Henrik Pilegaard - Academia.edu (original) (raw)

Papers by Henrik Pilegaard

ACM Computing Surveys, 2012

In Section 2 of the main article, we have shown how to develop a Flow Logic for the π-calculus an... more In Section 2 of the main article, we have shown how to develop a Flow Logic for the π-calculus and in Section 3, we have covered a number of techniques that can increase the precision of the Flow Logic. In this section we are going to illustrate how the development may be extended to address language features that go beyond those of the standard π-calculus. We shall focus on the notions of distribution and code mobility that have been extensively investigated in the context of calculi as the Dπ-calculus [Hennessy 2007], KLAIM [Bettini et al. 2003], and Mobile Ambients [Cardelli and Gordon 2000] to name just a few. We have decided to follow the approach of the Dπ-calculus [Hennessy 2007] as it most directly extends the concepts from the π-calculus. We conclude with a few pointers to the literature. Proofs may be found in Appendix B.4. The material reported here is a collaboration between the authors of the main article and our students Piotr Filipiuk, Alejandro Hernandez, Lei Song, and Fuyuan Zhang as part of an intensive PhD course on Flow Logic. A.1 The Process Calculus The fundamental idea of the Dπ-calculus [Hennessy 2007] is that processes are spatially distributed over a collection of named localities. The syntax of networks, processes and actions are given by the following.

Nordic Journal of Computing, Dec 1, 2003

... a method that allows natural modelling of real-time (cost) properties of security protocols.P... more ... a method that allows natural modelling of real-time (cost) properties of security protocols.Proof support for the theory developed here is ... Some small examples of protocols are treated and properties are shown via interactive theorem proving. ... Bibliometrics: publication history ...

Lecture Notes in Computer Science, 2011

... Pilegaard2 1 DTU Informatics, Technical University of Denmark, Denmark {riis,nielson}@imm.dtu... more ... Pilegaard2 1 DTU Informatics, Technical University of Denmark, Denmark {riis,nielson}@imm.dtu.dk 2 Institut für Informatik, Technische Universität München, Germany joba@model.in.tum.de, henrik@pilegaard.org Abstract. ...

Dagstuhl Seminar Proceedings, 2006

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. As for other ambient calculi static program analysis can be used to compute safe approximations of the behaviour of system models. We use these tools to model and analyse the production of cholesterol in living cells and show that we are able to pinpoint the difference in behaviour between models of healthy systems and models of mutated systems giving rise to known diseases.

Electronic Notes in Theoretical Computer Science, May 1, 2007

In the context of process algebras it is customary to define semantics in the form of a reaction ... more In the context of process algebras it is customary to define semantics in the form of a reaction relation supported by a structural congruence relation. Recently process algebras have grown more expressive in order to meet the modelling demands of fields as diverse as business modelling and systems biology. This leads to combining various features, such as general choice and parallelism that were previously studied separately, and it often becomes difficult to define the reaction semantics. We present a general approach based on active evaluation contexts that allows the reaction semantics to be easily constructed.

Lecture Notes in Computer Science, 2004

Programming language technology can contribute to the development and understanding of Systems Bi... more Programming language technology can contribute to the development and understanding of Systems Biology by providing formal calculi for specifying and analysing the dynamic behaviour of biological systems. Our focus is on BioAmbients, a variation of the ambient calculi developed for modelling mobility in computer systems. We present a static analysis for capturing the spatial structure of biological systems and we illustrate it on a few examples.

Nordic Workshop Programming Theory, 2009

 Users may download and print one copy of any publication from the public portal for the purpose... more  Users may download and print one copy of any publication from the public portal for the purpose of private study or research.  You may not further distribute the material or use it for any profit-making activity or commercial gain  You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

The Journal of Logic and Algebraic Programming, May 1, 2012

Process algebras formalism is highly suitable for producing succinct descriptions of reactive con... more Process algebras formalism is highly suitable for producing succinct descriptions of reactive concurrent systems. Process algebras allow to represent them in a compositional way, as processes that run in parallel and interact, for example, through synchronisation or message passing. On the other hand, checking properties on process algebraic descriptions is often hard, while "unfolding" them into the Labelled Transition Systems can lead to the infamous state space explosion problem. In this work we use a subtype of Data Flow Analysis on systems defined by finite-state process algebras with CSP-type synchronisation-in particular, on our variant of IMC with a more permissive syntax, i.e. with a possibility to start a bounded number of new processes. We prove that the defined Pathway Analysis captures all the properties of the systems, i.e. is precise. The results of the Pathway Analysis can be therefore used as an intermediate representation format, which is more concise than the Labelled Transition System with all the states explicitly represented and more suitable for devising efficient verification algorithms of concurrent systems than their process algebraic descriptions-see, for example, the reachability algorithm in Skrypnyuk and Nielson (2011) [17].

arXiv (Cornell University), Sep 27, 2012

We perform a direct comparison of the Succinct Solver v2.0 and XSB Prolog v2.6 based on experimen... more We perform a direct comparison of the Succinct Solver v2.0 and XSB Prolog v2.6 based on experiments with Control Flow Analyses of scalable Discretionary Ambient programs and Carmel programs. To facilitate this comparison we expand ALFP clauses accepted by the Succinct Solver into more general Normal clauses accepted by both solvers and run the experiments for all three possible combinations of input and solver. This allows the solvers to be tested on even ground and enables the reuse of existing analyses and their corresponding ALFP constraint generators. The performance of the Succinct Solver is at worst a small constant factor worse than XSB Prolog. In optimum cases the Succinct Solver outperforms XSB Prolog by having a substantially lower asymptotic complexity.

