Papers
Topics
Authors
Recent
Gemini 2.5 Flash
Gemini 2.5 Flash
157 tokens/sec
GPT-4o
43 tokens/sec
Gemini 2.5 Pro Pro
43 tokens/sec
o3 Pro
4 tokens/sec
GPT-4.1 Pro
47 tokens/sec
DeepSeek R1 via Azure Pro
28 tokens/sec
2000 character limit reached

Data-Driven Score-Based Models for Generating Stable Structures with Adaptive Crystal Cells (2310.10695v1)

Published 16 Oct 2023 in physics.comp-ph and cs.LG

Abstract: The discovery of new functional and stable materials is a big challenge due to its complexity. This work aims at the generation of new crystal structures with desired properties, such as chemical stability and specified chemical composition, by using machine learning generative models. Compared to the generation of molecules, crystal structures pose new difficulties arising from the periodic nature of the crystal and from the specific symmetry constraints related to the space group. In this work, score-based probabilistic models based on annealed Langevin dynamics, which have shown excellent performance in various applications, are adapted to the task of crystal generation. The novelty of the presented approach resides in the fact that the lattice of the crystal cell is not fixed. During the training of the model, the lattice is learned from the available data, whereas during the sampling of a new chemical structure, two denoising processes are used in parallel to generate the lattice along the generation of the atomic positions. A multigraph crystal representation is introduced that respects symmetry constraints, yielding computational advantages and a better quality of the sampled structures. We show that our model is capable of generating new candidate structures in any chosen chemical system and crystal group without any additional training. To illustrate the functionality of the proposed method, a comparison of our model to other recent generative models, based on descriptor-based metrics, is provided.

