644 research outputs found
Modeling biological systems with delays in Bio-PEPA
Delays in biological systems may be used to model events for which the
underlying dynamics cannot be precisely observed, or to provide abstraction of
some behavior of the system resulting more compact models. In this paper we
enrich the stochastic process algebra Bio-PEPA, with the possibility of
assigning delays to actions, yielding a new non-Markovian process algebra:
Bio-PEPAd. This is a conservative extension meaning that the original syntax of
Bio-PEPA is retained and the delay specification which can now be associated
with actions may be added to existing Bio-PEPA models. The semantics of the
firing of the actions with delays is the delay-as-duration approach, earlier
presented in papers on the stochastic simulation of biological systems with
delays. These semantics of the algebra are given in the Starting-Terminating
style, meaning that the state and the completion of an action are observed as
two separate events, as required by delays. Furthermore we outline how to
perform stochastic simulation of Bio-PEPAd systems and how to automatically
translate a Bio-PEPAd system into a set of Delay Differential Equations, the
deterministic framework for modeling of biological systems with delays. We end
the paper with two example models of biological systems with delays to
illustrate the approach.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
Extended Differential Aggregations in Process Algebra for Performance and Biology
We study aggregations for ordinary differential equations induced by fluid
semantics for Markovian process algebra which can capture the dynamics of
performance models and chemical reaction networks. Whilst previous work has
required perfect symmetry for exact aggregation, we present approximate fluid
lumpability, which makes nearby processes perfectly symmetric after a
perturbation of their parameters. We prove that small perturbations yield
nearby differential trajectories. Numerically, we show that many heterogeneous
processes can be aggregated with negligible errors.Comment: In Proceedings QAPL 2014, arXiv:1406.156
Analysis of Timed and Long-Run Objectives for Markov Automata
Markov automata (MAs) extend labelled transition systems with random delays
and probabilistic branching. Action-labelled transitions are instantaneous and
yield a distribution over states, whereas timed transitions impose a random
delay governed by an exponential distribution. MAs are thus a nondeterministic
variation of continuous-time Markov chains. MAs are compositional and are used
to provide a semantics for engineering frameworks such as (dynamic) fault
trees, (generalised) stochastic Petri nets, and the Architecture Analysis &
Design Language (AADL). This paper considers the quantitative analysis of MAs.
We consider three objectives: expected time, long-run average, and timed
(interval) reachability. Expected time objectives focus on determining the
minimal (or maximal) expected time to reach a set of states. Long-run
objectives determine the fraction of time to be in a set of states when
considering an infinite time horizon. Timed reachability objectives are about
computing the probability to reach a set of states within a given time
interval. This paper presents the foundations and details of the algorithms and
their correctness proofs. We report on several case studies conducted using a
prototypical tool implementation of the algorithms, driven by the MAPA
modelling language for efficiently generating MAs.Comment: arXiv admin note: substantial text overlap with arXiv:1305.705
Rate-Based Transition Systems for Stochastic Process Calculi
A variant of Rate Transition Systems (RTS), proposed by Klin and Sassone, is introduced and used as the basic model for defining stochastic behaviour of processes. The transition relation used in our variant associates to each process, for each action, the set of possible futures paired with a measure indicating their rates. We show how RTS can be used for providing the operational semantics of stochastic extensions of classical formalisms, namely CSP and CCS. We also show that our semantics for stochastic CCS guarantees associativity of parallel composition. Similarly, in contrast with the original definition by Priami, we argue that a semantics for stochastic Ļ-calculus can be provided that guarantees associativity of parallel composition
Efficient Modelling and Generation of Markov Automata (extended version)
This paper introduces a framework for the efficient modelling and generation of Markov automata. It consists of (1) the data-rich process-algebraic language MAPA, allowing concise modelling of systems with nondeterminism, probability and Markovian timing; (2) a restricted form of the language, the MLPPE, enabling easy state space generation and parallel composition; and (3) several syntactic reduction techniques on the MLPPE format, for generating equivalent but smaller models. Technically, the framework relies on an encoding of MAPA into the existing prCRL language for probabilistic automata. First, we identify a class of transformations on prCRL that can be lifted to the Markovian realm using our encoding. Then, we employ this result to reuse prCRL's linearisation procedure to transform any MAPA specification to an equivalent MLPPE, and to lift three prCRL reduction techniques to MAPA. Additionally, we define two novel reduction techniques for MLPPEs. All our techniques treat data as well as Markovian and interactive behaviour in a fully symbolic manner, working on specifications instead of models and thus reducing state spaces prior to their construction. The framework has been implemented in our tool SCOOP, and a case study on polling systems and mutual exclusion protocols shows its practical applicability
Syntactic Markovian Bisimulation for Chemical Reaction Networks
In chemical reaction networks (CRNs) with stochastic semantics based on
continuous-time Markov chains (CTMCs), the typically large populations of
species cause combinatorially large state spaces. This makes the analysis very
difficult in practice and represents the major bottleneck for the applicability
of minimization techniques based, for instance, on lumpability. In this paper
we present syntactic Markovian bisimulation (SMB), a notion of bisimulation
developed in the Larsen-Skou style of probabilistic bisimulation, defined over
the structure of a CRN rather than over its underlying CTMC. SMB identifies a
lumpable partition of the CTMC state space a priori, in the sense that it is an
equivalence relation over species implying that two CTMC states are lumpable
when they are invariant with respect to the total population of species within
the same equivalence class. We develop an efficient partition-refinement
algorithm which computes the largest SMB of a CRN in polynomial time in the
number of species and reactions. We also provide an algorithm for obtaining a
quotient network from an SMB that induces the lumped CTMC directly, thus
avoiding the generation of the state space of the original CRN altogether. In
practice, we show that SMB allows significant reductions in a number of models
from the literature. Finally, we study SMB with respect to the deterministic
semantics of CRNs based on ordinary differential equations (ODEs), where each
equation gives the time-course evolution of the concentration of a species. SMB
implies forward CRN bisimulation, a recently developed behavioral notion of
equivalence for the ODE semantics, in an analogous sense: it yields a smaller
ODE system that keeps track of the sums of the solutions for equivalent
species.Comment: Extended version (with proofs), of the corresponding paper published
at KimFest 2017 (http://kimfest.cs.aau.dk/
Compositional Performance Modelling with the TIPPtool
Stochastic process algebras have been proposed as compositional specification formalisms for performance models. In this paper, we describe a tool which aims at realising all beneficial aspects of compositional performance modelling, the TIPPtool. It incorporates methods for compositional specification as well as solution, based on state-of-the-art techniques, and wrapped in a user-friendly graphical front end. Apart from highlighting the general benefits of the tool, we also discuss some lessons learned during development and application of the TIPPtool. A non-trivial model of a real life communication system serves as a case study to illustrate benefits and limitations
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