Abstract We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjace... more abstractAbstract We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate.

Journal Name: PLoS Genetics

Publication Date: Dec 20, 2012

Operational support is a specific type of process mining that assists users while process instances are being executed. Examples are predicting the remaining processing time of a running insurance claim and recommendi... more abstractOperational support is a specific type of process mining that assists users while process instances are being executed. Examples are predicting the remaining processing time of a running insurance claim and recommending the action that minimizes the treatment costs of a particular patient. Whereas it is easy to evaluate prediction techniques using cross validation, the evaluation of recommendation techniques is challenging as the recommender influences the execution of the process.

Journal Name: Application and Theory of Petri Nets

Publication Date: 2012

Abstract. Model checking tools and techniques are being applied for verification of concurrent systems by users having different skills and background. This ranges from formal methods experts with detailed knowledge o... more abstractAbstract. Model checking tools and techniques are being applied for verification of concurrent systems by users having different skills and background. This ranges from formal methods experts with detailed knowledge of the inner workings of the tools over students learning about model checking techniques to engineers that are mostly interested in applying the technology as a black-box. This paper proposes JoSEL, a visual language for specification of executable model checking jobs.

Publication Date: 2008

Abstract. The ComBack method is a memory reduction technique for explicit state space search algorithms. It enhances hash compaction with state reconstruction to resolve hash conflicts on-the-fly thereby ensuring full... more abstractAbstract. The ComBack method is a memory reduction technique for explicit state space search algorithms. It enhances hash compaction with state reconstruction to resolve hash conflicts on-the-fly thereby ensuring full coverage of the state space.

Journal Name: Transactions on Petri Nets and Other Models of Concurrency III

Publication Date: 2009

The ASCoVeCo State space Analysis Platform (ASAP) is a tool for performing explicit state space analysis of coloured Petri nets (CPNs) and other formalisms. ASAP supports a wide range of state space reduction techniqu... more abstractThe ASCoVeCo State space Analysis Platform (ASAP) is a tool for performing explicit state space analysis of coloured Petri nets (CPNs) and other formalisms. ASAP supports a wide range of state space reduction techniques and is intended to be easy to extend and to use, making it a suitable tool for students, researchers, and industrial users that would like to analyze protocols and/or experiment with different algorithms. This paper presents ASAP from these two perspectives.

Journal Name: Applications and Theory of Petri Nets

Publication Date: 2009

This paper is concerned with a memory-efficient representation of reachability graphs. We describe a technique that enables us to represent each reachable marking in a number of bits close to the theoretical minimum n... more abstractThis paper is concerned with a memory-efficient representation of reachability graphs. We describe a technique that enables us to represent each reachable marking in a number of bits close to the theoretical minimum needed for explicit state enumeration. The technique maps each state vector onto a number between zero and the number of reachable states and uses the sweep-line method to delete the state vectors themselves. A prototype of the proposed technique has been implemented and experimental results are reported.

Journal Name: Tools and Algorithms for the Construction and Analysis of Systems

Publication Date: 2004

Abstract. Coloured Petri nets (CP-nets or CPNs) is a widely used formalism for describing concurrent systems. CPN Tools provides a mature environment for constructing, simulating, and performing analysis of CPN models... more abstractAbstract. Coloured Petri nets (CP-nets or CPNs) is a widely used formalism for describing concurrent systems. CPN Tools provides a mature environment for constructing, simulating, and performing analysis of CPN models. CPN Tools also has limitations if, for example, one wishes to extend the analysis capabilities or to integrate CPN models into external applications. In this paper we present Access/CPN, a framework that facilitates such extensions.

Journal Name: Applications and Theory of Petri Nets

Publication Date: 2009

This paper describes the BRITNeY suite, a tool which enables users to create visualizations of formal models. BRITNeY suite is integrated with CPN Tools, and we give an example of how to extend a simple stop-and-wait ... more abstractThis paper describes the BRITNeY suite, a tool which enables users to create visualizations of formal models. BRITNeY suite is integrated with CPN Tools, and we give an example of how to extend a simple stop-and-wait protocol with a visualization in the form of message sequence charts. We also show examples of animations created during industrial projects to give an impression of what is possible with the BRITNeY suite.

Journal Name: Petri Nets and Other Models of Concurrency-ICATPN 2006

Publication Date: 2006

Abstract. This paper describes a platform, the BRITNeY Suite, for experimenting with Coloured Petri nets. The BRITNeY Suite provides access to data-structures and a simulator for Coloured Petri nets via a powerful scr... more abstractAbstract. This paper describes a platform, the BRITNeY Suite, for experimenting with Coloured Petri nets. The BRITNeY Suite provides access to data-structures and a simulator for Coloured Petri nets via a powerful scripting language and plug-in-mechanism, thereby making it easy to perform customized simulations and visualizations of Coloured Petri net models. Additionally it is possible to make elaborate extensions building on top of well-designed interfaces to Coloured Petri nets created using CPN Tools.

Journal Name: Proceedings of Seventh Workshop on Practical Use of Coloured Petri Nets and the CPN Tools. Århus, Denmark

Publication Date: Oct 2006

Abstract. Coloured Petri nets have proved to be a useful formalism for modeling distributed algorithms, ie, algorithms where nodes communicate via message passing. Here we describe an approach for modeling parallel al... more abstractAbstract. Coloured Petri nets have proved to be a useful formalism for modeling distributed algorithms, ie, algorithms where nodes communicate via message passing. Here we describe an approach for modeling parallel algorithms and programs, ie, algorithms and programs where processes communicate via shared memory. The model is verified for correctness, here to prove absence of mutual exclusion violations and to find dead-and live-locks.

Journal Name: Transactions on Petri Nets and Other Models of Concurrency VI

Publication Date: 2012