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Experimental Design for Dynamics Identification of Cellular Processes

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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. (PLoS ONE 3(8):e3105, 2008) and independently in M.M. Donahue et al. (IET Syst. Biol. 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.

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Acknowledgements

All authors partially supported by NSF grant DMS-0900277.

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Authors and Affiliations

  1. Department of Mathematics, Purdue University, 150 N. University Street, West Lafayette, IN, 47907, USA

    Vu Dinh & Gregery T. Buzzard

  2. Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Drive, West Lafayette, IN, 47907, USA

    Ann E. Rundell

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  1. Vu Dinh
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  2. Ann E. Rundell
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  3. Gregery T. Buzzard
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Correspondence to Vu Dinh.

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Dinh, V., Rundell, A.E. & Buzzard, G.T. Experimental Design for Dynamics Identification of Cellular Processes. Bull Math Biol 76, 597–626 (2014). https://doi.org/10.1007/s11538-014-9935-9

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  • DOI: https://doi.org/10.1007/s11538-014-9935-9

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