A study of Population MCMC for estimating Bayes Factors over nonlinear ODE models

Higher resolution biological data is now becoming available in ever greater quantities, allowing the complex behaviour of fundamental biological processes to be studied in much more detail. The area of Systems Biology is in desperate need of methods for inferring the most likely topology of the underlying genetic networks from this oftentimes noisy and poorly sampled data, to support the construction and testing of new model hypotheses. Towards that end, Bayesian methodology provides an ideal framework for tackling such challenges, and in particular offers a means of objectively comparing competing plausible models through the estimation of Bayes factors. There are, however, formidable obstacles which must be overcome to allow model inference using Bayes factors to be of practical use. Many important biological processes may be most accurately represented using nonlinear models based on systems of ordinary differential equations (ODEs), however parameter inference over these models often produces correspondingly nonlinear posterior distributions, which are very challenging to sample from, often resulting in biased marginal likelihood estimates with large variances. Such problems are commonly encountered when modelling circardian rhythms, which exhibit highly nonlinear oscillatory dynamics and play a central role in the overall functioning of most organisms. In this thesis I investigate tools for calculating Bayes factors to distinguish between ODE-based Goodwin oscillator models of varying complexity, which form the basic building blocks for describing this ubiquitous circadian behaviour. The main result in Chapter 3 of this thesis demonstrates how Population Markov Chain Monte Carlo may be employed in conjunction with thermodynamic integration methods to estimate Bayes factors which may accurately distinguish between two nonlinear oscillator models of varying complexity, given noisy experimental data generated from each of the models. In addition, it is shown how alternative methods may fail drastically in this setting, in particular harmonic mean based estimates. Suggestions are given regarding the optimal temperature schedule which should be employed for Population MCMC, and several ideas for future research extending this work are also discussed

3 sampled-data control of nonlinear systems

This chapter provides some of the main ideas resulting from recent developments in sampled-data control of nonlinear systems. We have tried to bring the basic parts of the new developments within the comfortable grasp of graduate students. Instead of presenting the more general results that are available in the literature, we opted to present their less general versions that are easier to understand and whose proofs are easier to follow. We note that some of the proofs we present have not appeared in the literature in this simplified form. Hence, we believe that this chapter will serve as an important reference for students and researchers that are willing to learn about this area of research

Fuzzy H-infinity output feedback control of nonlinear systems under sampled measurements

This paper studies the problem of designing an H∞ fuzzy feedback control for a class of nonlinear systems described by a continuous-time fuzzy system model under sampled output measurements. The premise variables of the fuzzy system model are allowed to be unavailable. We develop a technique for designing an H∞ fuzzy feedback control that guarantees the L2 gain from an exogenous input to a controlled output is less than or equal to a prescribed value. A design algorithm for constructing the H∞ fuzzy feedback controller is given

Contracting Nonlinear Observers: Convex Optimization and Learning from Data

A new approach to design of nonlinear observers (state estimators) is proposed. The main idea is to (i) construct a convex set of dynamical systems which are contracting observers for a particular system, and (ii) optimize over this set for one which minimizes a bound on state-estimation error on a simulated noisy data set. We construct convex sets of continuous-time and discrete-time observers, as well as contracting sampled-data observers for continuous-time systems. Convex bounds for learning are constructed using Lagrangian relaxation. The utility of the proposed methods are verified using numerical simulation.Comment: conference submissio

Recent advances on filtering and control for nonlinear stochastic complex systems with incomplete information: A survey

This Article is provided by the Brunel Open Access Publishing Fund - Copyright @ 2012 Hindawi PublishingSome recent advances on the filtering and control problems for nonlinear stochastic complex systems with incomplete information are surveyed. The incomplete information under consideration mainly includes missing measurements, randomly varying sensor delays, signal quantization, sensor saturations, and signal sampling. With such incomplete information, the developments on various filtering and control issues are reviewed in great detail. In particular, the addressed nonlinear stochastic complex systems are so comprehensive that they include conventional nonlinear stochastic systems, different kinds of complex networks, and a large class of sensor networks. The corresponding filtering and control technologies for such nonlinear stochastic complex systems are then discussed. Subsequently, some latest results on the filtering and control problems for the complex systems with incomplete information are given. Finally, conclusions are drawn and several possible future research directions are pointed out.This work was supported in part by the National Natural Science Foundation of China under Grant nos. 61134009, 61104125, 61028008, 61174136, 60974030, and 61074129, the Qing Lan Project of Jiangsu Province of China, the Project sponsored by SRF for ROCS of SEM of China, the Engineering and Physical Sciences Research Council EPSRC of the UK under Grant GR/S27658/01, the Royal Society of the UK, and the Alexander von Humboldt Foundation of Germany