Structural characterization of decomposition in rate-insensitive stochastic Petri nets

This paper focuses on stochastic Petri nets that have an equilibrium distribution that is a product form over the number of tokens at the places. We formulate a decomposition result for the class of nets that have a product form solution irrespective of the values of the transition rates. These nets where algebraically characterized by Haddad et al.~as $S\Pi^2$ nets. By providing an intuitive interpretation of this algebraical characterization, and associating state machines to sets of $T$-invariants, we obtain a one-to-one correspondence between the marking of the original places and the places of the added state machines. This enables us to show that the subclass of stochastic Petri nets under study can be decomposed into subnets that are identified by sets of its $T$-invariants

Performance Bounds for Synchronized Queueing Networks

Las redes de Petri estocásticas constituyen un modelo unificado de las diferentes extensiones de redes de colas con sincronizaciones existentes en la literatura, válido para el diseño y análisis de prestaciones de sistemas informáticos distribuidos. En este trabajo se proponen técnicas de cálculo de cotas superiores e inferiores de las prestaciones de redes de Petri estocásticas en estado estacionario. Las cotas obtenidas son calculables en tiempo polinómico en el tamaño del modelo, por medio de la resolución de ciertos problemas de programación lineal definidos a partir de la matriz de incidencia de la red (en este sentido, las técnicas desarrolladas pueden considerarse estructurales). Las cotas calculadas dependen sólamente de los valores medios de las variables aleatorias que describen la temporización del sistema, y son independientes de los momentos de mayor orden. Esta independencia de la forma de las distribuciones de probabilidad asociadas puede considerarse como una útil generalización de otros resultados existentes para distribuciones particulares, puesto que los momentos de orden superior son, habitualmente, desconocidos en la realidad y difíciles de estimar. Finalmente, las técnicas desarrolladas se aplican al análisis de diferentes ejemplos tomados de la literatura sobre sistemas informáticos distribuidos y sistemas de fabricación. ******* Product form queueing networks have long been used for the performance evaluation of computer systems. Their success has been due to their capability of naturally expressing sharing of resources and queueing, that are typical situations of traditional computer systems, as well as to their efficient solution algorithms, of polynomial complexity on the size of the model. Unfortunately, the introduction of synchronization constraints usually destroys the product form solution, so that general concurrent and distributed systems are not easily studied with this class of models. Petri nets have been proved specially adequate to model parallel and distributed systems. Moreover, they have a well-founded theory of analysis that allows to investigate a great number of qualitative properties of the system. In the original definition, Petri nets did not include the notion of time, and tried to model only the logical behaviour of systems by describing the causal relations existing among events. This approach showed its power in the specification and analysis of concurrent systems in a way independent of the concept of time. Nevertheless the introduction of a timing specification is essential if we want to use this class of models for the performance evaluation of distributed systems. One of the main problems in the actual use of timed and stochastic Petri net models for the quantitative evaluation of large systems is the explosion of the computational complexity of the analysis algorithms. In general, exact performance results are obtained from the numerical solution of a continuous time Markov chain, whose dimension is given by the size of the state space of the model. Structural computation of exact performance measures has been possible for some subclasses of nets such as those with state machine topology. These nets, under certain assumptions on the stochastic interpretation are isomorphic to Gordon and Newell's networks, in queueing theory terminology. In the general case, efficient methods for the derivation of performance measures are still needed. Two complementary approaches to the derivation of exact measures for the analysis of distributed systems are the utilization of approximation techniques and the computation of bounds. Approximate values for the performance parameters are in general more efficiently derived than the exact ones. On the other hand, "exactness" only exists in theory! In other words, numerical algorithms must be applied in practice for the computation of exact values, therefore making errors is inevitable. Performance bounds are useful in the preliminary phases of the design of a system, in which many parameters are not known accurately. Several alternatives for those parameters should be quickly evaluated, and rejected those that are clearly bad. Exact (and even approximate) solutions would be computationally very expensive. Bounds become useful in these instances since they usually require much less computation effort. The computation of upper and lower bounds for the steady-state performance of timed and stochastic Petri nets is considered in this work. In particular, we study the throughput of transitions, defined as the average number of firings per time unit. For this measure we try to compute upper and lower bounds in polynomial time on the size of the net model, by means of proper linear programming problems defined from the incidence matrix of the net (in this sense, we develop structural techniques). These bounds depend only on the mean values and not on the higher moments of the probability distribution functions of the random variables that describe the timing of the system. The independence of the probability distributions can be viewed as a useful generalization of the performance results, since higher moments of the delays are usually unknown for real cases, and difficult to estimate and assess. From a different perspective, the obtained results can be applied to the analysis of queueing networks extended with some synchronization schemes. Monoclass queueing networks can be mapped on stochastic Petri nets. On the other hand, stochastic Petri nets can be interpreted as monoclass queueing networks augmented with synchronization primitives. Concerning the presentation of this manuscript, it should be mentioned that chapter 1 has been written with the object of giving the reader an outline of the stochastic Petri net model: its definition, terminology, basic properties, and related concepts, together with its deep relation with other classic stochastic network models. Chapter 2 is devoted to the presentation of the net subclasses considered in the rest of the work. The classification presented here is quite different from the one which is usual in the framework of Petri nets. The reason lies on the fact that our classification criterion, the computability of visit ratios for transitions, is introduced for the first time in the field of stochastic Petri nets in this work. The significance of that criterion is based on the important role that the visit ratios play in the computation of upper and lower bounds for the performance of the models. Nevertheless, classical important net subclasses are identified here in terms of the computability of their visit ratios from different parameters of the model. Chapter 3 is concerned with the computation of reachable upper and lower bounds for the most restrictive subclass of those presented in chapter 2: marked graphs. The explanation of this fact is easy to understand. The more simple is the model the more accessible will be the techniques an ideas for the development of good results. Chapter 4 provides a generalization for live and bounded free choice nets of the results presented in the previous chapter. Quality of obtained bounds is similar to that for strongly connected marked graphs: throughput lower bounds are reachable for bounded nets while upper bounds are reachable for 1-bounded nets. Chapter 5 considers the extension to other net subclasses, like mono-T-semiflow nets, FRT-nets, totally open deterministic systems of sequential processes, and persistent nets. The results are of diverse colours. For mono-T-semiflow nets and, therefore, for general FRT-nets, it is not possible (so far) to obtain reachable throughput bounds. On the other hand, for bounded ordinary persistent nets, tight throughput upper bounds are derived. Moreover, in the case of totally open deterministic systems of sequential processes the exact steady-state performance measures can be computed in polynomial time on the net size. In chapter 6 bounds for other interesting performance measures are derived from throughput bounds and from classical queueing theory laws. After that, we explore the introduction of more information from the probability distribution functions of service times in order to improve the bounds. In particular, for Coxian service delay of transitions it is possible to improve the throughput upper bounds of previous chapters which held for more general forms of distribution functions. This improvement shows to be specially fruitful for live and bounded free choice nets. Chapter 7 is devoted to case studies. Several examples taken from literature in the fields of distributed computing systems and manufacturing systems are modelled by means of stochastic Petri nets and evaluated using the techniques developed in previous chapters. Finally, some concluding remarks and considerations on possible extensions of the work are presented

