Low-frequency local field potentials in primate motor cortex and their application to neural interfaces

PhD ThesisFor patients with spinal cord injury and paralysis, there are currently very limited options for clinical therapy. Brain-machine interfaces (BMIs) are neuroprosthetic devices that are being developed to record from the motor cortex in such patients, bypass the spinal lesion, and use decoded signals to control an effector, such as a prosthetic limb. The ideal BMI would be durable, reliable, totally predictable, fully-implantable, and have generous battery life. Current, state-of-the-art BMIs are limited in all of these domains; partly because the typical signals used—neuronal action potentials, or ‘spikes’—are very susceptible to micro-movement of recording electrodes. Recording spikes from the same neurons over many months is therefore difficult, and decoder behaviour may be unpredictable from day-today. Spikes also need to be digitized at high frequencies (~104 Hz) and heavily processed. As a result, devices are energy-hungry and difficult to miniaturise. Low-frequency local field potentials (lf-LFPs; < 5 Hz) are an alternative cortical signal. They are more stable and can be captured and processed at much lower frequencies (~101 Hz). Here we investigate rhythmical lf-LFP activity, related to the firing of local cortical neurons, during isometric wrist movements in Rhesus macaques. Multichannel spike-related slow potentials (SRSPs) can be used to accurately decode the firing rates of individual motor cortical neurons, and subjects can control a BMI task using this synthetic signal, as if they were controlling the actual firing rate. Lf-LFP–based firing rate estimates are stable over time – even once actual spike recordings have been lost. Furthermore, the dynamics of lf-LFPs are distinctive enough, that an unsupervised approach can be used to train a decoder to extract movement-related features for use in biofeedback BMIs. Novel electrode designs may help us optimise the recording of these signals, and facilitate progress towards a new generation of robust, implantable BMIs for patients.Research Studentship from the MRC, and Andy Jackson’s laboratory (hence this work) is supported by the Wellcome Trust

Algorithms for Neural Prosthetic Applications

abstract: In the last 15 years, there has been a significant increase in the number of motor neural prostheses used for restoring limb function lost due to neurological disorders or accidents. The aim of this technology is to enable patients to control a motor prosthesis using their residual neural pathways (central or peripheral). Recent studies in non-human primates and humans have shown the possibility of controlling a prosthesis for accomplishing varied tasks such as self-feeding, typing, reaching, grasping, and performing fine dexterous movements. A neural decoding system comprises mainly of three components: (i) sensors to record neural signals, (ii) an algorithm to map neural recordings to upper limb kinematics and (iii) a prosthetic arm actuated by control signals generated by the algorithm. Machine learning algorithms that map input neural activity to the output kinematics (like finger trajectory) form the core of the neural decoding system. The choice of the algorithm is thus, mainly imposed by the neural signal of interest and the output parameter being decoded. The various parts of a neural decoding system are neural data, feature extraction, feature selection, and machine learning algorithm. There have been significant advances in the field of neural prosthetic applications. But there are challenges for translating a neural prosthesis from a laboratory setting to a clinical environment. To achieve a fully functional prosthetic device with maximum user compliance and acceptance, these factors need to be addressed and taken into consideration. Three challenges in developing robust neural decoding systems were addressed by exploring neural variability in the peripheral nervous system for dexterous finger movements, feature selection methods based on clinically relevant metrics and a novel method for decoding dexterous finger movements based on ensemble methods.Dissertation/ThesisDoctoral Dissertation Bioengineering 201

Learning Hybrid System Models for Supervisory Decoding of Discrete State, with applications to the Parietal Reach Region

Based on Gibbs sampling, a novel method to identify mathematical models of neural activity in response to temporal changes of behavioral or cognitive state is presented. This work is motivated by the developing field of neural prosthetics, where a supervisory controller is required to classify activity of a brain region into suitable discrete modes. Here, neural activity in each discrete mode is modeled with nonstationary point processes, and transitions between modes are modeled as hidden Markov models. The effectiveness of this framework is first demonstrated on a simulated example. The identification algorithm is then applied to extracellular neural activity recorded from multi-electrode arrays in the parietal reach region of a rhesus monkey, and the results demonstrate the ability to decode discrete changes even from small data sets

