Jan Hasenauer

Clemens Schächter, Maren Hackenberg, Michelle Pfaffenlehner et al.

Many rare diseases offer limited established treatment options, leading patients to switch therapies when new medications emerge. To analyze the impact of such treatment switches within the low sample size limitations of rare disease trials, it is important to use all available data sources. This, however, is complicated when usage of measurement instruments change during the observation period, for example when instruments are adapted to specific age ranges. The resulting disjoint longitudinal data trajectories, complicate the application of traditional modeling approaches like mixed-effects regression. We tackle this by mapping observations of each instrument to a aligned low-dimensional temporal trajectory, enabling longitudinal modeling across instruments. Specifically, we employ a set of variational autoencoder architectures to embed item values into a shared latent space for each time point. Temporal disease dynamics and treatment switch effects are then captured through a mixed-effects regression model applied to latent representations. To enable statistical inference, we present a novel statistical testing approach that accounts for the joint parameter estimation of mixed-effects regression and variational autoencoders. The methodology is applied to quantify the impact of treatment switches for patients with spinal muscular atrophy. Here, our approach aligns motor performance items from different measurement instruments for mixed-effects regression and maps estimated effects back to the observed item level to quantify the treatment switch effect. Our approach allows for model selection as well as for assessing effects of treatment switching. The results highlight the potential of modeling in joint latent representations for addressing small data challenges.

Maren Philipps, Antonia Körner, Jakob Vanhoefer et al.

Universal differential equations (UDEs) leverage the respective advantages of mechanistic models and artificial neural networks and combine them into one dynamic model. However, these hybrid models can suffer from unrealistic solutions, such as negative values for biochemical quantities. We present non-negative UDE (nUDEs), a constrained UDE variant that guarantees non-negative values. Furthermore, we explore regularisation techniques to improve generalisation and interpretability of UDEs.

Nina Schmid, David Fernandes del Pozo, Willem Waegeman et al.

Scientific Machine Learning is a new class of approaches that integrate physical knowledge and mechanistic models with data-driven techniques for uncovering governing equations of complex processes. Among the available approaches, Universal Differential Equations (UDEs) are used to combine prior knowledge in the form of mechanistic formulations with universal function approximators, like neural networks. Integral to the efficacy of UDEs is the joint estimation of parameters within mechanistic formulations and the universal function approximators using empirical data. The robustness and applicability of resultant models, however, hinge upon the rigorous quantification of uncertainties associated with these parameters, as well as the predictive capabilities of the overall model or its constituent components. With this work, we provide a formalisation of uncertainty quantification (UQ) for UDEs and investigate important frequentist and Bayesian methods. By analysing three synthetic examples of varying complexity, we evaluate the validity and efficiency of ensembles, variational inference and Markov chain Monte Carlo sampling as epistemic UQ methods for UDEs.