Learning Dynamical Systems from Multiple Sparse Datasets: A Hierarchical Bayesian Modeling Approach

Deep learning has proven highly effective for nonlinear system identification, but heavily parameterized neural networks are prone to overfitting in low-data regimes and lack reliable uncertainty quantification. The recently developed manifold meta-learning framework addresses the data efficiency problem by restricting the model parameters to a meta-learned low-dimensional manifold. However, that method is purely deterministic. We propose a fully probabilistic extension of the manifold meta-learning framework, based on amortized Variational Inference, where a generative prior over the low-dimensional parameter manifold is learned. During task-specific adaptation, we combine Maximum A Posteriori estimation with the Laplace approximation to yield a mathematically grounded posterior approximation. Evaluated on a static regression task and the Bouc--Wen dynamical system benchmark, the proposed approach achieves predictive accuracy comparable to its deterministic counterpart while successfully providing calibrated uncertainty bounds in severely low-data regimes.

State-space models (SSMs) are the standard formalism for Bayesian treatment of dynamical systems, with natural applications in statistics, signal processing, and machine learning. Despite their importance in both theory and application, dynamical systems have proven difficult to incorporate in modern probabilistic programming languages (PPLs), making state-of-the-art methods less accessible to practitioners and introducing friction in following the "Bayesian workflow." We introduce dynestyx, a probabilistic programming library with first-class support for SSMs, including state-of-the-art methods in the estimation of both states and parameters. Through a single, unified interface, users may specify arbitrary priors for discrete-time or continuous-time dynamical systems, perform inference over mixed-effect data, and make state and parameter estimates with principled uncertainty quantification.

Dynamical modelling is central to many scientific domains, including pharmacometrics, systems biology, physiology, and epidemiology. In these settings, heterogeneity is often intrinsic: different subjects or units follow related but distinct continuous-time dynamics. Classical nonlinear mixed-effects Ordinary Differential Equation (ODE) models address this by combining population-level structure with subject-specific effects, but they rely on a parametric vector field and are therefore vulnerable to structural misspecification and unmodelled mechanisms. This motivates nonparametric approaches that can retain principled uncertainty quantification, yet existing nonparametric ODE methods typically assume a single shared dynamical system rather than an explicit mixed-effect hierarchy over subject-specific dynamics. We propose MEGPODE, a Bayesian nonparametric mixed-effect ODE model in which each subject's vector field is decomposed into a shared population component and a subject-specific deviation, both endowed with Gaussian process (GP) priors. To avoid repeated ODE solves per subject during training, we combine state-space GP trajectory priors with virtual collocation observations, yielding Kalman-smoothing trajectory updates and closed-form regressions for the vector fields. Across controlled heterogeneous ODE benchmarks spanning oscillatory, biomedical systems, MEGPODE improves population-field recovery and subject-level trajectory prediction relative to strong baselines.