A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks.

We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model. Within this setup, we tackle the Bayesian estimation of a subset of the model parameters. Specifically, we compare three Monte Carlo based numerical methods for the approximation of the posterior probability density function of the unknown parameters given a set of partial and noisy observations of the system. The schemes we assess are the particle Metropolis-Hastings (PMH) algorithm, the nonlinear population Monte Carlo (NPMC) method and the approximate Bayesian computation sequential Monte Carlo (ABC-SMC) scheme. We present an extensive numerical simulation study, which shows that while the three techniques can effectively solve the problem there are significant differences both in estimation accuracy and computational efficiency.

A Rao-Blackwellized particle filter for joint parameter estimation and biomass tracking in a stochastic predator-prey system.

Functional response estimation and population tracking in predator-prey systems are critical problems in ecology. In this paper we consider a stochastic predator-prey system with a Lotka-Volterra functional response and propose a particle filtering method for: (a) estimating the behavioral parameter representing the rate of effective search per predator in the functional response and (b) forecasting the population biomass using field data. In particular, the proposed technique combines a sequential Monte Carlo sampling scheme for tracking the time-varying biomass with the analytical integration of the unknown behavioral parameter. In order to assess the performance of the method, we show results for both synthetic and observed data collected in an acarine predator-prey system, namely the pest mite Tetranychus urticae and the predatory mite Phytoseiulus persimilis.

Robust global synchronization of two complex dynamical networks.

We investigate the synchronization of two coupled complex dynamical networks, a problem that has been termed outer synchronization in the literature. Our approach relies on (a) a basic lemma on the eigendecomposition of matrices resulting from Kronecker products and (b) a suitable choice of Lyapunov function related to the synchronization error dynamics. Starting from these two ingredients, a theorem that provides a sufficient condition for outer synchronization of the networks is proved. The condition in the theorem is expressed as a linear matrix inequality. When satisfied, synchronization is guaranteed to occur globally, i.e., independently of the initial conditions of the networks. The argument of the proof includes the design of the gain of the synchronizer, which is a constant square matrix with dimension dependent on the number of dynamic variables in a single network node, but independent of the size of the overall network, which can be much larger. This basic result is subsequently elaborated to simplify the design of the synchronizer, to avoid unnecessarily restrictive assumptions (e.g., diffusivity) on the coupling matrix that defines the topology of the networks and, finally, to obtain synchronizers that are robust to model errors in the parameters of the coupled networks. An illustrative numerical example for the outer synchronization of two networks of classical Lorenz nodes with perturbed parameters is presented.

Robust outer synchronization between two complex networks with fractional order dynamics.

Synchronization between two coupled complex networks with fractional-order dynamics, hereafter referred to as outer synchronization, is investigated in this work. In particular, we consider two systems consisting of interconnected nodes. The state variables of each node evolve with time according to a set of (possibly nonlinear and chaotic) fractional-order differential equations. One of the networks plays the role of a master system and drives the second network by way of an open-plus-closed-loop (OPCL) scheme. Starting from a simple analysis of the synchronization error and a basic lemma on the eigenvalues of matrices resulting from Kronecker products, we establish various sets of conditions for outer synchronization, i.e., for ensuring that the errors between the state variables of the master and response systems can asymptotically vanish with time. Then, we address the problem of robust outer synchronization, i.e., how to guarantee that the states of the nodes converge to common values when the parameters of the master and response networks are not identical, but present some perturbations. Assuming that these perturbations are bounded, we also find conditions for outer synchronization, this time given in terms of sets of linear matrix inequalities (LMIs). Most of the analytical results in this paper are valid both for fractional-order and integer-order dynamics. The assumptions on the inner (coupling) structure of the networks are mild, involving, at most, symmetry and diffusivity. The analytical results are complemented with numerical examples. In particular, we show examples of generalized and robust outer synchronization for networks whose nodes are governed by fractional-order Lorenz dynamics.

Monte Carlo method for adaptively estimating the unknown parameters and the dynamic state of chaotic systems.

We propose a Monte Carlo methodology for the joint estimation of unobserved dynamic variables and unknown static parameters in chaotic systems. The technique is sequential, i.e., it updates the variable and parameter estimates recursively as new observations become available, and, hence, suitable for online implementation. We demonstrate the validity of the method by way of two examples. In the first one, we tackle the estimation of all the dynamic variables and one unknown parameter of a five-dimensional nonlinear model using a time series of scalar observations experimentally collected from a chaotic CO2 laser. In the second example, we address the estimation of the two dynamic variables and the phase parameter of a numerical model commonly employed to represent the dynamics of optoelectronic feedback loops designed for chaotic communications over fiber-optic links.

Monte Carlo method for multiparameter estimation in coupled chaotic systems.

We address the problem of estimating multiple parameters of a chaotic dynamical model from the observation of a scalar time series. We assume that the series is produced by a chaotic system with the same functional form as the model, so that synchronization between the two systems can be achieved by an adequate coupling. In this scenario, we propose an efficient Monte Carlo optimization algorithm that iteratively updates the model parameters in order to minimize the synchronization error. As an example, we apply it to jointly estimate the three static parameters of a chaotic Lorenz system.

Adaptive approximation method for joint parameter estimation and identical synchronization of chaotic systems.

We introduce a numerical approximation method for estimating an unknown parameter of a (primary) chaotic system which is partially observed through a scalar time series. Specifically, we show that the recursive minimization of a suitably designed cost function that involves the dynamic state of a fully observed (secondary) system and the observed time series can lead to the identical synchronization of the two systems and the accurate estimation of the unknown parameter. The salient feature of the proposed technique is that the only external input to the secondary system is the unknown parameter which needs to be adjusted. We present numerical examples for the Lorenz system which show how our algorithm can be considerably faster than some previously proposed methods.