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L1 regularization
bernhardsteiert edited this page Sep 3, 2016
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L1 penalty terms can be used to detect cell type-specific parameters, triggering specific behavior of signaling pathways or gene regulatory networks. Such differences may reveal drug targets that selectively affect only malignant cells while leaving healthy cells unaffected.
- Steiert B., et al. L1 regularization facilitates detection of cell type-specific parameters in dynamical systems. Bioinformatics 32(17), i718-i726, 2016.
The benchmark model used in the publication is located in the folder /Examples/Dream6_L1.
One example of identifying cell type-specific parameters is shown in the example application JAK2/STAT5 signaling model.
- 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?