Efficient parametric analysis of the chemical master equation through model order reduction

Background: Stochastic biochemical reaction networks are commonly modelled by the chemical master equation, and can be simulated as first order linear differential equations through a finite state projection. Due to the very high state space dimension of these equations, numerical simulations are computationally expensive. This is a particular problem for analysis tasks requiring repeated simulations for different parameter values. Such tasks are computationally expensive to the point of infeasibility with the chemical master equation. Results: In this article, we apply parametric model order reduction techniques in order to construct accurate low-dimensional parametric models of the chemical master equation. These surrogate models can be used in various parametric analysis task such as identifiability analysis, parameter estimation, or sensitivity analysis. As biological examples, we consider two models for gene regulation networks, a bistable switch and a network displaying stochastic oscillations. Conclusions: The results show that the parametric model reduction yields efficient models of stochastic biochemical reaction networks, and that these models can be useful for systems biology applications involving parametric analysis problems such as parameter exploration, optimization, estimation or sensitivity analysis.Comment: 23 pages, 8 figures, 2 table

Reduced basis methods for pricing options with the Black-Scholes and Heston model

In this paper, we present a reduced basis method for pricing European and American options based on the Black-Scholes and Heston model. To tackle each model numerically, we formulate the problem in terms of a time dependent variational equality or inequality. We apply a suitable reduced basis approach for both types of options. The characteristic ingredients used in the method are a combined POD-Greedy and Angle-Greedy procedure for the construction of the primal and dual reduced spaces. Analytically, we prove the reproduction property of the reduced scheme and derive a posteriori error estimators. Numerical examples are provided, illustrating the approximation quality and convergence of our approach for the different option pricing models. Also, we investigate the reliability and effectivity of the error estimators.Comment: 25 pages, 27 figure

Kernel Methods for Surrogate Modeling

This chapter deals with kernel methods as a special class of techniques for surrogate modeling. Kernel methods have proven to be efficient in machine learning, pattern recognition and signal analysis due to their flexibility, excellent experimental performance and elegant functional analytic background. These data-based techniques provide so called kernel expansions, i.e., linear combinations of kernel functions which are generated from given input-output point samples that may be arbitrarily scattered. In particular, these techniques are meshless, do not require or depend on a grid, hence are less prone to the curse of dimensionality, even for high-dimensional problems. In contrast to projection-based model reduction, we do not necessarily assume a high-dimensional model, but a general function that models input-output behavior within some simulation context. This could be some micro-model in a multiscale-simulation, some submodel in a coupled system, some initialization function for solvers, coefficient function in PDEs, etc. First, kernel surrogates can be useful if the input-output function is expensive to evaluate, e.g. is a result of a finite element simulation. Here, acceleration can be obtained by sparse kernel expansions. Second, if a function is available only via measurements or a few function evaluation samples, kernel approximation techniques can provide function surrogates that allow global evaluation. We present some important kernel approximation techniques, which are kernel interpolation, greedy kernel approximation and support vector regression. Pseudo-code is provided for ease of reproducibility. In order to illustrate the main features, commonalities and differences, we compare these techniques on a real-world application. The experiments clearly indicate the enormous acceleration potentia

Dictionary-based Online-adaptive Structure-preserving Model Order Reduction for Parametric Hamiltonian Systems

Classical model order reduction (MOR) for parametric problems may become computationally inefficient due to large sizes of the required projection bases, especially for problems with slowly decaying Kolmogorov n-widths. Additionally, Hamiltonian structure of dynamical systems may be available and should be preserved during the reduction. In the current presentation, we address these two aspects by proposing a corresponding dictionary-based, online-adaptive MOR approach. The method requires dictionaries for the state-variable, non-linearities and discrete empirical interpolation (DEIM) points. During the online simulation, local basis extensions/simplifications are performed in an online-efficient way, i.e. the runtime complexity of basis modifications and online simulation of the reduced models do not depend on the full state dimension. Experiments on a linear wave equation and a non-linear Sine-Gordon example demonstrate the efficiency of the approach.Comment: 29 pages, 13 figure