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Register a new userRepresentation learning for neural population activity with Neural Data Transformers
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Neural population activity is theorized to reflect an underlying dynamical structure. This structure can be accurately captured using state space models with explicit dynamics, such as those based on recurrent neural networks (RNNs). However, using recurrence to explicitly model dynamics necessitates sequential processing of data, slowing real-time applications such as brain-computer interfaces. Here we introduce the Neural Data Transformer (NDT), a non-recurrent alternative. We test the NDTs ability to capture autonomous dynamical systems by applying it to synthetic datasets with known dynamics and data from monkey motor cortex during a reaching task well-modeled by RNNs. The NDT models these datasets as well as state-of-the-art recurrent models. Further, its non-recurrence enables 3.9ms inference, well within the loop time of real-time applications and more than 6 times faster than recurrent baselines on the monkey reaching dataset. These results suggest that an explicit dynamics model is not necessary to model autonomous neural population dynamics. Code: https://github.com/snel-repo/neural-data-transformers
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Despite rapid advances in machine learning tools, the majority of neural decoding approaches still use traditional methods. Modern machine learning tools, which are versatile and easy to use, have the potential to significantly improve decoding performance. This tutorial describes how to effectively apply these algorithms for typical decoding problems. We provide descriptions, best practices, and code for applying common machine learning methods, including neural networks and gradient boosting. We also provide detailed comparisons of the performance of various methods at the task of decoding spiking activity in motor cortex, somatosensory cortex, and hippocampus. Modern methods, particularly neural networks and ensembles, significantly outperform traditional approaches, such as Wiener and Kalman filters. Improving the performance of neural decoding algorithms allows neuroscientists to better understand the information contained in a neural population and can help advance engineering applications such as brain machine interfaces.
In recent years, artificial neural networks have achieved state-of-the-art performance for predicting the responses of neurons in the visual cortex to natural stimuli. However, they require a time consuming parameter optimization process for accurately modeling the tuning function of newly observed neurons, which prohibits many applications including real-time, closed-loop experiments. We overcome this limitation by formulating the problem as $K$-shot prediction to directly infer a neurons tuning function from a small set of stimulus-response pairs using a Neural Process. This required us to developed a Factorized Neural Process, which embeds the observed set into a latent space partitioned into the receptive field location and the tuning function properties. We show on simulated responses that the predictions and reconstructed receptive fields from the Factorized Neural Process approach ground truth with increasing number of trials. Critically, the latent representation that summarizes the tuning function of a neuron is inferred in a quick, single forward pass through the network. Finally, we validate this approach on real neural data from visual cortex and find that the predictive accuracy is comparable to -- and for small $K$ even greater than -- optimization based approaches, while being substantially faster. We believe this novel deep learning systems identification framework will facilitate better real-time integration of artificial neural network modeling into neuroscience experiments.
How can animals behave effectively in conditions involving different motivational contexts? Here, we propose how reinforcement learning neural networks can learn optimal behavior for dynamically changing motivational salience vectors. First, we show that Q-learning neural networks with motivation can navigate in environment with dynamic rewards. Second, we show that such networks can learn complex behaviors simultaneously directed towards several goals distributed in an environment. Finally, we show that in Pavlovian conditioning task, the responses of the neurons in our model resemble the firing patterns of neurons in the ventral pallidum (VP), a basal ganglia structure involved in motivated behaviors. We show that, similarly to real neurons, recurrent networks with motivation are composed of two oppositely-tuned classes of neurons, responding to positive and negative rewards. Our model generates predictions for the VP connectivity. We conclude that networks with motivation can rapidly adapt their behavior to varying conditions without changes in synaptic strength when expected reward is modulated by motivation. Such networks may also provide a mechanism for how hierarchical reinforcement learning is implemented in the brain.
Periodic neural activity not locked to the stimulus or to motor responses is usually ignored. Here, we present new tools for modeling and quantifying the information transmission based on periodic neural activity that occurs with quasi-random phase relative to the stimulus. We propose a model to reproduce characteristic features of oscillatory spike trains, such as histograms of inter-spike intervals and phase locking of spikes to an oscillatory influence. The proposed model is based on an inhomogeneous Gamma process governed by a density function that is a product of the usual stimulus-dependent rate and a quasi-periodic function. Further, we present an analysis method generalizing the direct method (Rieke et al, 1999; Brenner et al, 2000) to assess the information content in such data. We demonstrate these tools on recordings from relay cells in the lateral geniculate nucleus of the cat.
We investigate the possibility that narrowband oscillations may emerge from completely asynchronous, independent neural firing. We find that a population of asynchronous neurons may produce narrowband oscillations if each neuron fires quasi-periodically, and we deduce bounds on the degree of variability in neural spike-timing which will permit the emergence of such oscillations. These results suggest a novel mechanism of neural rhythmogenesis, and they help to explain recent experimental reports of large-amplitude local field potential oscillations in the absence of neural spike-timing synchrony. Simply put, although synchrony can produce oscillations, oscillations do not always imply the existence of synchrony.
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