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Charles Windolf

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3 papers

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NeurIPS Conference 2023 Conference Paper

Bypassing spike sorting: Density-based decoding using spike localization from dense multielectrode probes

Yizi Zhang
Tianxiao He
Julien Boussard
Charles Windolf
Olivier Winter
Eric Trautmann
Noam Roth
Hailey Barrell

Neural decoding and its applications to brain computer interfaces (BCI) are essential for understanding the association between neural activity and behavior. A prerequisite for many decoding approaches is spike sorting, the assignment of action potentials (spikes) to individual neurons. Current spike sorting algorithms, however, can be inaccurate and do not properly model uncertainty of spike assignments, therefore discarding information that could potentially improve decoding performance. Recent advances in high-density probes (e. g. , Neuropixels) and computational methods now allow for extracting a rich set of spike features from unsorted data; these features can in turn be used to directly decode behavioral correlates. To this end, we propose a spike sorting-free decoding method that directly models the distribution of extracted spike features using a mixture of Gaussians (MoG) encoding the uncertainty of spike assignments, without aiming to solve the spike clustering problem explicitly. We allow the mixing proportion of the MoG to change over time in response to the behavior and develop variational inference methods to fit the resulting model and to perform decoding. We benchmark our method with an extensive suite of recordings from different animals and probe geometries, demonstrating that our proposed decoder can consistently outperform current methods based on thresholding (i. e. multi-unit activity) and spike sorting. Open source code is available at https: //github. com/yzhang511/density_decoding.

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NeurIPS Conference 2020 Conference Paper

A Biologically Plausible Neural Network for Slow Feature Analysis

David Lipshutz
Charles Windolf
Siavash Golkar
Dmitri Chklovskii

Learning latent features from time series data is an important problem in both machine learning and brain function. One approach, called Slow Feature Analysis (SFA), leverages the slowness of many salient features relative to the rapidly varying input signals. Furthermore, when trained on naturalistic stimuli, SFA reproduces interesting properties of cells in the primary visual cortex and hippocampus, suggesting that the brain uses temporal slowness as a computational principle for learning latent features. However, despite the potential relevance of SFA for modeling brain function, there is currently no SFA algorithm with a biologically plausible neural network implementation, by which we mean an algorithm operates in the online setting and can be mapped onto a neural network with local synaptic updates. In this work, starting from an SFA objective, we derive an SFA algorithm, called Bio-SFA, with a biologically plausible neural network implementation. We validate Bio-SFA on naturalistic stimuli.

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NeurIPS Conference 2018 Conference Paper

Learning long-range spatial dependencies with horizontal gated recurrent units

Drew Linsley
Junkyung Kim
Vijay Veerabadran
Charles Windolf
Thomas Serre

Progress in deep learning has spawned great successes in many engineering applications. As a prime example, convolutional neural networks, a type of feedforward neural networks, are now approaching -- and sometimes even surpassing -- human accuracy on a variety of visual recognition tasks. Here, however, we show that these neural networks and their recent extensions struggle in recognition tasks where co-dependent visual features must be detected over long spatial ranges. We introduce a visual challenge, Pathfinder, and describe a novel recurrent neural network architecture called the horizontal gated recurrent unit (hGRU) to learn intrinsic horizontal connections -- both within and across feature columns. We demonstrate that a single hGRU layer matches or outperforms all tested feedforward hierarchical baselines including state-of-the-art architectures with orders of magnitude more parameters.

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