John S. Choi

Evaluating dependence in spike train metric spaces

Assessing dependence between two sets of spike trains or between a set of input stimuli and the corresponding generated spike trains is crucial in many neuroscientific applications, such as in analyzing functional connectivity among neural assemblies, and in neural coding. Dependence between two random variables is traditionally assessed in terms of mutual information. However, although well explored in the context of real or vector valued random variables, estimating mutual information still remains a challenging issue when the random variables exist in more exotic spaces such as the space of spike trains. In the statistical literature, on the other hand, the concept of dependence between two random variables has been presented in many other ways, e.g. using copula, or using measures of association such as Spearmans ρ, and Kendalls τ. Although these methods are usually applied on the real line, their simplicity, both in terms of understanding and estimating, make them worth investigating in the context of spike train dependence. In this paper, we generalize the concept of association to any abstract metric spaces. This new approach is an attractive alternative to mutual information, since it can be easily estimated from realizations without binning or clustering. It also provides an intuitive understanding of what dependence implies in the context of realizations. We show that this new methodology effectively captures dependence between sets of stimuli and spike trains. Moreover, the estimator has desirable small sample characteristic, and it often outperforms an existing similar metric based approach.

An adaptive decoder from spike trains to micro-stimulation using kernel least-mean-squares (KLMS)

This paper proposes a nonlinear adaptive decoder for somatosensory micro-stimulation based on the kernel least mean square (KLMS) algorithm applied directly on the space of spike trains. Instead of using a binned representation of spike trains, we transform the vector of spike times into a function in reproducing kernel Hilbert space (RKHS), where the inner product of two spike time vectors is defined by a nonlinear cross intensity kernel. This representation encapsulates the statistical description of the point process that generates the spike trains, and bypasses the curse of dimensionality-resolution of the binned spike representations. We compare our method with two other methods based on binned data: GLM and KLMS, in reconstructing biphasic micro-stimulation. The results indicate that the KLMS based on RKHS for spike train is able to detect the timing, the shape and the amplitude of the biphasic stimulation with the best accuracy.

Control of a center-out reaching task using a reinforcement learning Brain-Machine Interface

In this work, we develop an experimental primate test bed for a center-out reaching task to test the performance of reinforcement learning based decoders for Brain-Machine Interfaces. Neural recordings obtained from the primary motor cortex were used to adapt a decoder using only sequences of neuronal activation and reinforced interaction with the environment. From a naïve state, the system was able to achieve 100% of the targets without any a priori knowledge of the correct neural-to-motor mapping. Results show that the coupling of motor and reward information in an adaptive BMI decoder has the potential to create more realistic and functional models necessary for future BMI control.

Neural decoding with kernel-based metric learning

In studies of the nervous system, the choice of metric for the neural responses is a pivotal assumption. For instance, a well-suited distance metric enables us to gauge the similarity of neural responses to various stimuli and assess the variability of responses to a repeated stimulus—exploratory steps in understanding how the stimuli are encoded neurally. Here we introduce an approach where the metric is tuned for a particular neural decoding task. Neural spike train metrics have been used to quantify the information content carried by the timing of action potentials. While a number of metrics for individual neurons exist, a method to optimally combine single-neuron metrics into multineuron, or population-based, metrics is lacking. We pose the problem of optimizing multineuron metrics and other metrics using centered alignment, a kernel-based dependence measure. The approach is demonstrated on invasively recorded neural data consisting of both spike trains and local field potentials. The experimental paradigm consists of decoding the location of tactile stimulation on the forepaws of anesthetized rats. We show that the optimized metrics highlight the distinguishing dimensions of the neural response, significantly increase the decoding accuracy, and improve nonlinear dimensionality reduction methods for exploratory neural analysis.

A tensor-product-kernel framework for multiscale neural activity decoding and control

Brain machine interfaces (BMIs) have attracted intense attention as a promising technology for directly interfacing computers or prostheses with the brains motor and sensory areas, thereby bypassing the body. The availability of multiscale neural recordings including spike trains and local field potentials (LFPs) brings potential opportunities to enhance computational modeling by enriching the characterization of the neural system state. However, heterogeneity on data type (spike timing versus continuous amplitude signals) and spatiotemporal scale complicates the model integration of multiscale neural activity. In this paper, we propose a tensor-product-kernel-based framework to integrate the multiscale activity and exploit the complementary information available in multiscale neural activity. This provides a common mathematical framework for incorporating signals from different domains. The approach is applied to the problem of neural decoding and control. For neural decoding, the framework is able to identify the nonlinear functional relationship between the multiscale neural responses and the stimuli using general purpose kernel adaptive filtering. In a sensory stimulation experiment, the tensor-product-kernel decoder outperforms decoders that use only a single neural data type. In addition, an adaptive inverse controller for delivering electrical microstimulation patterns that utilizes the tensor-product kernel achieves promising results in emulating the responses to natural stimulation.

