Foundation Models for Discovery and Exploration in Chemical Space
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2025
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| author | Wadell, Alexius Bhutani, Anoushka Azumah, Victor Ellis-Mohr, Austin R. Stier, Andrew J. Hegazy, Kareem Brace, Alexander Zhao, Hancheng Kelly, Celia Nayak, Anuj K. Chen, Yuhan Simatos, Dimitrios Lin, Hongyi Emani, Murali Vishwanath, Venkatram Gering, Kevin Alkan, Melisa Gibbs, Tom Wells, Jack Qian, Wesley W. Gerkin, Richard C. Amorelli, Benjamin Wiltschko, Alexander B. Varshney, Lav R. Ramsundar, Bharath Duraisamy, Karthik Mahoney, Michael W. Ramanathan, Arvind Viswanathan, Venkatasubramanian |
| author_facet | Wadell, Alexius Bhutani, Anoushka Azumah, Victor Ellis-Mohr, Austin R. Stier, Andrew J. Hegazy, Kareem Brace, Alexander Zhao, Hancheng Kelly, Celia Nayak, Anuj K. Chen, Yuhan Simatos, Dimitrios Lin, Hongyi Emani, Murali Vishwanath, Venkatram Gering, Kevin Alkan, Melisa Gibbs, Tom Wells, Jack Qian, Wesley W. Gerkin, Richard C. Amorelli, Benjamin Wiltschko, Alexander B. Varshney, Lav R. Ramsundar, Bharath Duraisamy, Karthik Mahoney, Michael W. Ramanathan, Arvind Viswanathan, Venkatasubramanian |
| contents | Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to navigate chemical space efficiently. Scientific foundation models trained on large unlabelled datasets offer a path towards navigating chemical space across application domains. Here, we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenizer, Smirk, which comprehensively captures nuclear, electronic, and geometric information, MIST learns a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure-property relationships and have been shown to match or exceed state-of-the-art performance across diverse benchmarks, from physiology to electrochemistry. We demonstrate the ability of these models to solve real-world problems across chemical space from multiobjective electrolyte solvent screening to stereochemical reasoning for organometallics and mixture property prediction. The clearest demonstration of a foundation model is its ability to solve problems that were neither explicit targets of training nor central to the intentions of its developers. We identify olfactory perception mapping as such a problem, and show that MIST accurately predicted scent profiles and learned a hierarchical representation of olfactory space consistent with hyperbolic geometry. We formulated hyperparameter aware Bayesian neural scaling laws which eliminate the need for hyperparameter sweeps at every scale, making training large compute-optimal models feasible on a limited compute budget. The methods and findings presented here represent a significant step towards accelerating materials discovery, design, and optimization using foundation models. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2510_18900 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Foundation Models for Discovery and Exploration in Chemical Space Wadell, Alexius Bhutani, Anoushka Azumah, Victor Ellis-Mohr, Austin R. Stier, Andrew J. Hegazy, Kareem Brace, Alexander Zhao, Hancheng Kelly, Celia Nayak, Anuj K. Chen, Yuhan Simatos, Dimitrios Lin, Hongyi Emani, Murali Vishwanath, Venkatram Gering, Kevin Alkan, Melisa Gibbs, Tom Wells, Jack Qian, Wesley W. Gerkin, Richard C. Amorelli, Benjamin Wiltschko, Alexander B. Varshney, Lav R. Ramsundar, Bharath Duraisamy, Karthik Mahoney, Michael W. Ramanathan, Arvind Viswanathan, Venkatasubramanian Chemical Physics Materials Science Machine Learning Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to navigate chemical space efficiently. Scientific foundation models trained on large unlabelled datasets offer a path towards navigating chemical space across application domains. Here, we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenizer, Smirk, which comprehensively captures nuclear, electronic, and geometric information, MIST learns a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure-property relationships and have been shown to match or exceed state-of-the-art performance across diverse benchmarks, from physiology to electrochemistry. We demonstrate the ability of these models to solve real-world problems across chemical space from multiobjective electrolyte solvent screening to stereochemical reasoning for organometallics and mixture property prediction. The clearest demonstration of a foundation model is its ability to solve problems that were neither explicit targets of training nor central to the intentions of its developers. We identify olfactory perception mapping as such a problem, and show that MIST accurately predicted scent profiles and learned a hierarchical representation of olfactory space consistent with hyperbolic geometry. We formulated hyperparameter aware Bayesian neural scaling laws which eliminate the need for hyperparameter sweeps at every scale, making training large compute-optimal models feasible on a limited compute budget. The methods and findings presented here represent a significant step towards accelerating materials discovery, design, and optimization using foundation models. |
| title | Foundation Models for Discovery and Exploration in Chemical Space |
| topic | Chemical Physics Materials Science Machine Learning |
| url | https://arxiv.org/abs/2510.18900 |