Tutorial Workshop on Parameter Estimation for Biological Models

NC State University, July 28-31, 2016

Co-organizers: Andrea Arnold, Franz Hamilton, Alun Lloyd and Mette Olufsen.

Confirmed speakers include Tom Banks (NC State), Daniela Calvetti (Case Western), Marisa Eisenberg (University of Michigan), Kevin Flores (NC State), Ralph Smith (NC State), Hien Tran (NC State) and Hulin Wu (University of Texas Health Science Center at Houston).

Final program for workshop: includes PDFs of presentations and videos of (most of) the talks.
Abstracts for talks and practicals

This workshop is aimed at graduate students (and others) who have an interest in confronting mathematical models with biological data. Tutorials will cover estimation of model parameters and associated uncertainties, parameter identifiability, and uncertainty quantification. Lectures will be accompanied by hands-on computer exercises.

Individuals wishing to participate should contact Mette Olufsen. Financial support is available to support attendance of a limited number of United States student and postdoc participants. If you wish to request financial support please attach a copy of your CV to your email and ask your advisor to email a letter of recommendation to us. Full consideration will be given to applications (for participation and/or support) received by May 1st.

Link to workshop announcement.

See information on previous workshop (August 2014).


Talks: SAS Hall 1102; Coffee Breaks: SAS Hall 4104

Thursday July 28th. Theme: Least Squares Estimation
8:00 – 9:00 Registration SAS Hall 4104
9:00 – 9:15 Welcome to the workshop (M.S. Olufsen / A.L. Lloyd)
9:15 – 10:45 Tutorial lecture: Introduction to parameter estimation in a least squares framework (Kevin Flores) PDF of slides and slides on sensitivities ; Video of talk
10:45 – 11:15 Coffee break
11:15 – 12:00 Research talk: A mathematical methodology for determining information content in demographic data for ecotoxicology studies (H.T. Banks) PDF of slides (Apologies: no video)
12:00 – 1:30 Lunch break
1:30 – 2:15 Research talk: Parameter estimation in cardiovascular dynamics modeling (Mette S. Olufsen) PDF of slides ; Video of talk
2:30 – 4:30 Computer Practical: Sensitivity Analysis and Least Squares Parameter Estimation for an Epidemic Model (Alun L. Lloyd) Code and other materials
5:00 – 7:00 Poster session (light refreshments provided)
Friday July 29th. Themes: Identifiability and Forward Propagation of Uncertainty
9:00 – 10:30 Tutorial lecture: Identifiability (Marisa Eisenberg) PDF of slides ; Video of talk
10:30 – 11:00 Coffee break
11:00 – 12:30 Computer practical on identifiability (Marisa Eisenberg and Chris Durden)
Materials for practical
12:30 – 2:00 Lunch break
2:00 – 3:30 Tutorial lecture: Uncertainty quantification for biological models (Ralph Smith)
PDF of slides ; Video of talk
3:30 – 5:00 Computer practical: Numerical techniques for active subspaces, surrogate model construction and uncertainty propagation (Ralph Smith)
Slides and code for practical
5:00 – 5:30 Coffee break
5.30 – 6.30 Keynote talk: Connecting models with data: identifiability and parameter estimation of multiple transmission pathways (Marisa Eisenberg) Video of talk
Saturday July 30th. Themes: Bayesian Approaches and Filtering Methods
9:00 – 10:30 Tutorial lecture: Inverse problems in the Bayesian framework (Daniela Calvetti) PDF of slides ; Video of talk
10:30 – 11:00 Coffee break
11:00 – 12:30 Computer practical on nonsequential Bayesian (A. Arnold/ F. Hamilton)
PDF of slides and zip fie of codes
12:30 – 2:00 Lunch break
2:00 – 3:00 Keynote talk: Compensating for lack of data with expert knowledge: how hierarchical models can be used to solve the very underdetermined MEG inverse problem (Daniela Calvetti) (Apologies: no video)
3:00 – 4:00 Tutorial lecture: Bayesian filtering (Franz Hamilton & Andrea Arnold)
PDF of slides (Apologies: no video)
4:00 – 4:30 Coffee break
4:30 – 5:30 Computer practical: Kalman filtering in a mass-spring system (Arnold/Hamilton)
PDF of slides
Dinner: outing to downtown Raleigh. Local participants will drive.
Sunday July 31st. Theme: Mixed Effects Models
9:00 – 10:30 Tutorial talk: Introduction to mixed-effects modeling (H. Tran) PDF of slides ; Video of talk: part 1 and part 2
10:30 – 11:00 Coffee break
11:00 – 12:00 Keynote talk: Mixed-effects biological models: estimation and inference (Hulin Wu) PDF of slides ; Video of talk
12:00 End of workshop

Abstracts for talks and practicals

To 2018 workshop page