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Revision as of 14:27, 9 August 2018
Contents
20 Benchmark Problem 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.
Download
The 20 benchmark models are available with version control on github [REF].
Overview
An overview about the benchmark models is also provided at the github repository [REF].
Bechmarking Studies
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].
Convexity
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].
