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D. Bošnački

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My research interest is in applications of mathematics and computer science in biology and medicine and formal verification of hardware and software. Recently I grew interested in deep learning, mainly for biomedical applications.

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Vrije Universiteit Brussel

University of Wollongong

Kansas State University

Oxford Brookes University

Institut Curie

Politecnico di Milano

Marius Treutwein

Universitätsklinikum Regensburg

Nelson Mauro Maldonato

Università degli Studi di Napoli "Federico II"

shanmuk srinivas

Savitribai Phule Pune University

University of British Columbia

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Papers by D. Bošnački

On verification challenges at the Large Hadron Collider

Tens of images can suffice to train neural networks for malignant leukocyte detection

Scientific Reports, 2021

Convolutional neural networks (CNNs) excel as powerful tools for biomedical image classification.... more Convolutional neural networks (CNNs) excel as powerful tools for biomedical image classification. It is commonly assumed that training CNNs requires large amounts of annotated data. This is a bottleneck in many medical applications where annotation relies on expert knowledge. Here, we analyze the binary classification performance of a CNN on two independent cytomorphology datasets as a function of training set size. Specifically, we train a sequential model to discriminate non-malignant leukocytes from blast cells, whose appearance in the peripheral blood is a hallmark of leukemia. We systematically vary training set size, finding that tens of training images suffice for a binary classification with an ROC-AUC over 90%. Saliency maps and layer-wise relevance propagation visualizations suggest that the network learns to increasingly focus on nuclear structures of leukocytes as the number of training images is increased. A low dimensional tSNE representation reveals that while the two...

Modeling the interference between shear and longitudinal waves under high intensity focused ultrasound propagation in bone

Physics in Medicine & Biology, 2018

DOI to the publisher's website. • The final author version and the galley proof are versions of t... more DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • 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 the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User Agreement:

Modelling the temperature evolution of bone under high intensity focused ultrasound

Physics in medicine and biology, Jan 21, 2016

Magnetic resonance-guided high intensity focused ultrasound (MR-HIFU) has been clinically shown t... more Magnetic resonance-guided high intensity focused ultrasound (MR-HIFU) has been clinically shown to be effective for palliative pain management in patients suffering from skeletal metastasis. The underlying mechanism is supposed to be periosteal denervation caused by ablative temperatures reached through ultrasound heating of the cortex. The challenge is exact temperature control during sonication as MR-based thermometry approaches for bone tissue are currently not available. Thus, in contrast to the MR-HIFU ablation of soft tissue, a thermometry feedback to the HIFU is lacking, and the treatment of bone metastasis is entirely based on temperature information acquired in the soft tissue adjacent to the bone surface. However, heating of the adjacent tissue depends on the exact sonication protocol and requires extensive modelling to estimate the actual temperature of the cortex. Here we develop a computational model to calculate the spatial temperature evolution in bone and the adjacen...

Model Checking Software: Proceedings. Toronto, Canada, May 19-20, 2001

PDMC 2010 Workshop Organization

2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology, 2010

Program Chairs Jiří Barnat, Masaryk University, Czech Republic Michael Weber, University of Twent... more Program Chairs Jiří Barnat, Masaryk University, Czech Republic Michael Weber, University of Twente, The Netherlands ... Program Committee Henri Bal, Free University Amsterdam, The Netherlands Dragan Bošnački, TU Eindhoven, The Netherlands Luboš Brim, Masaryk University Brno, Czech Republic Stefan Edelkamp, TZI Bremen, Germany Ganesh Gopalakrishnan, University of Utah, USA Keijo Heljanko, Aalto University, Finland Gerard Holzmann, NASA/JPL, USA William Knottenbelt, Imperial College, United Kingdom Radu Mateescu, INRIA Grenoble, France ...

