Model Reduction for Parameter Estimation
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.
| 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: GH 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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