Region-Based Analysis of Hybrid Petri Nets with a Single General One-Shot Transition

Recently, hybrid Petri nets with a single general one-shot transition (HPnGs) have been introduced together with an algorithm to analyze their underlying state space using a conditioning/deconditioning approach. In this paper we propose a considerably more efficient algorithm for analysing HPnGs. The proposed algorithm maps the underlying state-space onto a plane for all possible firing times of the general transition s and for all possible systems times t. The key idea of the proposed method is that instead of dealing with infinitely many points in the t-s-plane, we can partition the state space into several regions, such that all points inside one region are associated with the same system state. To compute the probability to be in a specific system state at time τ, it suffices to find all regions intersecting the line t = τ and decondition the firing time over the intersections. This partitioning results in a considerable speed-up and provides more accurate results. A scalable case study illustrates the efficiency gain with respect to the previous algorithm

Hybrid Petri nets with multiple stochastic transition firings

This paper introduces an algorithm for the efficient computation of transient measures of interest in Hybrid Petri nets in which the stochastic transitions are allowed to fire an arbitrary but finite number of times. Each firing increases the dimensionality of the underlying discrete/continuous state space. The algorithm evolves around a partitioning of the multi-dimensional state-space into regions, making use of advanced algorithms (and libraries) for computational geometry. To bound the number of stochastic transition firings the notion of control tokens is newly introduced. While the new partitioning algorithm is general, the implementation is currently limited to only two stochastic firings. The feasibility and usefulness of the new algorithm is illustrated in a case study of a water refinery plant with cascading failures

Fluid Survival Tool: A Model Checker for Hybrid Petri Nets

Recently, algorithms for model checking Stochastic Time Logic (STL) on Hybrid Petri nets with a single general one-shot transition (HPNG) have been introduced. This paper presents a tool for model checking HPNG models against STL formulas. A graphical user interface (GUI) not only helps to demonstrate and validate existing algorithms, it also eases use. From the output of the model checker, 2D and 3D plots can be generated. The extendable object-oriented tool has been developed using the Model-View-Controller and Facade patterns, Doxygen for documentation and Qt for GUI development written in C++

Calculus for decision systems

The conceptualization of the term system has become highly dependent on the application domain. What a physicist means by the term system might be different than what a sociologist means by the same term. In 1956, Bertalanffy [1] defined a system as a set of units with relationships among them . This and many other definitions of system share the idea of a system as a black box that has parts or elements interacting between each other. This means that at some level of abstraction all systems are similar, what eventually differentiates one system from another is the set of underlining equations which describe how these parts interact within the system. ^ In this dissertation we develop a framework that allows us to characterize systems from an interaction level, i.e., a framework that gives us the capability to capture how/when the elements of the system interact. This framework is a process algebra called Calculus for Decision Systems (CDS). This calculus provides means to create mathematical expressions that capture how the systems interact and react to different stimuli. It also provides the ability to formulate procedures to analyze these interactions and to further derive other interesting insights of the system. ^ After defining the syntax and reduction rules of the CDS, we develop a notion of behavioral equivalence for decision systems. This equivalence, called bisimulation, allows us to compare decision systems from the behavioral standpoint. We apply our results to games in extensive form, some physical systems, and cyber-physical systems. ^ Using the CDS for the study of games in extensive form we were able to define the concept of subgame perfect equilibrium for a two-person game with perfect information. Then, we investigate the behavior of two games played in parallel by one of the players. We also explore different couplings between games, and compare - using bisimulation - the behavior of two games that are the result of two different couplings. The results showed that, with some probability, the behavior of playing a game as first player, or second player, could be irrelevant. ^ Decision systems can be comprised by multiple decision makers. We show that in the case where two decision makers interact, we can use extensive games to represent the conflict resolution. For the case where there are more than two decision makers, we presented how to characterize the interactions between elements within an organizational structure. Organizational structures can be perceived as multiple players interacting in a game. In the context of organizational structures, we use the CDS as an information sharing mechanism to transfer the inputs and outputs from one extensive game to another. We show the suitability of our calculus for the analysis of organizational structures, and point out some potential research extensions for the analysis of organizational structures. ^ The other general area we investigate using the CDS is cyber-physical systems. Cyber-physical systems or CPS is a class of systems that are characterized by a tight relationship between systems (or processes) in the areas of computing, communication and physics. We use the CDS to describe the interaction between elements in some simple mechanical system, as well as a particular case of the generalized railroad crossing (GRC) problem, which is a typical case of CPS. We show two approaches to the solution of the GRC problem. ^ This dissertation does not intend to develop new methods to solve game theoretical problems or equations of motion of a physical system, it aims to be a seminal work towards the creation of a general framework to study systems and equivalence of systems from a formal standpoint, and to increase the applications of formal methods to real-world problems

Computational Techniques for the Structural and Dynamic Analysis of Biological Networks

The analysis of biological systems involves the study of networks from different omics such as genomics, transcriptomics, metabolomics and proteomics. In general, the computational techniques used in the analysis of biological networks can be divided into those that perform (i) structural analysis, (ii) dynamic analysis of structural prop- erties and (iii) dynamic simulation. Structural analysis is related to the study of the topology or stoichiometry of the biological network such as important nodes of the net- work, network motifs and the analysis of the flux distribution within the network. Dy- namic analysis of structural properties, generally, takes advantage from the availability of interaction and expression datasets in order to analyze the structural properties of a biological network in different conditions or time points. Dynamic simulation is useful to study those changes of the biological system in time that cannot be derived from a structural analysis because it is required to have additional information on the dynamics of the system. This thesis addresses each of these topics proposing three computational techniques useful to study different types of biological networks in which the structural and dynamic analysis is crucial to answer to specific biological questions. In particu- lar, the thesis proposes computational techniques for the analysis of the network motifs of a biological network through the design of heuristics useful to efficiently solve the subgraph isomorphism problem, the construction of a new analysis workflow able to integrate interaction and expression datasets to extract information about the chromo- somal connectivity of miRNA-mRNA interaction networks and, finally, the design of a methodology that applies techniques coming from the Electronic Design Automation (EDA) field that allows the dynamic simulation of biochemical interaction networks and the parameter estimation

Measurements, Models, Systems and Design

531 s.

Ninth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, October 20-22, 2008

This booklet contains the proceedings of the Ninth Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, October 20-22, 2008. The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop0