Showing papers by "Maciej Koutny published in 2011"

Causality in structured occurrence nets

Abstract: Structured occurrence nets consist of multiple occurrence nets -- each recording causality and concurrency in an execution of a component of a concurrent system. These occurrence nets are linked together by means of various types of relationships, aimed at representing dependencies between communicating and evolving sub-systems. In this paper, we investigate causality in the basic class of communication structured occurrence nets (cso-nets). We start by introducing the corresponding system-level model of communication structured Place Transition Nets (cspt-nets) which extend Place Transition Nets with an explicit structuring into communicating sub-systems and process interaction based on a combination of synchronous and asynchronous communication. After that we develop a cso-net based process semantics for cspt-nets showing that causality in cso-nets is underpinned by stratified order structures extending causal partial orders with weak causality.

Timed Mobility in Process Algebra and Petri Nets

Abstract: Abstract We present a process algebra called TiMo in which timeouts of interactions and adaptable migrations in a distributed environment with explicit locations can be specified. Timing constraints allow to control the communication between co-located mobile processes, and a migration action with variable destination supports flexible movement from one location to another. The model of time is based on local clocks rather than a global clock. We provide a structural translation of TiMo into behaviourally equivalent high level timed Petri nets. As a result, we obtain a formal net semantics for timed interaction and migration which is both structural and allows one to deal directly with concurrency and causality.

Step Semantics of Boolean Nets

Abstract: Boolean nets are a family of Petri net models with very simple markings which are sets of places. We investigate several classes of boolean nets distinguished by different kinds of individual connections between places and transitions, as well as different ways in which these connections are combined in order to specify the effect of executing steps of transitions. The latter aspect can be captured by connection monoids. A key advantage of using connection monoids is that by describing the step semantics of a class of Petri nets in terms of a connection monoid, one can apply results developed within a general theory of Petri net synthesis. In this paper, we provide an extensive classification of boolean nets which can be described by connection monoids. This classification is based on the realisation that the different ways of interpreting combinations of connections can be made explicit using a higher level monoid. Moreover, we demonstrate that connection monoids can capture other behavioural properties of boolean nets, such as structural conflicts between transitions.

Mutex Causality in Processes and Traces of General Elementary Nets

Abstract: A concurrent history represented by a causality structure that captures the intrinsic, invariant dependencies between its actions, can be interpreted as defining a set of closely related observations e.g., step sequences. Depending on the relationships observed in the histories of a system, the concurrency paradigm to which it adheres may be identified, with different concurrency paradigms underpinned by different kinds of causality structures. Elementary net systems with inhibitor arcs and mutex arcs ENIM-systems are a system model that through its process semantics and associated causality structures fits the least restrictive concurrency paradigm. One can also investigate the abstract behaviour of an ENIM-system by grouping together step sequences in equivalence classes generalised comtraces using the structural relations between its transitions. The resulting concurrent histories of the ENIM-system are consistent with the generalised stratified order structures underlying its processes. The paper establishes a link between ENIM-systems and trace theory allowing one to discuss different observations of concurrent behaviour in a way that is consistent with the causality semantics defined by the operationally defined processes.

Timed migration and interaction with access permissions

Abstract: We introduce and study a process algebra able to model the systems composed of processes (agents) which may migrate within a distributed environment comprising a number of distinct locations. Two processes may communicate if they are present in the same location and, in addition, they have appropriate access permissions to communicate over a channel. Access permissions are dynamic, and processes can acquire new access permissions or lose some existing permissions while migrating from one location to another. Timing constraints coordinate and control both the communication between processes and migration between locations. We completely characterise those situations when a process is always guaranteed to possess safe access permissions. The consequences of such a result are twofold. First, we are able to validate systems where one does not need to check (at least partially) access permissions as they are guaranteed not to be violated, improving efficiency of implementation. Second, one can design systems in which processes are not blocked (deadlocked) because of the lack of dynamically changing access permissions.