Improved spike-based brain-machine interface using bayesian adaptive kernel smoother and deep learning

Multiunit activity (MUA) has been proposed to mitigate the robustness issue faced by single-unit activity (SUA)-based brain-machine interfaces (BMIs). Most MUA-based BMIs still employ a binning method for estimating firing rates and linear decoder for decoding behavioural parameters. The limitations of binning and linear decoder lead to suboptimal performance of MUA-based BMIs. To address this issue, we propose a method which consists of Bayesian adaptive kernel smoother (BAKS) as the firing rate estimation algorithm and deep learning, particularly quasi-recurrent neural network (QRNN), as the decoding algorithm. We evaluated the proposed method for reconstructing (offline) hand kinematics from intracortical neural data chronically recorded from the primary motor cortex of two non-human primates. Extensive empirical results across recording sessions and subjects showed that the proposed method consistently outperforms other combinations of firing rate estimation algorithm and decoding algorithm. Overall results suggest the effectiveness of the proposed method for improving the decoding performance of MUA-based BMIs

A control algorithm for autonomous optimization of extracellular recordings

This paper develops a control algorithm that can autonomously position an electrode so as to find and then maintain an optimal extracellular recording position. The algorithm was developed and tested in a two-neuron computational model representative of the cells found in cerebral cortex. The algorithm is based on a stochastic optimization of a suitably defined signal quality metric and is shown capable of finding the optimal recording position along representative sampling directions, as well as maintaining the optimal signal quality in the face of modeled tissue movements. The application of the algorithm to acute neurophysiological recording experiments and its potential implications to chronic recording electrode arrays are discussed

Particle-filtering approaches for nonlinear Bayesian decoding of neuronal spike trains

The number of neurons that can be simultaneously recorded doubles every seven years. This ever increasing number of recorded neurons opens up the possibility to address new questions and extract higher dimensional stimuli from the recordings. Modeling neural spike trains as point processes, this task of extracting dynamical signals from spike trains is commonly set in the context of nonlinear filtering theory. Particle filter methods relying on importance weights are generic algorithms that solve the filtering task numerically, but exhibit a serious drawback when the problem dimensionality is high: they are known to suffer from the 'curse of dimensionality' (COD), i.e. the number of particles required for a certain performance scales exponentially with the observable dimensions. Here, we first briefly review the theory on filtering with point process observations in continuous time. Based on this theory, we investigate both analytically and numerically the reason for the COD of weighted particle filtering approaches: Similarly to particle filtering with continuous-time observations, the COD with point-process observations is due to the decay of effective number of particles, an effect that is stronger when the number of observable dimensions increases. Given the success of unweighted particle filtering approaches in overcoming the COD for continuous- time observations, we introduce an unweighted particle filter for point-process observations, the spike-based Neural Particle Filter (sNPF), and show that it exhibits a similar favorable scaling as the number of dimensions grows. Further, we derive rules for the parameters of the sNPF from a maximum likelihood approach learning. We finally employ a simple decoding task to illustrate the capabilities of the sNPF and to highlight one possible future application of our inference and learning algorithm

Deciphering Elapsed Time and Predicting Action Timing from Neuronal Population Signals

The proper timing of actions is necessary for the survival of animals, whether in hunting prey or escaping predators. Researchers in the field of neuroscience have begun to explore neuronal signals correlated to behavioral interval timing. Here, we attempt to decode the lapse of time from neuronal population signals recorded from the frontal cortex of monkeys performing a multiple-interval timing task. We designed a Bayesian algorithm that deciphers temporal information hidden in noisy signals dispersed within the activity of individual neurons recorded from monkeys trained to determine the passage of time before initiating an action. With this decoder, we succeeded in estimating the elapsed time with a precision of approximately 1 s throughout the relevant behavioral period from firing rates of 25 neurons in the pre-supplementary motor area. Further, an extended algorithm makes it possible to determine the total length of the time-interval required to wait in each trial. This enables observers to predict the moment at which the subject will take action from the neuronal activity in the brain. A separate population analysis reveals that the neuronal ensemble represents the lapse of time in a manner scaled relative to the scheduled interval, rather than representing it as the real physical time