A central objective in neuroscience is to understand how the brain orchestrates movement. Recent advances in automated tracking technologies have made it possible to document behavior with unprecedented temporal resolution and scale, generating rich datasets which can be exploited to gain insights into the neural control of movement. One common approach is to identify stereotypical motor primitives using cluster analysis. However, this categorical description can limit our ability to model the effect of more continuous control schemes. Here we take a control theoretic approach to behavioral modeling and argue that movements can be understood as the output of a controlled dynamical system. Previously, models of movement dynamics, trained solely on behavioral data, have been effective in reproducing observed features of neural activity. These models addressed specific scenarios where animals were trained to execute particular movements upon receiving a prompt. In this study, we extend this approach to analyze the full natural locomotor repertoire of an animal: the zebrafish larva. Our findings demonstrate that this repertoire can be effectively generated through a sparse control signal driving a latent Recurrent Neural Network (RNN). Our model's learned latent space preserves key kinematic features and disentangles different categories of movements. To further interpret the latent dynamics, we used balanced model reduction to yield a simplified model. Collectively, our methods serve as a case study for interpretable system identification, and offer a novel framework for understanding neural activity in relation to movement.

Second-order optimization has been shown to accelerate the training of deep neural networks in many applications, often yielding faster progress per iteration on the training loss compared to first-order optimizers. However, the generalization properties of second-order methods are still being debated. Theoretical investigations have proved difficult to carry out outside the tractable settings of heavily simplified model classes - thus, the relevance of existing theories to practical deep learning applications remains unclear. Similarly, empirical studies in large-scale models and real datasets are significantly confounded by the necessity to approximate second-order updates in practice. It is often unclear whether the observed generalization behaviour arises specifically from the second-order nature of the parameter updates, or instead reflects the specific structured (e.g. Kronecker) approximations used or any damping-based interpolation towards first-order updates. Here, we show for the first time that exact Gauss-Newton (GN) updates take on a tractable form in a class of deep reversible architectures that are sufficiently expressive to be meaningfully applied to common benchmark datasets. We exploit this novel setting to study the training and generalization properties of the GN optimizer. We find that exact GN generalizes poorly. In the mini-batch training setting, this manifests as rapidly saturating progress even on the training loss, with parameter updates found to overfit each mini-batch without producing the features that would support generalization to other mini-batches. In contrast to previous work, we show that our experiments run in the feature learning regime, in which the neural tangent kernel (NTK) changes during the course of training. However, changes in the NTK are not associated with any significant change in neural representations, explaining the lack of generalization.

A common source of anxiety for the computational neuroscience student is the question “will my recurrent neural network (RNN) model finally learn that task?”. Unlike in machine learning where any architectural modification of an RNN (e.g. GRU or LSTM) is acceptable if it speeds up training, the RNN models trained as _models of brain dynamics_ are subject to plausibility constraints that fundamentally exclude the usual machine learning hacks. The “vanilla” RNNs commonly used in computational neuroscience find themselves plagued by ill-conditioned loss surfaces that complicate training and significantly hinder our capacity to investigate the brain dynamics underlying complex tasks. Moreover, some tasks may require very long time horizons which backpropagation cannot handle given typical GPU memory limits. Here, we develop SOFO, a second-order optimizer that efficiently navigates loss surfaces whilst _not_ requiring backpropagation. By relying instead on easily parallelized batched forward-mode differentiation, SOFO enjoys constant memory cost in time. Morever, unlike most second-order optimizers which involve inherently sequential operations, SOFO's effective use of GPU parallelism yields a per-iteration wallclock time essentially on par with first-order gradient-based optimizers. We show vastly superior performance compared to Adam on a number of RNN tasks, including a difficult double-reaching motor task and the learning of an adaptive Kalman filter algorithm trained over a long horizon.

