7 Search Results for "Schätz, Bernhard"

Document
DOI: 10.4230/LIPIcs.WABI.2025.20
A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences

Authors: Haonan Wu, Antonio Blanca, and Paul Medvedev

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al. 2016) can accurately estimate the substitution rate between two low-repetitive sequences from their k-mer sketches; however, it is inaccurate on repetitive sequences such as the centromere of a human chromosome. Follow-up work by Blanca et al. (2021) has attempted to model how mutations affect k-mer sets based on strong assumptions that the sequence is non-repetitive and that mutations do not create spurious k-mer matches. However, the theoretical foundations for extending an estimator like Mash to work in the presence of repeat sequences have been lacking. In this work, we relax the non-repetitive assumption and propose a novel estimator for the mutation rate. We derive theoretical bounds on our estimator’s bias. Our experiments show that it remains accurate for repetitive genomic sequences, such as the alpha satellite higher order repeats in centromeres. We demonstrate our estimator’s robustness across diverse datasets and various ranges of the substitution rate and k-mer size. Finally, we show how sketching can be used to avoid dealing with large k-mer sets while retaining accuracy. Our software is available at https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator.
Cite as

Haonan Wu, Antonio Blanca, and Paul Medvedev. A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wu_et_al:LIPIcs.WABI.2025.20,
  author =	{Wu, Haonan and Blanca, Antonio and Medvedev, Paul},
  title =	{{A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{20:1--20:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.20},
  URN =		{urn:nbn:de:0030-drops-239465},
  doi =		{10.4230/LIPIcs.WABI.2025.20},
  annote =	{Keywords: k-mers, sketching, mutation rates}
}
Document
DOI: 10.4230/DagRep.4.2.17
The Pacemaker Challenge: Developing Certifiable Medical Devices (Dagstuhl Seminar 14062)

Authors: Dominique Méry, Bernhard Schätz, and Alan Wassyng

Published in: Dagstuhl Reports, Volume 4, Issue 2 (2014)

Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 14062 "The Pacemaker Challenge: Developing Certifiable Medical Devices". The aim of the seminar was to bring together leading researchers and industrial partners of this field; the seminary ended up with 24 participants from 8 countries: Canada, Denmark, France, The Unites States, Germany, United Kingdom, Brazil. Through a series of presentations, discussions, and working group meetings, the seminar attempted to get a general view of the field of medical devices and certification issues through the pacemaker challenge. The seminar brought together, on the one hand, researchers from the different notations and various tools. The main outcome of the seminar is the exchange of information between different groups and the project of a book.
Cite as

Dominique Méry, Bernhard Schätz, and Alan Wassyng. The Pacemaker Challenge: Developing Certifiable Medical Devices (Dagstuhl Seminar 14062). In Dagstuhl Reports, Volume 4, Issue 2, pp. 17-37, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)

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@Article{mery_et_al:DagRep.4.2.17,
  author =	{M\'{e}ry, Dominique and Sch\"{a}tz, Bernhard and Wassyng, Alan},
  title =	{{The Pacemaker Challenge: Developing Certifiable Medical Devices (Dagstuhl Seminar 14062)}},
  pages =	{17--37},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2014},
  volume =	{4},
  number =	{2},
  editor =	{M\'{e}ry, Dominique and Sch\"{a}tz, Bernhard and Wassyng, Alan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.4.2.17},
  URN =		{urn:nbn:de:0030-drops-45436},
  doi =		{10.4230/DagRep.4.2.17},
  annote =	{Keywords: Embedded systems, Real-time systems, Medical devices, Model-driven development, Software certification, Validation \& verification, Formal methods}
}
Document
DOI: 10.4230/DagRep.1.11.1
Science and Engineering of Cyber-Physical Systems (Dagstuhl Seminar 11441)

Authors: Holger Giese, Bernhard Rumpe, Bernhard Schätz, and Janos Sztipanovits

Published in: Dagstuhl Reports, Volume 1, Issue 11 (2012)

Abstract
Today, a new category of engineering systems is emerging that combines the physical with the computational in a holistic way: Cyber-physical systems (CPS). The key property of these systems is that functionality and salient system properties are emerging from an intensive interaction of physical and computational components. Traditional separation along engineering disciplines in the design of such systems leads to various quality, maintainability and evolutionary problems, and integrated theories and engineering techniques are urgently needed. The purpose of the seminar is to bring together researchers from the field, from both academia and industry to discuss the new scientific foundations and engineering principles for the vastly emerging field of CPS.
Cite as

