Dagstuhl Reports, Volume 9, Issue 8



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Complete Issue
Dagstuhl Reports, Volume 9, Issue 8, August 2019, Complete Issue

Abstract
Dagstuhl Reports, Volume 9, Issue 8, August 2019, Complete Issue

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Dagstuhl Reports, Volume 9, Issue 8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@Article{DagRep.9.8,
  title =	{{Dagstuhl Reports, Volume 9, Issue 8, August 2019, Complete Issue}},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2020},
  volume =	{9},
  number =	{8},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8},
  URN =		{urn:nbn:de:0030-drops-118392},
  doi =		{10.4230/DagRep.9.8},
  annote =	{Keywords: Dagstuhl Reports, Volume 9, Issue 8, August 2019, Complete Issue}
}
Document
Front Matter
Dagstuhl Reports, Table of Contents, Volume 9, Issue 8, 2019

Abstract
Dagstuhl Reports, Table of Contents, Volume 9, Issue 8, 2019

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Dagstuhl Reports, Volume 9, Issue 8, pp. i-ii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@Article{DagRep.9.8.i,
  title =	{{Dagstuhl Reports, Table of Contents, Volume 9, Issue 8, 2019}},
  pages =	{i--ii},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2020},
  volume =	{9},
  number =	{8},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8.i},
  URN =		{urn:nbn:de:0030-drops-118405},
  doi =		{10.4230/DagRep.9.8.i},
  annote =	{Keywords: Table of Contents, Frontmatter}
}
Document
Software Protection Decision Support and Evaluation Methodologies (Dagstuhl Seminar 19331)

Authors: Bjorn De Sutter, Christian Collberg, Mila Dalla Preda, and Brecht Wyseur


Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 19331 ``Software Protection Decision Support and Evaluation Methodologies''. The seminar is situated in the domain of software protection against so-called man-at-the-end attacks, in which attackers have white-box access to the software that embeds valuable assets with security requirements such as confidentiality and integrity. The attackers try to compromise those by reverse-engineering the software and by tampering with it. Within this domain, the seminar focused mainly on three aspects: 1) how to evaluate newly proposed protections and attackers thereon; 2) how to create an appropriate benchmark suite to be used in such evaluations; 3) how to build decision support to aid users of protection tool with the selection of appropriate protections. The major outcomes are a structure for a white-paper on software protection evaluation methodologies, with some concrete input collected on the basis of four case studies explored during the seminar, and a plan for creating a software protection benchmark suite.

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Bjorn De Sutter, Christian Collberg, Mila Dalla Preda, and Brecht Wyseur. Software Protection Decision Support and Evaluation Methodologies (Dagstuhl Seminar 19331). In Dagstuhl Reports, Volume 9, Issue 8, pp. 1-25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@Article{desutter_et_al:DagRep.9.8.1,
  author =	{De Sutter, Bjorn and Collberg, Christian and Dalla Preda, Mila and Wyseur, Brecht},
  title =	{{Software Protection Decision Support and Evaluation Methodologies (Dagstuhl Seminar 19331)}},
  pages =	{1--25},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{9},
  number =	{8},
  editor =	{De Sutter, Bjorn and Collberg, Christian and Dalla Preda, Mila and Wyseur, Brecht},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8.1},
  URN =		{urn:nbn:de:0030-drops-116825},
  doi =		{10.4230/DagRep.9.8.1},
  annote =	{Keywords: Benchmarks, Decision Support Systems, Evaluation Methodology, man-at-the-end attacks, metrics, predictive models, reverse engineering and tampering, software protection}
}
Document
Algorithms and Complexity for Continuous Problems (Dagstuhl Seminar 19341)

Authors: Dmitriy Bilyk, Aicke Hinrichs, Frances Y. Kuo, and Klaus Ritter


Abstract
From 18.08. to 23.08.2019, the Dagstuhl Seminar 19341 Algorithms and Complexity for Continuous Problems was held in the International Conference and Research Center (LZI), Schloss Dagstuhl. During the seminar, participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar can be found in this report. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.