Dagstuhl Seminar Proceedings, 2006

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. The technical contribution of this paper is to extend the Flow Logic approach to static analysis with a couple of new techniques in order to give precise information about the behaviour of systems written in BioAmbients. Applying the development to a simple model of a cell releasing nutrients from food compunds we illustrate how the proposed analysis does indeed improve on previous efforts.

Information Processing Letters, Aug 1, 2007

There are two popular approaches to specifying the semantics of process algebras: labelled transi... more There are two popular approaches to specifying the semantics of process algebras: labelled transition semantics and reaction semantics. While the notion of free name is rather unproblematic for labelled transition semantics this is not so for reaction semantics in the presence of a structural congruence for unfolding recursive declarations. We show that the standard definition of free name is not preserved under the structural congruence. We then develop a fixed point approach to the set of free names and show that it is invariant under the structural congruence.

Springer eBooks, Jul 13, 2008

In service-oriented computing, correlations are used to determine links between service providers... more In service-oriented computing, correlations are used to determine links between service providers and users. A correlation contains values for some variables received in a communication. Subsequent messages will only be received when they match the values of the correlation. Correlations allow for the implementation of sessions, local shared memory, gradually provided input, or input provided in arbitrary order-thus presenting a challenge to static analysis. In this work, we present a static analysis in relational form of correlations. It is defined in terms of a fragment of the process calculus COWS that itself builds on the Fusion Calculus. The analysis is implemented and practical experiments allow us to automatically establish properties of the flow of information between services.

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. The technical contribution of this paper is to extend the Flow Logic approach to static analysis with a couple of new techniques in order to give precise information about the behaviour of systems written in BioAmbients. Applying the development to a simple model of a cell releasing nutrients from food compunds we illustrate how the proposed analysis does indeed improve on previous efforts.

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. As for other ambient calculi static program analysis can be used to compute safe approximations of the behaviour of system models. We use these tools to model and analyse the production of cholesterol in living cells and show that we are able to pinpoint the difference in behaviour between models of healthy systems and models of mutated systems giving rise to known diseases.

ACM Computing Surveys, 2012

In Section 2 of the main article, we have shown how to develop a Flow Logic for the π-calculus an... more In Section 2 of the main article, we have shown how to develop a Flow Logic for the π-calculus and in Section 3, we have covered a number of techniques that can increase the precision of the Flow Logic. In this section we are going to illustrate how the development may be extended to address language features that go beyond those of the standard π-calculus. We shall focus on the notions of distribution and code mobility that have been extensively investigated in the context of calculi as the Dπ-calculus [Hennessy 2007], KLAIM [Bettini et al. 2003], and Mobile Ambients [Cardelli and Gordon 2000] to name just a few. We have decided to follow the approach of the Dπ-calculus [Hennessy 2007] as it most directly extends the concepts from the π-calculus. We conclude with a few pointers to the literature. Proofs may be found in Appendix B.4. The material reported here is a collaboration between the authors of the main article and our students Piotr Filipiuk, Alejandro Hernandez, Lei Song, and Fuyuan Zhang as part of an intensive PhD course on Flow Logic. A.1 The Process Calculus The fundamental idea of the Dπ-calculus [Hennessy 2007] is that processes are spatially distributed over a collection of named localities. The syntax of networks, processes and actions are given by the following.

Nordic Journal of Computing, Dec 1, 2003

... a method that allows natural modelling of real-time (cost) properties of security protocols.P... more ... a method that allows natural modelling of real-time (cost) properties of security protocols.Proof support for the theory developed here is ... Some small examples of protocols are treated and properties are shown via interactive theorem proving. ... Bibliometrics: publication history ...

Lecture Notes in Computer Science, 2011

... Pilegaard2 1 DTU Informatics, Technical University of Denmark, Denmark {riis,nielson}@imm.dtu... more ... Pilegaard2 1 DTU Informatics, Technical University of Denmark, Denmark {riis,nielson}@imm.dtu.dk 2 Institut für Informatik, Technische Universität München, Germany joba@model.in.tum.de, henrik@pilegaard.org Abstract. ...

Dagstuhl Seminar Proceedings, 2006

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. As for other ambient calculi static program analysis can be used to compute safe approximations of the behaviour of system models. We use these tools to model and analyse the production of cholesterol in living cells and show that we are able to pinpoint the difference in behaviour between models of healthy systems and models of mutated systems giving rise to known diseases.

