A deep learning and data archaeology approach for mosquito repellent discovery

Jennifer N. Wei, Marnix Vlot, Benjamin Manuel Sanchez, Brian Lee, Luuk Berning, Martijn W Vos, Rob W.M. Henderson, Wesley Wei Qian, D. Michael Ando, Kurt M. Groetsch, Richard C Gerkin, Alexander B Wiltschko, Koen J Dechering

Keywords: machine learning, cheminformatics, data archaeology, insect control

TL;DR: We apply ML to identify new mosquito repellent candidates, using a historical dataset of mosquito repellent activity to train an initial model and refining the model through prospective validation of candidate compounds on a membrane feeder assay.

Abstract: Insect-borne diseases kill >0.5 million people annually. Currently available repellents for personal or household protection are limited in their efficacy, applicability, and safety profile. Here, we describe a machine-learning-driven high-throughput method for the discovery of novel repellent molecules. To achieve this, we digitized a large, historic dataset containing ~19,000 mosquito repellency measurements. We then trained a graph neural network (GNN) to map molecular structure and repellency. We applied this model to select 317 candidate molecules to test in parallelizable behavioral assays, quantifying repellency in multiple pest species and in follow-up trials with human volunteers. The GNN approach outperformed a chemoinformatics model and produced a hit rate that increased with training data size, suggesting that both model innovation and novel data collection were integral to predictive accuracy. We identified >10 molecules with repellency similar to or greater than the most widely used repellents. This approach enables computational screening of billions of possible molecules to identify empirically tractable numbers of candidate repellents, leading to accelerated progress towards solving a global health challenge.

Paper Track: Papers

Submission Category: AI-Guided Design