I propose a novel framework that integrates stochastic differential equations (SDEs) with deep generative models to improve uncertainty quantification in machine learning applications involving structured and temporal data. This approach, termed Stochastic Latent Differential Inference (SLDI), embeds an Itô SDE in the latent space of a variational autoencoder, allowing for flexible, continuous-time modeling of uncertainty while preserving a principled mathematical foundation. The drift and diffusion terms of the SDE are parameterized by neural networks, enabling data-driven inference and generalizing classical time series models to handle irregular sampling and complex dynamic structure. A central theoretical contribution is the co-parameterization of the adjoint state with a dedicated neural network, forming a coupled forward-backward system that captures not only latent evolution but also gradient dynamics. I introduce a pathwise-regularized adjoint loss and analyze variance-reduced gradient flows through the lens of stochastic calculus, offering new tools for improving training stability in deep latent SDEs. My paper unifies and extends variational inference, continuous-time generative modeling, and control-theoretic optimization, providing a rigorous foundation for future developments in stochastic probabilistic machine learning.

Aligning neural dynamics with movements is a fundamental goal in neuroscience and brain-machine interfaces. However, there is still a lack of dimensionality reduction methods that can effectively align low-dimensional latent dynamics with movements. To address this gap, we propose Neural Embeddings Rank (NER), a technique that embeds neural dynamics into a 3D latent space and contrasts the embeddings based on movement ranks. NER learns to regress continuous representations of neural dynamics (i.e., embeddings) on continuous movements. We apply NER and six other dimensionality reduction techniques to neurons in the primary motor cortex (M1), dorsal premotor cortex (PMd), and primary somatosensory cortex (S1) as monkeys perform reaching tasks.

Real-world applications of reinforcement learning often involve environments where agents operate on complex, high-dimensional observations, but the underlying (``latent'') dynamics are comparatively simple. However, beyond restrictive settings such as tabular latent dynamics, the fundamental statistical requirements and algorithmic principles for are poorly understood. This paper addresses the question of reinforcement learning under from a statistical and algorithmic perspective. On the statistical side, our main negativeresult shows that well-studied settings for reinforcement learning with function approximation become intractable when composed with rich observations; we complement this with a positive result, identifying as ageneral condition that enables statistical tractability. Algorithmically, we develop provably efficient reductions ---that is, reductions that transform an arbitrary algorithm for the latent MDP into an algorithm that can operate on rich observations--- in two settings: one where the agent has access to hindsightobservations of the latent dynamics (Lee et al., 2023) and onewhere the agent can estimate latent models (Schwarzer et al., 2020). Together, our results serve as a first step toward a unified statistical and algorithmic theory forreinforcement learning under latent dynamics.

Functional magnetic resonance imaging (fMRI) enables measuring human brain activity, in vivo. Yet, the fMRI hemodynamic response unfolds over very slow timescales (<0.1-1

A recently proposed class of models attempts to learn latent dynamics from high-dimensional observations, like images, using priors informed by Hamiltonian mechanics. While these models have important potential applications in areas like robotics or autonomous driving, there is currently no good way to evaluate their performance: existing methods primarily rely on image reconstruction quality, which does not always reflect the quality of the learnt latent dynamics. In this work, we empirically highlight the problems with the existing measures and develop a set of new measures, including a binary indicator of whether the underlying Hamiltonian dynamics have been faithfully captured, which we call Symplecticity Metric or SyMetric. Our measures take advantage of the known properties of Hamiltonian dynamics and are more discriminative of the model's ability to capture the underlying dynamics than reconstruction error. Using SyMetric, we identify a set of architectural choices that significantly improve the performance of a previously proposed model for inferring latent dynamics from pixels, the Hamiltonian Generative Network (HGN). Unlike the original HGN, the new SyMetric is able to discover an interpretable phase space with physically meaningful latents on some datasets. Furthermore, it is stable for significantly longer rollouts on a diverse range of 13 datasets, producing rollouts of essentially infinite length both forward and backwards in time with no degradation in quality on a subset of the datasets.

An influential framework within systems neuroscience posits that neural computations can be understood in terms of low-dimensional dynamics in recurrent circuits. A number of methods have thus been developed to extract latent dynamical systems from neural recordings, but inferring models that are both predictive and interpretable remains a difficult challenge. Here we propose a new method called Low-rank Inference from Neural Trajectories (LINT), based on a class of low-rank recurrent neural networks (lrRNNs) for which a link between connectivity and dynamics has been previously demonstrated. By fitting such networks to trajectories of neural activity, LINT yields a mechanistic model of latent dynamics, as well as a set of axes for dimensionality reduction and verifiable predictions for inactivations of specific populations of neurons. Here, we first demonstrate the consistency of our method and apply it to two use cases: (i) we reverse-engineer black-box vanilla RNNs trained to perform cognitive tasks, and (ii) we infer latent dynamics and neural contributions from electrophysiological recordings of nonhuman primates performing a similar task.

Modern neural interfaces allow access to the activity of up to a million neurons within brain circuits. However, bandwidth limits often create a trade-off between greater spatial sampling (more channels or pixels) and the temporal frequency of sampling. Here we demonstrate that it is possible to obtain spatio-temporal super-resolution in neuronal time series by exploiting relationships among neurons, embedded in latent low-dimensional population dynamics. Our novel neural network training strategy, selective backpropagation through time (SBTT), enables learning of deep generative models of latent dynamics from data in which the set of observed variables changes at each time step. The resulting models are able to infer activity for missing samples by combining observations with learned latent dynamics. We test SBTT applied to sequential autoencoders and demonstrate more efficient and higher-fidelity characterization of neural population dynamics in electrophysiological and calcium imaging data. In electrophysiology, SBTT enables accurate inference of neuronal population dynamics with lower interface bandwidths, providing an avenue to significant power savings for implanted neuroelectronic interfaces.

Our algorithm scales to data comprising millions of observed dimensions, making it possible to access dynamics distributed across large populations or multiple brain areas.