Representing Conversations for Scalable Overhearing

Open distributed multi-agent systems are gaining interest in the academic community and in industry. In such open settings, agents are often coordinated using standardized agent conversation protocols. The representation of such protocols (for analysis, validation, monitoring, etc) is an important aspect of multi-agent applications. Recently, Petri nets have been shown to be an interesting approach to such representation, and radically different approaches using Petri nets have been proposed. However, their relative strengths and weaknesses have not been examined. Moreover, their scalability and suitability for different tasks have not been addressed. This paper addresses both these challenges. First, we analyze existing Petri net representations in terms of their scalability and appropriateness for overhearing, an important task in monitoring open multi-agent systems. Then, building on the insights gained, we introduce a novel representation using Colored Petri nets that explicitly represent legal joint conversation states and messages. This representation approach offers significant improvements in scalability and is particularly suitable for overhearing. Furthermore, we show that this new representation offers a comprehensive coverage of all conversation features of FIPA conversation standards. We also present a procedure for transforming AUML conversation protocol diagrams (a standard human-readable representation), to our Colored Petri net representation

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

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

A tool for model-checking Markov chains

Markov chains are widely used in the context of the performance and reliability modeling of various systems. Model checking of such chains with respect to a given (branching) temporal logic formula has been proposed for both discrete [34, 10] and continuous time settings [7, 12]. In this paper, we describe a prototype model checker for discrete and continuous-time Markov chains, the Erlangen-Twente Markov Chain Checker EÎMC2, where properties are expressed in appropriate extensions of CTL. We illustrate the general benefits of this approach and discuss the structure of the tool. Furthermore, we report on successful applications of the tool to some examples, highlighting lessons learned during the development and application of EÎMC2

Event structures for Petri nets with persistence

Event structures are a well-accepted model of concurrency. In a seminal paper by Nielsen, Plotkin and Winskel, they are used to establish a bridge between the theory of domains and the approach to concurrency proposed by Petri. A basic role is played by an unfolding construction that maps (safe) Petri nets into a subclass of event structures, called prime event structures, where each event has a uniquely determined set of causes. Prime event structures, in turn, can be identified with their domain of configurations. At a categorical level, this is nicely formalised by Winskel as a chain of coreflections. Contrary to prime event structures, general event structures allow for the presence of disjunctive causes, i.e., events can be enabled by distinct minimal sets of events. In this paper, we extend the connection between Petri nets and event structures in order to include disjunctive causes. In particular, we show that, at the level of nets, disjunctive causes are well accounted for by persistent places. These are places where tokens, once generated, can be used several times without being consumed and where multiple tokens are interpreted collectively, i.e., their histories are inessential. Generalising the work on ordinary nets, Petri nets with persistence are related to a new subclass of general event structures, called locally connected, by means of a chain of coreflections relying on an unfolding construction

An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

Model Checking Markov Chains with Actions and State Labels

In the past, logics of several kinds have been proposed for reasoning about discrete- or continuous-time Markov chains. Most of these logics rely on either state labels (atomic propositions) or on transition labels (actions). However, in several applications it is useful to reason about both state-properties and action-sequences. For this purpose, we introduce the logic asCSL which provides powerful means to characterize execution paths of Markov chains with actions and state labels. asCSL can be regarded as an extension of the purely state-based logic asCSL (continuous stochastic logic). \ud In asCSL, path properties are characterized by regular expressions over actions and state-formulas. Thus, the truth value of path-formulas does not only depend on the available actions in a given time interval, but also on the validity of certain state formulas in intermediate states.\ud We compare the expressive power of CSL and asCSL and show that even the state-based fragment of asCSL is strictly more expressive than CSL if time intervals starting at zero are employed. Using an automaton-based technique, an asCSL formula and a Markov chain with actions and state labels are combined into a product Markov chain. For time intervals starting at zero we establish a reduction of the model checking problem for asCSL to CSL model checking on this product Markov chain. The usefulness of our approach is illustrated by through an elaborate model of a scalable cellular communication system for which several properties are formalized by means of asCSL-formulas, and checked using the new procedure