9,564 research outputs found
A survey on efficient diagnosability tests for automata and bounded Petri nets
This paper presents a survey and evaluation of the efficiency of polynomial diagnosability algorithms for systems modeled by Petri nets and automata. A modified verification algorithm that reduces the state space by exploiting symmetry and abstracting unobservable transitions is also proposed. We show the importance of minimal explanations on the performance of diagnosability verifiers.
Different verifiers are compared in terms of state space
and elapsed time. It is shown that the minimal explanation
notion involved in the modified basis reachability
graph, a graph presented by Cabasino et al. [3] for diagnosability analysis of Petri nets, has great impact also
on automata-based diagnosability methods. The evaluation
often shows improved computation times of a factor
1000 or more when the concept of minimal explanation is
included in the computation
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
Scale-invariant cellular automata and self-similar Petri nets
Two novel computing models based on an infinite tessellation of space-time
are introduced. They consist of recursively coupled primitive building blocks.
The first model is a scale-invariant generalization of cellular automata,
whereas the second one utilizes self-similar Petri nets. Both models are
capable of hypercomputations and can, for instance, "solve" the halting problem
for Turing machines. These two models are closely related, as they exhibit a
step-by-step equivalence for finite computations. On the other hand, they
differ greatly for computations that involve an infinite number of building
blocks: the first one shows indeterministic behavior whereas the second one
halts. Both models are capable of challenging our understanding of
computability, causality, and space-time.Comment: 35 pages, 5 figure
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
The Hardness of Finding Linear Ranking Functions for Lasso Programs
Finding whether a linear-constraint loop has a linear ranking function is an
important key to understanding the loop behavior, proving its termination and
establishing iteration bounds. If no preconditions are provided, the decision
problem is known to be in coNP when variables range over the integers and in
PTIME for the rational numbers, or real numbers. Here we show that deciding
whether a linear-constraint loop with a precondition, specifically with
partially-specified input, has a linear ranking function is EXPSPACE-hard over
the integers, and PSPACE-hard over the rationals. The precise complexity of
these decision problems is yet unknown. The EXPSPACE lower bound is derived
from the reachability problem for Petri nets (equivalently, Vector Addition
Systems), and possibly indicates an even stronger lower bound (subject to open
problems in VAS theory). The lower bound for the rationals follows from a novel
simulation of Boolean programs. Lower bounds are also given for the problem of
deciding if a linear ranking-function supported by a particular form of
inductive invariant exists. For loops over integers, the problem is PSPACE-hard
for convex polyhedral invariants and EXPSPACE-hard for downward-closed sets of
natural numbers as invariants.Comment: In Proceedings GandALF 2014, arXiv:1408.5560. I thank the organizers
of the Dagstuhl Seminar 14141, "Reachability Problems for Infinite-State
Systems", for the opportunity to present an early draft of this wor
On functional module detection in metabolic networks
Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models
Parallel symbolic state-space exploration is difficult, but what is the alternative?
State-space exploration is an essential step in many modeling and analysis
problems. Its goal is to find the states reachable from the initial state of a
discrete-state model described. The state space can used to answer important
questions, e.g., "Is there a dead state?" and "Can N become negative?", or as a
starting point for sophisticated investigations expressed in temporal logic.
Unfortunately, the state space is often so large that ordinary explicit data
structures and sequential algorithms cannot cope, prompting the exploration of
(1) parallel approaches using multiple processors, from simple workstation
networks to shared-memory supercomputers, to satisfy large memory and runtime
requirements and (2) symbolic approaches using decision diagrams to encode the
large structured sets and relations manipulated during state-space generation.
Both approaches have merits and limitations. Parallel explicit state-space
generation is challenging, but almost linear speedup can be achieved; however,
the analysis is ultimately limited by the memory and processors available.
Symbolic methods are a heuristic that can efficiently encode many, but not all,
functions over a structured and exponentially large domain; here the pitfalls
are subtler: their performance varies widely depending on the class of decision
diagram chosen, the state variable order, and obscure algorithmic parameters.
As symbolic approaches are often much more efficient than explicit ones for
many practical models, we argue for the need to parallelize symbolic
state-space generation algorithms, so that we can realize the advantage of both
approaches. This is a challenging endeavor, as the most efficient symbolic
algorithm, Saturation, is inherently sequential. We conclude by discussing
challenges, efforts, and promising directions toward this goal
Algorithmic Verification of Asynchronous Programs
Asynchronous programming is a ubiquitous systems programming idiom to manage
concurrent interactions with the environment. In this style, instead of waiting
for time-consuming operations to complete, the programmer makes a non-blocking
call to the operation and posts a callback task to a task buffer that is
executed later when the time-consuming operation completes. A co-operative
scheduler mediates the interaction by picking and executing callback tasks from
the task buffer to completion (and these callbacks can post further callbacks
to be executed later). Writing correct asynchronous programs is hard because
the use of callbacks, while efficient, obscures program control flow.
We provide a formal model underlying asynchronous programs and study
verification problems for this model. We show that the safety verification
problem for finite-data asynchronous programs is expspace-complete. We show
that liveness verification for finite-data asynchronous programs is decidable
and polynomial-time equivalent to Petri Net reachability. Decidability is not
obvious, since even if the data is finite-state, asynchronous programs
constitute infinite-state transition systems: both the program stack and the
task buffer of pending asynchronous calls can be potentially unbounded.
Our main technical construction is a polynomial-time semantics-preserving
reduction from asynchronous programs to Petri Nets and conversely. The
reduction allows the use of algorithmic techniques on Petri Nets to the
verification of asynchronous programs.
We also study several extensions to the basic models of asynchronous programs
that are inspired by additional capabilities provided by implementations of
asynchronous libraries, and classify the decidability and undecidability of
verification questions on these extensions.Comment: 46 pages, 9 figure
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