Dynestyx: A Probabilistic Programming Library for Dynamical Systems

Estimating parameters of dynamical systems from sparse, noisy, and irregularly sampled data is often severely ill-conditioned. When multiple related datasets are available, they provide additional information if the shared structure and variability are properly modeled. We propose a hierarchical Bayesian framework for probabilistic meta-learning in dynamical systems, modeling dataset-specific parameters as draws from a shared population distribution. A numerical ODE solver is embedded within gradient-based MCMC to enable efficient posterior inference of the shared population and dataset-specific parameter distribution. Experiments show improved predictive performance over unpooled methods, highlighting the potential for data-efficient system identification in settings with sparse data.

Latent state space systems are ubiquitous in statistical modelling, arising naturally when time series are observed through noisy measurements. However, training deep state space models (DSSMs) at scale remains difficult. Two largely distinct strategies have emerged for training DSSMs. The first, auto-encoding DSSMs, trains generative models by optimising a variational lower bound. The second backpropagates through the outputs of classical sequential Monte Carlo (SMC) algorithms. Such approaches can train DSSMs for both discriminative and generative tasks, but their inherently sequential forward passes scale poorly on modern hardware. We propose \emph{parallel variational Monte Carlo} (PVMC), a new training method that bridges these paradigms and robustly trains DSSMs for both discriminative and generative tasks. Across a set of benchmark experiments, PVMC matches or exceeds state-of-the-art performance while training $10\times$ faster than the fastest competing SMC-based approach.

Due to their explicit priors and ability to model uncertainty, Bayesian methods have played a major role in dynamical latent variable modeling of single-cell neural recordings. However, modern-sized datasets have made overparameterized deep networks the preferred methods of choice due to their predictive power and favorable computational scaling. While many posterior approximations exist, all incur approximation errors. Recent work accounts for this error in the form of computational uncertainty but comes at the cost of quadratic complexity and assumes fixed model hyperparameters. Here we extend this development to model selection, including a novel training loss and optimization scheme, which yields tractable inference in large state-spaces. We introduce a framework, the Computation-Aware State-Space Model (CASSM), specifically designed for the scale-imbalanced regime, where the number of trials is significantly lower than the number of recorded neurons. In this regime, for both synthetic and real data, we show that our method is competitive with data-hungry deep networks, with significantly improved uncertainty calibration over previous attempts to scale Bayesian methods. Our experiments provide a roadmap to neuroscience researchers in choosing from a host of potential dynamical latent variable models given key dataset properties and constraints.