A neural network for online spike classification that improves decoding accuracy

Brain-wide arousal signals are segregated from movement planning in the superior colliculus

The superior colliculus (SC) is traditionally considered a brain region that functions as an interface between processing visual inputs and generating eye movement outputs. Although its role as a primary reflex center is thought to be conserved across vertebrate species, evidence suggests that the SC has evolved to support higher-order cognitive functions including spatial attention. When it comes to oculomotor areas such as the SC, it is critical that high precision fixation and eye movements are maintained even in the presence of signals related to ongoing changes in cognition and brain state, both of which have the potential to interfere with eye position encoding and movement generation. In this study, we recorded spiking responses of neuronal populations in the SC while monkeys performed a memory-guided saccade task and found that the activity of some of the neurons fluctuated over tens of minutes. By leveraging the statistical power afforded by high-dimensional neuronal recordings, we were able to identify a low-dimensional pattern of activity that was correlated with the subjects' arousal levels. Importantly, we found that the spiking responses of deep-layer SC neurons were less correlated with this brain-wide arousal signal, and that neural activity associated with changes in pupil size and saccade tuning did not overlap in population activity space with movement initiation signals. Taken together, these findings provide a framework for understanding how signals related to cognition and arousal can be embedded in the population activity of oculomotor structures without compromising the fidelity of the motor output.

Compact deep neural network models of visual cortex

A powerful approach to understanding the computations carried out in visual cortex is to develop models that predict neural responses to arbitrary images. Deep neural network (DNN) models have worked remarkably well at predicting neural responses [1, 2, 3], yet their underlying computations remain buried in millions of parameters. Have we simply replaced one complicated system in vivo with another in silico ? Here, we train a data-driven deep ensemble model that predicts macaque V4 responses ∼50% more accurately than currently-used task-driven DNN models. We then compress this deep ensemble to identify compact models that have 5,000x fewer parameters yet equivalent accuracy as the deep ensemble. We verified that the stimulus preferences of the compact models matched those of the real V4 neurons by measuring V4 responses to both 'maximizing' and adversarial images generated using compact models. We then analyzed the inner workings of the compact models and discovered a common circuit motif: Compact models share a similar set of filters in early stages of processing but then specialize by heavily consolidating this shared representation with a precise readout. This suggests that a V4 neuron's stimulus preference is determined entirely by its consolidation step. To demonstrate this, we investigated the compression step of a dot-detecting compact model and found a set of simple computations that may be carried out by dot-selective V4 neurons. Overall, our work demonstrates that the DNN models currently used in computational neuroscience are needlessly large; our approach provides a new way forward for obtaining explainable, high-accuracy models of visual cortical neurons.

DualSort: online spike sorting with a running neural network

Objective.Spike sorting, i.e. the detection and separation of measured action potentials from different extracellularly recorded neurons, remains one of the bottlenecks in deciphering the brain. In recent years, the application of neural networks (NNs) for spike sorting has garnered significant attention. Most methods focus on specific sub-problems within the conventional spike sorting pipeline, such as spike detection or feature extraction, and attempt to solve them with complex network architectures. This paper presents DualSort, a simple NN that gets combined with downstream post-processing for real-time spike sorting. It shows high efficiency, low complexity, and requires a comparatively small amount of human interaction.Approach.Synthetic and experimentally obtained extracellular single-channel recordings were utilized to train and evaluate the proposed NN. For training, spike waveforms were labeled with respect to their associated neuron and position in the signal, allowing the detection and categorization of spikes in unison. DualSort classifies a single spike multiple times in succession, as it runs over the signal in a step-by-step manner and uses a post-processing algorithm that transmits the network output into spike trains. Main results.With the used datasets, DualSort was able to detect and distinguish different spike waveforms and separate them from background activity. The post-processing algorithm significantly strengthened the overall performance of the model, making the system more robust as a whole. Although DualSort is an end-to-end solution that efficiently transforms filtered signals into spike trains, it competes with contemporary state-of-the-art technologies that exclusively target single sub-problems in the conventional spike sorting pipeline.Significance.This work demonstrates that even under high noise levels, complex NNs are not necessary by any means to achieve high performance in spike detection and sorting. The utilization of data augmentation on a limited quantity of spikes could substantially decrease hand-labeling compared to other studies. Furthermore, the proposed framework can be utilized without human interaction when combined with an unsupervised technique that provides pseudo labels for DualSort. Due to the low complexity of our network, it works efficiently and enables real-time processing on basic hardware. The proposed approach is not limited to spike sorting, as it may also be used to process different signals, such as electroencephalogram (EEG), which needs to be investigated in future research.