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Dmitriy Bilyk, Aicke Hinrichs, Frances Y. Kuo, and Klaus Ritter. Algorithms and Complexity for Continuous Problems (Dagstuhl Seminar 19341). In Dagstuhl Reports, Volume 9, Issue 8, pp. 26-48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@Article{bilyk_et_al:DagRep.9.8.26,
  author =	{Bilyk, Dmitriy and Hinrichs, Aicke and Kuo, Frances Y. and Ritter, Klaus},
  title =	{{Algorithms and Complexity for Continuous Problems (Dagstuhl Seminar 19341)}},
  pages =	{26--48},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{9},
  number =	{8},
  editor =	{Bilyk, Dmitriy and Hinrichs, Aicke and Kuo, Frances Y. and Ritter, Klaus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8.26},
  URN =		{urn:nbn:de:0030-drops-116835},
  doi =		{10.4230/DagRep.9.8.26},
  annote =	{Keywords: applied harmonic analysis, computational stochastics, computing and complexity in infinite dimensions, discrepancy theory, tractability analysis}
}
Document
Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342)

Authors: Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, and Gabriele Varani


Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 19342 ``Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction''.

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Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, and Gabriele Varani. Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342). In Dagstuhl Reports, Volume 9, Issue 8, pp. 49-69, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@Article{backofen_et_al:DagRep.9.8.49,
  author =	{Backofen, Rolf and Mandel-Gutfreund, Yael and Ohler, Uwe and Varani, Gabriele},
  title =	{{Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342)}},
  pages =	{49--69},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{9},
  number =	{8},
  editor =	{Backofen, Rolf and Mandel-Gutfreund, Yael and Ohler, Uwe and Varani, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8.49},
  URN =		{urn:nbn:de:0030-drops-116843},
  doi =		{10.4230/DagRep.9.8.49},
  annote =	{Keywords: Machine learning, algorithms, genomics analysis, gene expression net- works, big data analysis, quantitative prediction, proteins, RNA, CLIP-Seq}
}
Document
Computational Proteomics (Dagstuhl Seminar 19351)

Authors: Nuno Bandeira and Lennart Martens


Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 19351 ``Computational Proteomics''. The Seminar was originally built around four topics, identification and quantification of DIA data; algorithms for the analysis of protein cross-linking data; creating an online view on complete, browsable proteomes from public data; and detecting interesting biology from proteomics findings. These four topics were led to four correpsonding breakout sessions, which in turn led to five offshoot breakout sessions. The abstracts presented here first describe the four topic introduction talks, as well as a fifth, cross-cutting topic talk on bringin proteomics data into clinical trials. These talk abstracts are followed by one abstract each per breakout session, documenting that breakout's discussion and outcomes. An Executive Summary is also provided, which details the overall seminar structure, the relationship between the breakout sessions and topics, and the most important conclusions for the four topic-derived breakouts.

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Nuno Bandeira and Lennart Martens. Computational Proteomics (Dagstuhl Seminar 19351). In Dagstuhl Reports, Volume 9, Issue 8, pp. 70-83, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@Article{bandeira_et_al:DagRep.9.8.70,
  author =	{Bandeira, Nuno and Martens, Lennart},
  title =	{{Computational Proteomics (Dagstuhl Seminar 19351)}},
  pages =	{70--83},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{9},
  number =	{8},
  editor =	{Bandeira, Nuno and Martens, Lennart},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8.70},
  URN =		{urn:nbn:de:0030-drops-117724},
  doi =		{10.4230/DagRep.9.8.70},
  annote =	{Keywords: computational biology, computational mass spectrometry, proteomics}
}
Document
Computation in Low-Dimensional Geometry and Topology (Dagstuhl Seminar 19352)

Authors: Maarten Löffler, Anna Lubiw, Saul Schleimer, and Erin Moriarty Wolf Chambers


Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 19352 ``Computation in Low-Dimensional Geometry and Topology''. The seminar participants investigated problems in: knot theory, trajectory analysis, algorithmic topology, computational geometry of curves, and graph drawing, with an emphasis on how low-dimensional structures change over time.

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Maarten Löffler, Anna Lubiw, Saul Schleimer, and Erin Moriarty Wolf Chambers. Computation in Low-Dimensional Geometry and Topology (Dagstuhl Seminar 19352). In Dagstuhl Reports, Volume 9, Issue 8, pp. 84-112, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@Article{loffler_et_al:DagRep.9.8.84,
  author =	{L\"{o}ffler, Maarten and Lubiw, Anna and Schleimer, Saul and Wolf Chambers, Erin Moriarty},
  title =	{{Computation in Low-Dimensional Geometry and Topology (Dagstuhl Seminar 19352)}},
  pages =	{84--112},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{9},
  number =	{8},
  editor =	{L\"{o}ffler, Maarten and Lubiw, Anna and Schleimer, Saul and Wolf Chambers, Erin Moriarty},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8.84},
  URN =		{urn:nbn:de:0030-drops-117734},
  doi =		{10.4230/DagRep.9.8.84},
  annote =	{Keywords: Geometric topology, Graph Drawing, Computational Geometry}
}

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