# MCGM: Multi-stage Clustered Global Modeling for Long-range Interactions in Molecules

arXiv: https://arxiv.org/abs/2509.22028 · HTML: https://mlsanity.com/paper/2509.22028/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 42 references that are in the map.
- First posted on arXiv 26 Sep 2025.

## Builds on (most cited first, 18 of 18)

- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [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)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [Learning Local Equivariant Representations for Large-Scale Atomistic Dynamics](https://mlsanity.com/paper/2204.05249/) (2022)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [Graph neural networks for materials science and chemistry](https://mlsanity.com/paper/2208.09481/) (2022)
- [SpookyNet: Learning Force Fields with Electronic Degrees of Freedom and Nonlocal Effects](https://mlsanity.com/paper/2105.00304/) (2021)
- [Ewald-based Long-Range Message Passing for Molecular Graphs](https://mlsanity.com/paper/2303.04791/) (2023)
- [Latent Ewald summation for machine learning of long-range interactions](https://mlsanity.com/paper/2408.15165/) (2024)
- [Accelerating Molecular Graph Neural Networks via Knowledge Distillation](https://mlsanity.com/paper/2306.14818/) (2023)
- [Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel](https://mlsanity.com/paper/2311.01276/) (2023)
- [Neural P3M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs](https://mlsanity.com/paper/2409.17622/) (2024)

## Abstract (arXiv)

Geometric graph neural networks (GNNs) excel at capturing molecular geometry, yet their locality-biased message passing hampers the modeling of long-range interactions. Current solutions have fundamental limitations: extending cutoff radii causes computational costs to scale cubically with distance; physics-inspired kernels (e.g., Coulomb, dispersion) are often system-specific and lack generality; Fourier-space methods require careful tuning of multiple parameters (e.g., mesh size, k-space cutoff) with added computational overhead. We introduce Multi-stage Clustered Global Modeling (MCGM), a lightweight, plug-and-play module that endows geometric GNNs with hierarchical global context through efficient clustering operations. MCGM builds a multi-resolution hierarchy of atomic clusters, distills global information via dynamic hierarchical clustering, and propagates this context back through learned transformations, ultimately reinforcing atomic features via residual connections. Seamlessly integrated into four diverse backbone architectures, MCGM reduces OE62 energy prediction error by an average of 26.2%. On AQM, MCGM achieves state-of-the-art accuracy (17.0 meV for energy, 4.9 meV/AA for forces) while using 20% fewer parameters than Neural P3M. Code will be made available upon acceptance.