Ordinary differential equations (ODEs) can provide mechanistic models of temporally local changes of processes, where parameters are often informed by external knowledge. While ODEs are popular in systems modeling, they are less established for statistical modeling of longitudinal cohort data, e.g., in a clinical setting. Yet, modeling of local changes could also be attractive for assessing the trajectory of an individual in a cohort in the immediate future given its current status, where ODE parameters could be informed by further characteristics of the individual. However, several hurdles so far limit such use of ODEs, as compared to regression-based function fitting approaches. The potentially higher level of noise in cohort data might be detrimental to ODEs, as the shape of the ODE solution heavily depends on the initial value. In addition, larger numbers of variables multiply such problems and might be difficult to handle for ODEs. To address this, we propose to use each observation in the course of time as the initial value to obtain multiple local ODE solutions and build a combined estimator of the underlying dynamics. Neural networks are used for obtaining a low-dimensional latent space for dynamic modeling from a potentially large number of variables, and for obtaining patient-specific ODE parameters from baseline variables. Simultaneous identification of dynamic models and of a latent space is enabled by recently developed differentiable programming techniques. We illustrate the proposed approach in an application with spinal muscular atrophy patients and a corresponding simulation study. In particular, modeling of local changes in health status at any point in time is contrasted to the interpretation of functions obtained from a global regression. This more generally highlights how different application settings might demand different modeling strategies.

This A fundamental challenge in physics-informed is because the standard ML part of PIML, which tends to machine learning (PIML) is the design of robust learn spurious associations, will perform poorly in our OOD PIML methods for out-of-distribution (OOD) setting. We then propose a promising solution: Combine forecasting tasks. These OOD tasks require meta learning with causal structure discovery to learn an learning-to-learn from observations of the same ODE model that is robust to OOD initial conditions and can (ODE) dynamical system with different unknown adapt to OOD parameters of the dynamical system. In our ODE parameters, and demand accurate forecasts OOD tasks, OOD robustness means that the robustness is even under out-of-support initial conditions and tied to interventions over the initial conditions and unknown out-of-support ODE parameters. In this work we parameters of the system, not on arbitrary interventions as propose a solution for such tasks, which we define the system evolves from the initial state. This is an important as a meta-learning procedure for causal structure distinction. There can be multiple ODE models that discovery (including invariant risk minimization).

Deep networks have become increasingly of interest in dynamical system prediction, but generalization remains elusive. In this work, we consider the physical parameters of ODEs as factors of variation of the data generating process. By leveraging ideas from supervised disentanglement in VAEs, we aim to separate the ODE parameters from the dynamics in the latent space. Experiments show that supervised disentanglement allows VAEs to capture the variability in the dynamics and extrapolate better to ODE parameter spaces that were not present in the training data.

Longitudinal biomedical data are often characterized by a sparse time grid and individual-specific development patterns. Specifically, in epidemiological cohort studies and clinical registries we are facing the question of what can be learned from the data in an early phase of the study, when only a baseline characterization and one follow-up measurement are available. Inspired by recent advances that allow to combine deep learning with dynamic modeling, we investigate whether such approaches can be useful for uncovering complex structure, in particular for an extreme small data setting with only two observations time points for each individual. Irregular spacing in time could then be used to gain more information on individual dynamics by leveraging similarity of individuals. We provide a brief overview of how variational autoencoders (VAEs), as a deep learning approach, can be linked to ordinary differential equations (ODEs) for dynamic modeling, and then specifically investigate the feasibility of such an approach that infers individual-specific latent trajectories by including regularity assumptions and individuals' similarity. We also provide a description of this deep learning approach as a filtering task to give a statistical perspective. Using simulated data, we show to what extent the approach can recover individual trajectories from ODE systems with two and four unknown parameters and infer groups of individuals with similar trajectories, and where it breaks down. The results show that such dynamic deep learning approaches can be useful even in extreme small data settings, but need to be carefully adapted.

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.

Sequential data often originates from diverse domains across which statistical regularities and domain specifics exist. To specifically learn cross-domain sequence representations, we introduce disentangled state space models (DSSM) -- a class of SSM in which domain-invariant state dynamics is explicitly disentangled from domain-specific information governing that dynamics. We analyze how such separation can improve knowledge transfer to new domains, and enable robust prediction, sequence manipulation and domain characterization. We furthermore propose an unsupervised VAE-based training procedure to implement DSSM in form of Bayesian filters. In our experiments, we applied VAE-DSSM framework to achieve competitive performance in online ODE system identification and regression across experimental settings, and controlled generation and prediction of bouncing ball video sequences across varying gravitational influences.

We introduce a novel generative formulation of deep probabilistic models implementing "soft" constraints on their function dynamics. In particular, we develop a flexible methodological framework where the modeled functions and derivatives of a given order are subject to inequality or equality constraints. We then characterize the posterior distribution over model and constraint parameters through stochastic variational inference. As a result, the proposed approach allows for accurate and scalable uncertainty quantification on the predictions and on all parameters. We demonstrate the application of equality constraints in the challenging problem of parameter inference in ordinary differential equation models, while we showcase the application of inequality constraints on the problem of monotonic regression of count data. The proposed approach is extensively tested in several experimental settings, leading to highly competitive results in challenging modeling applications, while offering high expressiveness, flexibility and scalability.