Combining Insertion and Deletion in RNA-editing Preserves Regularity

Electronic Proceedings in Theoretical Computer Science, 2012

Inspired by RNA-editing as occurs in transcriptional processes in the living cell, we introduce a... more Inspired by RNA-editing as occurs in transcriptional processes in the living cell, we introduce an abstract notion of string adjustment, called guided rewriting. This formalism allows simultaneously inserting and deleting elements. We prove that guided rewriting preserves regularity: for every regular language its closure under guided rewriting is regular too. This contrasts an earlier abstraction of RNA-editing separating insertion and deletion for which it was proved that regularity is not preserved. The particular automaton construction here relies on an auxiliary notion of slice sequence which enables to sweep from left to right through a completed rewrite sequence.

GPU-Based Graph Decomposition into Strongly Connected and Maximal End Components

Lecture Notes in Computer Science, 2014

GPUexplore: Many-Core On-the-Fly State Space Exploration Using GPUs

Lecture Notes in Computer Science, 2014

In recent years, General Purpose Graphics Processors (GPUs) have been successfully applied in mul... more In recent years, General Purpose Graphics Processors (GPUs) have been successfully applied in multiple application domains to drastically speed up computations. Model checking is an automatic method to formally verify the correctness of a system specification. Such specifications can be viewed as implicit descriptions of a large directed graph or state space, and for most model checking operations, this graph must be analysed. Constructing it, or on-the-fly exploring it, however, is computationally intensive, so it makes sense to try to implement this for GPUs. In this paper, we explain the limitations involved, and how to overcome these. We discuss the possible approaches involving related work, and propose an alternative, using a new hash table approach for GPUs. Experimental results with our prototype implementations show significant speed-ups compared to the established sequential counterparts.

Improving Spin’s Partial-Order Reduction for Breadth-First Search

Lecture Notes in Computer Science, 2005

ABSTRACT We describe an improvement of the partial-order reduction algorithm for breadth-first se... more ABSTRACT We describe an improvement of the partial-order reduction algorithm for breadth-first search which was introduced in Spin version 4.0. Our improvement is based on the algorithm by Alur et al. for symbolic state model checking for local safety properties [1]. The crux of the improvement is an optimization in the context of explicit state model checking of the condition that prevents action ignoring, also known as the cycle proviso. There is an interesting duality between the cycle provisos for the breadth-first search (BFS) and depth first search (DFS) exploration of the state space, which is reflected in the role of the BFS queue and the DFS stack, respectively. The improved version of the algorithm is supported in the current version of Spin and can be shown to perform significantly better than the initial version.

Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets

Communications in Computer and Information Science, 2008

ABSTRACT We describe an improvement of an algorithm for detecting frequently occurring patterns a... more ABSTRACT We describe an improvement of an algorithm for detecting frequently occurring patterns and modules in biological networks. The improvement is based on the observation that the problem of finding frequent network parts can be reduced to the problem of finding maximal frequent item sets (MFI). The MFI problem is a classical problem in the data mining community and there exist numerous efficient tools for it, most of them publicly available. We apply MFI tools to find frequent subgraphs in metabolic pathways from the KEGG database. Our experimental results show that, compared to the existing specialized tools for frequent subgraphs detection, the MFI tools coupled with an adequate postprocessing are much more efficient with regard to the running time and the size of the frequent graphs.

Improving GPU Sparse Matrix-Vector Multiplication for Probabilistic Model Checking

Lecture Notes in Computer Science, 2012

ABSTRACT We present several methods to improve the run times of probabilistic model checking on g... more ABSTRACT We present several methods to improve the run times of probabilistic model checking on general-purpose graphics processing units (GPUs). The methods enhance sparse matrix-vector multiplica-tions, which are in the core of the probabilistic model checking algo-rithms. The improvement is based on the analysis of the transition matrix structures corresponding to state spaces of a selection of examples from the literature. Our first method defines an enumeration of the matrix elements (states of the Markov chains), based on breadth-first search which can lead to a more regular representation of the matrices. We introduce two additional methods that adjust the execution paths and memory access patterns of the individual processors of the GPU. They exploit the specific features of the transition matrices arising from probabilis-tic/stochastic models as well as the logical and physical architectures of the device. We implement the matrix reindexing and the efficient memory access methods in GPU-PRISM, an extension of the probabilistic model checker PRISM. The experiments with the prototype implementation show that each of the methods can bring a significant run time improvement -more than four times compared to the previous version of GPU-PRISM. Moreover, in some cases, the methods are orthogonal and can be used in combination to achieve even greater speed ups.

