Matbench Discovery -- A framework to evaluate machine learning crystal stability predictions

Matbench Discovery simulates the deployment of machine learning (ML) energy models in a high-throughput search for stable inorganic crystals. We address the disconnect between (i) thermodynamic stability and formation energy and (ii) in-domain vs out-of-distribution performance. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with further insights into trade-offs between various performance metrics. To answer the question which ML methodology performs best at materials discovery, our initial release explores a variety of models including random forests, graph neural networks (GNN), one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials (UIP). Ranked best-to-worst by their test set F1 score on thermodynamic stability prediction, we find CHGNet>M3GNet>MACE>ALIGNN>MEGNet>CGCNN>CGCNN+P>Wrenformer>BOWSR>Voronoi tessellation fingerprints with random forest. The top 3 models are UIPs, the winning methodology for ML-guided materials discovery, achieving F1 scores of ~0.6 for crystal stability classification and discovery acceleration factors (DAF) of up to 5x on the first 10k most stable predictions compared to dummy selection from our test set. We also highlight a sharp disconnect between commonly used global regression metrics and more task-relevant classification metrics. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV/atom above the convex hull where most materials are. Our results highlight the need to focus on classification metrics that actually correlate with improved stability hit rate.

[1]  Rhys E. A. Goodall,et al.  Pushing the Pareto front of band gap and permittivity: ML-guided search for dielectric materials , 2024, arXiv.org.

[2]  Christopher J. Bartel,et al.  CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling , 2023, Nature Machine Intelligence.

[3]  Brian L. DeCost,et al.  Exploiting redundancy in large materials datasets for efficient machine learning with less data , 2023, Nature communications.

[4]  Samuel M. Blau,et al.  Chemical reaction networks and opportunities for machine learning , 2023, Nature Computational Science.

[5]  Simon L. Batzner,et al.  Fast Uncertainty Estimates in Deep Learning Interatomic Potentials , 2022, The Journal of chemical physics.

[6]  Brian L. DeCost,et al.  A critical examination of robustness and generalizability of machine learning prediction of materials properties , 2022, npj Computational Materials.

[7]  Eric S. Muckley,et al.  Quantifying the performance of machine learning models in materials discovery , 2022, Digital Discovery.

[8]  Zachary W. Ulissi,et al.  The Open Catalyst 2022 (OC22) Dataset and Challenges for Oxide Electrocatalysis , 2022, ACS Catalysis.

[9]  Gábor Csányi,et al.  MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields , 2022, NeurIPS.

[10]  R. Hennig,et al.  Data-augmentation for graph neural network learning of the relaxed energies of unrelaxed structures , 2022, npj Computational Materials.

[11]  Chi Chen,et al.  A universal graph deep learning interatomic potential for the periodic table , 2022, Nature Computational Science.

[12]  J. Corbeil,et al.  On the robustness of generalization of drug–drug interaction models , 2021, BMC Bioinformatics.

[13]  Rhys E. A. Goodall,et al.  Rapid discovery of stable materials by coordinate-free coarse graining , 2021, Science advances.

[14]  Brian L. DeCost,et al.  Atomistic Line Graph Neural Network for improved materials property predictions , 2021, npj Computational Materials.

[15]  Anubhav Jain,et al.  A framework for quantifying uncertainty in DFT energy corrections , 2021, Scientific Reports.

[16]  Chi Chen,et al.  Accelerating materials discovery with Bayesian optimization and graph deep learning , 2021, Materials Today.

[17]  M. Marques,et al.  Predicting stable crystalline compounds using chemical similarity , 2021, npj Computational Materials.

[18]  Joseph H. Montoya,et al.  Rational Solid-State Synthesis Routes for Inorganic Materials. , 2021, Journal of the American Chemical Society.

[19]  Jonathan P. Mailoa,et al.  E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials , 2021, Nature Communications.

[20]  G. Hart,et al.  The AFLOW Library of Crystallographic Prototypes: Part 3 , 2020, Computational Materials Science.

[21]  Volker L. Deringer,et al.  A general-purpose machine-learning force field for bulk and nanostructured phosphorus , 2020, Nature Communications.

[22]  Weihua Hu,et al.  The Open Catalyst 2020 (OC20) Dataset and Community Challenges , 2020, ACS Catalysis.

