A machine learning Automated Recommendation Tool for synthetic biology

Tijana Radivojević, Zak Costello, Kenneth Workman and Hector Garcia Martin ()
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Tijana Radivojević: DOE Agile BioFoundry
Zak Costello: DOE Agile BioFoundry
Kenneth Workman: DOE Agile BioFoundry
Hector Garcia Martin: DOE Agile BioFoundry

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, fatty acids, and tryptophan. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing.

Date: 2020
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DOI: 10.1038/s41467-020-18008-4

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