Matrix-geometric solution of infinite stochastic Petri nets

We characterize a class of stochastic Petri nets that can be solved using matrix geometric techniques. Advantages of such on approach are that very efficient mathematical technique become available for practical usage, as well as that the problem of large state spaces can be circumvented. We first characterize the class of stochastic Petri nets of interest by formally defining a number of constraints that have to be fulfilled. We then discuss the matrix geometric solution technique that can be employed and present some boundary conditions on tool support. We illustrate the practical usage of the class of stochastic Petri nets with two examples: a queueing system with delayed service and a model of connection management in ATM network

About Dynamical Systems Appearing in the Microscopic Traffic Modeling

Motivated by microscopic traffic modeling, we analyze dynamical systems which have a piecewise linear concave dynamics not necessarily monotonic. We introduce a deterministic Petri net extension where edges may have negative weights. The dynamics of these Petri nets are well-defined and may be described by a generalized matrix with a submatrix in the standard algebra with possibly negative entries, and another submatrix in the minplus algebra. When the dynamics is additively homogeneous, a generalized additive eigenvalue may be introduced, and the ergodic theory may be used to define a growth rate under additional technical assumptions. In the traffic example of two roads with one junction, we compute explicitly the eigenvalue and we show, by numerical simulations, that these two quantities (the additive eigenvalue and the growth rate) are not equal, but are close to each other. With this result, we are able to extend the well-studied notion of fundamental traffic diagram (the average flow as a function of the car density on a road) to the case of two roads with one junction and give a very simple analytic approximation of this diagram where four phases appear with clear traffic interpretations. Simulations show that the fundamental diagram shape obtained is also valid for systems with many junctions. To simulate these systems, we have to compute their dynamics, which are not quite simple. For building them in a modular way, we introduce generalized parallel, series and feedback compositions of piecewise linear concave dynamics.Comment: PDF 38 page

Computational models for inferring biochemical networks

Biochemical networks are of great practical importance. The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects, which contributed to a vast amount of biological information. The construction of biochemical systems (systems of chemical reactions), which include both topology and kinetic constants of the chemical reactions, is NP-hard and is a well-studied system biology problem. In this paper, we propose a hybrid architecture, which combines genetic programming and simulated annealing in order to generate and optimize both the topology (the network) and the reaction rates of a biochemical system. Simulations and analysis of an artificial model and three real models (two models and the noisy version of one of them) show promising results for the proposed method.The Romanian National Authority for Scientific Research, CNDI–UEFISCDI, Project No. PN-II-PT-PCCA-2011-3.2-0917

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Performance modeling of e-procurement workflow using Generalised Stochastic Petri net (GSPN)

This paper proposes a Generalised Stochastic Petri net (GSPN) model representing a generic e-procurement workflow process. The model displays the dynamic behaviour of the system and shows the inter relationship of process activities. An analysis based on matrix equation approach enabled users to analyse the critical system's states, and thus justify the process performance. The results obtained allow users for better decision making in improving e-procurement workflow performance

Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable