Scientific Machine Learning (SciML) is a burgeoning field that synergistically combines domain-aware and interpretable models with agnostic machine learning techniques. In this work, we introduce GOKU-UI, an evolution of the SciML generative model GOKU-nets. GOKU-UI not only broadens the original model's spectrum to incorporate other classes of differential equations, such as Stochastic Differential Equations (SDEs), but also integrates attention mechanisms and a novel multiple shooting training strategy in the latent space. These modifications have led to a significant increase in its performance in both reconstruction and forecast tasks, as demonstrated by our evaluation of simulated and empirical data. Specifically, GOKU-UI outperformed all baseline models on synthetic datasets even with a training set 16-fold smaller, underscoring its remarkable data efficiency. Furthermore, when applied to empirical human brain data, while incorporating stochastic Stuart-Landau oscillators into its dynamical core, our proposed enhancements markedly increased the model's effectiveness in capturing complex brain dynamics. This augmented version not only surpassed all baseline methods in the reconstruction task, but also demonstrated lower prediction error of future brain activity up to 15 seconds ahead. By training GOKU-UI on resting state fMRI data, we encoded whole-brain dynamics into a latent representation, learning a low-dimensional dynamical system model that could offer insights into brain functionality and open avenues for practical applications such as the classification of mental states or psychiatric conditions. Ultimately, our research provides further impetus for the field of Scientific Machine Learning, showcasing the potential for advancements when established scientific insights are interwoven with modern machine learning.

In several crucial applications, domain knowledge is encoded by a system of ordinary differential equations (ODE). A motivating example is intensive care unit patients: The dynamics of some vital physiological variables such as heart rate, blood pressure and arterial compliance can be approximately described by a known system of ODEs. Typically, some of the ODE variables are directly observed while some are unobserved, and in addition many other variables are observed but not modeled by the ODE, for example body temperature. Importantly, the unobserved ODE variables are ``known-unknowns'': We know they exist and their functional dynamics, but cannot measure them directly, nor do we know the function tying them to all observed measurements. Estimating these known-unknowns is often highly valuable to physicians. Under this scenario we wish to: (i) learn the static parameters of the ODE generating each observed time-series (ii) infer the dynamic sequence of all ODE variables including the known-unknowns, and (iii) extrapolate the future of the ODE variables and the observations of the time-series. We address this task with a variational autoencoder incorporating the known ODE function, called GOKU-net for Generative ODE modeling with Known Unknowns. We test our method on videos of pendulums with unknown length, and a model of the cardiovascular system.