An Electric Field Model for Prediction of Somatosensory (S1) Cortical Field Potentials Induced by Ventral Posterior Lateral (VPL) Thalamic Microstimulation

Microstimulation (MiSt) is used experimentally and clinically to activate localized populations of neural elements. However, it is difficult to predict-and subsequently control-neural responses to simultaneous current injection through multiple electrodes in an array. This is due to the unknown locations of neuronal elements in the extracellular medium that are excited by the superposition of multiple parallel current sources. We, therefore, propose a model that maps the computed electric field in the 3-D space surrounding the stimulating electrodes in one brain region to the local field potential (LFP) fluctuations evoked in a downstream region. Our model is trained with the recorded LFP waveforms in the primary somatosensory cortex (S1) resulting from MiSt applied in multiple electrode configurations in the ventral posterolateral nucleus (VPL) of the quiet awake rat. We then predict the cortical responses to MiSt in “novel” electrode configurations, a result that suggests that this technique could aid in the design of spatially optimized MiSt patterns through a multielectrode array.

Optimizing microstimulation using a reinforcement learning framework

The ability to provide sensory feedback is desired to enhance the functionality of neuroprosthetics. Somatosensory feedback provides closed-loop control to the motor system, which is lacking in feedforward neuroprosthetics. In the case of existing somatosensory function, a template of the natural response can be used as a template of desired response elicited by electrical microstimulation. In the case of no initial training data, microstimulation parameters that produce responses close to the template must be selected in an online manner. We propose using reinforcement learning as a framework to balance the exploration of the parameter space and the continued selection of promising parameters for further stimulation. This approach avoids an explicit model of the neural response from stimulation. We explore a preliminary architecture — treating the task as a k-armed bandit — using offline data recorded for natural touch and thalamic microstimulation, and we examine the methods efficiency in exploring the parameter space while concentrating on promising parameter forms. The best matching stimulation parameters, from k = 68 different forms, are selected by the reinforcement learning algorithm consistently after 334 realizations.

Subspace matching thalamic microstimulation to tactile evoked potentials in rat somatosensory cortex

We show experimental results that the evoked local field potentials of the rat somatosensory cortex from natural tactile touch of forepaw digits and matched thalamic microstimulation can be qualitatively and quantitively similar. In ongoing efforts to optimize the microstimulation settings (e.g., location, amplitude, etc.) to match the natural response, we investigate whether subspace projection methods, specifically the eigenface approach proposed in the computer vision community (Turk and Pentland 1991 [1]), can be used to choose the parameters of microstimulation such that the response matches a single tactile touch realization. Since the evoked potentials from multiple electrodes are high dimensional spatio-temporal data, the subspace projections improve computational efficiency and can reduce the effect of noisy realizations. In computing the PCA projections we use the peristimulus averages instead of the realizations. The dataset is pruned of unreliable stimulation types. A new subspace is computed for the pruned stimulation type, and is used to estimate a sequence of microstimulations to best match the natural responses. This microstimulation sequence is applied in vivo and quantitative analysis shows that per realization matching does statistically better than choosing randomly from the pruned subset.

Eliciting naturalistic cortical responses with a sensory prosthesis via optimized microstimulation

OBJECTIVE Lost sensations, such as touch, could one day be restored by electrical stimulation along the sensory neural pathways. Such stimulation, when informed by electronic sensors, could provide naturalistic cutaneous and proprioceptive feedback to the user. Perceptually, microstimulation of somatosensory brain regions produces localized, modality-specific sensations, and several spatiotemporal parameters have been studied for their discernibility. However, systematic methods for encoding a wide array of naturally occurring stimuli into biomimetic percepts via multi-channel microstimulation are lacking. More specifically, generating spatiotemporal patterns for explicitly evoking naturalistic neural activation has not yet been explored. APPROACH We address this problem by first modeling the dynamical input-output relationship between multichannel microstimulation and downstream neural responses, and then optimizing the input pattern to reproduce naturally occurring touch responses as closely as possible. MAIN RESULTS Here we show that such optimization produces responses in the S1 cortex of the anesthetized rat that are highly similar to natural, tactile-stimulus-evoked counterparts. Furthermore, information on both pressure and location of the touch stimulus was found to be highly preserved. SIGNIFICANCE Our results suggest that the currently presented stimulus optimization approach holds great promise for restoring naturalistic levels of sensation.

Decoding stimuli from multi-source neural responses

Spike trains and local field potentials (LFPs) are two different manifestations of neural activity recorded simultaneously from the same electrode array and contain complementary information of stimuli or behaviors. This paper proposes a tensor product kernel based decoder, which allows modeling the sample from different sources individually and mapping them onto the same reproducing kernel Hilbert space (RKHS) defined by the tensor product of the individual kernels for each source, where linear regression is conducted to identify the nonlinear mapping from the multi-type neural responses to the stimuli. The decoding results of the rat sensory stimulation experiment show that the tensor-product-kernel-based decoder outperforms the decoders with either single-type neural activities.