Holger Giese, Bernhard Rumpe, Bernhard Schätz, and Janos Sztipanovits. Science and Engineering of Cyber-Physical Systems (Dagstuhl Seminar 11441). In Dagstuhl Reports, Volume 1, Issue 11, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@Article{giese_et_al:DagRep.1.11.1,
  author =	{Giese, Holger and Rumpe, Bernhard and Sch\"{a}tz, Bernhard and Sztipanovits, Janos},
  title =	{{Science and Engineering of Cyber-Physical Systems (Dagstuhl Seminar 11441)}},
  pages =	{1--22},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2012},
  volume =	{1},
  number =	{11},
  editor =	{Giese, Holger and Rumpe, Bernhard and Sch\"{a}tz, Bernhard and Sztipanovits, Janos},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.1.11.1},
  URN =		{urn:nbn:de:0030-drops-33752},
  doi =		{10.4230/DagRep.1.11.1},
  annote =	{Keywords: Embedded systems, real-time systems, control, composition, system integration, design automation, model-driven development, validation \& verification}
}
Document
DOI: 10.4230/DagSemProc.07451.1
07451 Abstracts Collection – Model-Based Engineering of Embedded Real-Time Systems

Authors: Holger Giese, Gabor Karsai, Edward Lee, Bernhard Rumpe, and Bernhard Schätz

Published in: Dagstuhl Seminar Proceedings, Volume 7451, Model-Based Engineering of Embedded Real-Time Systems (2007)

Abstract
From 04.11. to 09.11.2007, the Dagstuhl Seminar 07451 ``Model-Based Engineering of Embedded Real-Time Systems'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Holger Giese, Gabor Karsai, Edward Lee, Bernhard Rumpe, and Bernhard Schätz. 07451 Abstracts Collection – Model-Based Engineering of Embedded Real-Time Systems. In Model-Based Engineering of Embedded Real-Time Systems. Dagstuhl Seminar Proceedings, Volume 7451, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)

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@InProceedings{giese_et_al:DagSemProc.07451.1,
  author =	{Giese, Holger and Karsai, Gabor and Lee, Edward and Rumpe, Bernhard and Sch\"{a}tz, Bernhard},
  title =	{{07451 Abstracts Collection – Model-Based Engineering of Embedded Real-Time Systems}},
  booktitle =	{Model-Based Engineering of Embedded Real-Time Systems},
  pages =	{1--14},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2007},
  volume =	{7451},
  editor =	{Holger Giese and Gabor Karsai and Edward Lee and Bernhard Rumpe and Bernhard Sch\"{a}tz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.07451.1},
  URN =		{urn:nbn:de:0030-drops-12718},
  doi =		{10.4230/DagSemProc.07451.1},
  annote =	{Keywords: Models, model-based, MDD, embedded systems, real-time systems, validation \& verification, tool-support, domain-specific, languages}
}
Document
DOI: 10.4230/DagSemProc.07451.2
07451 Summary – Model-Based Engineering of Embedded Real-Time Systems

Authors: Holger Giese, Gabor Karsai, Edward Lee, Bernhard Rumpe, and Bernhard Schätz

Published in: Dagstuhl Seminar Proceedings, Volume 7451, Model-Based Engineering of Embedded Real-Time Systems (2007)

Abstract
Today, embedded software plays a central role in most advanced technical systems such as airplanes, cell phones, and cars, and has become the main driver for innovation. Development, evolution, configuration and maintenance of embedded and distributed software nowadays often are serious challenges as a drastic increase of the software complexity can be observed in practice. The application of model-based engineering technologies to embedded real-time systems seems to be a good candidate to tackle some of the resulting problems.
Cite as

Holger Giese, Gabor Karsai, Edward Lee, Bernhard Rumpe, and Bernhard Schätz. 07451 Summary – Model-Based Engineering of Embedded Real-Time Systems. In Model-Based Engineering of Embedded Real-Time Systems. Dagstuhl Seminar Proceedings, Volume 7451, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)

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@InProceedings{giese_et_al:DagSemProc.07451.2,
  author =	{Giese, Holger and Karsai, Gabor and Lee, Edward and Rumpe, Bernhard and Sch\"{a}tz, Bernhard},
  title =	{{07451 Summary – Model-Based Engineering of Embedded Real-Time Systems}},
  booktitle =	{Model-Based Engineering of Embedded Real-Time Systems},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2007},
  volume =	{7451},
  editor =	{Holger Giese and Gabor Karsai and Edward Lee and Bernhard Rumpe and Bernhard Sch\"{a}tz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.07451.2},
  URN =		{urn:nbn:de:0030-drops-12720},
  doi =		{10.4230/DagSemProc.07451.2},
  annote =	{Keywords: Models, model-based, MDD, embedded systems, real-time systems, validation \& verification, tool-support, domain-specific languages}
}
Document
DOI: 10.4230/DagSemProc.06351.4
A Model-Based Approach To Requirements Analysis

