A Low-Power Spike Detection and Alignment Algorithm

Objective. Translational efforts on spike-signal-based implantable brain-machine interfaces (BMIs) are increasingly aiming to minimise bandwidth while maintaining decoding performance. Developing these BMIs requires advances in neuroscience and electronic technology, as well as using low-complexity spike detection algorithms and high-performance machine learning models. While some state-of-the-art BMI systems jointly design spike detection algorithms and machine learning models, it remains unclear how the detection performance affects decoding. Approach. We propose the co-design of the neural decoder with an ultra-low complexity spike detection algorithm. The detection algorithm is designed to attain a target firing rate, which the decoder uses to modulate the input features preserving statistical invariance in long term (over several months). Main results. We demonstrate a multiplication-free fixed-point spike detection algorithm with an average detection accuracy of 97% across different noise levels on a synthetic dataset and the lowest hardware complexity among studies we have seen. By co-designing the system to incorporate statistically invariant features, we observe significantly improved long-term stability, with decoding accuracy degrading by less than 10% after 80 days of operation. Our analysis also reveals a nonlinear relationship between spike detection and decoding performance. Increasing the detection sensitivity improves decoding accuracy and long-term stability, which means the activity of more neurons is beneficial despite the detection of more noise. Reducing the spike detection sensitivity still provides acceptable decoding accuracy whilst reducing the bandwidth by at least 30%. Significance. Our findings regarding the relationship between spike detection and decoding performance can provide guidance on setting the threshold for spike detection rather than relying on training or trial-and-error. The trade-off between data bandwidth and decoding performance can be effectively managed using appropriate spike detection settings. We demonstrate improved decoding performance by maintaining statistical invariance of input features. We believe this approach can motivate further research focused on improving decoding performance through the manipulation of data itself (based on a hypothesis) rather than using more complex decoding models.

Spike detection is often the first step in neural signal processing. It has profound effects on subsequent steps down the signal processing pipeline. Most existing spike detection algorithms require manual setting of detection threshold, which is very inconvenient for long-term neural interface. Furthermore, these algorithms are usually only evaluated using simulated dataset. Few studies are devoted to evaluating how different spike detection algorithms affect decoding performance in brain-computer interface. We have proposed a new spike detection algorithm called "exponential component - power component" (EC-PC) that offers fully automatic unsupervised spike detection. In this study, we compared the performance of a motor decoding task when different spike detection algorithms were used. EC-PC is shown to produce a higher decoding accuracy compared with other existing algorithms. Our results suggest that EC-PC can help improve motor decoding performance of brain-computer interface.

In a previous study the authors showed that rolandic spikes are characterised by typical field distributions of the spectral parameters instantaneous power and instantaneous frequency [14]. According to localisation of the focus and lateralisation of instantaneous power seven topographic spike classes were determined visually and verified with a Neural Network classifier (multi layer perceptron - MLP) [9]. Based on these results an algorithm for simultaneous detection and classification of rolandic spike activity was developed [7]. Aim of this study was to check the results of visual spike classification by means of a global optimising cluster algorithm and to test additional classifiers - Linear Discriminant Analysis (LDA) and a Cascade Correlation net (CC) - for topographic spike classification and their application in the developed spike detection algorithm. Essentially, the results of cluster analysis confirmed the visual spike classification. The number of „correct” classifications of visually selected instantaneous power distributions of rolandic spikes (7 classes) and non-spike activities (alpha- and EMC-activities) of 10 Routine EEG records was nearly the same for the three classifiers LDA, MLP and CC. Routine EEG records of three further children containing more than 900 spikes were used to compare the performance of the spike detection algorithm using LDA, MLP or CC with the results of visual spike detection by two experienced electroencephalographers. The best results were obtained with the MLP as classifier in the developed detection algorithm. The number of „false/positive” detections was significant lower than when using LDA or CC.

The increasing data rate has become a major issue confronting next-generation intracortical brain-machine interfaces (iBMIs). The scaling number of recording sites requires complex analog wiring and lead to huge digitization power consumption. Compressive event-based neural frontends have been used in high-density neural implants to support the simultaneous recording of more channels. Event-based frontends (EBF) convert recorded signals into asynchronous digital events via delta modulation and can inherently achieve considerable compression. But EBFs are prone to false events that do not correspond to neural and may affect the output firing rate, which is the key feature for neural decoding. Spike detection (SPD) is a key process in the iBMI pipeline to detect neural spikes and further reduce the data rate. However, conventional digital SPD suffers from the increasing buffer size and frequent memory access power, and conventional spike emphasizers are not compatible with EBFs. In this work we introduced an event-based spike detection (Ev-SPD) algorithm for scalable compressive EBFs. To implement the algorithm effectively, we proposed a novel low-power 10-T eDRAM-SRAM hybrid random-access memory (HRAM) in-memory computing (IMC) bitcell for event processing. We fabricated the proposed 1024-channel IMC SPD macro in a 65nm process and tested the macro with both synthetic dataset and Neuropixel recordings. The proposed macro achieved a high spike detection accuracy of 96.06% on a synthetic dataset and 95.08% similarity and 0.05 firing pattern MAE on Neuropixel recordings. Our event-based IMC SPD macro achieved a high per channel spike detection energy efficiency of 23.9 nW per channel and an area efficiency of 375 μm2 per channel. Our work presented a SPD scheme compatible with compressive EBFs for high-density iBMIs, achieving ultra-low power consumption with an IMC architecture while maintaining considerable accuracy.

