Natalja Strelkowa

Aivar Sootla, Natalja Strelkowa, Damien Ernst et al.

In this paper, we consider the periodic reference tracking problem in the framework of batch-mode reinforcement learning, which studies methods for solving optimal control problems from the sole knowledge of a set of trajectories. In particular, we extend an existing batch-mode reinforcement learning algorithm, known as Fitted Q Iteration, to the periodic reference tracking problem. The presented periodic reference tracking algorithm explicitly exploits a priori knowledge of the future values of the reference trajectory and its periodicity. We discuss the properties of our approach and illustrate it on the problem of reference tracking for a synthetic biology gene regulatory network known as the generalised repressilator. This system can produce decaying but long-lived oscillations, which makes it an interesting system for the tracking problem. In our companion paper we also take a look at the regulation problem of the toggle switch system, where the main goal is to drive the system's states to a specific bounded region in the state space.

Aivar Sootla, Natalja Strelkowa, Damien Ernst et al.

In this paper, we consider the problem of optimal exogenous control of gene regulatory networks. Our approach consists in adapting an established reinforcement learning algorithm called the fitted Q iteration. This algorithm infers the control law directly from the measurements of the system's response to external control inputs without the use of a mathematical model of the system. The measurement data set can either be collected from wet-lab experiments or artificially created by computer simulations of dynamical models of the system. The algorithm is applicable to a wide range of biological systems due to its ability to deal with nonlinear and stochastic system dynamics. To illustrate the application of the algorithm to a gene regulatory network, the regulation of the toggle switch system is considered. The control objective of this problem is to drive the concentrations of two specific proteins to a target region in the state space.