Proceedings First Workshop on GRAPH Inspection and Traversal Engineering

Electronic Proceedings in Theoretical Computer Science, 2012

GPU-PRISM: An Extension of PRISM for General Purpose Graphics Processing Units

2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology, 2010

AbstractWe present an extension of the model checker PRISM for (general purpose) graphics proces... more

Using Fairness to Make Abstractions Work

Lecture Notes in Computer Science, 2004

ions often introduce infinite traces which have no corresponding traces at the concrete level and... more ions often introduce infinite traces which have no corresponding traces at the concrete level and may lead to failure of the verification. Refinement does not always help to eliminate those traces. In this paper, we consider a timer abstraction that introduces a cyclic behaviour on abstract timers and we show how one can exclude cycles by imposing a strong fairness constraint on the abstract model. By employing the fact that the loop on the abstract timer is a self-loop, we render the strong fairness constraint into a weak fairness constraint and embed it into the verification algorithm. We implemented the algorithm in the DTSpin model checker and showed its efficiency on case studies. The same approach can be used for other data abstractions that introduce self-loops.

Efficient Approximate Verification of Promela Models Via Symmetry Markers

Lecture Notes in Computer Science, 2007

Page 1. Efficient Approximate Verification of Promela Models Via Symmetry Markers Dragan Bonacki... more

The Attributed Pi Calculus

Lecture Notes in Computer Science, 2008

The attributed pi calculus (f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L))({\phi({\mathcal L... more The attributed pi calculus (f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L))({\phi({\mathcal L})}) forms an extension of the pi calculus with attributed processes and attribute dependent synchronization. To ensure flexibility, the calculus is parametrized with the language L{\mathcal L} which defines possible values of attributes. f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L){\phi({\mathcal L})} can express polyadic synchronization as in pi@ and thus diverse compartment organizations. A non-deterministic and a stochastic semantics, where rates may depend on attribute values, is introduced. The stochastic semantics is based on continuous time Markov chains. A simulation algorithm is developed which is firmly rooted in this stochastic semantics. Two examples underline the applicability of f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L){\phi({\mathcal L})} to systems biology: Euglena’s movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda.

Efficient Probabilistic Model Checking on General Purpose Graphics Processors

Lecture Notes in Computer Science, 2009

We present algorithms for parallel probabilistic model checking on general purpose graphic proces... more We present algorithms for parallel probabilistic model checking on general purpose graphic processing units (GPGPUs). For this purpose we exploit the fact that some of the basic algorithms for probabilistic model checking rely on matrix vector multiplication. Since this kind of linear algebraic operations are implemented very efficiently on GPGPUs, the new parallel algorithms can achieve considerable runtime improvements compared to their counterparts on standard architectures. We implemented our parallel algorithms on top of the probabilistic model checker PRISM. The prototype implementation was evaluated on several case studies in which we observed significant speedup over the standard CPU implementation of the tool.

Cluster-Based Partial-Order Reduction

Automated Software Engineering, 2004

DOI to the publisher's website. • The final author version and the galley proof are versions of t... more DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • 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 the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User Agreement:

Survey on Directed Model Checking

Lecture Notes in Computer Science, 2009

This article surveys and gives historical accounts to the algorithmic essentials of directed mode... more This article surveys and gives historical accounts to the algorithmic essentials of directed model checking, a promising bug-hunting technique to mitigate the state explosion problem. In the enumeration process, successor selection is prioritized. We discuss existing guidance and methods to automatically generate them by exploiting system abstractions. We extend the algorithms to feature partial-order reduction and show how liveness problems can be adapted by lifting the search space. For deterministic, finite domains we instantiate the algorithms to directed symbolic, external and distributed search. For real-time domains we discuss the adaption of the algorithms to timed automata and for probabilistic domains we show the application to counterexample generation. Last but not least, we explain how directed model checking helps to accelerate finding solutions to scheduling problems.

On verification challenges at the Large Hadron Collider

Tens of images can suffice to train neural networks for malignant leukocyte detection

Scientific Reports, 2021

Convolutional neural networks (CNNs) excel as powerful tools for biomedical image classification.... more Convolutional neural networks (CNNs) excel as powerful tools for biomedical image classification. It is commonly assumed that training CNNs requires large amounts of annotated data. This is a bottleneck in many medical applications where annotation relies on expert knowledge. Here, we analyze the binary classification performance of a CNN on two independent cytomorphology datasets as a function of training set size. Specifically, we train a sequential model to discriminate non-malignant leukocytes from blast cells, whose appearance in the peripheral blood is a hallmark of leukemia. We systematically vary training set size, finding that tens of training images suffice for a binary classification with an ROC-AUC over 90%. Saliency maps and layer-wise relevance propagation visualizations suggest that the network learns to increasingly focus on nuclear structures of leukocytes as the number of training images is increased. A low dimensional tSNE representation reveals that while the two...

Modeling the interference between shear and longitudinal waves under high intensity focused ultrasound propagation in bone

Physics in Medicine & Biology, 2018

DOI to the publisher's website. • The final author version and the galley proof are versions of t... more DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • 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 the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User Agreement:

Modelling the temperature evolution of bone under high intensity focused ultrasound

Physics in medicine and biology, Jan 21, 2016

Magnetic resonance-guided high intensity focused ultrasound (MR-HIFU) has been clinically shown t... more Magnetic resonance-guided high intensity focused ultrasound (MR-HIFU) has been clinically shown to be effective for palliative pain management in patients suffering from skeletal metastasis. The underlying mechanism is supposed to be periosteal denervation caused by ablative temperatures reached through ultrasound heating of the cortex. The challenge is exact temperature control during sonication as MR-based thermometry approaches for bone tissue are currently not available. Thus, in contrast to the MR-HIFU ablation of soft tissue, a thermometry feedback to the HIFU is lacking, and the treatment of bone metastasis is entirely based on temperature information acquired in the soft tissue adjacent to the bone surface. However, heating of the adjacent tissue depends on the exact sonication protocol and requires extensive modelling to estimate the actual temperature of the cortex. Here we develop a computational model to calculate the spatial temperature evolution in bone and the adjacen...

Model Checking Software: Proceedings. Toronto, Canada, May 19-20, 2001

PDMC 2010 Workshop Organization

2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology, 2010

Program Chairs Jiří Barnat, Masaryk University, Czech Republic Michael Weber, University of Twent... more Program Chairs Jiří Barnat, Masaryk University, Czech Republic Michael Weber, University of Twente, The Netherlands ... Program Committee Henri Bal, Free University Amsterdam, The Netherlands Dragan Bošnački, TU Eindhoven, The Netherlands Luboš Brim, Masaryk University Brno, Czech Republic Stefan Edelkamp, TZI Bremen, Germany Ganesh Gopalakrishnan, University of Utah, USA Keijo Heljanko, Aalto University, Finland Gerard Holzmann, NASA/JPL, USA William Knottenbelt, Imperial College, United Kingdom Radu Mateescu, INRIA Grenoble, France ...

Combining Insertion and Deletion in RNA-editing Preserves Regularity

Electronic Proceedings in Theoretical Computer Science, 2012

Inspired by RNA-editing as occurs in transcriptional processes in the living cell, we introduce a... more Inspired by RNA-editing as occurs in transcriptional processes in the living cell, we introduce an abstract notion of string adjustment, called guided rewriting. This formalism allows simultaneously inserting and deleting elements. We prove that guided rewriting preserves regularity: for every regular language its closure under guided rewriting is regular too. This contrasts an earlier abstraction of RNA-editing separating insertion and deletion for which it was proved that regularity is not preserved. The particular automaton construction here relies on an auxiliary notion of slice sequence which enables to sweep from left to right through a completed rewrite sequence.

