Optimal Experiment Design, Signal Transduction Pathways

Definition

Optimal experiment design is a key component for building accurate models of signal transduction pathways (Kreutz and Timmer 2009). Since experiment design is conducted prior to parameter estimation, any experiment design procedure needs to explicitly be able to deal with parameter uncertainty.

For a mathematical definition of optimal experiment design, assume that a regression model is given by

$$ {\mathbf{y}} = {\mathbf{g}}\left( {{\mathbf{\theta }};{\mathbf{\xi }}} \right) $$

(1)

where ${\mathbf{y}} \in {\mathbb{R}^m}$ is the output vector, ${\mathbf{\theta }} \in {\mathbb{R}^n}$ is the parameter vector, and ${\mathbf{\xi }} \in {\mathbb{R}^p}$ denotes the experimental conditions. Experiment design is often formulated as an optimization problem where a set of experimental criteria are available to evaluate the quality of a designed experiment (Atkinson et al. 2007). The experimental criteria are named alphabetically, and a popular one is the D-criterion which...