Parameter Inference for Stochastic and Deterministic Dynamic Biological Processes

Module MA5603

This Module is offered by Department of Mathematics.

This module handbook serves to describe contents, learning outcome, methods and examination type as well as linking to current dates for courses and module examination in the respective sections.

Module version of WS 2014/5 (current)

There are historic module descriptions of this module. A module description is valid until replaced by a newer one.

Whether the module’s courses are offered during a specific semester is listed in the section Courses, Learning and Teaching Methods and Literature below.

available module versions
WS 2014/5	SS 2012	WS 2011/2

Basic Information

MA5603 is a semester module in English language at Master’s level which is offered every semester.

This Module is included in the following catalogues within the study programs in physics.

Catalogue of non-physics elective courses

Total workload	Contact hours	Credits (ECTS)
150 h	45 h	5 CP

Content, Learning Outcome and Preconditions

Content

Scientific skills:
1. Modelling
a. Ordinary differential equation
b. Partial differential equation
c. Markov jump processes
d. Chemical Master Equation
2. Probability theory
3. Nonlinear optimization
4. Parameter inference
a. Bayesian
b. Maximum likelihood
5. Uncertainty analysis
a. Asymptotic methods
b. Bootstrapping
c. Profile likelihood
d. Bayesian analysis
Programming skills:
The participants will develop several MATLAB programs for parameter estimation.
Soft skills:
The participants will work in groups and present recent advances in the field. This will improve team working and presentation skills.

Learning Outcome

1) The participants can model deterministic and stochastic biological processes and simulate them using MATLAB.
2) The participants can independently solve common parameter estimation problems for in dynamical systems.
3) The participants can analyze the uncertainty of parameter estimates using different methods.
4) The participants can present own results and critically evaluate them.

Preconditions

Bachelor in mathematics, bioinformatics, statistics or related fields.

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

Please keep in mind that course announcements are regularly only completed in the semester before.

WS 2012/3

Type	SWS	Title	Lecturer(s)	Dates	Links
VO	2	Parameter Inference for Stochastic and Deterministic Dynamic Biological Processes	Hasenauer, J. Theis, F.		documents

Learning and Teaching Methods

lecture, exercise module, student`s participation, project work

Media

Blackboard and slides

Literature

A. Tarantola. Inverse Problem Theory and Methods for Model Parameter Estimation. SIAM. Url: http://www.ipgp.fr/~tarantola/Files/Professional/Books/InverseProblemTheory.pdf

Module Exam

Description of exams and course work

Presentation. The lecturers will provide each student with two papers on a certain lecture-related topic. The content of these papers has to be summarized and discussed in a presentation (20-30 minutes). The students are allowed to use the beamer as well as the blackboard.

Exam Repetition

The exam may be repeated at the end of the semester.