Authors: Bernhard Schätz, Eva Geisberger, and Johannes Grünbauer

Published in: Dagstuhl Seminar Proceedings, Volume 6351, Methods for Modelling Software Systems (MMOSS) (2007)

Abstract
A major task in designing embedded systems is the systematic elaboration of functional system requirements and their integration into the environment of the complete technical system. The main challenge is to handle the versatile tasks of coordinating a definition of behavior, which is appropriate to the problem. The problem- and design-specifications of the customer related product definition have to be adjusted with and integrated into the manifold requirements of the technical system design. Accordingly, the model-based requirements analysis and system-definition presented here defines a well-structured modeling approach, which systematically aids the goal-oriented formulation and adjustment of the different stakeholder-requirements with the aid of views onto the system and descriptive specification techniques. Thus it allows a clear specification of a consistent and complete system design. The central steps of this approach are implemented in a requirements management (RM) tool prototype called AutoRAID
Cite as

Bernhard Schätz, Eva Geisberger, and Johannes Grünbauer. A Model-Based Approach To Requirements Analysis. In Methods for Modelling Software Systems (MMOSS). Dagstuhl Seminar Proceedings, Volume 6351, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)

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@InProceedings{schatz_et_al:DagSemProc.06351.4,
  author =	{Sch\"{a}tz, Bernhard and Geisberger, Eva and Gr\"{u}nbauer, Johannes},
  title =	{{A Model-Based Approach To Requirements Analysis}},
  booktitle =	{Methods for Modelling Software Systems (MMOSS)},
  pages =	{1--9},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2007},
  volume =	{6351},
  editor =	{Ed Brinksma and David Harel and Angelika Mader and Perdita Stevens and Roel Wieringa},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.06351.4},
  URN =		{urn:nbn:de:0030-drops-8663},
  doi =		{10.4230/DagSemProc.06351.4},
  annote =	{Keywords: Requirements, model-based, tool support}
}
Document
DOI: 10.4230/DagSemProc.05022.1
Tagungsband Dagstuhl-Workshop MBEES: Modellbasierte Entwicklung eingebetteter Systeme 2005

Authors: Torsten Klein, Bernhard Rumpe, and Bernhard Schätz

Published in: Dagstuhl Seminar Proceedings, Volume 5022, Model-Based Development of Embedded Systems (2005)

Abstract
Die modellbasierte Entwicklung eingebetteter, softwarebasierter Systeme beruht auf der anwendungsorientierten Modellierung der zu realisierenden Systeme sowohl unter Nutzung von Standardsprachen, wie der UML und deren Elementen, wie Komponenten, Nachrichten, oder Zustände, als auch von domäenspezifischen Konzepten, wie etwa zeitbehafteten Ereignissen oder Signalen, synchronem oder asynchronem Datenfluss und Priorisierungs- und Unterbrechungskonzepten. Durch den Einsatz anwendungsorientierter statt codezentrierter Modelle können Aspekte der Implementierung (z.B. Bus- oder Task-Schedules, Implementierungstypen) abstrahiert werden, während besonders wichtige und kritische Aspekte explizit und frühzeitig modelliert werden (z.B. Zeit, Prioritäten oder Kommunikationsaspekte). Die Anwendung analytischer und generativer Verfahren auf diesen Modellen erlaubt die effiziente Entwicklung hochqualitativer Software.
Cite as

Torsten Klein, Bernhard Rumpe, and Bernhard Schätz. Tagungsband Dagstuhl-Workshop MBEES: Modellbasierte Entwicklung eingebetteter Systeme 2005. In Model-Based Development of Embedded Systems. Dagstuhl Seminar Proceedings, Volume 5022, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2005)

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@InProceedings{klein_et_al:DagSemProc.05022.1,
  author =	{Klein, Torsten and Rumpe, Bernhard and Sch\"{a}tz, Bernhard},
  title =	{{Tagungsband Dagstuhl-Workshop MBEES: Modellbasierte Entwicklung eingebetteter Systeme 2005}},
  booktitle =	{Model-Based Development of Embedded Systems},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2005},
  volume =	{5022},
  editor =	{Torsten Klein and Bernhard Rumpe and Bernhard Sch\"{a}tz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05022.1},
  URN =		{urn:nbn:de:0030-drops-312},
  doi =		{10.4230/DagSemProc.05022.1},
  annote =	{Keywords: Modellbasierte Entwicklung , eingebettete Systeme model-based development , embedded systems}
}
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