HyperODE is introduced, a surrogate capable of operating across an entire class of approximately mass-conserving compartmental models without retraining, by mapping the structure of ordinary differential equations into directed hypergraphs, which decouples the functional form of system interactions from the neural network architecture.
Abstract
Understanding and controlling complex dynamical systems often requires executing thousands of numerical simulations across vast parametric landscapes, which is time-consuming. Machine learning surrogates significantly accelerate simulation by predicting state trajectories across different initializations and parameter values. However, surrogate models are specialized to one simulation model. Modifying the underlying differential equations - e.g., adding a physiological state or altering an epidemiological contact network - renders trained models obsolete and forces computationally expensive retraining from scratch. We introduce HyperODE, a surrogate capable of operating across an entire class of approximately mass-conserving compartmental models without retraining. By mapping the structure of ordinary differential equations (ODEs) into directed hypergraphs, HyperODE decouples the functional form of system interactions from the neural network architecture. HyperODE takes a compartmental model in the form of an ODE with an arbitrary parameter distribution defined through quantiles and transforms it into a hypergraph. It outputs the distribution of the trajectories for all the states in the original ODE in the form of quantiles. We then use this surrogate to build an encoder that takes a noisy trajectory and outputs a distribution over the parameters of the original ODE, thus calibrating the model in a single pass. On families and system sizes never seen in training, HyperODE produces calibrated quantile bands in a single forward pass, with weighted-interval score and coverage on par with specialized surrogates for each structure. For inverse inference, HyperODE produces calibration from noisy state trajectories in a few milliseconds with a single shared encoder, competitive with existing methods. HyperODE extends zero-shot to ODEs that break mass conservation and to external forcing.
Reconstructing population dynamics is a central problem in the physical and data sciences. Often, the dynamics are modeled as a Wasserstein gradient flow (WGF): a curve of distributions driven by an energy functional. Though there are multiple mathematical characterizations of a WGF, the dominant algorithmic approach relies on the Jordan--Kinderlehrer--Otto (JKO) scheme. JKO-based methods are inflexible to time discretisation and require solving costly optimal transport problems. We take a residual approach, enforcing the continuity equations via a non-negative loss function whose minimum is the WGF. Combined with a data-fitting divergence, this gives a single global objective. This perspective unifies several existing methods and leads to a new particle-based method, stitching, that is simulation-free and robust to large gaps between observations. We demonstrate that the stitching method achieves state-of-the-art performance across trajectory inference benchmarks. For code see github.com/BasisResearch/wasserstein-residuals.
Markus Heinonen, Yair Shenfeld, R. Baptista et al.· 0 citations
Foundation models for time-dependent partial differential equations (PDEs) are trained on large and diverse collections of physical systems and can generalize effectively to new downstream tasks. After fine-tuning on only a few trajectories from a target domain, they can achieve strong accuracy in low-data regimes. However, these models are typically large and computationally intensive, limiting their usefulness as fast surrogates for numerical solvers. We propose Teacher Rollout Extension (TREX), a knowledge distillation framework that transfers the predictive capability of a pretrained foundation model into a compact and efficient student. Starting from a fine-tuned teacher, TREX augments limited downstream data by generating long synthetic trajectories through teacher rollouts, optionally with periodic noise injection. This procedure samples from the teacher-induced rollout distribution without requiring explicit knowledge of the initial-condition distribution, while exposing the student to long-horizon states and local recovery behavior around states encountered during autoregressive prediction. The student can further incorporate task-specific inductive biases, such as equivariance, that the teacher does not necessarily enforce. We evaluate TREX on multiple PDE benchmarks. The resulting students can match or surpass the teacher's accuracy while reducing the number of parameters by several orders of magnitude and achieving more than an order-of-magnitude speedup in inference.
Daniel Musekamp, Boshra Ariguib, Andrei Manolache et al.· 0 citations
Inferring continuous system evolution from sparse temporal snapshots is a key challenge in generative modeling and single-cell omics. While Optimal Transport (OT) is popular, existing frameworks are largely restricted to first-order dynamics, assuming memoryless velocity fields. This limits expressiveness, as first-order systems fail to account for regulatory momentum and time-delayed responses inherent in processes like cell differentiation. Here, we introduce TracingFlow, a simulation-free Flow Matching framework generalizing to second-order dynamics. By using neural networks to regress the acceleration field, TracingFlow provides an exact, efficient solution to the Dynamical Optimal Acceleration Transport (DOAT) problem. Unlike first-order methods yielding over-smoothed trajectories, our second-order formulation captures high-curvature transitions and nonlinear evolutions by learning the underlying force fields. Evaluated on complex synthetic and large-scale scRNA-seq datasets, TracingFlow achieves superior accuracy in distributional reconstruction and trajectory faithfulness. Moreover, by integrating lineage tracing priors, it recovers dynamical structures that are both mathematically optimal and biologically plausible.
