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Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

Brian Hie, Bryan D. Bryson, Bonnie A. Berger

Machine learning that generates biological hypotheses has transformative potential, but most learning algorithms are susceptible to pathological failure when exploring regimes beyond the training data distribution. A solution to address this issue is to quantify prediction uncertainty so that algorithms can gracefully handle novel phenomena that confound standard methods. Here, we demonstrate the broad utility of robust uncertainty prediction in biological discovery. By leveraging Gaussian process-based uncertainty prediction on modern pre-trained features, we train a model on just 72 compounds to make predictions over a 10,833-compound library, identifying and experimentally validating compounds with nanomolar affinity for diverse kinases and whole-cell growth inhibition of Mycobacterium tuberculosis. Uncertainty facilitates a tight iterative loop between computation and experimentation and generalizes across biological domains as diverse as protein engineering and single-cell transcriptomics. More broadly, our work demonstrates that uncertainty should play a key role in the increasing adoption of machine learning algorithms into the experimental lifecycle.

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