STOCHASTIC KINETIC MODELS: DYNAMIC INDEPENDENCE, MODULARITY AND GRAPHS

The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular systems. We identify SKM subprocesses with the corresponding counting processes and propose a directed, cyclic graph (the kinetic independence graph or KIG) that encodes the local independence structure of their conditional intensities. Given a partition [A, D, B] of the vertices, the graphical separation A ⊥ B|D in the undirected KIG has an intuitive chemical interpretation and implies that A is locally independent of B given A ∪ D. It is proved that this separation also results in global independence of the internal histories of A and B conditional on a history of the jumps in D which, under conditions we derive, corresponds to the internal history of D. The results enable mathematical definition of a modularization of an SKM using its implied dynamics. Graphical decomposition methods are developed for the identification and efficient computation of nested modularizations. Application to an SKM of the red blood cell advances understanding of this biochemical system.     

On positive harris recurrence of stochastic fluid networks

The stochastic fluid networks we consider here are open multiclass fluid networks with Markov-modulated inflow rate. They are typically used as models for manufacturing and telecommunication systems. The main aim of this paper is to investigate the question of positive Harris recurrence of the joint process of buffer content and inflow rate. It will turn out that a Markovian server allocation exists under which the process is positive Harris recurrent if the usual traffic conditions are satisfied on average. Moreover, for special networks like single-server networks, re-entrant lines and Jackson networks it is possible to show that certain service disciplines induce positive Harris recurrent state processes. As a by-product we show that these stochastic fluid networks converge under appropriately defined scaling to solutions of deterministic fluid models.     

Curved Chaotic Map Time Series Models and Their Stochastic Reversals

This paper considers two types of chaotic map time series models, including the well-known tent, logistic and binary-shift maps as special cases; these are called curved tent and curved binary families. Deterministic behaviour is investigated by invariant distributions, Lyapunov exponents, and by serial dependency. Stochastic time reversal of the families is shown to produce models which have a broader range of stochastic and chaotic properties than their deterministic counterparts. The marginal distributions may have concentrations and restricted supports and are shown to be a non-standard class of invariant distribution. Dependenc y is generally weaker with the reversed stochastic models. The work gives a broad statistical account of deterministic and stochastically reversed map models, such as are emerging in random number generation, communica tion systems and cryptography     

TWO-SPECIES SYSTEMS IN RANDOM ENVIRONMENT

An exactly solvable model for two interacting species with stochastic parameters is investigated. The parameter describing the interaction is assumed to be characterized by a dichotomic Markov process. It is remarkable that in contrast to the usual oscillatory behaviour in the deterministic case the expected value of the logarithm of each population size, as a consequence of parametric stochastic perturbations, attains a stable value as time increases. check that in their absence the damping term vanishes, leading to the deterministic model of Gomatam.     

Non parametric estimation of the structural expectation of a stochastic increasing function

This article introduces a non parametric warping model for functional data. When the outcome of an experiment is a sample of curves, data can be seen as realizations of a stochastic process, which takes into account the variations between the different observed curves. The aim of this work is to define a mean pattern which represents the main behaviour of the set of all the realizations. So, we define the structural expectation of the underlying stochastic function. Then, we provide empirical estimators of this structural expectation and of each individual warping function. Consistency and asymptotic normality for such estimators are proved.     

Two Applications of Statistics to Traffic Models

Two statistical applications for estimation and prediction of flows in traffic networks are presented. In the first, the number of route users are assumed to be independent α-shifted gamma Γ(θ, λ₀) random variables denoted H(α, θ, λ₀), with common λ₀. As a consequence, the link, OD (origin-destination) and node flows are also H(α, θ, λ₀) variables. We assume that the main source of information is plate scanning, which permits us to identify, totally or partially, the vehicle route, OD and link flows by scanning their corresponding plate numbers at an adequately selected subset of links. A Bayesian approach using conjugate families is proposed that allows us to estimate different traffic flows. In the second application, a stochastic demand dynamic traffic model to predict some traffic variables and their time evolution in real networks is presented. The Bayesian network model considers that the variables are generalized Beta variables such that when marginally transformed to standard normal become multivariate normal. The model is able to provide a point estimate, a confidence interval or the density of the variable being predicted. Finally, the models are illustrated by their application to the Nguyen Dupuis network and the Vermont-State example. The resulting traffic predictions seem to be promising for real traffic networks and can be done in real time.     

Extended lasso-type MARS (LMARS) model in the description of biological network

The multivariate adaptive regression splines (MARS) model is one of the well-known, additive non-parametric models that can deal with highly correlated and nonlinear datasets successfully. From our previous analyses, we have seen that lasso-type MARS (LMARS) can be a strong alternative of the Gaussian graphical model (GGM) which is a well-known probabilistic method to describe the steady-state behaviour of the complex biological systems via the lasso regression. In this study, we extend our original LMARS model by taking into account the second-order interaction effects of genes as the representative of the feed-forward loop in biological networks. By this way, we can describe both linear and nonlinear activations of the genes in the same model. We evaluate the performance of our new model under different dimensional simulated and real systems, and then compare the accuracy of the estimates with GGM and LMARS outputs. The results show the advantage of this new model over its close alternatives.     

