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Encrypted machine learning of molecular quantum properties
Dec 22, 2022
Large machine learning models with improved predictions have become widely available in the chemical sciences. Unfortunately, these models do not protect the privacy necessary within commercial settings, prohibiting the use of potentially extremely valuable data by others. Encrypting the prediction process can solve this problem by double-blind model evaluation and prohibits the extraction of training or query data. However, contemporary ML models based on fully homomorphic encryption or federated learning are either too expensive for practical use or have to trade higher speed for weaker security. We have implemented secure and computationally feasible encrypted machine learning models using oblivious transfer enabling and secure predictions of molecular quantum properties across chemical compound space. However, we find that encrypted predictions using kernel ridge regression models are a million times more expensive than without encryption. This demonstrates a dire need for a compact machine learning model architecture, including molecular representation and kernel matrix size, that minimizes model evaluation costs.
SELFIES and the future of molecular string representations
Mar 31, 2022
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.