6 Search Results for "Meier, Michael"

Document
DOI: 10.4230/LIPIcs.SEA.2024.17
Barcode Selection and Layout Optimization in Spatial Transcriptomics

Authors: Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
An important special case of the quadratic assignment problem arises in the synthesis of DNA microarrays for high-resolution spatial transcriptomics. The task is to select a suitable subset from a set of barcodes, i. e. short DNA strings that serve as unique identifiers, and to assign the selected barcodes to positions on a two-dimensional array in such a way that a position-dependent cost function is minimized. A typical microarray with dimensions of 768×1024 requires 786,432 many barcodes to be placed, leading to very challenging large-scale combinatorial optimization problems. The general quadratic assignment problem is well-known for its hardness, both in theory and in practice. It turns out that this also holds for the special case of the barcode layout problem. We show that the problem is even hard to approximate: It is MaxSNP-hard. An ILP formulation theoretically allows the computation of optimal results, but it is only applicable for tiny instances. Therefore, we have developed layout constructing and improving heuristics with the aim of computing near-optimal solutions for instances of realistic size. These include a sorting-based algorithm, a greedy algorithm, 2-OPT-based local search and a genetic algorithm. To assess the quality of the results, we compare the generated solutions with the expected cost of a random layout and with lower bounds. A combination of the greedy algorithm and 2-OPT local search produces the most promising results in terms of both quality and runtime. Solutions to large-scale instances with arrays of dimension 768×1024 show a 37% reduction in cost over a random solution and can be computed in about 3 minutes. Since the universe of suitable barcodes is much larger than the number of barcodes needed, this can be exploited. Experiments with different surpluses of barcodes show that a significant improvement in layout quality can be achieved at the cost of a reasonable increase in runtime. Another interesting finding is that the restriction of the barcode design space by biochemical constraints is actually beneficial for the overall layout cost.
Cite as

Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann. Barcode Selection and Layout Optimization in Spatial Transcriptomics. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 17:1-17:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{jatzkowski_et_al:LIPIcs.SEA.2024.17,
  author =	{Jatzkowski, Frederik L. and Schmidt, Antonia and Mank, Robert and Sch\"{u}ler, Steffen and M\"{u}ller-Hannemann, Matthias},
  title =	{{Barcode Selection and Layout Optimization in Spatial Transcriptomics}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{17:1--17:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.17},
  URN =		{urn:nbn:de:0030-drops-203821},
  doi =		{10.4230/LIPIcs.SEA.2024.17},
  annote =	{Keywords: Spatial Transcriptomics, Array Layout, Optimization, Computational Complexity, GPU Computing, Integer Linear Programming, Metaheuristics}
}
Document
Survey
DOI: 10.4230/TGDK.2.1.3
Semantic Web: Past, Present, and Future

Authors: Ansgar Scherp, Gerd Groener, Petr Škoda, Katja Hose, and Maria-Esther Vidal

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
Ever since the vision was formulated, the Semantic Web has inspired many generations of innovations. Semantic technologies have been used to share vast amounts of information on the Web, enhance them with semantics to give them meaning, and enable inference and reasoning on them. Throughout the years, semantic technologies, and in particular knowledge graphs, have been used in search engines, data integration, enterprise settings, and machine learning. In this paper, we recap the classical concepts and foundations of the Semantic Web as well as modern and recent concepts and applications, building upon these foundations. The classical topics we cover include knowledge representation, creating and validating knowledge on the Web, reasoning and linking, and distributed querying. We enhance this classical view of the so-called "Semantic Web Layer Cake" with an update of recent concepts that include provenance, security and trust, as well as a discussion of practical impacts from industry-led contributions. We conclude with an outlook on the future directions of the Semantic Web. This is a living document. If you like to contribute, please contact the first author and visit: https://github.com/ascherp/semantic-web-primer
Cite as

