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Generalized Method of Moments for Stochastic Reaction Networks in Equilibrium

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Computational Methods in Systems Biology (CMSB 2016)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9859))

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Abstract

Calibrating parameters is a crucial problem within quantitative modeling approaches to reaction networks. Existing methods for stochastic models rely either on statistical sampling or can only be applied to small systems. Here we present an inference procedure for stochastic models in equilibrium that is based on a moment matching scheme with optimal weighting and that can be used with high-throughput data like the one collected by flow cytometry. Our method does not require an approximation of the underlying equilibrium probability distribution and, if reaction rate constants have to be learned, the optimal values can be computed by solving a linear system of equations. We evaluate the effectiveness of the proposed approach on three case studies.

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Notes

  1. 1.

    The existence and convergence of moments is treated Gupta et al. [11]. It can be proved for the models in Sect. 4 with positive rate constants.

  2. 2.

    The case of both repressors being bound, would result in samples around the origin, which can be neglected if there are no such samples.

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Authors and Affiliations

  1. Computer Science Department, Saarland University, Saarbrücken, Germany

    Michael Backenköhler, Luca Bortolussi & Verena Wolf

  2. Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy

    Luca Bortolussi

Authors
  1. Michael Backenköhler
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  2. Luca Bortolussi
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  3. Verena Wolf
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Correspondence to Verena Wolf .

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Editors and Affiliations

  1. TU Wien, Vienna, Austria

    Ezio Bartocci

  2. Computer Laboratory, University of Cambridge, Cambridge, United Kingdom

    Pietro Lio

  3. Department of Computer Science, University of Oxford, Oxford, United Kingdom

    Nicola Paoletti

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Backenköhler, M., Bortolussi, L., Wolf, V. (2016). Generalized Method of Moments for Stochastic Reaction Networks in Equilibrium. In: Bartocci, E., Lio, P., Paoletti, N. (eds) Computational Methods in Systems Biology. CMSB 2016. Lecture Notes in Computer Science(), vol 9859. Springer, Cham. https://doi.org/10.1007/978-3-319-45177-0_2

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  • DOI: https://doi.org/10.1007/978-3-319-45177-0_2

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