Yuhao Sun, Zekun Wu, Zixun Huang et al.· 0 citations
We benchmark transport-based generative models as well as distillation-based few-step methods for the probabilistic forecasting of stochastic fluid flows, with a particular focus on performance under limited inference budgets. All methods are evaluated on a two-dimensional Kolmogorov flow with stochastic forcing. We measure one-step distributional accuracy against large simulated reference ensembles and assess whether the invariant measure is preserved during autoregressive rollouts via the enstrophy spectrum. On the stochastic task, flow matching achieves the most accurate one-step conditional distribution at high inference budgets, while the second-order exponential integrator DPM-2 is strongest at very low NFE. Few-step distillation methods are competitive with the multi-step methods and preserve the enstrophy spectrum particularly well. A deterministic control task, in which the forcing over the prediction interval is observed, separates aleatoric from epistemic uncertainty. Model performance does not translate between the two settings: the distilled models are competitive on the stochastic task but least accurate on the control task. While stochastic diffusion samplers such as DDPM better preserve the enstrophy spectrum during rollouts in the stochastic setting, deterministic samplers such as DDIM and DPM-2 show better spectral preservation in the deterministic setting.
Sebastian Pfister, Benjamin J. Holzschuh, Nils Thürey· 0 citations
Deploying machine learning surrogates in scientific simulations faces multifaceted challenges, primary among which is the lack of Continual Learning (CL) capabilities—specifically, the inability to adapt to new physical regimes without significantly degrading performance on prior ones. This is particularly problematic for autoregressive surrogates of time-dependent Partial Differential Equations (PDEs), where small prediction errors can accumulate over long rollouts and new physical regimes overwrite previously learned dynamics. We formulate this adaptation as a CL problem, demonstrating that while standard Experience Replay (ER) is a robust baseline across Advection-Diffusion, Burgers’, and Navier-Stokes equations, storing full high-resolution rollouts can be memory-inefficient. To address this, we introduce Replay-TS, a temporal-slicing replay strategy that stores compact autoregressive windows sampled across past simulations. Through empirical analysis, we show that Replay-TS exploits the low-frequency spectral redundancy of physical systems to enable sparse supervision for rollout steps. By preserving the contiguous historical context and sparsely penalizing the autoregressive target steps, Replay-TS improves retention performance under a fixed memory budget by leveraging higher sample diversity. Replay-TS consistently outperforms standard ER methods across standard 1D and 2D streams, achieving over a 30% MSE reduction in a mixed-physics stream, while remaining architecture-agnostic.
Hamed Hemati, Binh Duong Nguyen, Stefan Sandfeld· Machine Learning for Computa...· 0 citations
Continuous-time Markov chains (CTMCs) provide the backbone for modeling discrete stochastic dynamics across applied, physical, and biological sciences. Their integration with modern gradient-based machine learning, however, is limited by the hard categorical event selection intrinsic to Gillespie-type simulation algorithms. We exploit the affine state update to obtain the exact one-step conditional-mean sensitivity by differentiating normalized reaction propensities. We pair this backward rule with exact forward trajectories to define the propensity straight-through (PST) estimator. At the trajectory level, we show that one-step sensitivities composed across events can depart from the exact multistep sensitivity. We derive the resulting per-step discrepancy in closed form and prove that it vanishes identically for affine downstream dependence. PST matches the accuracy of Gumbel-Softmax straight-through across all benchmarks: reversible dimerization (0.06% error), a genetic oscillator (1.7% error), a 50-task repressilator suite (0.17% median error), and patch-clamp ion-channel recordings ($R^2$ = 0.988). Under matched settings, PST converges 3.0-fold faster on the oscillator and 2.1-fold faster on the ion channel. At deep-learning scale, PST trains a 203,796-parameter stochastic reaction network with hard sampling, reaching 98.22% MNIST digit classification accuracy. By differentiating an exact conditional mean rather than a relaxed sample, PST offers a temperature- and Gumbel-free path to scalable gradient-based learning through exact stochastic trajectories.
