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A central task in computational drug discovery is to construct models from known active molecules to find further promising molecules for subsequent screening. However, typically only very few active molecules are known. Therefore, few-shot learning methods have the potential to improve the effectiveness of this critical phase of the drug discovery process. We introduce a new method for few-shot drug discovery. Its main idea is to enrich a molecule representation by knowledge about known context or reference molecules. Our novel concept for molecule representation enrichment is to associate molecules from both the support set and the query set with a large set of reference (context) molecules through a Modern Hopfield Network. Intuitively, this enrichment step is analogous to a human expert who would associate a given molecule with familiar molecules whose properties are known. The enrichment step reinforces and amplifies the covariance structure of the data, while simultaneously removing spurious correlations arising from the decoration of molecules. Our approach is compared with other few-shot methods for drug discovery on the FS-Mol benchmark dataset. On FS-Mol, our approach outperforms all compared methods and therefore sets a new state-of-the art for few-shot learning in drug discovery. An ablation study shows that the enrichment step of our method is the key to improve the predictive quality. In a domain shift experiment, we further demonstrate the robustness of our method. Code is available at https://github.com/ml-jku/MHNfs.

Due to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs. We conducted a large-scale virtual screening for small molecules that are potential CoV-2 inhibitors. To this end, we utilized "ChemAI", a deep neural network trained on more than 220M data points across 3.6M molecules from three public drug-discovery databases. With ChemAI, we screened and ranked one billion molecules from the ZINC database for favourable effects against CoV-2. We then reduced the result to the 30,000 top-ranked compounds, which are readily accessible and purchasable via the ZINC database. Additionally, we screened the DrugBank using ChemAI to allow for drug repurposing, which would be a fast way towards a therapy. We provide these top-ranked compounds of ZINC and DrugBank as a library for further screening with bioassays at https://github.com/ml-jku/sars-cov-inhibitors-chemai., Comment: Additional results added. Various corrections to formulations and typos