Recent developments in nonlinear stochastic modelling of social processes

After a brief review of social applications of Markov chains, the paper discusses nonlinear (“interactive”) Markov models in discrete and continuous time. The rather subtle relationship between the deterministic and stochastic versions of such models is explored by means of examples. It is shown that the behaviour of nonlinear systems over time periods of practical interest depends critically on the total size as well as on the system parameters. Particular attention is paid to strong and weak forms of quasi-stationarity exhibited by stochastic systems.     

Delay Estimation for Some Stationary Diffusion-type Processes

In this paper the asymptotic behaviour of the maximum likelihood and Bayesian estimators of a delay parameter is studied. The observed process is supposed to be the solution of a linear stochastic differential equation with one time delay term. It is shown that these estimators are consistent and their limit distributions are described. The behaviour of the estimators is similar to the behaviour of corresponding estimators in change-point problems. The question of asymptotical efficiency is also discussed.     

Applications of bivariate and univariate local lyapunov exponents

Chaotic systems are characterized by sensitivity to initial conditions, and this property can be measured by global Lyapunov exponents, which are measures of the average divergence rate of initially close trajectories. Wolff (1992) introduced local Lyapunov exponents and used them to obtain two diagnostic plots for differentiating between stochastic and deterministic time series. We extend the definition of the local Lyapunov exponent and the diagnostic plots to accommodate time series that arise from bivariate maps and investigate the behaviour of the local Lyapunov exponents and the corresponding diagnostic plots for some dynamical systems and stochastic time series. We consider the application of these diagnostic plots to some heart rate variability data.     

Degree-based goodness-of-fit tests for heterogeneous random graph models: Independent and exchangeable cases

The degrees are a classical and relevant way to study the topology of a network. They can be used to assess the goodness of fit for a given random graph model. In this paper, we introduce goodness-of-fit tests for two classes of models. First, we consider the case of independent graph models such as the heterogeneous Erdös-Rényi model in which the edges have different connection probabilities. Second, we consider a generic model for exchangeable random graphs called the W-graph. The stochastic block model and the expected degree distribution model fall within this framework. We prove the asymptotic normality of the degree mean square under these independent and exchangeable models and derive formal tests. We study the power of the proposed tests and we prove the asymptotic normality under specific sparsity regimes. The tests are illustrated on real networks from social sciences and ecology, and their performances are assessed via a simulation study.     

Reverse engineering gene regulatory networks using approximate Bayesian computation

Gene regulatory networks are collections of genes that interact with one other and with other substances in the cell. By measuring gene expression over time using high-throughput technologies, it may be possible to reverse engineer, or infer, the structure of the gene network involved in a particular cellular process. These gene expression data typically have a high dimensionality and a limited number of biological replicates and time points. Due to these issues and the complexity of biological systems, the problem of reverse engineering networks from gene expression data demands a specialized suite of statistical tools and methodologies. We propose a non-standard adaptation of a simulation-based approach known as Approximate Bayesian Computing based on Markov chain Monte Carlo sampling. This approach is particularly well suited for the inference of gene regulatory networks from longitudinal data. The performance of this approach is investigated via simulations and using longitudinal expression data from a genetic repair system in Escherichia coli.     

Reified Bayesian modelling and inference for physical systems

We describe an approach, termed reified analysis, for linking the behaviour of mathematical models with inferences about the physical systems which the models represent. We describe the logical basis for the approach, based on coherent assessment of the implications of deficiencies in the mathematical model. We show how the statistical analysis may be carried out by specifying stochastic relationships between the model that we have, improved versions of the model that we might construct, and the system itself. We illustrate our approach with an example concerning the potential shutdown of the Thermohaline circulation in the Atlantic Ocean.     

General standby allocation in series and parallel systems

Stochastic orders are very useful tools to compare the lifetimes of two systems. Optimum lifetime of a series (resp. parallel) system with general standby component(s) depends on the allocation strategy of standby component(s) into the system. Here, we discuss three different models of one or more standby components. In each model, we compare different series (resp. parallel) systems (which are formed through different allocation strategies of standby component(s)) with respect to the usual stochastic order and the stochastic precedence order. The results related to the cold as well as the hot standby models are obtained as particular cases of the results discussed in this article because the model considered here is a general one.     

Bayesian multivariate GARCH models with dynamic correlations and asymmetric error distributions

The main goal in this paper is to develop and apply stochastic simulation techniques for GARCH models with multivariate skewed distributions using the Bayesian approach. Both parameter estimation and model comparison are not trivial tasks and several approximate and computationally intensive methods (Markov chain Monte Carlo) will be used to this end. We consider a flexible class of multivariate distributions which can model both skewness and heavy tails. Also, we do not fix tail behaviour when dealing with fat tail distributions but leave it subject to inference.     

