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Latent Gaussian process (GP) models are widely used in neuroscience to uncover hidden state evolutions from sequential observations, mainly in neural activity recordings. While latent GP models provide a principled and powerful solution in theory, the intractable posterior in non-conjugate settings necessitates approximate inference schemes, which may lack scalability. In this work, we propose cvHM, a general inference framework for latent GP models leveraging Hida-Matérn kernels and conjugate computation variational inference (CVI). With cvHM, we are able to perform variational inference of latent neural trajectories with linear time complexity for arbitrary likelihoods. The reparameterization of stationary kernels using Hida-Matérn GPs helps us connect the latent variable models that encode prior assumptions through dynamical systems to those that encode trajectory assumptions through GPs. In contrast to previous work, we use bidirectional information filtering, leading to a more concise implementation. Furthermore, we employ the Whittle approximate likelihood to achieve highly efficient hyperparameter learning. 

Latent variable models have become instrumental in computational neuroscience for reasoning about neural computation. This has fostered the development of powerful offline algorithms for extracting latent neural trajectories from neural recordings. However, despite the potential of real-time alternatives to give immediate feedback to experimentalists, and enhance experimental design, they have received markedly less attention. In this work, we introduce the exponential family variational Kalman filter (eVKF), an online recursive Bayesian method aimed at inferring latent trajectories while simultaneously learning the dynamical system generating them. eVKF works for arbitrary likelihoods and utilizes the constant base measure exponential family to model the latent state stochasticity. We derive a closed-form variational analog to the predict step of the Kalman filter which leads to a provably tighter bound on the ELBO compared to another online variational method. We validate our method on synthetic and real-world data, and, notably, show that it achieves competitive performance. 

In recent years, the efficacy of using artificial recurrent neural networks to model cortical dynamics has been a topic of interest. Gated recurrent units (GRUs) are specialized memory elements for building these recurrent neural networks. Despite their incredible success in natural language, speech, video processing, and extracting dynamics underlying neural data, little is understood about the specific dynamics representable in a GRU network, and how these dynamics play a part in performance and generalization. As a result, it is both difficult to know a priori how successful a GRU network will perform on a given task, and also their capacity to mimic the underlying behavior of their biological counterparts. Using a continuous time analysis, we gain intuition on the inner workings of GRU networks. We restrict our presentation to low dimensions, allowing for a comprehensive visualization. We found a surprisingly rich repertoire of dynamical features that includes stable limit cycles (nonlinear oscillations), multi-stable dynamics with various topologies, and homoclinic bifurcations. At the same time GRU networks are limited in their inability to produce continuous attractors, which are hypothesized to exist in biological neural networks. We contextualize the usefulness of different kinds of observed dynamics and support our claims experimentally. 

Brain dynamics can exhibit narrow-band nonlinear oscillations and multistability. For a subset of disorders of consciousness and motor control, we hypothesized that some symptoms originate from the inability to spontaneously transition from one attractor to another. Using external perturbations, such as electrical pulses delivered by deep brain stimulation devices, it may be possible to induce such transition out of the pathological attractors. However, the induction of transition may be non-trivial, rendering the current open-loop stimulation strategies insufficient. In order to develop next-generation neural stimulators that can intelligently learn to induce attractor transitions, we require a platform to test the efficacy of such systems. To this end, we designed an analog circuit as a model for the multistable brain dynamics. The circuit spontaneously oscillates stably on two periods as an instantiation of a 3-dimensional continuous-time gated recurrent neural network. To discourage simple perturbation strategies, such as constant or random stimulation patterns from easily inducing transition between the stable limit cycles, we designed a state-dependent nonlinear circuit interface for external perturbation. We demonstrate the existence of nontrivial solutions to the transition problem in our circuit implementation. 

The standard approach to fitting an autoregressive spike train model is to maximize the likelihood for one-step prediction. This maximum likelihood estimation (MLE) often leads to models that perform poorly when generating samples recursively for more than one time step. Moreover, the generated spike trains can fail to capture important features of the data and even show diverging firing rates. To alleviate this, we propose to directly minimize the divergence between neural recorded and model generated spike trains using spike train kernels. We develop a method that stochastically optimizes the maximum mean discrepancy induced by the kernel. Experiments performed on both real and synthetic neural data validate the proposed approach, showing that it leads to well-behaving models. Using different combinations of spike train kernels, we show that we can control the trade-off between different features which is critical for dealing with model-mismatch. 

Understanding the nature of representation in neural networks is a goal shared by neuroscience and machine learning. It is therefore exciting that both fields converge not only on shared questions but also on similar approaches. A pressing question in these areas is understanding how the structure of the representation used by neural networks affects both their generalization, and robustness to perturbations. In this work, we investigate the latter by juxtaposing experimental results regarding the covariance spectrum of neural representations in the mouse V1 (Stringer et al) with artificial neural networks. We use adversarial robustness to probe Stringer et al's theory regarding the causal role of a 1/n covariance spectrum. We empirically investigate the benefits such a neural code confers in neural networks, and illuminate its role in multi-layer architectures. Our results show that imposing the experimentally observed structure on artificial neural networks makes them more robust to adversarial attacks. Moreover, our findings complement the existing theory relating wide neural networks to kernel methods, by showing the role of intermediate representations. 

Recently mean field theory has been successfully used to analyze properties of wide, random neural networks. It gave rise to a prescriptive theory for initializing feed-forward neural networks with orthogonal weights, which ensures that both the forward propagated activations and the backpropagated gradients are near isometries and as a consequence training is orders of magnitude faster. Despite strong empirical performance, the mechanisms by which critical initializations confer an advantage in the optimization of deep neural networks are poorly understood. Here we show a novel connection between the maximum curvature of the optimization landscape (gradient smoothness) as measured by the Fisher information matrix (FIM) and the spectral radius of the input-output Jacobian, which partially explains why more isometric networks can train much faster. Furthermore, given that orthogonal weights are necessary to ensure that gradient norms are approximately preserved at initialization, we experimentally investigate the benefits of maintaining orthogonality throughout training, and we conclude that manifold optimization of weights performs well regardless of the smoothness of the gradients. Moreover, we observe a surprising yet robust behavior of highly isometric initializations --- even though such networks have a lower FIM condition number \emph{at initialization}, and therefore by analogy to convex functions should be easier to optimize, experimentally they prove to be much harder to train with stochastic gradient descent. We conjecture the FIM condition number plays a non-trivial role in the optimization.