Graph neural network interatomic potential ensembles with calibrated aleatoric and epistemic uncertainty on energy and forces

Research output: Contribution to journalJournal articleResearchpeer-review


  • Fulltext

    Final published version, 1.23 MB, PDF document

  • Jonas Busk
  • Mikkel N. Schmidt
  • Winther, Ole
  • Tejs Vegge
  • Peter Bjørn Jørgensen

Inexpensive machine learning (ML) potentials are increasingly being used to speed up structural optimization and molecular dynamics simulations of materials by iteratively predicting and applying interatomic forces. In these settings, it is crucial to detect when predictions are unreliable to avoid wrong or misleading results. Here, we present a complete framework for training and recalibrating graph neural network ensemble models to produce accurate predictions of energy and forces with calibrated uncertainty estimates. The proposed method considers both epistemic and aleatoric uncertainty and the total uncertainties are recalibrated post hoc using a nonlinear scaling function to achieve good calibration on previously unseen data, without loss of predictive accuracy. The method is demonstrated and evaluated on two challenging, publicly available datasets, ANI-1x (Smith et al. J. Chem. Phys., 2018, 148, 241733.) and Transition1x (Schreiner et al. Sci. Data, 2022, 9, 779.), both containing diverse conformations far from equilibrium. A detailed analysis of the predictive performance and uncertainty calibration is provided. In all experiments, the proposed method achieved low prediction error and good uncertainty calibration, with predicted uncertainty correlating with expected error, on energy and forces. To the best of our knowledge, the method presented in this paper is the first to consider a complete framework for obtaining calibrated epistemic and aleatoric uncertainty predictions on both energy and forces in ML potentials.

Original languageEnglish
JournalPhysical Chemistry Chemical Physics
Pages (from-to)25828-25837
Number of pages10
Publication statusPublished - 2023

Bibliographical note

Publisher Copyright:
© 2023 The Royal Society of Chemistry.

ID: 369347360