Exhaustive local chemical space exploration using a transformer model
Alessandro Tibo, Jiazhen He, Jon Paul Janet, Eva Nittinger, Ola Engkvist
Abstract
How many near-neighbors does a molecule have? This fundamental question in chemistry is crucial for molecular optimization problems under the similarity principle assumption. Generative models can sample molecules from a vast chemical space but lack explicit knowledge about molecular similarity. Therefore, these models need guidance from reinforcement learning to sample a relevant similar chemical space. However, they still miss a mechanism to measure the coverage of a specific region of the chemical space. To overcome these limitations, a source-target molecular transformer model, regularized via a similarity kernel function, is proposed. Trained on a largest dataset of ≥200 billion molecular pairs, the model enforces a direct relationship between generating a target molecule and its similarity to a source molecule. Results indicate that the regularization term significantly improves the correlation between generation probability and molecular similarity, enabling exhaustive exploration of molecule near-neighborhoods. Understanding molecular near neighbours is key for molecular optimization. Here, authors propose a transformer model that improves correlation between generation probability and molecular similarity, enhancing exploration of molecular neighbourhoods.