Accurate, Very Low Computational Complexity Spike Sorting Using Unsupervised Matched Subspace Learning

This paper presents an adaptable dictionary-based feature extraction approach for spike sorting offering high accuracy and low computational complexity for implantable applications. It extracts and learns identifiable features from evolving subspaces through matched unsupervised subspace filtering. To provide compatibility with the strict constraints in implantable devices such as the chip area and power budget, the dictionary contains arrays of {-1, 0 and 1} and the algorithm need only process addition and subtraction operations. Three types of such dictionary were considered. To quantify and compare the performance of the resulting three feature extractors with existing systems, a neural signal simulator based on several different libraries was developed. For noise levels $\sigma_N$ between 0.05 and 0.3 and groups of 3 to 6 clusters, all three feature extractors provide robust high performance with average classification errors of less than 8% over five iterations, each consisting of 100 generated data segments. To our knowledge, the proposed adaptive feature extractors are the first able to classify reliably 6 clusters for implantable applications. An ASIC implementation of the best performing dictionary-based feature extractor was synthesized in a 65-nm CMOS process. It occupies an area of 0.09 mm2 and dissipates up to about 10.48 μW from a 1 V supply voltage, when operating with 8-bit resolution at 30 kHz operating frequency

Efficient Approximation of Action Potentials with High-Order Shape Preservation in Unsupervised Spike Sorting

This paper presents a novel approximation unit added to the conventional spike processing chain which provides an appreciable reduction of complexity of the high-hardware cost feature extractors. The use of the Taylor polynomial is proposed and modelled employing its cascaded derivatives to non-uniformly capture the essential samples in each spike for reliable feature extraction and sorting. Inclusion of the approximation unit can provide 3X compression (i.e. from 66 to 22 samples) to the spike waveforms while preserving their shapes. Detailed spike waveform sequences based on in-vivo measurements have been generated using a customized neural simulator for performance assessment of the approximation unit tested on six published feature extractors. For noise levels σN between 0.05 and 0.3 and groups of 3 spikes in each channel, all the feature extractors provide almost same sorting performance before and after approximation. The overall implementation cost when including the approximation unit and feature extraction shows a large reduction (i.e. up to 8.7X) in the hardware costly and more accurate feature extractors, offering a substantial improvement in feature extraction design

A Deep Neural Network-Based Spike Sorting with Improved Channel Selection and Artefact Removal

In order to implement highly efficient brain-machine interface (BMI) systems, high-channel count sensing is often used to record extracellular action potentials. However, the extracellular recordings are typically severely contaminated by artefacts and various noise sources, rendering the separation of multi-unit neural recordings an immensely challenging task. Removing artefact and noise from neural events can improve the spike sorting performance and classification accuracy. This paper presents a deep learning technique called deep spike detection (DSD) with a strong learning ability of high-dimensional vectors for neural channel selection and artefacts removal from the selected neural channel. The proposed method significantly improves spike detection compared to the conventional methods by sequentially diminishing the noise level and discarding the active artefacts in the recording channels. The simulated and experimental results show that there is considerably better performance when the extracellular raw recordings are cleaned prior to assigning individual spikes to the neurons that generated them. The DSD achieves an overall classification accuracy of 91.53% and outperformes Wave_clus by 3.38% on the simulated dataset with various noise levels and artefacts