[23]  O. A. von Lilienfeld,et al.  Retrospective on a decade of machine learning for chemical discovery , 2020, Nature Communications.

[24]  Kristin A. Persson,et al.  A graph-based network for predicting chemical reaction pathways in solid-state materials synthesis , 2020, Nature Communications.

[25]  Anubhav Jain,et al.  Benchmarking materials property prediction methods: the Matbench test set and Automatminer reference algorithm , 2020, npj Computational Materials.

[26]  Christopher J. Bartel,et al.  A critical examination of compound stability predictions from machine-learned formation energies , 2020, npj Computational Materials.

[27]  Rhys E. A. Goodall,et al.  Predicting materials properties without crystal structure: deep representation learning from stoichiometry , 2019, Nature Communications.

[28]  Ralf Drautz,et al.  Atomic cluster expansion for accurate and transferable interatomic potentials , 2019, Physical Review B.

[29]  Chi Chen,et al.  Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals , 2018, Chemistry of Materials.

[30]  Kyle Chard,et al.  Matminer: An open source toolkit for materials data mining , 2018, Computational Materials Science.

[31]  Claudia Draxl,et al.  NOMAD: The FAIR concept for big data-driven materials science , 2018, MRS Bulletin.

[32]  Noam Bernstein,et al.  Machine Learning a General-Purpose Interatomic Potential for Silicon , 2018, Physical Review X.

[33]  Muratahan Aykol,et al.  Thermodynamic limit for synthesis of metastable inorganic materials , 2018, Science Advances.

[34]  Li Li,et al.  Tensor Field Networks: Rotation- and Translation-Equivariant Neural Networks for 3D Point Clouds , 2018, ArXiv.

[35]  Jeffrey C Grossman,et al.  Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties. , 2017, Physical review letters.

[36]  Finale Doshi-Velez,et al.  Decomposition of Uncertainty in Bayesian Deep Learning for Efficient and Risk-sensitive Learning , 2017, ICML.

[37]  Alok Choudhary,et al.  Including crystal structure attributes in machine learning models of formation energies via Voronoi tessellations , 2017 .

[38]  Lukasz Kaiser,et al.  Attention is All you Need , 2017, NIPS.

[39]  Vijay S. Pande,et al.  MoleculeNet: a benchmark for molecular machine learning , 2017, Chemical science.

[40]  Aron Walsh,et al.  Computational Screening of All Stoichiometric Inorganic Materials , 2016, Chem.

[41]  Miguel A. L. Marques,et al.  The optimal one dimensional periodic table: a modified Pettifor chemical scale from data mining , 2016 .

[42]  Logan T. Ward,et al.  A General-Purpose Machine Learning Framework for Predicting Properties of Inorganic Materials , 2016, 1606.09551.

[43]  Muratahan Aykol,et al.  Materials Design and Discovery with High-Throughput Density Functional Theory: The Open Quantum Materials Database (OQMD) , 2013 .

[44]  Kristin A. Persson,et al.  Commentary: The Materials Project: A materials genome approach to accelerating materials innovation , 2013 .

[45]  Kristof T. Schütt,et al.  How to represent crystal structures for machine learning: Towards fast prediction of electronic properties , 2013, 1307.1266.

[46]  S. Curtarolo,et al.  AFLOW: An automatic framework for high-throughput materials discovery , 2012, 1308.5715.

[47]  Anubhav Jain,et al.  Accuracy of density functional theory in predicting formation energies of ternary oxides from binary oxides and its implication on phase stability , 2012 .

[48]  K. Müller,et al.  Fast and accurate modeling of molecular atomization energies with machine learning. , 2011, Physical review letters.

[49]  Michele Parrinello,et al.  Generalized neural-network representation of high-dimensional potential-energy surfaces. , 2007, Physical review letters.

[50]  P. Luksch,et al.  New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design. , 2002, Acta crystallographica. Section B, Structural science.

[51]  I. D. Brown,et al.  The inorganic crystal structure data base , 1983, J. Chem. Inf. Comput. Sci..

[52]  Zachary W. Ulissi,et al.  AdsorbML: Accelerating Adsorption Energy Calculations with Machine Learning , 2022, ArXiv.

[53]  Frank H. Allen,et al.  Crystallographic Databases and Knowledge Bases in Materials Design , 1999 .