So, in these experiments, we performed a logarithmic parameter sweep of s from insignificant (s=10−6) to dominant (s=1).
Deterministic and stochastic optimization routines are combined by fitting in logarithmic parameter space allowing for robust parameter calibration.
Red line is a synthetic velocity change modeled by a logarithmic velocity recovery with the median model parameters.
As in regression, optimisation of parameters was performed by a logarithmic grid search over an extensive range of values, that is, C=(2−15,…,2) and γ=(2−20,…,2−20
All parameter estimation steps (step 1 of the work flow) are carried out in logarithmic parameter space to efficiently cover a large search area (cf. [ 31]).
All model parameters are defined to be strictly positive, and to introduce prior knowledge on the parameter ranges, we use standard normal prior distributions in logarithmic parameter space and assume that a priori dependencies between the parameters do not exist.
The relationship between these two parameters was best fitted by a logarithmic regression curve.
PW is a comprehensive framework for data-based modeling in Systems Biology comprising multi-experiment fitting in normal and logarithmic parameter space.
Optimisation of the C parameter (linear and Gaussian kernels) and γ (Gaussian kernel) was performed by a logarithmic grid search of base 2 over an extensive range of values.
The measurement signal is quantized by a logarithmic quantizer.
