Workshop on Statistical Inference for Dynamical Systems
Mathematical models are essential tools in systems biology and systems medicine. They contribute to an understanding of structure and dynamics of cellular and tissue dynamics far beyond their isolated parts, as well as to the prevention, diagnosis and therapy of diseases. Yet, model topology as well as model parameters are often unknown and need to be inferred from experimental data.
Over the last years, there was substantial progress in the development of standardized model selection and parameter estimation pipelines. Furthermore, optimization and sampling methods have been improved, and novel concepts introduced (e.g., at the interface of mechanistic modelling and machine learning).
In this workshop, the state-of-the-art in the field of model selection and parameter estimation will be introduced. This will include basics and advanced methods for statistical inference as well as problem standardization such as PEtab. Furthermore, software tools for different programming languages will be presented, along with materials and examples to get started.
The workshop is intended for persons interested in parameter estimation and models selection. It will feature introductory level presentations by experts in the field of systems and computational biology. Furthermore, it will provide time and space to work on statistical inference problems together with tool developers.
| 14.00 - 14.15 | Welcome and brief introduction (Jan Hasenauer, 15 min) |
| 14.15 - 15.15 | Parameter estimation |
| Maximum likelihood estimation and profile likelihoods (Fabian Fröhlich, 30 min) | |
| Maximum a posteriori estimation and sampling (Jan Hasenauer, 30 min) | |
| 15.15 - 15.30 | Break |
| 15.30 - 16.30 | Model selection and standardisation |
| Model selection criteria and algorithms (Clemens Kreutz, 30 min) | |
|
Standardisation for parameter estimation (Daniel Weindl, 15 min) and model selection (Dilan Pathirana, 15 min) |
|
| 16.30 - 16.45 | Break |
| 16.45 - 17.25 | Software tools |
| Copasi (Frank Bergmann, 10 min) | |
| Data2Dynamics (Clemens Kreutz, 10 min) | |
| Dmod (Severin Bang, 10 min) | |
| AMICI/pyPESTO (Daniel Weindl, 10 min) | |
| 17.25 - 17.30 | Closing remarks (all, 5 min) |
Jan Hasenauer (jan.hasenauer@uni-bonn.de) and Daniel Weindl (daniel.weindl@helmholtz-muenchen.de)
- Severin Bang, Institute of Physics, University of Freiburg
- Frank Bergmann, Department of Modeling of Biological Processes, University of Heidelberg
- Fabian Fröhlich, Institute of Computational Biomedicine, Heidelberg University
- Jan Hasenauer, Life and Medical Sciences (LIMES) Institute, University of Bonn
- Clemens Kreutz, Institute of Medical Biometry and Statistics, Albert-Ludwigs-Universität Freiburg
- Dilan Pathirana, Life and Medical Sciences (LIMES) Institute, University of Bonn
- Daniel Weindl, Institute for Computational Biology, Helmholtz Center Munich
Humboldt-Universität zu Berlin
Invalidenstraße 42
10115 Berlin
Room 312
Friday, October 7, 2022
2 - 5:30 pm
Remark: As this is a satellite event to the ICSB 2022, we can only accept participants who registered for this conference.
Background in mathematical modelling of biological processes.
