Spike sorting is a critical first step in extracting neural signals from large-scale electrophysiological data. This manuscript describes an efficient, reliable pipeline for spike sorting on dense multi-electrode arrays (MEAs), where neural signals appear across many electrodes and spike sorting currently represents a major computational bottleneck. We present several new techniques that make dense MEA spike sorting more robust and scalable.

New silicon technology is enabling large-scale electrophysiological recordings in vivo from hundreds to thousands of channels. Interpreting these recordings requires scalable and accurate automated methods for spike sorting, which should minimize the time required for manual curation of the results. Here we introduce KiloSort, a new integrated spike sorting framework that uses template matching both during spike detection and during spike clustering. KiloSort models the electrical voltage as a sum of template waveforms triggered on the spike times, which allows overlapping spikes to be identified and resolved. Unlike previous algorithms that compress the data with PCA, KiloSort operates on the raw data which allows it to construct a more accurate model of the waveforms. Processing times are faster than in previous algorithms thanks to batch-based optimization on GPUs. We compare KiloSort to an established algorithm and show favorable performance, at much reduced processing times. A novel post-clustering merging step based on the continuity of the templates further reduced substantially the number of manual operations required on this data, for the neurons with near-zero error rates, paving the way for fully automated spike sorting of multichannel electrode recordings.

Frequency-specific patterns of neural activity are traditionally interpreted as sustained rhythmic oscillations, and related to cognitive mechanisms such as attention, high level visual processing or motor control. While alpha waves (8--12\,Hz) are known to closely resemble short sinusoids, and thus are revealed by Fourier analysis or wavelet transforms, there is an evolving debate that electromagnetic neural signals are composed of more complex waveforms that cannot be analyzed by linear filters and traditional signal representations. In this paper, we propose to learn dedicated representations of such recordings using a multivariate convolutional sparse coding (CSC) algorithm. Applied to electroencephalography (EEG) or magnetoencephalography (MEG) data, this method is able to learn not only prototypical temporal waveforms, but also associated spatial patterns so their origin can be localized in the brain. Our algorithm is based on alternated minimization and a greedy coordinate descent solver that leads to state-of-the-art running time on long time series. To demonstrate the implications of this method, we apply it to MEG data and show that it is able to recover biological artifacts. More remarkably, our approach also reveals the presence of non-sinusoidal mu-shaped patterns, along with their topographic maps related to the somatosensory cortex.

Recent progress in deep learning for audio synthesis opens the way to models that directly produce the waveform, shifting away from the traditional paradigm of relying on vocoders or MIDI synthesizers for speech or music generation. Despite their successes, current state-of-the-art neural audio synthesizers such as WaveNet and SampleRNN suffer from prohibitive training and inference times because they are based on autoregressive models that generate audio samples one at a time at a rate of 16kHz. In this work, we study the more computationally efficient alternative of generating the waveform frame-by-frame with large strides. We present a lightweight neural audio synthesizer for the original task of generating musical notes given desired instrument, pitch and velocity. Our model is trained end-to-end to generate notes from nearly 1000 instruments with a single decoder, thanks to a new loss function that minimizes the distances between the log spectrograms of the generated and target waveforms. On the generalization task of synthesizing notes for pairs of pitch and instrument not seen during training, SING produces audio with significantly improved perceptual quality compared to a state-of-the-art autoencoder based on WaveNet as measured by a Mean Opinion Score (MOS), and is about 32 times faster for training and 2, 500 times faster for inference.

Realistic music generation is a challenging task. When building generative models of music that are learnt from data, typically high-level representations such as scores or MIDI are used that abstract away the idiosyncrasies of a particular performance. But these nuances are very important for our perception of musicality and realism, so in this work we embark on modelling music in the raw audio domain. It has been shown that autoregressive models excel at generating raw audio waveforms of speech, but when applied to music, we find them biased towards capturing local signal structure at the expense of modelling long-range correlations. This is problematic because music exhibits structure at many different timescales. In this work, we explore autoregressive discrete autoencoders (ADAs) as a means to enable autoregressive models to capture long-range correlations in waveforms. We find that they allow us to unconditionally generate piano music directly in the raw audio domain, which shows stylistic consistency across tens of seconds.

However, developing effective foundation models for electronic health record (EHR) data in Emergency Medicine requires addressing several challenges.

This augmentation is applied to waveforms with a probability of 0.7. T emporal Jitter: This augmentation works through two steps. This augmentation is applied to waveforms with a probability of 0.5. We use a batch size of 128 and learning rate of 0.0001 for all multi-channel models. CEED benchmark models seems appropriate.

In CEED, we assume that waveforms are already extracted from an extracellular recording. Each waveform is then passed through our stochastic view generation module, where different views are obtained by applying transformations.

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