Electronic Notes in Theoretical Computer Science, May 1, 2007

In the context of process algebras it is customary to define semantics in the form of a reaction ... more In the context of process algebras it is customary to define semantics in the form of a reaction relation supported by a structural congruence relation. Recently process algebras have grown more expressive in order to meet the modelling demands of fields as diverse as business modelling and systems biology. This leads to combining various features, such as general choice and parallelism that were previously studied separately, and it often becomes difficult to define the reaction semantics. We present a general approach based on active evaluation contexts that allows the reaction semantics to be easily constructed.

Lecture Notes in Computer Science, 2004

Programming language technology can contribute to the development and understanding of Systems Bi... more Programming language technology can contribute to the development and understanding of Systems Biology by providing formal calculi for specifying and analysing the dynamic behaviour of biological systems. Our focus is on BioAmbients, a variation of the ambient calculi developed for modelling mobility in computer systems. We present a static analysis for capturing the spatial structure of biological systems and we illustrate it on a few examples.

Nordic Workshop Programming Theory, 2009

 Users may download and print one copy of any publication from the public portal for the purpose... more  Users may download and print one copy of any publication from the public portal for the purpose of private study or research.  You may not further distribute the material or use it for any profit-making activity or commercial gain  You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

The Journal of Logic and Algebraic Programming, May 1, 2012

Process algebras formalism is highly suitable for producing succinct descriptions of reactive con... more Process algebras formalism is highly suitable for producing succinct descriptions of reactive concurrent systems. Process algebras allow to represent them in a compositional way, as processes that run in parallel and interact, for example, through synchronisation or message passing. On the other hand, checking properties on process algebraic descriptions is often hard, while "unfolding" them into the Labelled Transition Systems can lead to the infamous state space explosion problem. In this work we use a subtype of Data Flow Analysis on systems defined by finite-state process algebras with CSP-type synchronisation-in particular, on our variant of IMC with a more permissive syntax, i.e. with a possibility to start a bounded number of new processes. We prove that the defined Pathway Analysis captures all the properties of the systems, i.e. is precise. The results of the Pathway Analysis can be therefore used as an intermediate representation format, which is more concise than the Labelled Transition System with all the states explicitly represented and more suitable for devising efficient verification algorithms of concurrent systems than their process algebraic descriptions-see, for example, the reachability algorithm in Skrypnyuk and Nielson (2011) [17].

arXiv (Cornell University), Sep 27, 2012

We perform a direct comparison of the Succinct Solver v2.0 and XSB Prolog v2.6 based on experimen... more We perform a direct comparison of the Succinct Solver v2.0 and XSB Prolog v2.6 based on experiments with Control Flow Analyses of scalable Discretionary Ambient programs and Carmel programs. To facilitate this comparison we expand ALFP clauses accepted by the Succinct Solver into more general Normal clauses accepted by both solvers and run the experiments for all three possible combinations of input and solver. This allows the solvers to be tested on even ground and enables the reuse of existing analyses and their corresponding ALFP constraint generators. The performance of the Succinct Solver is at worst a small constant factor worse than XSB Prolog. In optimum cases the Succinct Solver outperforms XSB Prolog by having a substantially lower asymptotic complexity.

Dagstuhl Seminar Proceedings, 2006

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. The technical contribution of this paper is to extend the Flow Logic approach to static analysis with a couple of new techniques in order to give precise information about the behaviour of systems written in BioAmbients. Applying the development to a simple model of a cell releasing nutrients from food compunds we illustrate how the proposed analysis does indeed improve on previous efforts.

Information Processing Letters, Aug 1, 2007

There are two popular approaches to specifying the semantics of process algebras: labelled transi... more There are two popular approaches to specifying the semantics of process algebras: labelled transition semantics and reaction semantics. While the notion of free name is rather unproblematic for labelled transition semantics this is not so for reaction semantics in the presence of a structural congruence for unfolding recursive declarations. We show that the standard definition of free name is not preserved under the structural congruence. We then develop a fixed point approach to the set of free names and show that it is invariant under the structural congruence.

Springer eBooks, Jul 13, 2008

In service-oriented computing, correlations are used to determine links between service providers... more In service-oriented computing, correlations are used to determine links between service providers and users. A correlation contains values for some variables received in a communication. Subsequent messages will only be received when they match the values of the correlation. Correlations allow for the implementation of sessions, local shared memory, gradually provided input, or input provided in arbitrary order-thus presenting a challenge to static analysis. In this work, we present a static analysis in relational form of correlations. It is defined in terms of a fragment of the process calculus COWS that itself builds on the Fusion Calculus. The analysis is implemented and practical experiments allow us to automatically establish properties of the flow of information between services.

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. The technical contribution of this paper is to extend the Flow Logic approach to static analysis with a couple of new techniques in order to give precise information about the behaviour of systems written in BioAmbients. Applying the development to a simple model of a cell releasing nutrients from food compunds we illustrate how the proposed analysis does indeed improve on previous efforts.

BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting f... more BioAmbients is a derivative of mobile ambients that has shown promise of describing interesting features of the behaviour of biological systems. As for other ambient calculi static program analysis can be used to compute safe approximations of the behaviour of system models. We use these tools to model and analyse the production of cholesterol in living cells and show that we are able to pinpoint the difference in behaviour between models of healthy systems and models of mutated systems giving rise to known diseases.