# Crystal structure prediction using graph neural combinatorial optimization

arXiv: https://arxiv.org/abs/2604.23921 · HTML: https://mlsanity.com/paper/2604.23921/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 33 of its 75 references that are in the map.
- First posted on arXiv 27 Apr 2026.

## Builds on (most cited first, 30 of 33)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Sinkhorn Distances: Lightspeed Computation of Optimal Transportation Distances](https://mlsanity.com/paper/1306.0895/) (2013)
- [The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables](https://mlsanity.com/paper/1611.00712/) (2016)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [Machine Learning for Combinatorial Optimization: a Methodological Tour d'Horizon](https://mlsanity.com/paper/1811.06128/) (2018)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Understanding over-squashing and bottlenecks on graphs via curvature](https://mlsanity.com/paper/2111.14522/) (2021)
- [Flow Network based Generative Models for Non-Iterative Diverse Candidate Generation](https://mlsanity.com/paper/2106.04399/) (2021)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [PairNorm: Tackling Oversmoothing in GNNs](https://mlsanity.com/paper/1909.12223/) (2019)
- [Combinatorial optimization and reasoning with graph neural networks](https://mlsanity.com/paper/2102.09544/) (2021)
- [A Survey on Oversmoothing in Graph Neural Networks](https://mlsanity.com/paper/2303.10993/) (2023)
- [Learning a SAT Solver from Single-Bit Supervision](https://mlsanity.com/paper/1802.03685/) (2018)
- [Solving Mixed Integer Programs Using Neural Networks](https://mlsanity.com/paper/2012.13349/) (2020)
- [Learning Latent Permutations with Gumbel-Sinkhorn Networks](https://mlsanity.com/paper/1802.08665/) (2018)
- [Exphormer: Sparse Transformers for Graphs](https://mlsanity.com/paper/2303.06147/) (2023)
- [Erdos Goes Neural: an Unsupervised Learning Framework for Combinatorial Optimization on Graphs](https://mlsanity.com/paper/2006.10643/) (2020)
- [Combinatorial Optimization with Physics-Inspired Graph Neural Networks](https://mlsanity.com/paper/2107.01188/) (2021)
- [A Diffusion Model Framework for Unsupervised Neural Combinatorial Optimization](https://mlsanity.com/paper/2406.01661/) (2024)
- [Let the Flows Tell: Solving Graph Combinatorial Optimization Problems with GFlowNets](https://mlsanity.com/paper/2305.17010/) (2023)
- [The Machine Learning for Combinatorial Optimization Competition (ML4CO): Results and Insights](https://mlsanity.com/paper/2203.02433/) (2022)
- [Graph Coloring with Physics-Inspired Graph Neural Networks](https://mlsanity.com/paper/2202.01606/) (2022)

## Abstract (arXiv)

Crystalline materials are widely used in technological applications, yet their discovery remains a significant challenge. As their properties are driven by structure, crystal structure prediction (CSP) methods play a central role in computational approaches aiming to accelerate this process. Previously, CSP has been approached from a combinatorial optimization perspective, with the core challenge of allocating atoms on a fine grid of predefined discrete positions within a unit cell while minimizing their interaction energy. Exact mathematical optimization methods provide guaranteed solutions, but they become computationally expensive for large-scale instances, where the atomic configuration space grows rapidly, particularly in the absence of additional symmetry constraints. In this work, we introduce a neural combinatorial optimization approach to the atom allocation challenge and, subsequently, CSP, based on graph neural networks (GNNs), which can effectively sample from the distribution of feasible structures in an unsupervised manner. We leverage expander graphs to construct computational graphs over discrete positions that capture both short- and long-range interactions between atoms, and employ the Gumbel-Sinkhorn approach to enforce the desired stoichiometry of the generated structures. We demonstrate that our method outperforms classical heuristic approaches and is competitive with a commercial optimization solver across a range of chemical compositions. This enables the use of ever-expanding GPU infrastructure to tackle the inherent combinatorial challenges of CSP, paving the way for scaling beyond current capabilities.