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Priors in the d2d framework
Prior knowledge about parameters can be considered as well. If knowledge is available, it is used as a penalisation term for individual parameters by setting
#!matlab
ar.type(jp)=1;
for a quadratic penalty which corresponds to a normal distributed prior.
#!matlab
ar.type(jp)=2;
can be used to switch from hard lower and upper boundaries to quadratic penalization if p exceeds the lower bounds ar.lb or the upper bounds ar.ub. The default weight of such a penalty is 0.1. Within the bounds, there is no penalty.
The third possibility is
#!matlab
ar.type(jp)=3;
for a L1 penalisation term. L1-penalization is frequently applied for model discrimination, i.e. for finding sparse models with a reduced number of parameters.
For type 1 and 3, one needs to further specify the mean and the standard deviation of the required distribution. These parameters can be set at
#!matlab
ar.mean(jp)
and
#!matlab
ar.std(jp)
Utilizing priors as described enables Bayesian parameter estimation by maximizing the posterior.
For information on how priors enter the objective function of the parameter estimation process, consider the wiki-section about Objective function, likelihood and chi-square.
- Installation and system requirements
- Setting up models
- First steps
- Advanced events and pre-equilibration
- Computation of integration-based prediction bands
- How is the architecture of the code and the most important commands?
- What are the most important fields of the global variable ar?
- What are the most important functions?
- Optimization algorithms available in the d2d-framework
- Objective function, likelhood and chi-square in the d2d framework
- How to set up priors?
- How to set up steady state constraints?
- How do I restart the solver upon a step input?
- How to deal with integrator tolerances?
- How to implement a bolus injection?
- How to implement washing and an injection?
- How to implement a moment ODE model?
- How to run PLE calculations on a Cluster?