Recordings of extracellular spikes have been widely used in various fields ranging from basic neuroscientific research to clinical applications. However, in the extracellular recording system, how to accurately detect spikes from the recorded signal in real time is still a major challenging work. Although the existing algorithms for online spike detection have made great progress, there still remains much room for improvement in terms of accuracy. In this paper, we propose a new method for high accuracy and real time spike detection. Concretely, differential operator is firstly employed to accentuate spikes in the signal for its simplicity and strong capacity to detect significant changes. Then, by exploiting the structural features of spikes, the resolution parameter is introduced to improve the performance of differential operator. Finally, a simple and effective measure is utilized to further reduce the influence of background noise, which makes spike detection more accurate. The results of simulated and real data show that the proposed method is able to precisely detect spikes while maintaining low computational complexity.

We introduce algorithms and architectures for automatic spike detection and alignment that are designed for low power. Some of the algorithms are based on principal component analysis (PCA). Others employ a novel integral transform analysis and achieve 99% of the precision of a PCA detector, while requiring only 0.05% of the computational complexity. The algorithms execute autonomously, but require off-line training and setting of computational parameters. We employ pre-recorded neuronal signals to evaluate the accuracy of the proposed algorithms and architectures: the recorded data are processed by a standard PCA spike detection and alignment software algorithm, as well as by the several hardware algorithms, and the outcomes are compared.

This paper presents an experiment based comparison of absolute threshold (AT) and non-linear energy operator (NEO) spike detection algorithms in intra-cortical Brain Machine Interfaces (iBMIs). Results show an average increase in decoding performance of ≈5% in monkey A across 28 sessions recorded over 6 days and ≈2% in monkey B across 35 sessions recorded over 8 days when using NEO over AT. To the best of our knowledge, this is the first ever reported comparison of spike detection algorithms in an iBMI experimental framework involving two monkeys. Based on the improvements observed in an experimental setting backed by previously reported improvements in simulation studies, we advocate switching from state of the art spike detection technique - AT to NEO.

This thesis was to solve the problem that tremendous amount of data of neural signal seriously confined the number of transmission channels with a limited bandwidth in a digital telemetry system. Although a spike-detection algorithm designed for data reduction had been reported, the signal in between the spikes was lost. Moreover, various non-ideal factors greatly reduced the accuracy of spike detection. This thesis used the commercialized data-compression algorithm, MPEG Layer 3 (MP3), as our data reduction scheme and evaluated its performance on spike sorting. The evaluation results showed that MP3 kept at least 80% accuracy of unit isolation. For reducing the consumption of hardware resource by MP3, MP3 algorithm was further simplified and the corresponding performance was checked. All the algorithm simplification carried out in this thesis compromised barely discernible performance. At last this thesis discussed a method for multi-channel signal analysis, ICA. The effect of MP3 on ICA after the highest level of simplification was simulated. The results showed that the miss probabilities of MP3 were considerably low, regardless of the encoding bit rate. According to all the results mentioned above, we preliminarily validated MP3 a proper neural signal compressor.

Next generation sequencing (NGS) technologies have enabled cheap, large-scale, and high-throughput production of short DNA sequence reads and thereby have promoted the explosive growth of data volume. Unfortunately, the produced reads are short and prone to contain errors that are incurred during sequencing cycles. Both large data volume and sequencing errors have complicated the mapping of NGS reads onto the reference genome and have motivated the development of various aligners for very short reads, typically less than 100 base pairs (bps) in length. As read length continues to increase, propelled by advances in NGS technologies, these longer reads tend to have higher sequencing error rates and more true mutations (including substitutions, insertions, or deletions) to the genome. Such new characteristics make inefficient the aligners, which are optimized for very short reads and support only ungapped alignments or gapped alignments with very limited number of gaps (typically one gap), and thereby call for new aligners with fully gapped alignment supported. In this chapter, we present the CUSHAW software suite for NGS read alignment, which is open-source and consists of three individual aligners: CUSHAW, CUSHAW2, and CUSHAW3. This suite offers parallel and efficient NGS read alignments to large genomes, such as the human genome, by harnessing multi-core CPUs or compute unified device architecture (CUDA)-enabled graphics processing units (GPUs). Moreover, it has the capability to align both base-space and color-space reads and is consistently shown to be one of the best alignment tools through our performance evaluations.

