We consider the problem of variational Bayesian inference in a latent variable model where a (possibly complex) observed stochastic process is governed by the unobserved solution of a latent stochastic differential equation (SDE). Motivated by the challenges that arise when trying to learn a latent SDE in $\mathbb{R}^n$ from large-scale data, such as efficient gradient computation, we take a step back and study a specific subclass instead. In our case, the SDE evolves inside a homogeneous latent space and is induced by stochastic dynamics of the corresponding (matrix) Lie group. In the context of learning problems, SDEs on the $n$-dimensional unit sphere are arguably the most relevant incarnation of this setup. For variational inference, the sphere not only facilitates using a uniform prior on the initial state of the SDE, but we also obtain a particularly simple and intuitive expression for the KL divergence between the approximate posterior and prior process in the evidence lower bound. We provide empirical evidence that a latent SDE of the proposed type can be learned efficiently by means of an existing one-step geometric Euler-Maruyama scheme. Despite restricting ourselves to a less diverse class of SDEs, we achieve competitive or even state-of-the-art performance on a collection of time series interpolation and classification benchmarks.

Clinical time series data from electronic health records and medical registries offer unprecedented opportunities to understand patient trajectories and inform medical decision-making. However, leveraging such data presents significant challenges due to irregular sampling, complex latent physiology, and inherent uncertainties in both measurements and disease progression. To address these challenges, we propose a generative modeling framework based on latent neural stochastic differential equations (SDEs) that views clinical time series as discrete-time partial observations of an underlying controlled stochastic dynamical system. This formulation naturally handles irregularly sampled observations, learns complex non-linear interactions, and captures the stochasticity of disease progression and measurement noise within a unified scalable probabilistic framework. Results show that our framework outperforms ordinary differential equation and long short-term memory baseline models in accuracy and uncertainty estimation. These results highlight its potential for enabling precise, uncertainty-aware predictions to support clinical decision-making. Introduction Predicting patient trajectories is critical for enabling timely interventions, better understanding of disease progression, and developing personalized medicine [1]. For instance, early detection of sepsis has been shown to significantly reduce the risk of organ failure and mortality [2]. This potential is increasingly becoming feasible due to the rapid growth of available healthcare data like electronic health records (EHRs) [3]. A defining feature of healthcare data are their temporal nature, reflecting the dynamic evolution of patient conditions over time. These temporal patterns highlight the need for time series models specifically tailored to the complexities of clinical data. However, healthcare time series have unique characteristics such as missing values, irregular sampling, aleatoric uncertainty, and patient-specific variability, that make modeling them particularly challenging [5, 6]. Traditional time series models, such as autoregressive moving average (ARIMA) models, have been applied to healthcare data but often struggle with its complexity and irregularity [7].

The Latent Stochastic Differential Equation (SDE) is a powerful tool for time series and sequence modeling. However, training Latent SDEs typically relies on adjoint sensitivity methods, which depend on simulation and backpropagation through approximate SDE solutions, which limit scalability. In this work, we propose SDE Matching, a new simulation-free method for training Latent SDEs. Inspired by modern Score- and Flow Matching algorithms for learning generative dynamics, we extend these ideas to the domain of stochastic dynamics for time series and sequence modeling, eliminating the need for costly numerical simulations. Our results demonstrate that SDE Matching achieves performance comparable to adjoint sensitivity methods while drastically reducing computational complexity.

We consider the problem of variational Bayesian inference in a latent variable model where a (possibly complex) observed stochastic process is governed by the unobserved solution of a latent stochastic differential equation (SDE). Motivated by the challenges that arise when trying to learn a latent SDE in \mathbb{R} n from large-scale data, such as efficient gradient computation, we take a step back and study a specific subclass instead. In our case, the SDE evolves inside a homogeneous latent space and is induced by stochastic dynamics of the corresponding (matrix) Lie group. In the context of learning problems, SDEs on the n -dimensional unit sphere are arguably the most relevant incarnation of this setup. For variational inference, the sphere not only facilitates using a uniform prior on the initial state of the SDE, but we also obtain a particularly simple and intuitive expression for the KL divergence between the approximate posterior and prior process in the evidence lower bound.

Particle filtering is a standard Monte-Carlo approach for a wide range of sequential inference tasks. The key component of a particle filter is a set of particles with importance weights that serve as a proxy of the true posterior distribution of some stochastic process. In this work, we propose continuous latent particle filters, an approach that extends particle filtering to the continuous-time domain. We demonstrate how continuous latent particle filters can be used as a generic plug-in replacement for inference techniques relying on a learned variational posterior. Our experiments with different model families based on latent neural stochastic differential equations demonstrate superior performance of continuous-time particle filtering in inference tasks like likelihood estimation and sequential prediction for a variety of stochastic processes.