GPU-Based Graph Decomposition into Strongly Connected and Maximal End Components

Lecture Notes in Computer Science, 2014

GPUexplore: Many-Core On-the-Fly State Space Exploration Using GPUs

Lecture Notes in Computer Science, 2014

In recent years, General Purpose Graphics Processors (GPUs) have been successfully applied in mul... more In recent years, General Purpose Graphics Processors (GPUs) have been successfully applied in multiple application domains to drastically speed up computations. Model checking is an automatic method to formally verify the correctness of a system specification. Such specifications can be viewed as implicit descriptions of a large directed graph or state space, and for most model checking operations, this graph must be analysed. Constructing it, or on-the-fly exploring it, however, is computationally intensive, so it makes sense to try to implement this for GPUs. In this paper, we explain the limitations involved, and how to overcome these. We discuss the possible approaches involving related work, and propose an alternative, using a new hash table approach for GPUs. Experimental results with our prototype implementations show significant speed-ups compared to the established sequential counterparts.

Improving Spin’s Partial-Order Reduction for Breadth-First Search

Lecture Notes in Computer Science, 2005

ABSTRACT We describe an improvement of the partial-order reduction algorithm for breadth-first se... more ABSTRACT We describe an improvement of the partial-order reduction algorithm for breadth-first search which was introduced in Spin version 4.0. Our improvement is based on the algorithm by Alur et al. for symbolic state model checking for local safety properties [1]. The crux of the improvement is an optimization in the context of explicit state model checking of the condition that prevents action ignoring, also known as the cycle proviso. There is an interesting duality between the cycle provisos for the breadth-first search (BFS) and depth first search (DFS) exploration of the state space, which is reflected in the role of the BFS queue and the DFS stack, respectively. The improved version of the algorithm is supported in the current version of Spin and can be shown to perform significantly better than the initial version.

Finding Frequent Subgraphs in Biological Networks Via Maximal Item Sets

Communications in Computer and Information Science, 2008

ABSTRACT We describe an improvement of an algorithm for detecting frequently occurring patterns a... more ABSTRACT We describe an improvement of an algorithm for detecting frequently occurring patterns and modules in biological networks. The improvement is based on the observation that the problem of finding frequent network parts can be reduced to the problem of finding maximal frequent item sets (MFI). The MFI problem is a classical problem in the data mining community and there exist numerous efficient tools for it, most of them publicly available. We apply MFI tools to find frequent subgraphs in metabolic pathways from the KEGG database. Our experimental results show that, compared to the existing specialized tools for frequent subgraphs detection, the MFI tools coupled with an adequate postprocessing are much more efficient with regard to the running time and the size of the frequent graphs.

Improving GPU Sparse Matrix-Vector Multiplication for Probabilistic Model Checking

Lecture Notes in Computer Science, 2012

ABSTRACT We present several methods to improve the run times of probabilistic model checking on g... more ABSTRACT We present several methods to improve the run times of probabilistic model checking on general-purpose graphics processing units (GPUs). The methods enhance sparse matrix-vector multiplica-tions, which are in the core of the probabilistic model checking algo-rithms. The improvement is based on the analysis of the transition matrix structures corresponding to state spaces of a selection of examples from the literature. Our first method defines an enumeration of the matrix elements (states of the Markov chains), based on breadth-first search which can lead to a more regular representation of the matrices. We introduce two additional methods that adjust the execution paths and memory access patterns of the individual processors of the GPU. They exploit the specific features of the transition matrices arising from probabilis-tic/stochastic models as well as the logical and physical architectures of the device. We implement the matrix reindexing and the efficient memory access methods in GPU-PRISM, an extension of the probabilistic model checker PRISM. The experiments with the prototype implementation show that each of the methods can bring a significant run time improvement -more than four times compared to the previous version of GPU-PRISM. Moreover, in some cases, the methods are orthogonal and can be used in combination to achieve even greater speed ups.

