Project 20 Benchmark Problems for Modelling Intracellular Processes
Ordinary differential equation (ODE) models are frequently applied to describe intracellular biochemical processes. Here, we provide a set of 20 published benchmark models which should serve as test cases for assessing methodology for modelling.
An overview about the benchmark models is also provided at the github repository [REF].
The 20 benchmark models are available with version control on github [REF].
Studies based on the 20 Benchmark problems
Here, we summarize several outcomes of benchmark studies performed on the 20 benchmark problems.
Optimization at the Log-Scale
It has been shown [REF] that optimization algorithms have superior performance if parameters are optimized at the log-scale [REF].
It has been shown [REF] that the negative log-likelihood which has to be minimized for parameter estimation is more convex if the parameters are evaluated at the log-scale. It has been concluded that this fact is one reason for performance benefits of deterministic optimization algorithms if optimization is performed at the log-scale [REF].