Proceedings ArticleDOI
Structural identification of GMA models: algorithm and model comparison
Graciano Dieck Kattas,Peter Gennemark,Dag Wedelin +2 more
- pp 107-113
TLDR
A local search algorithm for structural identification of Generalized Mass Action models from time course data is proposed and is able to find as good or better models than any of the other approaches.Abstract:
We propose a local search algorithm for structural identification of Generalized Mass Action (GMA) models from time course data. The algorithm has been implemented as part of our existing system for identification of dynamical systems.We compare this approach to existing alternatives in terms of analytical GMA models, analytical GMA models with parameter estimation from time course data, S-systems, and linear models. This is done on three new test problems designed to exhibit different characteristic properties of biochemical pathways, and which are defined with chemical rate reactions. By applying state-of-the-art algorithmic methods we are able to make a full investigation for the test problems also with noisy data.The results show that on the tested problems, our structural identification algorithm is able to find as good or better models than any of the other approaches. It can therefore be expected to be a useful tool for identifying models of unknown systems from time course data.All test problems are available on the web.read more
Citations
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Journal ArticleDOI
Biochemical Systems Theory: A Review
TL;DR: This paper depicts major developments in BST up to the current state of the art in 2012 and is intended as a guide for investigators entering the fascinating field of biological systems analysis and as a resource for practitioners and experts.
Journal ArticleDOI
ODEion--a software module for structural identification of ordinary differential equations.
Peter Gennemark,Dag Wedelin +1 more
TL;DR: ODEion is a software module for structural identification of ordinary differential equations that implements computationally efficient algorithms that have been shown to efficiently handle sparse and noisy data and can run a range of realistic problems that previously required a supercomputer.
Journal ArticleDOI
Optimal Design in Population Kinetic Experiments by Set-Valued Methods
Peter Gennemark,Peter Gennemark,Alexander S. Danis,Joakim Nyberg,Andrew C. Hooker,Warwick Tucker +5 more
TL;DR: A new method for optimal experimental design of population pharmacometric experiments based on global search methods using interval analysis; all variables and parameters are represented as intervals rather than real numbers, similar to robust optimal design.
Book ChapterDOI
Building computational models of swarms from simulated positional data
TL;DR: The results show the retrieved models are capable of emulating the collective behavior well, especially when the interaction structure resembles the one of the source model.
References
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Journal ArticleDOI
Distilling Free-Form Natural Laws from Experimental Data
Michael D. Schmidt,Hod Lipson +1 more
TL;DR: In this article, the authors proposed a method for automatically searching motion-tracking data captured from various physical systems, ranging from simple harmonic oscillators to chaotic double-pendula, without any prior knowledge about physics, kinematics, or geometry, the algorithm discovered Hamiltonians, Lagrangians, and other laws of geometric and momentum conservation.
Supporting Online Material for Distilling Free-Form Natural Laws from Experimental Data
Michael Schmidt,Hod Lipson +1 more
TL;DR: This work proposes a principle for the identification of nontriviality, and demonstrated this approach by automatically searching motion-tracking data captured from various physical systems, ranging from simple harmonic oscillators to chaotic double-pendula, and discovered Hamiltonians, Lagrangians, and other laws of geometric and momentum conservation.
Journal ArticleDOI
Automated reverse engineering of nonlinear dynamical systems
Josh C. Bongard,Hod Lipson +1 more
TL;DR: This work introduces for the first time a method that can automatically generate symbolic equations for a nonlinear coupled dynamical system directly from time series data, applicable to any system that can be described using sets of ordinary nonlinear differential equations.
Book
Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists
TL;DR: This work presents a graphical representation of biochemical systems, a sequence of models describing purine metabolism, and a model of the tricarboxylic acid cycle in Dictyostelium discoideum, which shows the importance of knowing the initial steps of the Glycolytic-Glycogenolytic pathway.