Proportional lumpability and proportional bisimilarity

3noIn this paper, we deal with the lumpability approach to cope with the state space explosion problem inherent to the computation of the stationary performance indices of large stochastic models. The lumpability method is based on a state aggregation technique and applies to Markov chains exhibiting some structural regularity. Moreover, it allows one to efficiently compute the exact values of the stationary performance indices when the model is actually lumpable. The notion of quasi-lumpability is based on the idea that a Markov chain can be altered by relatively small perturbations of the transition rates in such a way that the new resulting Markov chain is lumpable. In this case, only upper and lower bounds on the performance indices can be derived. Here, we introduce a novel notion of quasi-lumpability, named proportional lumpability, which extends the original definition of lumpability but, differently from the general definition of quasi-lumpability, it allows one to derive exact stationary performance indices for the original process. We then introduce the notion of proportional bisimilarity for the terms of the performance process algebra PEPA. Proportional bisimilarity induces a proportional lumpability on the underlying continuous-time Markov chains. Finally, we prove some compositionality results and show the applicability of our theory through examples.openopenMarin A.; Piazza C.; Rossi S.Marin, A.; Piazza, C.; Rossi, S

Contextual Lumpability

Quantitative analysis of computer systems is often based on Markovian models. Among the formalisms that are used in practice, Markovian process algebras have found many applications, also thanks to their compositional nature that allows one to specify systems as interacting individual automata that carry out actions. Nevertheless, as with all state-based modelling techniques, Markovian process algebras suffer from the well-known state space explosion problem. State aggregation, specifically lumping, is one of the possible methods for tackling this problem. In this paper we revisit the notion of Markovian bisimulation which has previously been shown to induce a lumpable relation in the underlying Markov process. Here we consider the coarser relation of contextual lumpability, and taking the specific example of strong equivalence in PEPA, we propose a slightly relaxed definition of Markovian bisimulation, named lumpable bisimilarity, and prove that this is a characterisation of the notion of contextual lumpability for PEPA components. Moreover, we show that lumpable bisimilarity induces the largest contextual lumping over the Markov process underlying any PEPA component. We provide an algorithm for lumpable bisimilarity and study both its time and space complexity. 1

Symbolic Computation of Differential Equivalences

Ordinary differential equations (ODEs) are widespread in manynatural sciences including chemistry, ecology, and systems biology,and in disciplines such as control theory and electrical engineering. Building on the celebrated molecules-as-processes paradigm, they have become increasingly popular in computer science, with high-level languages and formal methods such as Petri nets, process algebra, and rule-based systems that are interpreted as ODEs. We consider the problem of comparing and minimizing ODEs automatically. Influenced by traditional approaches in the theory of programming, we propose differential equivalence relations. We study them for a basic intermediate language, for which we have decidability results, that can be targeted by a class of high-level specifications. An ODE implicitly represents an uncountable state space, hence reasoning techniques cannot be borrowed from established domains such as probabilistic programs with finite-state Markov chain semantics. We provide novel symbolic procedures to check an equivalence and compute the largest one via partition refinement algorithms that use satisfiability modulo theories. We illustrate the generality of our framework by showing that differential equivalences include (i) well-known notions for the minimization of continuous-time Markov chains (lumpability),(ii) bisimulations for chemical reaction networks recently proposedby Cardelli et al., and (iii) behavioral relations for process algebra with ODE semantics. With a prototype implementation we are able to detect equivalences in biochemical models from the literature thatcannot be reduced using competing automatic techniques

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

Bounds Computation for Symmetric Nets

Monotonicity in Markov chains is the starting point for quantitative abstraction of complex probabilistic systems leading to (upper or lower) bounds for probabilities and mean values relevant to their analysis. While numerous case studies exist in the literature, there is no generic model for which monotonicity is directly derived from its structure. Here we propose such a model and formalize it as a subclass of Stochastic Symmetric (Petri) Nets (SSNs) called Stochastic Monotonic SNs (SMSNs). On this subclass the monotonicity is proven by coupling arguments that can be applied on an abstract description of the state (symbolic marking). Our class includes both process synchronizations and resource sharings and can be extended to model open or cyclic closed systems. Automatic methods for transforming a non monotonic system into a monotonic one matching the MSN pattern, or for transforming a monotonic system with large state space into one with reduced state space are presented. We illustrate the interest of the proposed method by expressing standard monotonic models and modelling a flexible manufacturing system case study

Algorithms for Performance, Dependability, and Performability Evaluation using Stochastic Activity Networks

Modeling tools and technologies are important for aerospace development. At the University of Illinois, we have worked on advancing the state of the art in modeling by Markov reward models in two important areas: reducing the memory necessary to numerically solve systems represented as stochastic activity networks and other stochastic Petri net extensions while still obtaining solutions in a reasonable amount of time, and finding numerically stable and memory-efficient methods to solve for the reward accumulated during a finite mission time. A long standing problem when modeling with high level formalisms such as stochastic activity networks is the so-called state space explosion, where the number of states increases exponentially with size of the high level model. Thus, the corresponding Markov model becomes prohibitively large and solution is constrained by the the size of primary memory. To reduce the memory necessary to numerically solve complex systems, we propose new methods that can tolerate such large state spaces that do not require any special structure in the model (as many other techniques do). First, we develop methods that generate row and columns of the state transition-rate-matrix on-the-fly, eliminating the need to explicitly store the matrix at all. Next, we introduce a new iterative solution method, called modified adaptive Gauss-Seidel, that exhibits locality in its use of data from the state transition-rate-matrix, permitting us to cache portions of the matrix and hence reduce the solution time. Finally, we develop a new memory and computationally efficient technique for Gauss-Seidel based solvers that avoids the need for generating rows of A in order to solve Ax = b. This is a significant performance improvement for on-the-fly methods as well as other recent solution techniques based on Kronecker operators. Taken together, these new results show that one can solve very large models without any special structure

