-
STFlow: Data-Coupled Flow Matching for Geometric Trajectory Simulation
Authors:
Kiet Bennema ten Brinke,
Koen Minartz,
Vlado Menkovski
Abstract:
Simulating trajectories of dynamical systems is a fundamental problem 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 in deep generative modeling and geometric deep learning enable prob…
▽ More
Simulating trajectories of dynamical systems is a fundamental problem 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 in deep generative modeling and geometric deep learning enable probabilistic simulation by learning complex trajectory distributions while respecting intrinsic permutation and time-shift symmetries. However, trajectories of N-body systems are commonly characterized by high sensitivity to perturbations leading to bifurcations, as well as multi-scale temporal and spatial correlations. To address these challenges, we introduce STFlow (Spatio-Temporal Flow), a generative model based on graph neural networks and hierarchical convolutions. By incorporating data-dependent couplings within the Flow Matching framework, STFlow denoises starting from conditioned random-walks instead of Gaussian noise. This novel informed prior simplifies the learning task by reducing transport cost, increasing training and inference efficiency. We validate our approach on N-body systems, molecular dynamics, and human trajectory forecasting. Across these benchmarks, STFlow achieves the lowest prediction errors with fewer simulation steps and improved scalability.
△ Less
Submitted 27 May, 2026; v1 submitted 24 May, 2025;
originally announced May 2025.
-
Deep Neural Cellular Potts Models
Authors:
Koen Minartz,
Tim d'Hondt,
Leon Hillmann,
Jörn Starruß,
Lutz Brusch,
Vlado Menkovski
Abstract:
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 m…
▽ More
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.
△ Less
Submitted 4 February, 2025;
originally announced February 2025.
-
Understanding complex crowd dynamics with generative neural simulators
Authors:
Koen Minartz,
Fleur Hendriks,
Simon Martinus Koop,
Alessandro Corbetta,
Vlado Menkovski
Abstract:
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…
▽ More
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.
△ Less
Submitted 3 December, 2024; v1 submitted 2 December, 2024;
originally announced December 2024.
-
Accelerating Simulation of Two-Phase Flows with Neural PDE Surrogates
Authors:
Yoeri Poels,
Koen Minartz,
Harshit Bansal,
Vlado Menkovski
Abstract:
Simulation is a powerful tool to better understand physical systems, but generally requires computationally expensive numerical methods. Downstream applications of such simulations can become computationally infeasible if they require many forward solves, for example in the case of inverse design with many degrees of freedom. In this work, we investigate and extend neural PDE solvers as a tool to…
▽ More
Simulation is a powerful tool to better understand physical systems, but generally requires computationally expensive numerical methods. Downstream applications of such simulations can become computationally infeasible if they require many forward solves, for example in the case of inverse design with many degrees of freedom. In this work, we investigate and extend neural PDE solvers as a tool to aid in scaling simulations for two-phase flow problems, and simulations of oil expulsion from a pore specifically. We extend existing numerical methods for this problem to a more complex setting involving varying geometries of the domain to generate a challenging dataset. Further, we investigate three prominent neural PDE solver methods, namely the UNet, DRN, and U-FNO, and extend them for characteristics of the oil-expulsion problem: (1) spatial conditioning on the geometry; (2) periodicity in the boundary; (3) approximate mass conservation. We scale all methods and benchmark their speed-accuracy trade-off, evaluate qualitative properties, and perform an ablation study. We find that the investigated methods can accurately model the droplet dynamics with up to three orders of magnitude speed-up, that our extensions improve performance over the baselines, and that the introduced varying geometries constitute a significantly more challenging setting over the previously considered oil expulsion problem.
△ Less
Submitted 16 July, 2024; v1 submitted 27 May, 2024;
originally announced May 2024.
-
Efficient Probabilistic Modeling of Crystallization at Mesoscopic Scale
Authors:
Pol Timmer,
Koen Minartz,
Vlado Menkovski
Abstract:
Crystallization processes at the mesoscopic scale, where faceted, dendritic growth, and multigrain formation can be observed, are of particular interest within materials science and metallurgy. These processes are highly nonlinear, stochastic, and sensitive to small perturbations of system parameters and initial conditions. Methods for the simulation of these processes have been developed using di…
▽ More
Crystallization processes at the mesoscopic scale, where faceted, dendritic growth, and multigrain formation can be observed, are of particular interest within materials science and metallurgy. These processes are highly nonlinear, stochastic, and sensitive to small perturbations of system parameters and initial conditions. Methods for the simulation of these processes have been developed using discrete numerical models, but these are computationally expensive. This work aims to scale crystal growth simulation with a machine learning emulator. Specifically, autoregressive latent variable models are well suited for modeling the joint distribution over system parameters and the crystallization trajectories. However, successfully training such models is challenging due to the stochasticity and sensitivity of the system. Existing approaches consequently fail to produce diverse and faithful crystallization trajectories. In this paper, we introduce the Crystal Growth Neural Emulator (CGNE), a probabilistic model for efficient crystal growth emulation at the mesoscopic scale that overcomes these challenges. We validate CGNE results using the morphological properties of the crystals produced by numerical simulation. CGNE delivers a factor of 11 improvement in inference time and performance gains compared with recent state-of-the-art probabilistic models for dynamical systems.
△ Less
Submitted 26 May, 2024;
originally announced May 2024.
-
Fast Dynamic 1D Simulation of Divertor Plasmas with Neural PDE Surrogates
Authors:
Yoeri Poels,
Gijs Derks,
Egbert Westerhof,
Koen Minartz,
Sven Wiesen,
Vlado Menkovski
Abstract:
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 sur…
▽ More
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.
△ Less
Submitted 29 September, 2023; v1 submitted 30 May, 2023;
originally announced May 2023.
-
Equivariant Neural Simulators for Stochastic Spatiotemporal Dynamics
Authors:
Koen Minartz,
Yoeri Poels,
Simon Koop,
Vlado Menkovski
Abstract:
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,…
▽ More
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.
△ Less
Submitted 13 September, 2024; v1 submitted 23 May, 2023;
originally announced May 2023.
-
Towards Learned Simulators for Cell Migration
Authors:
Koen Minartz,
Yoeri Poels,
Vlado Menkovski
Abstract:
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…
▽ More
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.
△ Less
Submitted 2 November, 2022; v1 submitted 2 October, 2022;
originally announced October 2022.