Experimental design for dynamics identification of cellular processes
From MaRDI portal
Publication:2254657
DOI10.1007/S11538-014-9935-9zbMATH Open1329.92016arXiv1311.3261OpenAlexW2089221898WikidataQ35093349 ScholiaQ35093349MaRDI QIDQ2254657FDOQ2254657
Authors: Vu Dinh, Greg Buzzard, Ann E. Rundell 
Publication date: 6 February 2015
Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)
Abstract: We address the problem of using nonlinear models to design experiments to characterize the dynamics of cellular processes by using the approach of the Maximally Informative Next Experiment (MINE), which was introduced in [W. Dong, et al. Systems biology of the clock in neurospora crassa. {em PLoS ONE}, page e3105, 2008] and independently in [M. M. Donahue, et al. Experiment design through dynamical characterization of non-linear systems biology models utilising sparse grids. {em IET System Biology}, 4:249--262, 2010]. In this approach, existing data is used to define a probability distribution on the parameters; the next measurement point is the one that yields the largest model output variance with this distribution. Building upon this approach, we introduce the Expected Dynamics Estimator (EDE), which is the expected value using this distribution of the output as a function of time. We prove the consistency of this estimator (uniform convergence to true dynamics) even when the chosen experiments cluster in a finite set of points. We extend this proof of consistency to various practical assumptions on noisy data and moderate levels of model mismatch. Through the derivation and proof, we develop a relaxed version of MINE that is more computationally tractable and robust than the original formulation. The results are illustrated with numerical examples on two nonlinear ordinary differential equation models of biomolecular and cellular processes.
Full work available at URL: https://arxiv.org/abs/1311.3261
Recommendations
- Maximally informative next experiments for nonlinear models
- Identifiability and observability analysis for experimental design in nonlinear dynamical models
- Recent Advances in Nonlinear Experimental Design
- Experimental design for biological systems
- Dynamic system identification. Experiment design and data analysis
Cites Work
- Algorithm 847
- Response surface methodology. Process and product optimization using designed experiments
- Title not available (Why is that?)
- Quasi-Random Sequences and Their Discrepancies
- The theory of the design of experiments
- Stochastic effects and bistability in T cell receptor signaling
- Stability of closed invariant sets of semidynamical systems. The method of sign definite Lyapunov functions
- Model-oriented design of experiments
- Quasi-Monte Carlo methods and pseudo-random numbers
- An extension of the General Equivalence Theorem to nonlinear models
- Asymptotic properties of nonlinear estimates in stochastic models with finite design space
- One-step ahead adaptive \(D\)-optimal design on a finite design space is asymptotically optimal
- For differential equations with \(r\) parameters, \(2r+1\) experiments are enough for identification
- A global parallel model based design of experiments method to minimize model output uncer\-tainty
Cited In (7)
- Maximally informative next experiments for nonlinear models
- The role of mathematical models in understanding pattern formation in developmental biology
- Experimental design for nonparametric correction of misspecified dynamical models
- Evaluating the efficiency of cell mechanisms and systems
- Convergence of Griddy Gibbs sampling and other perturbed Markov chains
- D-optimal input design for nonlinear FIR-type systems: a dispersion-based approach
- Identifiability and observability analysis for experimental design in nonlinear dynamical models
Uses Software
This page was built for publication: Experimental design for dynamics identification of cellular processes
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2254657)
