Host-Aware Control of Gene Expression using Data-Enabled Predictive Control

TL;DR

This paper demonstrates that Data-enabled Predictive Control (DeePC) effectively manages gene expression in bacteria with minimal data, offering robustness to system variations and outperforming other control strategies.

Contribution

It introduces the application of DeePC with basis functions for host-aware gene regulation, highlighting its sample efficiency and robustness in biological systems.

Findings

DeePC performs among the best control strategies with minimal data.

DeePC remains robust to parameter variations.

Using basis functions improves handling of nonlinearities.

Abstract

Cybergenetic gene expression control in bacteria enables applications in engineering biology, drug development, and biomanufacturing. AI-based controllers offer new possibilities for real-time, single-cell-level regulation but typically require large datasets and re-training for new systems. Data-enabled Predictive Control (DeePC) offers better sample efficiency without prior modelling. We apply DeePC to a system with two inputs (optogenetic control and media concentration) and two outputs (expression of gene of interest and host growth rate). Using basis functions to address nonlinearities, we demonstrate that DeePC remains robust to parameter variations and performs among the best control strategies while using the least data.