consisting of an excitatory population with a linear adaptation term that directly regulates the activity of the excitatory population. Such a model has been used to replicate traveling wave data as observed in high density local field potential recordings (González-Ramírez et al. PLoS Computational Biology, 11(2), e1004065, 2015). In this work, we show that by adding an inhibitory population to this model we can still replicate wave properties as observed in human clinical data preceding seizure termination, but the parameter range over which such waves exist becomes more restricted...
June 2018: Journal of Computational Neuroscience
Deniz Kilinc, Alper Demir
Spike timing is believed to be a key factor in sensory information encoding and computations performed by the neurons and neuronal circuits. However, the considerable noise and variability, arising from the inherently stochastic mechanisms that exist in the neurons and the synapses, degrade spike timing precision. Computational modeling can help decipher the mechanisms utilized by the neuronal circuits in order to regulate timing precision. In this paper, we utilize semi-analytical techniques, which were adapted from previously developed methods for electronic circuits, for the stochastic characterization of neuronal circuits...
June 2018: Journal of Computational Neuroscience
Timothy D Matchen, Jeff Moehlis
Deep brain stimulation (DBS) is a common method of combating pathological conditions associated with Parkinson's disease, Tourette syndrome, essential tremor, and other disorders, but whose mechanisms are not fully understood. One hypothesis, supported experimentally, is that some symptoms of these disorders are associated with pathological synchronization of neurons in the basal ganglia and thalamus. For this reason, there has been interest in recent years in finding efficient ways to desynchronize neurons that are both fast-acting and low-power...
June 2018: Journal of Computational Neuroscience
Azamat Yeldesbay, Tibor Tóth, Silvia Daun
Detailed neural network models of animal locomotion are important means to understand the underlying mechanisms that control the coordinated movement of individual limbs. Daun-Gruhn and Tóth, Journal of Computational Neuroscience 31(2), 43-60 (2011) constructed an inter-segmental network model of stick insect locomotion consisting of three interconnected central pattern generators (CPGs) that are associated with the protraction-retraction movements of the front, middle and hind leg. This model could reproduce the basic locomotion coordination patterns, such as tri- and tetrapod, and the transitions between them...
June 2018: Journal of Computational Neuroscience
Alexandre Richard, Patricio Orio, Etienne Tanré
Long-range dependence (LRD) has been observed in a variety of phenomena in nature, and for several years also in the spiking activity of neurons. Often, this is interpreted as originating from a non-Markovian system. Here we show that a purely Markovian integrate-and-fire (IF) model, with a noisy slow adaptation term, can generate interspike intervals (ISIs) that appear as having LRD. However a proper analysis shows that this is not the case asymptotically. For comparison, we also consider a new model of individual IF neuron with fractional (non-Markovian) noise...
June 2018: Journal of Computational Neuroscience
Nikhil Krishnan, Daniel B Poll, Zachary P Kilpatrick
Working memory (WM) is limited in its temporal length and capacity. Classic conceptions of WM capacity assume the system possesses a finite number of slots, but recent evidence suggests WM may be a continuous resource. Resource models typically assume there is no hard upper bound on the number of items that can be stored, but WM fidelity decreases with the number of items. We analyze a neural field model of multi-item WM that associates each item with the location of a bump in a finite spatial domain, considering items that span a one-dimensional continuous feature space...
June 2018: Journal of Computational Neuroscience
Sungmin Han, Jun-Uk Chu, Jong Woong Park, Inchan Youn
Proprioceptive afferent activities recorded by a multichannel microelectrode have been used to decode limb movements to provide sensory feedback signals for closed-loop control in a functional electrical stimulation (FES) system. However, analyzing the high dimensionality of neural activity is one of the major challenges in real-time applications. This paper proposes a linear feature projection method for the real-time decoding of ankle and knee joint angles. Single-unit activity was extracted as a feature vector from proprioceptive afferent signals that were recorded from the L7 dorsal root ganglion during passive movements of ankle and knee joints...
May 15, 2018: Journal of Computational Neuroscience
Dominik S Kufel, Grzegorz M Wojcik
It was previously reported, that temperature may significantly influence neural dynamics on the different levels of brain function. Thus, in computational neuroscience, it would be useful to make models scalable for a wide range of various brain temperatures. However, lack of experimental data and an absence of temperature-dependent analytical models of synaptic conductance does not allow to include temperature effects at the multi-neuron modeling level. In this paper, we propose a first step to deal with this problem: A new analytical model of AMPA-type synaptic conductance, which is able to incorporate temperature effects in low-frequency stimulations...
May 11, 2018: Journal of Computational Neuroscience
Amin Karbasi, Amir Hesam Salavati, Martin Vetterli
The connectivity of a neuronal network has a major effect on its functionality and role. It is generally believed that the complex network structure of the brain provides a physiological basis for information processing. Therefore, identifying the network's topology has received a lot of attentions in neuroscience and has been the center of many research initiatives such as Human Connectome Project. Nevertheless, direct and invasive approaches that slice and observe the neural tissue have proven to be time consuming, complex and costly...
April 2018: Journal of Computational Neuroscience
Osamu Hoshino, Meihong Zheng, Kazuo Watanabe
Recurrent input to sensory cortex, via long-range reciprocal projections between motor and sensory cortices, is essential for accurate perceptual judgments. GABA levels in sensory cortices correlate with perceptual performance. We simulated a neuron-astrocyte network model to investigate how top-down, feedback signaling from a motor network (Nmot) to a sensory network (Nsen) affects perceptual judgments in association with ambient (extracellular) GABA levels. In the Nsen, astrocytic transporters modulated ambient GABA levels around pyramidal cells...
April 2018: Journal of Computational Neuroscience
Danielle Morel, Chandan Singh, William B Levy
In many theories of neural computation, linearly summed synaptic activation is a pervasive assumption for the computations performed by individual neurons. Indeed, for certain nominally optimal models, linear summation is required. However, the biophysical mechanisms needed to produce linear summation may add to the energy-cost of neural processing. Thus, the benefits provided by linear summation may be outweighed by the energy-costs. Using voltage-gated conductances in a relatively simple neuron model, this paper quantifies the cost of linearizing dendritically localized synaptic activation...
April 2018: Journal of Computational Neuroscience
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