# Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

arXiv: https://arxiv.org/abs/2508.12569 · HTML: https://mlsanity.com/paper/2508.12569/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 50 of its 148 references that are in the map.
- First posted on arXiv 18 Aug 2025.

## Builds on (most cited first, 30 of 50)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Dynamic Graph CNN for Learning on Point Clouds](https://mlsanity.com/paper/1801.07829/) (2018)
- [Learning to Simulate Complex Physics with Graph Networks](https://mlsanity.com/paper/2002.09405/) (2020)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [Hamiltonian Neural Networks](https://mlsanity.com/paper/1906.01563/) (2019)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [Machine learning accelerated computational fluid dynamics](https://mlsanity.com/paper/2102.01010/) (2021)
- [Self-Attention Graph Pooling](https://mlsanity.com/paper/1904.08082/) (2019)
- [Lagrangian Neural Networks](https://mlsanity.com/paper/2003.04630/) (2020)
- [3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data](https://mlsanity.com/paper/1807.02547/) (2018)
- [Modern Koopman Theory for Dynamical Systems](https://mlsanity.com/paper/2102.12086/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [Geometric and Physical Quantities Improve E(3) Equivariant Message Passing](https://mlsanity.com/paper/2110.02905/) (2021)
- [Deep Potential Molecular Dynamics: a scalable model with the accuracy of quantum mechanics](https://mlsanity.com/paper/1707.09571/) (2017)
- [EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations](https://mlsanity.com/paper/2306.12059/) (2023)
- [TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials](https://mlsanity.com/paper/2202.02541/) (2022)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [Clebsch-Gordan Nets: a Fully Fourier Space Spherical Convolutional Neural Network](https://mlsanity.com/paper/1806.09231/) (2018)
- [Spherical Message Passing for 3D Graph Networks](https://mlsanity.com/paper/2102.05013/) (2021)
- [Symplectic Recurrent Neural Networks](https://mlsanity.com/paper/1909.13334/) (2019)
- [Equivariant flow matching](https://mlsanity.com/paper/2306.15030/) (2023)
- [An Expert's Guide to Training Physics-informed Neural Networks](https://mlsanity.com/paper/2308.08468/) (2023)
- [Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs](https://mlsanity.com/paper/2302.03655/) (2023)
- [MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation](https://mlsanity.com/paper/2302.09048/) (2023)
- [Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations](https://mlsanity.com/paper/2210.07237/) (2022)
- [Hierarchical Graph Pooling with Structure Learning](https://mlsanity.com/paper/1911.05954/) (2019)

## Built on by (most cited first, 3 of 3)

- [Metriplector: From Field Theory to Neural Architecture](https://mlsanity.com/paper/2603.29496/) (2026)
- [Nonlinear GENERIC-Embedded Neural Networks (N-GENNs): Learning GENERIC dynamics with non-quadratic dissipation potentials](https://mlsanity.com/paper/2605.09058/) (2026)
- [Mesh Field Theory: Port-Hamiltonian Formulation of Mesh-Based Physics](https://mlsanity.com/paper/2605.00394/) (2026)

## Abstract (arXiv)

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.