Accelerated knowledge discovery from omics data by optimal experimental design

Xiaokang Wang, Navneet Rai, Beatriz Merchel Piovesan Pereira, Ameen Eetemadi and Ilias Tagkopoulos ()
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Xiaokang Wang: University of California
Navneet Rai: University of California
Beatriz Merchel Piovesan Pereira: University of California
Ameen Eetemadi: University of California
Ilias Tagkopoulos: University of California

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: Abstract How to design experiments that accelerate knowledge discovery on complex biological landscapes remains a tantalizing question. We present an optimal experimental design method (coined OPEX) to identify informative omics experiments using machine learning models for both experimental space exploration and model training. OPEX-guided exploration of Escherichia coli’s populations exposed to biocide and antibiotic combinations lead to more accurate predictive models of gene expression with 44% less data. Analysis of the proposed experiments shows that broad exploration of the experimental space followed by fine-tuning emerges as the optimal strategy. Additionally, analysis of the experimental data reveals 29 cases of cross-stress protection and 4 cases of cross-stress vulnerability. Further validation reveals the central role of chaperones, stress response proteins and transport pumps in cross-stress exposure. This work demonstrates how active learning can be used to guide omics data collection for training predictive models, making evidence-driven decisions and accelerating knowledge discovery in life sciences.

Date: 2020
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DOI: 10.1038/s41467-020-18785-y

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