Large language models design sequence-defined macromolecules via evolutionary optimization
Source abstract
Abstract
We demonstrate the ability of a large language model to perform evolutionary optimization for materials discovery. Anthropic’s Claude 3.5 model outperforms an active learning scheme with handcrafted surrogate models and an evolutionary algorithm in selecting monomer sequences to produce targeted morphologies in macromolecular self-assembly. Utilizing pre-trained language models can potentially reduce the need for hyperparameter tuning while offering new capabilities such as self-reflection. The model performs this task effectively with or without context about the task itself, but domain-specific context sometimes results in faster convergence to good solutions. Furthermore, when this context is withheld, the model infers an approximate notion of the task (e.g., calling it a protein folding problem). This work provides evidence of Claude 3.5’s ability to act as an evolutionary optimizer, a recently discovered emergent behavior of large language models, and demonstrates a practical use case in the study and design of soft materials.
Source: openalex_inverted_index · Quality: baseline
Research context
OpenAlex topics: DNA and Biological Computing · Machine Learning in Bioinformatics · Modular Robots and Swarm Intelligence
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (23)
Show source-provided references
1. Cummins, C. et al. Enabling future nanomanufacturing through block copolymer self-assembly: a review. Nano Today 35, 100936 (2020).10.1016/j.nantod.2020.100936 ↗
2. Dill, K. A. & MacCallum, J. L. The protein-folding problem, 50 years on. Science 338, 1042–1046 (2012).10.1126/science.1219021 ↗
3. Hakobyan, K., Noble, B. B. & Xu, J. The current science of sequence-defined macromolecules. Prog. Polym. Sci. 147, 101754 (2023).10.1016/j.progpolymsci.2023.101754 ↗
4. Statt, A., Kleeblatt, D. C. & Reinhart, W. F. Unsupervised learning of sequence-specific aggregation behavior for a model copolymer. Soft matter 17, 7697–7707 (2021).10.1039/D1SM01012C ↗
5. Bhattacharya, D., Kleeblatt, D. C., Statt, A. & Reinhart, W. F. Predicting aggregate morphology of sequence-defined macromolecules with recurrent neural networks. Soft Matter 18, 5037–5051 (2022).10.1039/D2SM00452F ↗
6. Statt, A., Casademunt, H., Brangwynne, C. & Panagiotopoulos, A. Model for intrinsically disordered proteins with a strong dependence of liquid-liquid phase separation on sequence. In: Bulletin of the American Physical Society 65 (2020).
7. Wu, X., Wu, S.-h., Wu, J., Feng, L. & Tan, K. C. Evolutionary computation in the era of large language model: Survey and roadmap. arXiv https://arxiv.org/abs/2401.10034 (2024).10.1109/TEVC.2024.3506731 ↗
8. Yang, C. et al. Large language models as optimizers. arXiv https://arxiv.org/abs/2309.03409 (2023).
9. Liu, F. et al. Large language model for multi-objective evolutionary optimization. arXiv https://arxiv.org/abs/2310.12541 (2023).
10. Brahmachary, S. et al. Large language model-based evolutionary optimizer: reasoning with elitism. arXiv https://arxiv.org/abs/2403.02054 (2024).
11. Anthropic. Claude 3.5 sonnet. https://www.anthropic.com/news/claude-3-5-sonnet (2024).
12. Kusne, A. G. et al. On-the-fly closed-loop materials discovery via bayesian active learning. Nat. Commun. 11, 5966 (2020).10.1038/s41467-020-19597-w ↗
13. Kim, C., Batra, R., Chen, L., Tran, H. & Ramprasad, R. Polymer design using genetic algorithm and machine learning. Computational Mater. Sci. 186, 110067 (2021).10.1016/j.commatsci.2020.110067 ↗
14. Abolhasani, M. & Kumacheva, E. The rise of self-driving labs in chemical and materials sciences. Nat. Synth. 2, 483–492 (2023).10.1038/s44160-022-00231-0 ↗
15. Wang, L. et al. Prompt engineering in consistency and reliability with the evidence-based guideline for llms. npj Digital Med. 7, 41 (2024).10.1038/s41746-024-01029-4 ↗
16. Bhattacharya, D., Kleeblatt, D., Statt, A. & Reinhart, W. Data for “Predicting aggregate morphology of sequence-defined macromolecules with Recurrent Neural Networks” (2022).10.1039/D2SM00452F ↗
17. Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).
18. Fortin, F.-A., De Rainville, F.-M., Gardner, M.-A., Parizeau, M. & Gagné, C. DEAP: Evolutionary algorithms made easy. J. Mach. Learn. Res. 13, 2171–2175 (2012).
19. Bäck, T. Evolutionary computation 1: Basic algorithms and operators (CRC press, 2018).
20. Anthropic. Anthropic python API library. https://github.com/anthropics/anthropic-sdk-python (2024).
21. Sclar, M., Choi, Y., Tsvetkov, Y. & Suhr, A. Quantifying language models’ sensitivity to spurious features in prompt design or: how i learned to start worrying about prompt formatting. arXiv https://arxiv.org/abs/2310.11324 (2023).
22. Errica, F., Siracusano, G., Sanvito, D. & Bifulco, R. What did i do wrong? quantifying llms’ sensitivity and consistency to prompt engineering. arXiv https://arxiv.org/abs/2406.12334 (2024).
23. Reinhart, W. & Statt, A. Data and code for, “Large language models design sequence-defined macromolecules via evolutionary optimization” https://doi.org/10.5281/zenodo.13489838 (2024).10.5281/zenodo.13489838 ↗