Membrane Systems with Qualitative Evolution Rules

Abstract: In membrane systems, biochemical reactions taking place in the compartments of a cell are abstracted to evolution rules that specify which and how many objects are consumed and produced. The recently proposed reaction systems also investigate processes carried by biochemical reactions, but the resulting computational model is remarkably different. A key difference is that in reaction systems, biochemical reactions are modeled using a qualitative rather than a quantitative approach. In this paper, we introduce so-called set membrane systems, a variant of membrane systems with qualitative evolution rules inspired by reaction systems. We then relate set membrane systems to Petri nets which leads to a new class of Petri nets: set-nets with localities. This Petri net model provides a faithful match with the operational semantics of set membrane systems.

Qualitative and Quantitative Aspects of a Model for Processes Inspired by the Functioning of the Living Cell

Abstract: Reaction systems are a formal model for processes inspired by the functioning of the living cell. The underlying idea of this model is that the functioning of the living cell is determined by the interactions of biochemical reactions, and these interactions are based on the mechanisms of facilitation and inhibition. In this paper we first review the main notions of the basic model of reaction systems which is a qualitative model. Then we discuss various ways of taking into account quantitative properties. About the authors Andrzej Ehrenfeucht is a Professor in the Department of Computer Science, University of Colorado, Boulder, USA. Jetty Kleijn is a visiting fellow within the School of Computing Science, Newcastle University. Maciej Koutny obtained his MSc (1982) and PhD (1984) from the Warsaw University of Technology. In 1985 he joined the then Computing Laboratory of the University of Newcastle upon Tyne to work as a Research Associate. In 1986 he became a Lecturer in Computing Science at Newcastle, and in 1994 was promoted to an established Readership at Newcastle. In 2000 he became a Professor of Computing Science. Grzegorz Rozenberg is a Professor of Computer Science at Leiden University, The Netherlands, and an Adjunct Professor at the Department of Computer Science of University of Colorado at Boulder, U.S.A. He is the head of the Theoretical Computer Science group at Leiden Institute of Advanced Computer Science (LIACS), and the scientific director of Leiden Center for Natural Computing (LCNC). He has published more than 500 papers, 6 books, and is a (co-)editor of about 90 books. He is a member of an editorial board of about 20 journals and book series. He has been a member of the program committees and invited speaker for practically all major conferences in theoretical computer science in Europe. He is a Foreign Member of the Finnish Academy of Sciences and Letters, a member of Academia Europaea, and he is holder of Honorary Doctorates of the University of Turku, Finland, the Technical University of Berlin, Germany, and the University of Bologna, Italy. He has received the Distinguished Achievements Award of the European Association for Theoretical Computer Science "in recognition of his outstanding scientific contributions to theoretical computer science". He is a Highly Cited Researcher by ISI. Suggested keywords REACTION SYSTEM GENERALISED REACTION SYSTEM LIVING CELL NATURAL COMPUTING GENETIC REGULATORY NETWORK TRANSITION SYSTEM, MEASUREMENT FUNCTION APPROXIMATION SIMULATION Qualitative and Quantitative Aspe ts of a Model for Pro esses Inspired by the Fun tioning of the Living Cell Andrzej Ehrenfeu ht1, Jetty Kleijn2, Ma iej Koutny3, and Grzegorz Rozenberg1,2 1 Department of Computer S ien e, University of Colorado at Boulder 430 UCB Boulder, CO 80309-0430, U.S.A. andrzej s. olorado.edu 2 LIACS, Leiden University, 2300 RA, The Netherlands {kleijn,rozenber} lia s.nl 3 S hool of Computing S ien e, New astle University, NE1 7RU, UK ma iej.koutny n l.a .uk Abstra t. Rea tion systems are a formal model for pro esses inspired by the fun tioning of the living ell. The underlying idea of this model is that the fun tioning of the living ell is determined by the intera tions of bio hemi al rea tions, and these intera tions are based on the me hanisms of fa ilitation and inhibition. In this paper we rst review the main notions of the basi model of rea tion systems whi h is a qualitative model. Then we dis uss various ways of taking into a ount quantitative properties.