Latent variable models are ubiquitous in the exploratory analysis of neural population recordings, where they allow researchers to summarize the activity of large populations of neurons in lower dimensional ‘latent’ spaces. Existing methods can generally be categorized into (i) Bayesian methods that facilitate flexible incorporation of prior knowledge and uncertainty estimation, but which typically do not scale to large datasets; and (ii) highly parameterized methods without explicit priors that scale better but often struggle in the low-data regime. Here, we bridge this gap by developing a fully Bayesian yet scalable version of Gaussian process factor analysis (bGPFA), which models neural data as arising from a set of inferred latent processes with a prior that encourages smoothness over time. Additionally, bGPFA uses automatic relevance determination to infer the dimensionality of neural activity directly from the training data during optimization. To enable the analysis of continuous recordings without trial structure, we introduce a novel variational inference strategy that scales near-linearly in time and also allows for non-Gaussian noise models appropriate for electrophysiological recordings. We apply bGPFA to continuous recordings spanning 30 minutes with over 14 million data points from primate motor and somatosensory cortices during a self-paced reaching task. We show that neural activity progresses from an initial state at target onset to a reach- specific preparatory state well before movement onset. The distance between these initial and preparatory latent states is predictive of reaction times across reaches, suggesting that such preparatory dynamics have behavioral relevance despite the lack of externally imposed delay periods. Additionally, bGPFA discovers latent processes that evolve over slow timescales on the order of several seconds and contain complementary information about reaction time. These timescales are longer than those revealed by methods which focus on individual movement epochs and may reflect fluctuations in e.g. task engagement.

Biological agents are known to learn many different tasks over the course of their lives, and to be able to revisit previous tasks and behaviors with little to no loss in performance. In contrast, artificial agents are prone to ‘catastrophic forgetting’ whereby performance on previous tasks deteriorates rapidly as new ones are acquired. This shortcoming has recently been addressed using methods that encourage parameters to stay close to those used for previous tasks. This can be done by (i) using specific parameter regularizers that map out suitable destinations in parameter space, or (ii) guiding the optimization journey by projecting gradients into subspaces that do not interfere with previous tasks. However, these methods often exhibit subpar performance in both feedforward and recurrent neural networks, with recurrent networks being of interest to the study of neural dynamics supporting biological continual learning. In this work, we propose Natural Continual Learning (NCL), a new method that unifies weight regularization and projected gradient descent. NCL uses Bayesian weight regularization to encourage good performance on all tasks at convergence and combines this with gradient projection using the prior precision, which prevents catastrophic forgetting during optimization. Our method outperforms both standard weight regularization techniques and projection based approaches when applied to continual learning problems in feedforward and recurrent networks. Finally, the trained networks evolve task-specific dynamics that are strongly preserved as new tasks are learned, similar to experimental findings in biological circuits.

A common problem in neuroscience is to elucidate the collective neural representations of behaviorally important variables such as head direction, spatial location, upcoming movements, or mental spatial transformations. Often, these latent variables are internal constructs not directly accessible to the experimenter. Here, we propose a new probabilistic latent variable model to simultaneously identify the latent state and the way each neuron contributes to its representation in an unsupervised way. In contrast to previous models which assume Euclidean latent spaces, we embrace the fact that latent states often belong to symmetric manifolds such as spheres, tori, or rotation groups of various dimensions. We therefore propose the manifold Gaussian process latent variable model (mGPLVM), where neural responses arise from (i) a shared latent variable living on a specific manifold, and (ii) a set of non-parametric tuning curves determining how each neuron contributes to the representation. Cross-validated comparisons of models with different topologies can be used to distinguish between candidate manifolds, and variational inference enables quantification of uncertainty. We demonstrate the validity of the approach on several synthetic datasets, as well as on calcium recordings from the ellipsoid body of Drosophila melanogaster and extracellular recordings from the mouse anterodorsal thalamic nucleus. These circuits are both known to encode head direction, and mGPLVM correctly recovers the ring topology expected from neural populations representing a single angular variable.

