A probabilistic foundation model for crystal structure denoising, phase classification, and order parameters

• URL: http://arxiv.org/abs/2512.11077v1
• Date: Thu, 11 Dec 2025 19:46:56 GMT
• Title: A probabilistic foundation model for crystal structure denoising, phase classification, and order parameters
• Abstract summary: Atomistic simulations generate large volumes of noisy structural data.<n>Existing tools such as PTM and CNA are restricted to a small set of hand-crafted lattices.<n>Here we introduce a log-probability foundation model that unifies denoising, phase classification, and OP extraction.
• Score: 2.4960857119636963
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Atomistic simulations generate large volumes of noisy structural data, but extracting phase labels, order parameters (OPs), and defect information in a way that is universal, robust, and interpretable remains challenging. Existing tools such as PTM and CNA are restricted to a small set of hand-crafted lattices (e.g.\ FCC/BCC/HCP), degrade under strong thermal disorder or defects, and produce hard, template-based labels without per-atom probability or confidence scores. Here we introduce a log-probability foundation model that unifies denoising, phase classification, and OP extraction within a single probabilistic framework. We reuse the MACE-MP foundation interatomic potential on crystal structures mapped to AFLOW prototypes, training it to predict per-atom, per-phase logits $l$ and to aggregate them into a global log-density $\log \hat{P}_θ(\boldsymbol{r})$ whose gradient defines a conservative score field. Denoising corresponds to gradient ascent on this learned log-density, phase labels follow from $\arg\max_c l_{ac}$, and the $l$ values act as continuous, defect-sensitive and interpretable OPs quantifying the Euclidean distance to ideal phases. We demonstrate universality across hundreds of prototypes, robustness under strong thermal and defect-induced disorder, and accurate treatment of complex systems such as ice polymorphs, ice--water interfaces, and shock-compressed Ti.

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