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49
BioPEPA: a framework for the modelling and analysis of biological systems
, 2008
"... In this work we present BioPEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use ..."
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Cited by 52 (18 self)
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In this work we present BioPEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use of general kinetic laws. The domain of application is the one of biochemical networks. BioPEPA may be seen as an intermediate, formal, compositional representation of biological systems, on which different kinds of analysis can be carried out. BioPEPA is enriched with some notions of equivalence. Specifically, the isomorphism and strong bisimulation for PEPA have been considered. Finally, we show the translation of three biological models into the new language and we report some analysis results.
A Logical Characterization of Bisimulation for Labeled Markov Processes
, 1998
"... This paper gives a logical characterization of probabilistic bisimulation for Markov processes introduced in [BDEP97]. The thrust of that work was an extension of the notion of bisimulation to systems with continuous state spaces; for example for systems where the state space is the real numbers. In ..."
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Cited by 34 (11 self)
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This paper gives a logical characterization of probabilistic bisimulation for Markov processes introduced in [BDEP97]. The thrust of that work was an extension of the notion of bisimulation to systems with continuous state spaces; for example for systems where the state space is the real numbers. In the present paper we study the logical characterization of probabilistic bisimulation for such general systems. This study revealed some unexpected results even for discrete probabilistic systems. ffl Bisimulation can be characterized by a very weak modal logic. The most striking feature is that one has no negation or any kind of negative proposition. ffl Bisimulation can be characterized by several inequivalent logics; we report five in this paper. ffl We do not need any finite branching assumption yet there is no need of infinitary conjunction. ffl The proofs that we give are of an entirely different character than the typical proofs of these results. They use quite subtle facts abou...
An Operational Semantics for Probabilistic Concurrent Constraint Programming
, 1998
"... This paper investigates a probabilistic version of the concurrent constraint programming paradigm (CCP). The aim is to introduce the possibility to formulate so called "randomised algorithms" within the CCP framework. Differently from common approaches in (imperative) highlevel programming language ..."
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Cited by 31 (13 self)
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This paper investigates a probabilistic version of the concurrent constraint programming paradigm (CCP). The aim is to introduce the possibility to formulate so called "randomised algorithms" within the CCP framework. Differently from common approaches in (imperative) highlevel programming languages, which rely on some kind of random() function, we introduce randomness in the very definition of the language by means of a probabilistic choice construct. This allows a program to make stochastic moves during its execution. We call the resulting language Probabilistic Concurrent Constraint Programming (PCCP). We present an operational semantics for PCCP by means of a probabilistic transition system such that the execution of a PCCP program may be seen as a stochastic process, i.e. as a random walk on the transition graph. The transition probabilities are given explicitly. This semantics captures a notion of observables which combines results of computations and the probability of those re...
PRISM: Probabilistic Model Checking for Performance and Reliability Analysis
 ACM SIGMETRICS Performance Evaluation Review
"... Probabilistic model checking is a formal verification technique for the modelling and analysis of stochastic systems. It has proved to be useful for studying a wide range of quantitative properties of models taken from many different application domains. This includes, for example, performance and r ..."
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Cited by 26 (1 self)
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Probabilistic model checking is a formal verification technique for the modelling and analysis of stochastic systems. It has proved to be useful for studying a wide range of quantitative properties of models taken from many different application domains. This includes, for example, performance and reliability properties of computer and communication systems. In this paper, we give an overview of the probabilistic model checking tool PRISM, focusing in particular on its support for continuoustime Markov chains and Markov reward models, and how these can be used to analyse performability properties. 1.
Quantitative Verification: Models, Techniques and Tools
, 2007
"... Automated verification is a technique for establishing if certain properties, usually expressed in temporal logic, hold for a system model. The model can be defined using a highlevel formalism or extracted directly from software using methods such as abstract interpretation. The verification procee ..."
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Cited by 14 (6 self)
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Automated verification is a technique for establishing if certain properties, usually expressed in temporal logic, hold for a system model. The model can be defined using a highlevel formalism or extracted directly from software using methods such as abstract interpretation. The verification proceeds through exhaustive exploration of the statetransition graph of the model and is therefore more powerful than testing. Quantitative verification is an analogous technique for establishing quantitative properties of a system model, such as the probability of battery power dropping below minimum, the expected time for message delivery and the expected number of messages lost before protocol termination. Models analysed through this method are typically variants of Markov chains, annotated with costs and rewards that describe resources and their usage during execution. Properties are expressed in temporal logic extended with probabilistic and reward operators. Quantitative verification involves a combination of a traversal of the statetransition graph of the model and numerical computation. This paper gives a brief overview of current research in quantitative verification, concentrating on the potential of the method and outlining future challenges. The modelling approach is described and the usefulness of the methodology illustrated with an example of a realworld protocol standard – Bluetooth device discovery – that has been analysed using the PRISM model checker (www.prismmodelchecker.org).