A common goal in the analysis of neural data is to compress large population recordings into sets of interpretable, low-dimensional latent trajectories. This problem can be approached using Gaussian process (GP)-based methods which provide uncertainty quantification and principled model selection. However, standard GP priors do not distinguish between underlying dynamical processes and other forms of temporal autocorrelation. Here, we propose a new family of “dynamical” priors over trajectories, in the form of GP covariance functions that express a property shared by most dynamical systems: temporal non-reversibility. Non-reversibility is a universal signature of autonomous dynamical systems whose state trajectories follow consistent flow fields, such that any observed trajectory could not occur in reverse. Our new multi-output GP kernels can be used as drop-in replacements for standard kernels in multivariate regression, but also in latent variable models such as Gaussian process factor analysis (GPFA). We therefore introduce GPFADS (Gaussian Process Factor Analysis with Dynamical Structure), which models single-trial neural population activity using low-dimensional, non-reversible latent processes. Unlike previously proposed non-reversible multi-output kernels, ours admits a Kronecker factorization enabling fast and memory-efficient learning and inference. We apply GPFADS to synthetic data and show that it correctly recovers ground truth phase portraits. GPFADS also provides a probabilistic generalization of jPCA, a method originally developed for identifying latent rotational dynamics in neural data. When applied to monkey M1 neural recordings, GPFADS discovers latent trajectories with strong dynamical structure in the form of rotations.

Stochastic gradient descent (SGD) remains the method of choice for deep learning, despite the limitations arising for ill-behaved objective functions. In cases where it could be estimated, the natural gradient has proven very effective at mitigating the catastrophic effects of pathological curvature in the objective function, but little is known theoretically about its convergence properties, and it has yet to find a practical implementation that would scale to very deep and large networks. Here, we derive an exact expression for the natural gradient in deep linear networks, which exhibit pathological curvature similar to the nonlinear case. We provide for the first time an analytical solution for its convergence rate, showing that the loss decreases exponentially to the global minimum in parameter space. Our expression for the natural gradient is surprisingly simple, computationally tractable, and explains why some approximations proposed previously work well in practice. This opens new avenues for approximating the natural gradient in the nonlinear case, and we show in preliminary experiments that our online natural gradient descent outperforms SGD on MNIST autoencoding while sharing its computational simplicity.

Hebbian changes of excitatory synapses are driven by and further enhance correlations between pre- and postsynaptic activities. Hence, Hebbian plasticity forms a positive feedback loop that can lead to instability in simulated neural networks. To keep activity at healthy, low levels, plasticity must therefore incorporate homeostatic control mechanisms. We find in numerical simulations of recurrent networks with a realistic triplet-based spike-timing-dependent plasticity rule (triplet STDP) that homeostasis has to detect rate changes on a timescale of seconds to minutes to keep the activity stable. We confirm this result in a generic mean-field formulation of network activity and homeostatic plasticity. Our results strongly suggest the existence of a homeostatic regulatory mechanism that reacts to firing rate changes on the order of seconds to minutes.

Although it is widely believed that reinforcement learning is a suitable tool for describing behavioral learning, the mechanisms by which it can be implemented in networks of spiking neurons are not fully understood. Here, we show that different learning rules emerge from a policy gradient approach depending on which features of the spike trains are assumed to influence the reward signals, i.e., depending on which neural code is in effect. We use the framework of Williams (1992) to derive learning rules for arbitrary neural codes. For illustration, we present policy-gradient rules for three different example codes - a spike count code, a spike timing code and the most general ``full spike train code - and test them on simple model problems. In addition to classical synaptic learning, we derive learning rules for intrinsic parameters that control the excitability of the neuron. The spike count learning rule has structural similarities with established Bienenstock-Cooper-Munro rules. If the distribution of the relevant spike train features belongs to the natural exponential family, the learning rules have a characteristic shape that raises interesting prediction problems.