Integrated OU Processes and Non-Gaussian OU-based Stochastic Volatility Models

Abstract. In this paper, we study the detailed distributional properties of integrated non-Gaussian Ornstein–Uhlenbeck (intOU) processes. Both exact and approximate results are given. We emphasize the study of the tail behaviour of the intOU process. Our results have many potential applications in financial economics, as OU processes are used as models of instantaneous variance in stochastic volatility (SV) models. In this case, an intOU process can be regarded as a model of integrated variance. Hence, the tail behaviour of the intOU process will determine the tail behaviour of returns generated by SV models.     

Rate estimation in partially observed Markov jump processes with measurement errors

We present a simulation methodology for Bayesian estimation of rate parameters in Markov jump processes arising for example in stochastic kinetic models. To handle the problem of missing components and measurement errors in observed data, we embed the Markov jump process into the framework of a general state space model. We do not use diffusion approximations. Markov chain Monte Carlo and particle filter type algorithms are introduced which allow sampling from the posterior distribution of the rate parameters and the Markov jump process also in data-poor scenarios. The algorithms are illustrated by applying them to rate estimation in a model for prokaryotic auto-regulation and the stochastic Oregonator, respectively.     

On weak convergence of long-range-dependent traffic processes

A possible model for communication traffic is that the amount of work arriving in successive time intervals is jointly Gaussian. This model seems to fly in the face of certain obvious and characteristic features of real traffic, such as the fact that it arrives in discrete bundles and that there is often a non-zero probability of zero traffic in a time interval of significant length. Also, the Gaussian model allows the possibility of negative traffic, which is clearly unrealistic. As the number of sources of traffic increases and the quantity of traffic in communication networks increases, however, under suitable conditions, the deviation between the distribution of real traffic and the Gaussian model will become less. The appropriate concept of topology/convergence must be used or the result will be meaningless. To identify an appropriate convergence framework, the performance statistics associated with a network, namely cell loss, delay, and, in general, statistics which can be expressed in terms of the network buffers which accumulate in the network may be used as a guide. Weak convergence of probability measures has the property that when the probability measures of traffic processes converge to that of a certain traffic process, the distribution of their performance characteristics, such as buffer occupancy, also converges in the same sense to the performance of the system to which they were converging. Real traffic appears, unambiguously, to be long-range dependent. There is an interesting example where aggregation of traffic does not seem to produce convergence to the queueing behaviour expected of Gaussian traffic, at any rate the tail characteristics do not converge to those of the Gaussian result. However, in Section 4, it is shown that if the variance of one traffic stream is finite and as a proportion of the variance of the whole traffic volume tends to zero, then the traffic in networks can be expected to converge to Gaussian in the sense of weak convergence of probability measures. It is then shown that, as a consequence, the traffic in the paradoxical example does converge in this sense also. The paradox is explained by noticing that asymptotic tail behaviour may become increasingly irrelevant as traffic is aggregated. This fact should sound a warning concerning the cavalier use of tail-behaviour as an indication of performance. Long-range dependence apparently places no inhibition on convergence to Gaussian behaviour. Convergence to a Gaussian distribution of increasing aggregates of traffic is only shown to occur for discrete time models. In fact it appears that continuous time Gaussian models do not share this property and their use for modelling real traffic may be problematic.     

A transient analysis of Markov fluid models with jumps

In this paper, we consider Markov fluid models with jumps which are useful for e.g. insurance risk modeling and the performance analysis of high-speed data networks. Recently, Ahn and Ramaswami [Ahn, S. & Ramaswami, V. (2004). Transient analysis of fluid flow models via stochastic coupling to a queue. Stochastic Models, 20 (1) 71–101] provided a transient analysis of the Markov modulated fluid flow model using stochastic coupling to a queueing model. Here we extend their results and provide a transient analysis of Markov fluid models with jumps. We also present some numerical examples.     

Information geodesics for gamma models of communication clustering

Recently, Akyildiz called for further work on non-Poisson models for communication arrivals in distributed networks such as cellular phone systems. The basic ‘random’ model for stochastic events is the Poisson process; for events on a line this resuits in an exponential disiribuuon of intervals between events. Network designers and managers need too monotor and quantify call clustering in order to optimize resaurce usage; the natural reference state from which to measure departures is that arising from a Poisson, process of calls. Here we consider gamma distributions, which contain exponential distributions as a special case. The surface representing gamma models has a natural Riemannian information metric and we obtain some geodesic sprays for this metric. The exponential distributions form a 1-dimensional subspace of the 2-dimensional space of all gamma distributions, so we have an isometric embedding of the random model as a subspace of the gamma models. This geometry may provide an appropriate structure on which to represent clustering as quantifiable departures from randomness and on which to impose dynamic control algorithms to optimize traffic at receiving nodes in distributed communication networks. In practice, we may expect correlation between call arrival times and call duration, reflecting for example peaks of different users of internet services. This would give rise to a twisted product of two surfaces with the twisting controlled by the correlation. Though bivariate gamma models do exist, such as Kibble's, none has tractabie information geometry nor sufficiently general marginal gammas,but a simulation method of approach is suggested.