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Parameter Estimation in Systems Biology
Pascal

Model Reduction for Parameter Estimation

author: Eric Mjolsness, University of California

Description

Estimating parameters in biochemical network models is a central but often difficult problem. A general approach that may be worth developing further is first to seek simplified or "reduced" models with fewer dynamical degrees of freedom, estimate parameters for the reduced models, and then use that information to constrain the corresponding parameters in the full model. This approach can leverage appropriate human expertise and could in principle be applied recursively. The choice of variables to eliminate during model reduction could also be made by clustering or other machine learning methods. Some relevant model reductions already exist for quasi-equilibrium models of transcriptional regulation networks, which could provide a starting point for this strategy.

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Slides
0:03 Model Reduction for Parameter Estimation
0:37 Topics
1:27 Transcriptional Gene Regulation Networks
2:34 GRN Parameter Optimization
5:31 GRN ANN Equations ’91
6:10 Model Reduction Example: Gene Regulation Network Derived from Stat Mech
7:45 Dynamical Model Reduction via Clustering
10:15 Core/Leaf Model Inference
12:17 SDE Advantages
12:58 Hierarchical Cooperative Activation: Alternative diagram notations
13:39 Hierarchical Cooperative Activation Model (HCA)
13:58 How to model transcriptional regulation?
14:25 Hard vs. Soft Logic
15:28 HCA- Z and ANN-like Equations
16:51 GRSN: Gene Regulation + Signal Transduction Network
17:59 Arabidopsis Shoot Apical Meristem (SAM)
18:29 WUS
19:14 CLV3/WUS networks
20:47 Biological scale hierarchies
22:10 Dynamical Grammar Aims
23:57 Elementary Reactions
24:14 Elementary Processes
24:52 Elementary process models
26:02 SPG Modeling Language: Semantics Semantic map Y: GH from Grammar to Stochastic Process
26:59 Time Ordered Product Expansion (TOPE)
27:42 Model Reduction for Dynamical Systems
29:22 Composition vs. Specialization in a Lattice of Models
31:07 A Parameter Estimation Future
31:59 Conclusions
32:47 For further information: www.ics.uci.edu/~emj www.computableplant.org Funding: US National Science Foundation FIBR program, NIH BISTI program Invitation…

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