Ansgar Scherp, Gerd Groener, Petr Škoda, Katja Hose, and Maria-Esther Vidal. Semantic Web: Past, Present, and Future. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 3:1-3:37, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{scherp_et_al:TGDK.2.1.3,
  author =	{Scherp, Ansgar and Groener, Gerd and \v{S}koda, Petr and Hose, Katja and Vidal, Maria-Esther},
  title =	{{Semantic Web: Past, Present, and Future}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:37},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.3},
  URN =		{urn:nbn:de:0030-drops-198607},
  doi =		{10.4230/TGDK.2.1.3},
  annote =	{Keywords: Linked Open Data, Semantic Web Graphs, Knowledge Graphs}
}
Document
DOI: 10.4230/LIPIcs.ESA.2019.46
Obviously Strategyproof Mechanisms for Machine Scheduling

Authors: Diodato Ferraioli, Adrian Meier, Paolo Penna, and Carmine Ventre

Published in: LIPIcs, Volume 144, 27th Annual European Symposium on Algorithms (ESA 2019)

Abstract
Catering to the incentives of people with limited rationality is a challenging research direction that requires novel paradigms to design mechanisms and approximation algorithms. Obviously strategyproof (OSP) mechanisms have recently emerged as the concept of interest to this research agenda. However, the majority of the literature in the area has either highlighted the shortcomings of OSP or focused on the "right" definition rather than on the construction of these mechanisms. We here give the first set of tight results on the approximation guarantee of OSP mechanisms for scheduling related machines. By extending the well-known cycle monotonicity technique, we are able to concentrate on the algorithmic component of OSP mechanisms and provide some novel paradigms for their design.
Cite as

Diodato Ferraioli, Adrian Meier, Paolo Penna, and Carmine Ventre. Obviously Strategyproof Mechanisms for Machine Scheduling. In 27th Annual European Symposium on Algorithms (ESA 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 144, pp. 46:1-46:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{ferraioli_et_al:LIPIcs.ESA.2019.46,
  author =	{Ferraioli, Diodato and Meier, Adrian and Penna, Paolo and Ventre, Carmine},
  title =	{{Obviously Strategyproof Mechanisms for Machine Scheduling}},
  booktitle =	{27th Annual European Symposium on Algorithms (ESA 2019)},
  pages =	{46:1--46:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-124-5},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{144},
  editor =	{Bender, Michael A. and Svensson, Ola and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2019.46},
  URN =		{urn:nbn:de:0030-drops-111677},
  doi =		{10.4230/LIPIcs.ESA.2019.46},
  annote =	{Keywords: Bounded Rationality, Extensive-form Mechanisms, Approximate Mechanism Design}
}
Document
DOI: 10.4230/DagSemProc.10061.5
Proof Complexity of Propositional Default Logic

Authors: Olaf Beyersdorff, Arne Meier, Sebastian Müller, Michael Thomas, and Heribert Vollmer

Published in: Dagstuhl Seminar Proceedings, Volume 10061, Circuits, Logic, and Games (2010)

Abstract
Default logic is one of the most popular and successful formalisms for non-monotonic reasoning. In 2002, Bonatti and Olivetti introduced several sequent calculi for credulous and skeptical reasoning in propositional default logic. In this paper we examine these calculi from a proof-complexity perspective. In particular, we show that the calculus for credulous reasoning obeys almost the same bounds on the proof size as Gentzen's system LK. Hence proving lower bounds for credulous reasoning will be as hard as proving lower bounds for LK. On the other hand, we show an exponential lower bound to the proof size in Bonatti and Olivetti's enhanced calculus for skeptical default reasoning.
Cite as

Olaf Beyersdorff, Arne Meier, Sebastian Müller, Michael Thomas, and Heribert Vollmer. Proof Complexity of Propositional Default Logic. In Circuits, Logic, and Games. Dagstuhl Seminar Proceedings, Volume 10061, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{beyersdorff_et_al:DagSemProc.10061.5,
  author =	{Beyersdorff, Olaf and Meier, Arne and M\"{u}ller, Sebastian and Thomas, Michael and Vollmer, Heribert},
  title =	{{Proof Complexity of Propositional Default Logic}},
  booktitle =	{Circuits, Logic, and Games},
  pages =	{1--14},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10061},
  editor =	{Benjamin Rossman and Thomas Schwentick and Denis Th\'{e}rien and Heribert Vollmer},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10061.5},
  URN =		{urn:nbn:de:0030-drops-25261},
  doi =		{10.4230/DagSemProc.10061.5},
  annote =	{Keywords: Proof complexity, default logic, sequent calculus}
}
Document
DOI: 10.4230/DagSemProc.10061.6
The Complexity of Reasoning for Fragments of Autoepistemic Logic