The Mutex Paradigm of Concurrency

Abstract: Concurrency can be studied at different yet consistent levels of abstraction: from individual behavioural observations, to more abstract concurrent histories which can be represented by causality structures capturing intrinsic, invariant dependencies between executed actions, to system level devices such as Petri nets or process algebra expressions. Histories can then be understood as sets of closely related observations (here step sequences of executed actions). Depending on the nature of the observed relationships between executed actions involved in a single concurrent history, one may identify different concurrency paradigms underpinned by different kinds of causality structures (e.g., the true concurrency paradigm is underpinned by causal partial orders with each history comprising all step sequences consistent with some causal partial order). For some paradigms there exist closely matching system models such as elementary net systems (EN-systems) for the true concurrency paradigm, or elementary net systems with inhibitor arcs (ENI-systems) for a paradigm where simultaneity of executed actions does not imply their unorderedness. In this paper, we develop a system model fitting the least restrictive concurrency paradigm and its associated causality structures. To this end, we introduce ENI-systems with mutex arcs (ENIM-systems). Each mutex arc relates two transitions which cannot be executed simultaneously, but can be executed in any order. To link ENIM-systems with causality structures we develop a notion of process following a generic approach (semantical framework) which includes a method to generate causality structures from the new class of processes.

Towards Quantitative Analysis of Opacity

Abstract: Opacity is a general approach for describing and unifying security properties expressed as predicates. A predicate is opaque if an observer of the system is unable to determine the satisfaction of the predicate in a given run of the system. The meaning of opacity is straightforward when considering the standard qualitative operational semantics, but there are a number of possible interpretations in a context where quantitative information about system evolutions is available. We propose four variants of quantitative opacity defined for probabilistic labelled transition systems, with each variant capturing a different aspect of quantifying the opacity of a predicate. Moreover, we present results showing how these four properties can be checked or approximated for specific classes of probabilistic labelled transition systems, observation functions, and system predicates.

The mutex paradigm of concurrency

Abstract: Concurrency can be studied at different yet consistent levels of abstraction: from individual behavioural observations, to more abstract concurrent histories which can be represented by causality structures capturing intrinsic, invariant dependencies between executed actions, to system level devices such as Petri nets or process algebra expressions. Histories can then be understood as sets of closely related observations (here step sequences of executed actions). Depending on the nature of the observed relationships between executed actions involved in a single concurrent history, one may identify different concurrency paradigms underpinned by different kinds of causality structures (e.g., the true concurrency paradigm is underpinned by causal partial orders with each history comprising all step sequences consistent with some causal partial order). For some paradigms there exist closely matching system models such as elementary net systems (EN-systems) for the true concurrency paradigm, or elementary net systems with inhibitor arcs (ENI-systems) for a paradigm where simultaneity of executed actions does not imply their unorderedness. In this paper, we develop a system model fitting the least restrictive concurrency paradigm and its associated causality structures. To this end, we introduce ENI-systems with mutex arcs (ENIM-systems). Each mutex arc relates two transitions which cannot be executed simultaneously, but can be executed in any order. To link ENIM-systems with causality structures we develop a notion of process following a generic approach (semantical framework) which includes a method to generate causality structures from the new class of processes.

Causality in Extensions of Petri Nets

Abstract: The causal semantics of standard net classes like Elementary Net Systems and Place/Transition Nets, is typically expressed in terms of partially ordered sets of transition occurrences. In each such partial order, causally related occurrences are ordered while concurrent transition occurrences remain unordered. Partial order semantics can, in particular, support model checking by efficient verification techniques based on net unfoldings.

Regions of Petri Nets with a/sync Connections

Abstract: Automated synthesis from behavioural specifications, such as transition systems, is an attractive way of constructing correct concurrent systems. In this paper, we investigate the synthesis of Petri nets which use special connections between transitions and places. Along these a/sync connections tokens can be transferred instantaneously between transitions executed in a single step. We show that for Place/Transition nets with a/sync connections the synthesis problem can be treated within the general approach based on regions of step transition systems. We also show that the problem is decidable for finite transition systems, and outline a suitable construction algorithm.