Scalable software and models for large-scale extracellular recordings

The brain represents information about the world through the electrical activity of populations of neurons. By placing an electrode near a neuron that is firing (spiking), it is possible to detect the resulting extracellular action potential (EAP) that is transmitted down an axon to other neurons. In this way, it is possible to monitor the communication of a group of neurons to uncover how they encode and transmit information. As the number of recorded neurons continues to increase, however, so do the data processing and analysis challenges. It is crucial that scalable software and analysis tools are developed and made available to the neuroscience community to keep up with the large amounts of data that are already being gathered. This thesis is composed of three pieces of work which I develop in order to better process and analyze large-scale extracellular recordings. My work spans all stages of extracellular analysis from the processing of raw electrical recordings to the development of statistical models to reveal underlying structure in neural population activity. In the first work, I focus on developing software to improve the comparison and adoption of different computational approaches for spike sorting. When analyzing neural recordings, most researchers are interested in the spiking activity of individual neurons, which must be extracted from the raw electrical traces through a process called spike sorting. Much development has been directed towards improving the performance and automation of spike sorting. This continuous development, while essential, has contributed to an over-saturation of new, incompatible tools that hinders rigorous benchmarking and complicates reproducible analysis. To address these limitations, I develop SpikeInterface, an open-source, Python framework designed to unify preexisting spike sorting technologies into a single toolkit and to facilitate straightforward benchmarking of different approaches. With this framework, I demonstrate that modern, automated spike sorters have low agreement when analyzing the same dataset, i.e. they find different numbers of neurons with different activity profiles; This result holds true for a variety of simulated and real datasets. Also, I demonstrate that utilizing a consensus-based approach to spike sorting, where the outputs of multiple spike sorters are combined, can dramatically reduce the number of falsely detected neurons. In the second work, I focus on developing an unsupervised machine learning approach for determining the source location of individually detected spikes that are recorded by high-density, microelectrode arrays. By localizing the source of individual spikes, my method is able to determine the approximate position of the recorded neuriii ons in relation to the microelectrode array. To allow my model to work with large-scale datasets, I utilize deep neural networks, a family of machine learning algorithms that can be trained to approximate complicated functions in a scalable fashion. I evaluate my method on both simulated and real extracellular datasets, demonstrating that it is more accurate than other commonly used methods. Also, I show that location estimates for individual spikes can be utilized to improve the efficiency and accuracy of spike sorting. After training, my method allows for localization of one million spikes in approximately 37 seconds on a TITAN X GPU, enabling real-time analysis of massive extracellular datasets. In my third and final presented work, I focus on developing an unsupervised machine learning model that can uncover patterns of activity from neural populations associated with a behaviour being performed. Specifically, I introduce Targeted Neural Dynamical Modelling (TNDM), a statistical model that jointly models the neural activity and any external behavioural variables. TNDM decomposes neural dynamics (i.e. temporal activity patterns) into behaviourally relevant and behaviourally irrelevant dynamics; the behaviourally relevant dynamics constitute all activity patterns required to generate the behaviour of interest while behaviourally irrelevant dynamics may be completely unrelated (e.g. other behavioural or brain states), or even related to behaviour execution (e.g. dynamics that are associated with behaviour generally but are not task specific). Again, I implement TNDM using a deep neural network to improve its scalability and expressivity. On synthetic data and on real recordings from the premotor (PMd) and primary motor cortex (M1) of a monkey performing a center-out reaching task, I show that TNDM is able to extract low-dimensional neural dynamics that are highly predictive of behaviour without sacrificing its fit to the neural data

From End to End: Gaining, Sorting, and Employing High-Density Neural Single Unit Recordings

The meaning behind neural single unit activity has constantly been a challenge, so it will persist in the foreseeable future. As one of the most sourced strategies, detecting neural activity in high-resolution neural sensor recordings and then attributing them to their corresponding source neurons correctly, namely the process of spike sorting, has been prevailing so far. Support from ever-improving recording techniques and sophisticated algorithms for extracting worthwhile information and abundance in clustering procedures turned spike sorting into an indispensable tool in electrophysiological analysis. This review attempts to illustrate that in all stages of spike sorting algorithms, the past 5 years innovations' brought about concepts, results, and questions worth sharing with even the non-expert user community. By thoroughly inspecting latest innovations in the field of neural sensors, recording procedures, and various spike sorting strategies, a skeletonization of relevant knowledge lays here, with an initiative to get one step closer to the original objective: deciphering and building in the sense of neural transcript

Developing robust movement decoders for local field potentials

textBrain Computer Interfaces (BCI) are devices that translate acquired neural signals to command and control signals. Applications of BCI include neural rehabilitation and neural prosthesis (thought controlled wheelchair, thought controlled speller etc.) to aid patients with disabilities and to augment human computer interaction. A successful practical BCI requires a faithful acquisition modality to record high quality neural signals; a signal processing system to construct appropriate features from these signals; and an algorithm to translate these features to appropriate outputs. Intracortical recordings like local field potentials provide reliable high SNR signals over long periods and suit BCI applications well. However, the non-stationarity of neural signals poses a challenge in robust decoding of subject behavior. Most BCI research focuses either on developing daily re-calibrated decoders that require exhaustive training sessions; or on providing cross-validation results. Such results ignore the variation of signal characteristics over different sessions and provide an optimistic estimate of BCI performance. Specifically, traditional BCI algorithms fail to perform at the same level on chronological data recordings. Neural signals are susceptible to variations in signal characteristics due to changes in subject behavior and learning, and variability in electrode characteristics due to tissue interactions. While training day-specific BCI overcomes signal variability, BCI re-training causes user frustration and exhaustion. This dissertation presents contributions to solve these challenges in BCI research. Specifically, we developed decoders trained on a single recording session and applied them on subsequently recorded sessions. This strategy evaluates BCI in a practical scenario with a potential to alleviate BCI user frustration without compromising performance. The initial part of the dissertation investigates extracting features that remain robust to changes in neural signal over several days of recordings. It presents a qualitative feature extraction technique based on ranking the instantaneous power of multichannel data. These qualitative features remain robust to outliers and changes in the baseline of neural recordings, while extracting discriminative information. These features form the foundation in developing robust decoders. Next, this dissertation presents a novel algorithm based on the hypothesis that multiple neural spatial patterns describe the variation in behavior. The presented algorithm outperforms the traditional methods in decoding over chronological recordings. Adapting such a decoder over multiple recording sessions (over 6 weeks) provided > 90% accuracy in decoding eight movement directions. In comparison, performance of traditional algorithms like Common Spatial Patterns deteriorates to 16% over the same time. Over time, adaptation reinforces some spatial patterns while diminishing others. Characterizing these spatial patterns reduces model complexity without user input, while retaining the same accuracy levels. Lastly, this dissertation provides an algorithm that overcomes the variation in recording quality. Chronic electrode implantation causes changes in signal-to-noise ratio (SNR) of neural signals. Thus, some signals and their corresponding features available during training become unavailable during testing and vice-versa. The proposed algorithm uses prior knowledge on spatial pattern evolution to estimate unknown neural features. This algorithm overcomes SNR variations and provides up to 93% decoding of eight movement directions over 6 weeks. Since model training requires only one session, this strategy reduces user frustration. In a practical closed-loop BCI, the user learns to produce stable spatial patterns, which improves performance of the proposed algorithms.Electrical and Computer Engineerin

Modeling and Analysis of Neural Spike Trains

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A discrete wavelet transform-based voice activity detection and noise classification with sub-band selection

A real-time discrete wavelet transform-based adaptive voice activity detector and sub-band selection for feature extraction are proposed for noise classification, which can be used in a speech processing pipeline. The voice activity detection and sub-band selection rely on wavelet energy features and the feature extraction process involves the extraction of mel-frequency cepstral coefficients from selected wavelet sub-bands and mean absolute values of all sub-bands. The method combined with a feedforward neural network with two hidden layers could be added to speech enhancement systems and deployed in hearing devices such as cochlear implants. In comparison to the conventional short-time Fourier transform-based technique, it has higher F1 scores and classification accuracies (with a mean of 0.916 and 90.1%, respectively) across five different noise types (babble, factory, pink, Volvo (car) and white noise), a significantly smaller feature set with 21 features, reduced memory requirement, faster training convergence and about half the computational cost

Automatic Detection and Classification of Neural Signals in Epilepsy

The success of an epilepsy treatment, such as resective surgery, relies heavily on the accurate identification and localization of the brain regions involved in epilepsy for which patients undergo continuous intracranial electroencephalogram (EEG) monitoring. The prolonged EEG recordings are screened for two main biomarkers of epilepsy: seizures and interictal spikes. Visual screening and quantitation of these two biomarkers in voluminous EEG recordings is highly subjective, labor-intensive, tiresome and expensive. This thesis focuses on developing new techniques to detect and classify these events in the EEG to aid the review of prolonged intracranial EEG recordings. It has been observed in the literature that reliable seizure detection can be made by quantifying the evolution of seizure EEG waveforms. This thesis presents three new computationally simple non-patient-specific (NPS) seizure detection systems that quantify the temporal evolution of seizure EEG. The first method is based on the frequency-weighted-energy, the second method on quantifying the EEG waveform sharpness, while the third method mimics EEG experts. The performance of these new methods is compared with that of three state-of-the-art NPS seizure detection systems. The results show that the proposed systems outperform these state-of-the-art systems. Epilepsy therapies are individualized for numerous reasons, and patient-specific (PS) seizure detection techniques are needed not only in the pre-surgical evaluation of prolonged EEG recordings, but also in the emerging neuro-responsive therapies. This thesis proposes a new model-based PS seizure detection system that requires only the knowledge of a template seizure pattern to derive the seizure model consisting of a set of basis functions necessary to utilize the statistically optimal null filters (SONF) for the detection of the subsequent seizures. The results of the performance evaluation show that the proposed system provides improved results compared to the clinically-used PS system. Quantitative analysis of the second biomarker, interictal spikes, may help in the understanding of epileptogenesis, and to identify new epileptic biomarkers and new therapies. However, such an analysis is still done manually in most of the epilepsy centers. This thesis presents an unsupervised spike sorting system that does not require a priori knowledge of the complete spike data