# Unsupervised Atomic Data Mining via Multi-Kernel Graph Autoencoders for Machine Learning Force Fields

arXiv: https://arxiv.org/abs/2509.12358 · HTML: https://mlsanity.com/paper/2509.12358/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 45 references that are in the map.
- First posted on arXiv 15 Sep 2025.

## Builds on (most cited first, 12 of 12)

- [Reproducible scaling laws for contrastive language-image learning](https://mlsanity.com/paper/2212.07143/) (2022)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [An Empirical Study of Example Forgetting during Deep Neural Network Learning](https://mlsanity.com/paper/1812.05159/) (2018)
- [Deep Learning on a Data Diet: Finding Important Examples Early in Training](https://mlsanity.com/paper/2107.07075/) (2021)
- [Beyond neural scaling laws: beating power law scaling via data pruning](https://mlsanity.com/paper/2206.14486/) (2022)
- [MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields](https://mlsanity.com/paper/2206.07697/) (2022)
- [D4: Improving LLM Pretraining via Document De-Duplication and Diversification](https://mlsanity.com/paper/2308.12284/) (2023)
- [Quality Not Quantity: On the Interaction between Dataset Design and Robustness of CLIP](https://mlsanity.com/paper/2208.05516/) (2022)
- [On the Predictability of Pruning Across Scales](https://mlsanity.com/paper/2006.10621/) (2020)
- [Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks](https://mlsanity.com/paper/2101.11588/) (2021)
- [Model-free quantification of completeness, uncertainties, and outliers in atomistic machine learning using information theory](https://mlsanity.com/paper/2404.12367/) (2024)
- [WACSF - Weighted Atom-Centered Symmetry Functions as Descriptors in Machine Learning Potentials](https://mlsanity.com/paper/1712.05861/) (2017)

## Built on by (most cited first, 1 of 1)

- [Maximizing Efficiency of Dataset Compression for Machine Learning Potentials With Information Theory](https://mlsanity.com/paper/2511.10561/) (2025)

## Abstract (arXiv)

Constructing a chemically diverse dataset while avoiding sampling bias is critical to training efficient and generalizable force fields. However, in computational chemistry and materials science, many common dataset generation techniques are prone to oversampling regions of the potential energy surface. Furthermore, these regions can be difficult to identify and isolate from each other or may not align well with human intuition, making it challenging to systematically remove bias in the dataset. While traditional clustering and pruning (down-sampling) approaches can be useful for this, they can often lead to information loss or a failure to properly identify distinct regions of the potential energy surface due to difficulties associated with the high dimensionality of atomic descriptors. In this work, we introduce the Multi-kernel Edge Attention-based Graph Autoencoder (MEAGraph) model, an unsupervised approach for analyzing atomic datasets. MEAGraph combines multiple linear kernel transformations with attention-based message passing to capture geometric sensitivity and enable effective dataset pruning without relying on labels or extensive training. Demonstrated applications on niobium, tantalum, and iron datasets show that MEAGraph efficiently groups similar atomic environments, allowing for the use of basic pruning techniques for removing sampling bias. This approach provides an effective method for representation learning and clustering that can be used for data analysis, outlier detection, and dataset optimization.