Authors: Nadia Creignou, Arne Meier, Michael Thomas, and Heribert Vollmer

Published in: Dagstuhl Seminar Proceedings, Volume 10061, Circuits, Logic, and Games (2010)

Abstract
Autoepistemic logic extends propositional logic by the modal operator L. A formula that is preceded by an L is said to be "believed". The logic was introduced by Moore 1985 for modeling an ideally rational agent's behavior and reasoning about his own beliefs. In this paper we analyze all Boolean fragments of autoepistemic logic with respect to the computational complexity of the three most common decision problems expansion existence, brave reasoning and cautious reasoning. As a second contribution we classify the computational complexity of counting the number of stable expansions of a given knowledge base. To the best of our knowledge this is the first paper analyzing the counting problem for autoepistemic logic.
Cite as

Nadia Creignou, Arne Meier, Michael Thomas, and Heribert Vollmer. The Complexity of Reasoning for Fragments of Autoepistemic Logic. In Circuits, Logic, and Games. Dagstuhl Seminar Proceedings, Volume 10061, pp. 1-10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{creignou_et_al:DagSemProc.10061.6,
  author =	{Creignou, Nadia and Meier, Arne and Thomas, Michael and Vollmer, Heribert},
  title =	{{The Complexity of Reasoning for Fragments of Autoepistemic Logic}},
  booktitle =	{Circuits, Logic, and Games},
  pages =	{1--10},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10061},
  editor =	{Benjamin Rossman and Thomas Schwentick and Denis Th\'{e}rien and Heribert Vollmer},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10061.6},
  URN =		{urn:nbn:de:0030-drops-25234},
  doi =		{10.4230/DagSemProc.10061.6},
  annote =	{Keywords: Autoepistemic logic, computational complexity, nonmonotonic reasoning, Post's lattice}
}
Document
DOI: 10.4230/DagSemProc.08102.2
2. 08102 Working Group – Early Warning Systems

Authors: Joachim Biskup, Bernhard Hämmerli, Michael Meier, Sebastian Schmerl, Jens Tölle, and Michael Vogel

Published in: Dagstuhl Seminar Proceedings, Volume 8102, Perspectives Workshop: Network Attack Detection and Defense (2008)

Abstract
Early Warning Systems aim at detecting unclassified but potentially harmful sys-tem behavior based on preliminary indications and are complementary to Intrusion Detection Systems. Both kinds of systems try to detect, identify and react before pos-sible damage occurs and contribute to an integrated and aggregated situation report (big picture). A particular emphasis of Early Warning Systems is to establish hypotheses and predictions as well as to generate advises in still not completely understood situations. Thus the term early has two meanings, a) to start early in time aiming to minimize damage, and b) to process uncertain and incomplete information.
Cite as

Joachim Biskup, Bernhard Hämmerli, Michael Meier, Sebastian Schmerl, Jens Tölle, and Michael Vogel. 2. 08102 Working Group – Early Warning Systems. In Perspectives Workshop: Network Attack Detection and Defense. Dagstuhl Seminar Proceedings, Volume 8102, pp. 1-2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{biskup_et_al:DagSemProc.08102.2,
  author =	{Biskup, Joachim and H\"{a}mmerli, Bernhard and Meier, Michael and Schmerl, Sebastian and T\"{o}lle, Jens and Vogel, Michael},
  title =	{{2. 08102 Working Group – Early Warning Systems}},
  booktitle =	{Perspectives Workshop: Network Attack Detection and Defense},
  pages =	{1--2},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8102},
  editor =	{Georg Carle and Falko Dressler and Richard A. Kemmerer and Hartmut K\"{o}nig and Christopher Kruegel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08102.2},
  URN =		{urn:nbn:de:0030-drops-14936},
  doi =		{10.4230/DagSemProc.08102.2},
  annote =	{Keywords: Intrusion detection and prevention, attack response and countermeasures, reactive security, automated security, survivability and self-protection, ma network monitoring, flow analysis, denial of service detection and response, event correlation}
}
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