Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

Robust ℋ2 Performance: Guaranteeing Margins for LQG Regulators

This paper shows that ℋ2 (LQG) performance specifications can be combined with structured uncertainty in the system, yielding robustness analysis conditions of the same nature and computational complexity as the corresponding conditions for ℋ∞ performance. These conditions are convex feasibility tests in terms of Linear Matrix Inequalities, and can be proven to be necessary and sufficient under the same conditions as in the ℋ∞ case. With these results, the tools of robust control can be viewed as coming full circle to treat the problem where it all began: guaranteeing margins for LQG regulators

Identification of Stochastic Wiener Systems using Indirect Inference

We study identification of stochastic Wiener dynamic systems using so-called indirect inference. The main idea is to first fit an auxiliary model to the observed data and then in a second step, often by simulation, fit a more structured model to the estimated auxiliary model. This two-step procedure can be used when the direct maximum-likelihood estimate is difficult or intractable to compute. One such example is the identification of stochastic Wiener systems, i.e.,~linear dynamic systems with process noise where the output is measured using a non-linear sensor with additive measurement noise. It is in principle possible to evaluate the log-likelihood cost function using numerical integration, but the corresponding optimization problem can be quite intricate. This motivates studying consistent, but sub-optimal, identification methods for stochastic Wiener systems. We will consider indirect inference using the best linear approximation as an auxiliary model. We show that the key to obtain a reliable estimate is to use uncertainty weighting when fitting the stochastic Wiener model to the auxiliary model estimate. The main technical contribution of this paper is the corresponding asymptotic variance analysis. A numerical evaluation is presented based on a first-order finite impulse response system with a cubic non-linearity, for which certain illustrative analytic properties are derived.Comment: The 17th IFAC Symposium on System Identification, SYSID 2015, Beijing, China, October 19-21, 201