Simulation and numerical solution of stochastic Petri nets with discrete and continuous timing

We introduce a novel stochastic Petri net formalism where discrete and continuous phase-type firing delays can appear in the same model. By capturing deterministic and generally random behavior in discrete or continuous time, as appropriate, the formalism affords higher modeling fidelity and efficiencies to use in practice. We formally specify the underlying stochastic process as a general state space Markov chain and show that it is regenerative, thus amenable to renewal theory techniques to obtain steady-state solutions. We present two steady-state analysis methods depending on the class of problem: one using exact numerical techniques, the other using simulation. Although regenerative structures that ease steady-state analysis exist in general, a noteworthy problem class arises when discrete-time transitions are synchronized. In this case, the underlying process is semi-regenerative and we can employ Markov renewal theory to formulate exact and efficient numerical solutions for the stationary distribution. We propose a solution method that shows promise in terms of time and space efficiency. Also noteworthy are the computational tradeoffs when analyzing the embedded versus the subordinate Markov chains that are hidden within the original process. In the absence of simplifying assumptions, we propose an efficient regenerative simulation method that identifies hidden regenerative structures within continuous state spaces. The new formalism and solution methods are demonstrated with two applications

A formalism for describing and simulating systems with interacting components.

This thesis addresses the problem of descriptive complexity presented by systems involving a high number of interacting components. It investigates the evaluation measure of performability and its application to such systems. A new description and simulation language, ICE and it's application to performability modelling is presented. ICE (Interacting ComponEnts) is based upon an earlier description language which was first proposed for defining reliability problems. ICE is declarative in style and has a limited number of keywords. The ethos in the development of the language has been to provide an intuitive formalism with a powerful descriptive space. The full syntax of the language is presented with discussion as to its philosophy. The implementation of a discrete event simulator using an ICE interface is described, with use being made of examples to illustrate the functionality of the code and the semantics of the language. Random numbers are used to provide the required stochastic behaviour within the simulator. The behaviour of an industry standard generator within the simulator and different methods of number allocation are shown. A new generator is proposed that is a development of a fast hardware shift register generator and is demonstrated to possess good statistical properties and operational speed. For the purpose of providing a rigorous description of the language and clarification of its semantics, a computational model is developed using the formalism of extended coloured Petri nets. This model also gives an indication of the language's descriptive power relative to that of a recognised and well developed technique. Some recognised temporal and structural problems of system event modelling are identified. and ICE solutions given. The growing research area of ATM communication networks is introduced and a sophisticated top down model of an ATM switch presented. This model is simulated and interesting results are given. A generic ICE framework for performability modelling is developed and demonstrated. This is considered as a positive contribution to the general field of performability research

Scalable Performance Analysis of Massively Parallel Stochastic Systems

The accurate performance analysis of large-scale computer and communication systems is directly inhibited by an exponential growth in the state-space of the underlying Markovian performance model. This is particularly true when considering massively-parallel architectures such as cloud or grid computing infrastructures. Nevertheless, an ability to extract quantitative performance measures such as passage-time distributions from performance models of these systems is critical for providers of these services. Indeed, without such an ability, they remain unable to offer realistic end-to-end service level agreements (SLAs) which they can have any confidence of honouring. Additionally, this must be possible in a short enough period of time to allow many different parameter combinations in a complex system to be tested. If we can achieve this rapid performance analysis goal, it will enable service providers and engineers to determine the cost-optimal behaviour which satisfies the SLAs. In this thesis, we develop a scalable performance analysis framework for the grouped PEPA stochastic process algebra. Our approach is based on the approximation of key model quantities such as means and variances by tractable systems of ordinary differential equations (ODEs). Crucially, the size of these systems of ODEs is independent of the number of interacting entities within the model, making these analysis techniques extremely scalable. The reliability of our approach is directly supported by convergence results and, in some cases, explicit error bounds. We focus on extracting passage-time measures from performance models since these are very commonly the language in which a service level agreement is phrased. We design scalable analysis techniques which can handle passages defined both in terms of entire component populations as well as individual or tagged members of a large population. A precise and straightforward specification of a passage-time service level agreement is as important to the performance engineering process as its evaluation. This is especially true of large and complex models of industrial-scale systems. To address this, we introduce the unified stochastic probe framework. Unified stochastic probes are used to generate a model augmentation which exposes explicitly the SLA measure of interest to the analysis toolkit. In this thesis, we deploy these probes to define many detailed and derived performance measures that can be automatically and directly analysed using rapid ODE techniques. In this way, we tackle applicable problems at many levels of the performance engineering process: from specification and model representation to efficient and scalable analysis