Definition Search Book Streamline Icon: https://streamlinehq.com
References (34)
  1. Le, T.; Winkler, D. Discovery and Optimization of Materials Using Evolutionary Approaches. Chem. Rev. 2016, 6107 – 6132
  2. Henson, A. B.; Gromski, P.; Cronin, L. Designing Algorithms To Aid Discovery by Chemical Robots. ACS Cent. Sci. 2018, 793–804
  3. Xie, Y.; Zhang, C.; Hu, X.; Zhang, C.; Kelly, S. P.; Atwood, J. L.; Lin, J. Machine learning assisted synthesis of metal-organic nanocapsules. J. Am. Chem. Soc. 2020, 1475 – 1481
  4. Ward, L.; Agrawal, A.; Choudhary, A.; Wolverton, C. A general- purpose machine learning framework for predicting properties of inorganic materials. npj Comput. Mater. 2016, 16026
  5. Dong, Y.; Wu, C.; Zhang, C.; Liu, Y.; Cheng, J.; Lin, J. Bandgap prediction by deep learning in configurationally hybridized graphene and boron nitride. npj Comput. Mater. 2019, 26
  6. Oliynyk, A. O.; Adutwum, L. A.; Rudyk, B. W.; Pisavadia, H.; Lotfi, S.; Hlukhyy, V.; Harynuk, J. J.; Mar, A.; Brgoch, J. Disentangling Structural Confusion through Machine Learning: Structure Prediction and Polymorphism of Equiatomic Ternary Phases ABC. J. Am. Chem. Soc. 2017, 17870–17881
  7. Raccuglia, P.; Elbert, K. C.; Adler, P.; Falk, C.; Wenny, M.; Mollo, A.; Zeller, M.; Friedler, S. A.; Schrier, J.; Norquist, A. Machine-learning-assisted materials discovery using failed experiments. Nature 2016, 73–76
  8. Ahneman, D. T.; Estrada, J. G.; Lin, S.; Dreher, S. D.; Doyle, A. Predicting reaction performance in C–N cross-coupling using machine learning. Science 2018, 186–190
  9. Granda, J. M.; Donina, L.; Dragone, V.; Long, D.-L.; Cronin, L. Controlling an organic synthesis robot with machine learning to search for new reactivity. Nature 2018, 377–381
  10. Moosavi, S. M.; Chidambaram, A.; Talirz, L.; Haranczyk, M.; Stylianou, K.; Smit, B. Capturing chemical intuition in synthesis of metal-organic frameworks. Nat. Commun. 2019, 539
  11. Coley, C. W.; Green, W. H.; Jensen, K. Machine Learning in Computer-Aided Synthesis Planning. Acc. Chem. Res. 2018, 1281–1289
  12. Voznyy, O.; Levina, L.; Fan, J. Z.; Askerka, M.; Jain, A.; Choi, M.-J.; Ouellette, O.; Todorovic, A. P.; Sagar, L.; Sargent, E. Machine Learning Accelerates Discovery of Optimal Colloidal Quantum Dot Synthesis. ACS Nano 2019, 11122–11128
  13. Kim, S.; Noh, J.; Go, G. H.; Aspuru-Guzik, A.; Jung, Y. Generative adversarial networks for crystal structure prediction. ACS Cent. Sci. 2020, 1412–1420
  14. Hoffmann, J.; Maestrati, L.; Sawada, Y.; Tang, J.; Sellier, J. M.; Bengio, Y. Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures. arXiv preprint 2019, 1909.00949
  15. Court, C. J.; Yildirim, B.; Jain, A.; Cole, J. M. 3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning. J. Chem. Inf. Model. 2020,
  16. Xie, T.; Fu, X.; Ganea, O.-E.; Barzilay, R.; Jaakkola, T. S. Crystal Diffusion Variational Autoencoder for Periodic Material Generation. International Conference on Learning Representations. 2022
  17. Nouira, A.; Sokolovska, N.; Crivello, J.-C. CrystalGAN: Learning to Discover Crystallographic Structures with Generative Adversarial Networks. AAAI 2019 Spring Symposium on Combining Machine Learning with Knowledge Engineering (AAAI-MAKE). 2019
  18. Kim, S.; Noh, J.; Gu, G. H.; Aspuru-Guzik, A.; Jung, Y. Generative Adversarial Networks for Crystal Structure Prediction. ACS Cent. Sci. 2020,
  19. Lim, J.; Ryu, S.; Kim, J. W.; others Molecular generative model based on conditional variational autoencoder for de novo molecular design. J. Cheminf. 2018, 10
  20. Fuhr, A. S.; Sumpter, B. G. Deep generative models for materials discovery and machine learning-accelerated innovation. Front. Mater. 2022, 8
  21. Shi, C.; Luo, S.; Xu, M.; Tang, J. Learning Gradient Fields for Molecular Conformation Generation. Proceedings of the 38th International Conference on Machine Learning. 2021; pp 9558–9568
  22. Hoogeboom, E.; Satorras, V. G.; Vignac, C.; Welling, M. Equivariant Diffusion for Molecule Generation in 3D. Proceedings of the 39th International Conference on Machine Learning. 2022; pp 8867–8887
  23. Xie, T.; Grossman, J. C. Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties. Phys. Rev. Lett. 2018, 120
  24. Gasteiger, J.; Giri, S.; Margraf, J. T.; Günnemann, S. Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules. 2020; https://arxiv.org/abs/2011.14115
  25. Gasteiger, J.; Becker, F.; Günnemann, S. GemNet: Universal Directional Graph Neural Networks for Molecules. Advances in Neural Information Processing Systems. 2021; pp 6790–6802
  26. Choudhary, K.; DeCost, B. Atomistic Line Graph Neural Network for improved materials property predictions. npj Comput. Mater. 2021, 7
  27. Ho, J.; Jain, A.; Abbeel, P. Denoising Diffusion Probabilistic Models. Advances in Neural Information Processing Systems. 2020; pp 6840–6851
  28. Song, Y.; Ermon, S. Generative Modeling by Estimating Gradients of the Data Distribution. Advances in Neural Information Processing Systems. 2019
  29. Yang, L.; Zhang, Z.; Hong, S.; Xu, R.; Zhao, Y.; Shao, Y.; Zhang, W.; Yang, M.-H.; Cui, B. Diffusion Models: A Comprehensive Survey of Methods and Applications. 2022; https://arxiv.org/abs/2209.00796
  30. Xu, M.; Yu, L.; Song, Y.; Shi, C.; Ermon, S.; Tang, J. GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation. International Conference on Learning Representations. 2022
  31. Ren, Z.; Noh, J.; Tian, S.; Oviedo, F.; Xing, G.; Liang, Q.; Aberle, A.; Liu, Y.; Li, Q.; Jayavelu, S.; others Inverse design of crystals using generalized invertible crystallographic representation. arXiv preprint arXiv:2005.07609 2020,
  32. Zhao, Y.; Al-Fahdi, M.; Hu, M.; Siriwardane, E.; Song, Y.; Nasiri, A.; Hu, J. High-throughput discovery of novel cubic crystal materials using deep generative neural networks. Adv. Sci. 2021, 8
  33. Zhao, Y.; Siriwardane, E. M. D.; Wu, Z.; Fu, N.; Al-Fahdi, M.; Hu, M.; Hu, J. Physics guided deep learning for generative design of crystal materials with symmetry constraints. npj Comput. Mater. 2023, 73–76
  34. Heusel, M.; Ramsauer, H.; Unterthiner, T.; Nessler, B.; Hochreiter, S. GANs Trained by a Two Time-Scale Update Rule Converge to a Local Nash Equilibrium. 2018; https://arxiv.org/abs/1706.08500
Citations (3)

Summary

We haven't generated a summary for this paper yet.