Ranking over Regression for Bayesian Optimization and Molecule Selection

Bayesian optimization (BO) has become an indispensable tool for autonomous decision-making across diverse applications from autonomous vehicle control to accelerated drug and materials discovery. With the growing interest in self-driving laboratories, BO of chemical systems is crucial for machine learning (ML) guided experimental planning. Typically, BO employs a regression surrogate model to predict the distribution of unseen parts of the search space. However, for the selection of molecules, picking the top candidates with respect to a distribution, the relative ordering of their properties may be more important than their exact values. In this paper, we introduce Rank-based Bayesian Optimization (RBO), which utilizes a ranking model as the surrogate. We present a comprehensive investigation of RBO's optimization performance compared to conventional BO on various chemical datasets. Our results demonstrate similar or improved optimization performance using ranking models, particularly for datasets with rough structure-property landscapes and activity cliffs. Furthermore, we observe a high correlation between the surrogate ranking ability and BO performance, and this ability is maintained even at early iterations of BO optimization when using ranking surrogate models. We conclude that RBO is an effective alternative to regression-based BO, especially for optimizing novel chemical compounds.

Calibration and generalizability of probabilistic models on low-data chemical datasets with DIONYSUS

Deep learning models that leverage large datasets are often the state of the art for modelling molecular properties. When the datasets are smaller (< 2000 molecules), it is not clear that deep learning approaches are the right modelling tool. In this work we perform an extensive study of the calibration and generalizability of probabilistic machine learning models on small chemical datasets. Using different molecular representations and models, we analyse the quality of their predictions and uncertainties in a variety of tasks (binary, regression) and datasets. We also introduce two simulated experiments that evaluate their performance: (1) Bayesian optimization guided molecular design, (2) inference on out-of-distribution data via ablated cluster splits. We offer practical insights into model and feature choice for modelling small chemical datasets, a common scenario in new chemical experiments. We have packaged our analysis into the DIONYSUS repository, which is open sourced to aid in reproducibility and extension to new datasets.

SELFIES and the future of molecular string representations

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction pathways, or the design of new molecules. The machine needs to read and write fluently in a chemical language for each of these tasks. Strings are a common tool to represent molecular graphs, and the most popular molecular string representation, SMILES, has powered cheminformatics since the late 1980s. However, in the context of AI and ML in chemistry, SMILES has several shortcomings -- most pertinently, most combinations of symbols lead to invalid results with no valid chemical interpretation. To overcome this issue, a new language for molecules was introduced in 2020 that guarantees 100\% robustness: SELFIES (SELF-referencIng Embedded Strings). SELFIES has since simplified and enabled numerous new applications in chemistry. In this manuscript, we look to the future and discuss molecular string representations, along with their respective opportunities and challenges. We propose 16 concrete Future Projects for robust molecular representations. These involve the extension toward new chemical domains, exciting questions at the interface of AI and robust languages and interpretability for both humans and machines. We hope that these proposals will inspire several follow-up works exploiting the full potential of molecular string representations for the future of AI in chemistry and materials science.