Extracellular chronic recordings have been used as important evidence in neuroscientific studies to unveil the fundamental neural network mechanisms in the brain. Spike detection is the first step in the analysis of recorded neural waveforms to decipher useful information and provide useful signals for brain-machine interface applications. The process of spike detection is to extract action potentials from the recordings, which are often compounded with noise from different sources. This study proposes a new detection algorithm that leverages a technique from wavelet-based image edge detection. It utilizes the correlation between wavelet coefficients at different sampling scales to create a robust spike detector. The algorithm has one tuning parameter, which potentially reduces the subjectivity of detection results. Both artificial benchmark data sets and real neural recordings are used to evaluate the detection performance of the proposed algorithm. Compared with other detection algorithms, the proposed method has a comparable or better detection performance. In this letter, we also demonstrate its potential for real-time implementation.

Localization of the epileptogenic zone (EZ) is very important for patients undergoing presurgical evaluation for resective epilepsy surgery. The detection of epileptiform spikes is of major importance for identifying the epileptogenic zone. The zone of cortex with interictal spikes is usually revealed intraoperatively, during acute electrocorticography (ECoG). The ECoG recordings cannot be completely visually reviewed, by a specialist, in a reasonable amount of time. So, computer algorithms for the automatic detection of spikes are very desirable. The article contains a proposal of spike detection algorithm, based on three ECoG signal parameters: signal energy, entropy and fractal dimension. The sensitivity of spike detection was 0.83, the specificity was 0.98 and the precision - 0.91.

When surface electromyography (EMG) signal is used in a real-time functional electrical stimulation (FES) system for feedback control, the artifact from electrical stimulation is a key challenge for EMG signal processing. To address this challenge, this study proposes a novel method to suppress stimulation artifacts in the EMG-driven closed-loop FES system. The proposed method is inspired by an experimental study that compares artifacts generated by electrical stimulations with different current intensities. It is found that (1) spikes of stimulation artifacts are susceptible to the current intensity and (2) tailing components are similar under different current intensities. Based on these observations, the proposed method combines the blanking and template subtracting strategies for suppressing stimulation artifact. The length of blanking window for suppressing the stimulation spike is adaptively determined by a spike detection algorithm and the first-order derivative analysis of signal. An autoregressive model is used to estimate the tailing part of stimulation artifact, which is an adaptive template for subtracting the artifact. The proposed method is evaluated on both semi-synthetic and experimental datasets. Verified on the semi-synthetic dataset, the proposed method achieves better performance than the classic blanking method. Validated on the experimental dataset, the proposed method substantially decreases the power of stimulation artifact in the EMG. These results indicate that the proposed method can effectively suppress the stimulation artifact while retains the useful EMG signal for an EMG-driven FES system.

Traditional methods for the development of a neuroprosthesis to perform closed-loop stimulation can be complex and the necessary technical knowledge and experience often present a high barrier for adoption. This paper takes a novel Model-Based Design approach to simplifying such closed-loop system development, and thereby lowering the adoption barrier. This work implements a computational model of different spike detection algorithms in Simulink® and compares their performances by taking advantage of synthetic neural signals to evaluate suitability for the intended embedded implementation. Clinical Relevance--- Closed-loop systems have been demonstrated to be suitable for brain repair strategies. Coupling two different brain areas by means of a neuroprosthesis can potentially lead to restoration of communication by inducing activity-dependent plasticity.

The rapid increase in the number of aerial and orbital Earth observation systems is generating a huge amount of remote sensing data that need to be readily transformed into useful information for policy and decision makers. This exposes an urgent demand for image interpretation tools that can deal efficiently with very large volumes of data. In this work, we introduce a set of methods that support distributed processing of georeferenced raster and vector data in a computer cluster, which may be a virtual cluster provided by cloud computing infrastructure services. The set of methods comprise a particular technique for indexing distributed georeferenced datasets, as well as strategies for distributing efficiently the processing of spatial context-aware operations. They provide the means for the development of scalable applications, capable of processing large volumes of geospatial data. We evaluated the proposed methods in a remote sensing image interpretation application, built on the MapReduce framework, and executed in a cloud computing infrastructure. The experimental results corroborate the capacity of the methods to support efficient handling of very large earth observation datasets.

Privacy preserving multi-party computation delegation for deep learning in cloud computing