Expectation reshapes V4 neuronal activity and improves perceptual performance

Recent visual experience creates expectations that heavily influence our visual perception. How does expectation shape the activity of cortical neurons to allow for improved perceptual discrimination of visual inputs? We recorded from populations of neurons in visual cortical area V4 while monkeys performed a natural image change detection task under different expectation conditions. We found that higher expectation led to an improvement in the ability to detect a change in an image. This improvement was associated with decreased neural responses to the image, providing evidence that a reduction in activity can improve stimulus encoding. The decrease in response could not be fully explained by short-timescale adaptation, suggesting partially separate mechanisms of adaptation and expectation. Additionally, higher expectation was associated with decreased trial-to-trial shared variability, indicating that a reduction in variability is a key means by which expectation influences perception. Taken together, the results of our study contribute to an understanding of how visual experience and expectation can shape our perception and behavior through modulating activity patterns across the visual cortex.

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.

Enhancing the decoding accuracy of EEG signals by the introduction of anchored-STFT and adversarial data augmentation method

Brain-computer interfaces (BCIs) enable communication between humans and machines by translating brain activity into control commands. Electroencephalography (EEG) signals are one of the most used brain signals in non-invasive BCI applications but are often contaminated with noise. Therefore, it is possible that meaningful patterns for classifying EEG signals are deeply hidden. State-of-the-art deep-learning algorithms are successful in learning hidden, meaningful patterns. However, the quality and the quantity of the presented inputs are pivotal. Here, we propose a feature extraction method called anchored Short Time Fourier Transform (anchored-STFT), which is an advanced version of STFT, as it minimizes the trade-off between temporal and spectral resolution presented by STFT. In addition, we propose a data augmentation method derived from l2-norm fast gradient sign method (FGSM), called gradient norm adversarial augmentation (GNAA). GNAA is not only an augmentation method but is also used to harness adversarial inputs in EEG data, which not only improves the classification accuracy but also enhances the robustness of the classifier. In addition, we also propose a CNN architecture, namely Skip-Net, for the classification of EEG signals. The proposed pipeline outperforms the current state-of-the-art methods and yields classification accuracies of 90.7% on BCI competition II dataset III and 89.5%, 81.8%, 76.0% and 85.4%, 69.1%, 80.9% on different data distributions of BCI Competition IV dataset 2b and 2a, respectively.

ELVISort: encoding latent variables for instant sorting, an artificial intelligence-based end-to-end solution

Objective.The growing number of recording sites of silicon-based probes means that an increasing amount of neural cell activities can be recorded simultaneously, facilitating the investigation of underlying complex neural dynamics. In order to overcome the challenges generated by the increasing number of channels, highly automated signal processing tools are needed. Our goal was to build a spike sorting model that can perform as well as offline solutions while maintaining high efficiency, enabling high-performance online sorting.Approach.In this paper we present ELVISort, a deep learning method that combines the detection and clustering of different action potentials in an end-to-end fashion.Main results.The performance of ELVISort is comparable with other spike sorting methods that use manual or semi-manual techniques, while exceeding the methods which use an automatic approach: ELVISort has been tested on three independent datasets and yielded average F₁scores of 0.96, 0.82 and 0.81, which comparable with the results of state-of-the-art algorithms on the same data. We show that despite the good performance, ELVISort is capable to process data in real-time: the time it needs to execute the necessary computations for a sample of given length is only 1/15.71 of its actual duration (i.e. the sampling time multiplied by the number of the sampling points).Significance.ELVISort, because of its end-to-end nature, can exploit the massively parallel processing capabilities of GPUs via deep learning frameworks by processing multiple batches in parallel, with the potential to be used on other cutting-edge AI-specific hardware such as TPUs, enabling the development of integrated, portable and real-time spike sorting systems with similar performance to offline sorters.