Koen Minartz

Koen Minartz, Yoeri Poels, Vlado Menkovski

Simulators driven by deep learning are gaining popularity as a tool for efficiently emulating accurate but expensive numerical simulators. Successful applications of such neural simulators can be found in the domains of physics, chemistry, and structural biology, amongst others. Likewise, a neural simulator for cellular dynamics can augment lab experiments and traditional computational methods to enhance our understanding of a cell's interaction with its physical environment. In this work, we propose an autoregressive probabilistic model that can reproduce spatiotemporal dynamics of single cell migration, traditionally simulated with the Cellular Potts model. We observe that standard single-step training methods do not only lead to inconsistent rollout stability, but also fail to accurately capture the stochastic aspects of the dynamics, and we propose training strategies to mitigate these issues. Our evaluation on two proof-of-concept experimental scenarios shows that neural methods have the potential to faithfully simulate stochastic cellular dynamics at least an order of magnitude faster than a state-of-the-art implementation of the Cellular Potts model.

Koen Minartz, Fleur Hendriks, Simon Martinus Koop et al.

Understanding the dynamics of pedestrian crowds is an outstanding challenge crucial for designing efficient urban infrastructure and ensuring safe crowd management. To this end, both small-scale laboratory and large-scale real-world measurements have been used. However, these approaches respectively lack statistical resolution and parametric controllability, both essential to discovering physical relationships underlying the complex stochastic dynamics of crowds. Here, we establish an investigation paradigm that offers laboratory-like controllability, while ensuring the statistical resolution of large-scale real-world datasets. Using our data-driven Neural Crowd Simulator (NeCS), which we train on large-scale data and validate against key statistical features of crowd dynamics, we show that we can perform effective surrogate crowd dynamics experiments without training on specific scenarios. We not only reproduce known experimental results on pairwise avoidance, but also uncover the vision-guided and topological nature of N-body interactions. These findings show how virtual experiments based on neural simulation enable data-driven scientific discovery.

Kiet Bennema ten Brinke, Koen Minartz, Vlado Menkovski

The simulation of N-body systems is a fundamental problem with applications in a wide range of fields, such as molecular dynamics, biochemistry, and pedestrian dynamics. Machine learning has become an invaluable tool for scaling physics-based simulators and developing models directly from experimental data. In particular, recent advances based on deep generative modeling and geometric deep learning have enabled probabilistic simulation by modeling complex distributions over trajectories while respecting the permutation symmetry that is fundamental to N-body systems. However, to generate realistic trajectories, existing methods must learn complex transformations starting from uninformed noise and do not allow for the exploitation of domain-informed priors. In this work, we propose STFlow to address this limitation. By leveraging flow matching and data-dependent couplings, STFlow facilitates physics-informed simulation of geometric trajectories without sacrificing model expressivity or scalability. Our evaluation on N-body dynamical systems, molecular dynamics, and pedestrian dynamics benchmarks shows that STFlow produces significantly lower prediction errors while enabling more efficient inference, highlighting the benefits of employing physics-informed prior distributions in probabilistic geometric trajectory modeling.

Koen Minartz, Tim d'Hondt, Leon Hillmann et al.

The cellular Potts model (CPM) is a powerful computational method for simulating collective spatiotemporal dynamics of biological cells. To drive the dynamics, CPMs rely on physics-inspired Hamiltonians. However, as first principles remain elusive in biology, these Hamiltonians only approximate the full complexity of real multicellular systems. To address this limitation, we propose NeuralCPM, a more expressive cellular Potts model that can be trained directly on observational data. At the core of NeuralCPM lies the Neural Hamiltonian, a neural network architecture that respects universal symmetries in collective cellular dynamics. Moreover, this approach enables seamless integration of domain knowledge by combining known biological mechanisms and the expressive Neural Hamiltonian into a hybrid model. Our evaluation with synthetic and real-world multicellular systems demonstrates that NeuralCPM is able to model cellular dynamics that cannot be accounted for by traditional analytical Hamiltonians.

Yoeri Poels, Gijs Derks, Egbert Westerhof et al.

Managing divertor plasmas is crucial for operating reactor scale tokamak devices due to heat and particle flux constraints on the divertor target. Simulation is an important tool to understand and control these plasmas, however, for real-time applications or exhaustive parameter scans only simple approximations are currently fast enough. We address this lack of fast simulators using neural PDE surrogates, data-driven neural network-based surrogate models trained using solutions generated with a classical numerical method. The surrogate approximates a time-stepping operator that evolves the full spatial solution of a reference physics-based model over time. We use DIV1D, a 1D dynamic model of the divertor plasma, as reference model to generate data. DIV1D's domain covers a 1D heat flux tube from the X-point (upstream) to the target. We simulate a realistic TCV divertor plasma with dynamics induced by upstream density ramps and provide an exploratory outlook towards fast transients. State-of-the-art neural PDE surrogates are evaluated in a common framework and extended for properties of the DIV1D data. We evaluate (1) the speed-accuracy trade-off; (2) recreating non-linear behavior; (3) data efficiency; and (4) parameter inter- and extrapolation. Once trained, neural PDE surrogates can faithfully approximate DIV1D's divertor plasma dynamics at sub real-time computation speeds: In the proposed configuration, 2ms of plasma dynamics can be computed in $\approx$0.63ms of wall-clock time, several orders of magnitude faster than DIV1D.

Koen Minartz, Yoeri Poels, Simon Koop et al.

Neural networks are emerging as a tool for scalable data-driven simulation of high-dimensional dynamical systems, especially in settings where numerical methods are infeasible or computationally expensive. Notably, it has been shown that incorporating domain symmetries in deterministic neural simulators can substantially improve their accuracy, sample efficiency, and parameter efficiency. However, to incorporate symmetries in probabilistic neural simulators that can simulate stochastic phenomena, we need a model that produces equivariant distributions over trajectories, rather than equivariant function approximations. In this paper, we propose Equivariant Probabilistic Neural Simulation (EPNS), a framework for autoregressive probabilistic modeling of equivariant distributions over system evolutions. We use EPNS to design models for a stochastic n-body system and stochastic cellular dynamics. Our results show that EPNS considerably outperforms existing neural network-based methods for probabilistic simulation. More specifically, we demonstrate that incorporating equivariance in EPNS improves simulation quality, data efficiency, rollout stability, and uncertainty quantification. We conclude that EPNS is a promising method for efficient and effective data-driven probabilistic simulation in a diverse range of domains.