Classifying Boolean Nets for Region-based Synthesis

Abstract: A Petri net model is referred to as Boolean if the only possible markings are sets, i.e., places are marked or not without further quantification; moreover, also the enabling conditions and firing rule are based on this principle of set-based token arithmetic. Elementary Net systems are an example of a class of Boolean nets, and so are the recently introduced set-nets. In our investigation of the synthesis problem for set-nets, it would be useful to know how this new net model can be fitted into the general theory of net synthesis based on the generic concept of τ -nets. Here, we demonstrate how set-nets and the idea of Boolean operations on tokens provide an opportunity to classify a wide variety of Boolean nets that are amenable to region-based net synthesis.

Membrane Systems with Qualitative Evolution Rules

Abstract: In membrane systems, biochemical reactions taking place in the compartments of a cell are abstracted to evolution rules that specify which and how many objects are consumed and produced. The recently proposed reaction systems also investigate processes carried by biochemical reactions, but the resulting computational model is remarkably different. A key difference is that in reaction systems, biochemical reactions are modeled using a qualitative rather than a quantitative approach. In this paper, we introduce so-called set membrane systems, a variant of membrane systems with qualitative evolution rules inspired by reaction systems. We then relate set membrane systems to Petri nets which leads to a new class of Petri nets: set-nets with localities. This Petri net model provides a faithful match with the operational semantics of set membrane systems.

Petri Nets for Biologically Motivated Computing

Abstract: Petri nets are a general and well-established model of concurrent and distributed computation and behaviour, including that taking place in biological systems. In this survey paper, we are concerned with intrinsic relationships between Petri nets and two formal models inspired by aspects of the functioning of the living cell: membrane systems and reaction systems. In particular, we are interested in the benefits that can result from establishing strong semantical links between Petri nets and membrane systems and reaction systems. We first discuss Petri nets with localities reflecting the compartmentalisation modelled in membrane systems. Then special attention is given to set-nets, a new Petri net model for reaction systems and their qualitative approach to the investigation of the processes carried out by biochemical reactions taking place in the living cell.

Coverability and Inhibitor Arcs: an example

Abstract: Inhibitor arcs pose a problem for the standard Coverability Tree Construction for Place/Transition Nets. A straightforward modification of the construction circumventing this problem works for PT-nets with one inhibitor place. Here it is shown that this modified construction may not terminate in case of two or more inhibitor places. © 2011 Newcastle University. Printed and published by Newcastle University, Computing Science, Claremont Tower, Claremont Road, Newcastle upon Tyne, NE1 7RU, England. Bibliographical details VAN DER VLUGT, S., KLEIJN, J., KOUTNY, M. Coverability and Inhibitor Arcs: an example [By] S. van der Vlugt, J. Kleijn, M. Koutny Newcastle upon Tyne: Newcastle University: Computing Science, 2011. (Newcastle University, Computing Science, Technical Report Series, No. CS-TR-1293)

Hasse Diagrams of Combined Traces

Abstract: One of the standard ways to represent concurrent behaviours is to use concepts originating from language theory, such as traces and comtraces. Traces can express notions such as concurrency and causality, whereas comtraces can also capture weak causality and simultaneity. This paper is concerned with the development of efficient data structures and algorithms for manipulating comtraces. We introduce Hasse diagrams for comtraces which are a generalisation of Hasse diagrams defined for partial orders and traces, and develop an efficient algorithm for deriving them from language theoretic representations of comtraces. We also explain how the new representation of comtraces can be used to implement efficiently some basic operations on comtraces.

Localities in Systems with a/sync Communication

Abstract: Localities and a/sync places are two recent extensions to the Petri net model. Whereas localities have been introduced as a modelling tool for membrane systems and more general GALS (globally asynchronous locally synchronous) systems, a/sync places make it possible to model synchronous communication between transitions. We investigate the interaction between locally synchronous execution and synchronous communication. Our focus is in particular on the causalities in the concurrent runs of a new Petri net model combining these features.

Petri Nets and Bio-Modelling - and how to benefit from their synergy

Abstract: In this talk we are concerned with the intrinsic similarities and differences between Petri nets on the one hand, and membrane systems and reaction systems on the other hand.