On Probabilistic CCP
 IN PROCEEDINGS OF APPIAGULPPRODE'97 JOINT CONFERENCE ON DECLARATIVE PROGRAMMING
, 1997
"... This paper investigates a probabilistic version of the concurrent constraint programming paradigm (CCP). The aim is to introduce the possibility to formulate so called "randomised algorithms" within the CCP framework. Our approach incorporates randomness directly within the (operational) semantics i ..."
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Cited by 11 (5 self)
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This paper investigates a probabilistic version of the concurrent constraint programming paradigm (CCP). The aim is to introduce the possibility to formulate so called "randomised algorithms" within the CCP framework. Our approach incorporates randomness directly within the (operational) semantics instead of referring to an "external" function or procedure call. We define the operational semantics of probabilistic concurrent constraint programming (PCCP) by means of a probabilistic transition system such that the execution of a PCCP program may be seen as a stochastic process, i.e. as a random walk on the transition graph. The transition probabilities are given explicitly.
Probabilistic Reachability for Parametric Markov Models ⋆
"... Abstract. Given a parametric Markov model, we consider the problem of computing the formula expressing the probability of reaching a given set of states. To attack this principal problem, Daws has suggested to first convert the Markov chain into a finite automaton, from which a regular expression is ..."
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Cited by 11 (2 self)
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Abstract. Given a parametric Markov model, we consider the problem of computing the formula expressing the probability of reaching a given set of states. To attack this principal problem, Daws has suggested to first convert the Markov chain into a finite automaton, from which a regular expression is computed. Afterwards, this expression is evaluated to a closed form expression representing the reachability probability. This paper investigates how this idea can be turned into an effective procedure. It turns out that the bottleneck lies in an exponential growth of the regular expression relative to the number of states. We therefore proceed differently, by tightly intertwining the regular expression computation with its evaluation. This allows us to arrive at an effective method that avoids the exponential blow up in most practical cases. We give a detailed account of the approach, also extending to parametric models with rewards and with nondeterminism. Experimental evidence is provided, illustrating that our implementation provides meaningful insights on nontrivial models. 1
Locationaware quality of service measurements for servicelevel agreements
 PROCEEDINGS OF THE THIRD INTERNATIONAL CONFERENCE ON TRUSTWORTHY GLOBAL COMPUTING (TGC’07). VOLUME 4912 OF LNCS., SPRINGERVERLAG
, 2008
"... We add specifications of locationaware measurements to performance models in a compositional fashion, promoting precision in performance measurement design. Using immediate actions to send control signals between measurement components we are able to obtain more accurate measurements from our stoc ..."
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Cited by 11 (6 self)
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We add specifications of locationaware measurements to performance models in a compositional fashion, promoting precision in performance measurement design. Using immediate actions to send control signals between measurement components we are able to obtain more accurate measurements from our stochastic models without disturbing their structure. A software tool processes both the model and the measurement specifications to give response time distributions and quantiles, an essential calculation in determining satisfaction of servicelevel agreements (SLAs).
Approximating Continuous Markov Processes
, 2000
"... Markov processes with continuous state spaces arise in the analysis of stochastic physical systems or stochastic hybrid systems. The standard logical and algorithmic tools for reasoning about discrete (finitestate) systems are, of course, inadequate for reasoning about such systems. In this work we ..."
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Cited by 9 (3 self)
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Markov processes with continuous state spaces arise in the analysis of stochastic physical systems or stochastic hybrid systems. The standard logical and algorithmic tools for reasoning about discrete (finitestate) systems are, of course, inadequate for reasoning about such systems. In this work we develop three related ideas for making such reasoning principles applicable to continuous systems. ffl We show how to approximate continuous systems by a countable family of finitestate probabilistic systems, we can reconstruct the full system from these finite approximants, ffl we define a metric between processes and show that the approximants converge in this metric to the full process, ffl we show that reasoning about properties definable in a rich logic can be carried out in terms of the approximants. The systems that we consider are Markov processes where the state space is continuous but the time steps are discrete. We allow such processes to interact with the environment by syn...
Scalable Differential Analysis of Process Algebra Models
"... The exact performance analysis of largescale software systems with discretestate approaches is difficult because of the wellknown problem of statespace explosion. This paper considers this problem with regard to the stochastic process algebra PEPA, presenting a deterministic approximation to the ..."
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Cited by 8 (3 self)
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The exact performance analysis of largescale software systems with discretestate approaches is difficult because of the wellknown problem of statespace explosion. This paper considers this problem with regard to the stochastic process algebra PEPA, presenting a deterministic approximation to the underlying Markov chain model based on ordinary differential equations. The accuracy of the approximation is assessed by means of a substantial case study of a distributed multithreaded application.