Proceedings First Workshop on GRAPH Inspection and Traversal Engineering

Electronic Proceedings in Theoretical Computer Science, 2012

GPU-PRISM: An Extension of PRISM for General Purpose Graphics Processing Units

2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology, 2010

AbstractWe present an extension of the model checker PRISM for (general purpose) graphics proces... more

Using Fairness to Make Abstractions Work

Lecture Notes in Computer Science, 2004

ions often introduce infinite traces which have no corresponding traces at the concrete level and... more ions often introduce infinite traces which have no corresponding traces at the concrete level and may lead to failure of the verification. Refinement does not always help to eliminate those traces. In this paper, we consider a timer abstraction that introduces a cyclic behaviour on abstract timers and we show how one can exclude cycles by imposing a strong fairness constraint on the abstract model. By employing the fact that the loop on the abstract timer is a self-loop, we render the strong fairness constraint into a weak fairness constraint and embed it into the verification algorithm. We implemented the algorithm in the DTSpin model checker and showed its efficiency on case studies. The same approach can be used for other data abstractions that introduce self-loops.

Efficient Approximate Verification of Promela Models Via Symmetry Markers

Lecture Notes in Computer Science, 2007

Page 1. Efficient Approximate Verification of Promela Models Via Symmetry Markers Dragan Bonacki... more

The Attributed Pi Calculus

Lecture Notes in Computer Science, 2008

The attributed pi calculus (f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L))({\phi({\mathcal L... more The attributed pi calculus (f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L))({\phi({\mathcal L})}) forms an extension of the pi calculus with attributed processes and attribute dependent synchronization. To ensure flexibility, the calculus is parametrized with the language L{\mathcal L} which defines possible values of attributes. f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L){\phi({\mathcal L})} can express polyadic synchronization as in pi@ and thus diverse compartment organizations. A non-deterministic and a stochastic semantics, where rates may depend on attribute values, is introduced. The stochastic semantics is based on continuous time Markov chains. A simulation algorithm is developed which is firmly rooted in this stochastic semantics. Two examples underline the applicability of f&amp;amp;amp;lt;/font &amp;amp;amp;gt;(L){\phi({\mathcal L})} to systems biology: Euglena’s movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda.

Efficient Probabilistic Model Checking on General Purpose Graphics Processors

Lecture Notes in Computer Science, 2009

We present algorithms for parallel probabilistic model checking on general purpose graphic proces... more We present algorithms for parallel probabilistic model checking on general purpose graphic processing units (GPGPUs). For this purpose we exploit the fact that some of the basic algorithms for probabilistic model checking rely on matrix vector multiplication. Since this kind of linear algebraic operations are implemented very efficiently on GPGPUs, the new parallel algorithms can achieve considerable runtime improvements compared to their counterparts on standard architectures. We implemented our parallel algorithms on top of the probabilistic model checker PRISM. The prototype implementation was evaluated on several case studies in which we observed significant speedup over the standard CPU implementation of the tool.

Cluster-Based Partial-Order Reduction

Automated Software Engineering, 2004

DOI to the publisher's website. • The final author version and the galley proof are versions of t... more DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • 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 the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User Agreement:

Survey on Directed Model Checking

Lecture Notes in Computer Science, 2009

This article surveys and gives historical accounts to the algorithmic essentials of directed mode... more This article surveys and gives historical accounts to the algorithmic essentials of directed model checking, a promising bug-hunting technique to mitigate the state explosion problem. In the enumeration process, successor selection is prioritized. We discuss existing guidance and methods to automatically generate them by exploiting system abstractions. We extend the algorithms to feature partial-order reduction and show how liveness problems can be adapted by lifting the search space. For deterministic, finite domains we instantiate the algorithms to directed symbolic, external and distributed search. For real-time domains we discuss the adaption of the algorithms to timed automata and for probabilistic domains we show the application to counterexample generation. Last but not least, we explain how directed model checking helps to accelerate finding solutions to scheduling problems.