22 Search Results for "Will, Sebastian"

Document
Invited Talk
DOI: 10.4230/LIPIcs.CSL.2024.4
Approximating Fixpoints of Approximated Functions (Invited Talk)

Authors: Barbara König

Published in: LIPIcs, Volume 288, 32nd EACSL Annual Conference on Computer Science Logic (CSL 2024)

Abstract
There is a large body of work on fixpoint theorems, guaranteeing the existence of fixpoints for certain functions and providing methods for computing them. This includes for instance Banachs’s fixpoint theorem, the well-known result by Knaster-Tarski that is frequently employed in computer science and Kleene iteration. It is less clear how to compute fixpoints if the function whose (least) fixpoint we are interested in is not known exactly, but can only be obtained by a sequence of subsequently better approximations. This scenario occurs for instance in the context of reinforcement learning, where the probabilities of a Markov decision process (MDP) - for which one wants to learn a strategy - are unknown and can only be sampled. There are several solutions to this problem where the fixpoint computation (for determining the value vector and the optimal strategy) and the exploration of the model are interleaved. However, these methods work only well for discounted MDPs, that is in the contractive setting, but not for general MDPs, that is for non-expansive functions. After describing and motivating the problem, we will in particular concentrate on the non-expansive case. There are many interesting systems who value vectors can be obtained by determining the fixpoints of non-expansive functions. Other than contractive functions, they do not guarantee uniqueness of the fixpoint, making it more difficult to approximate the least fixpoint by methods other than Kleene iteration. And also Kleene iteration fails if the function under consideration is only approximated. We hence describe a dampened Mann iteration scheme for (higher-dimensional) functions on the reals that converges to the least fixpoint from everywhere. This scheme can also be adapted to functions that are approximated, under certain conditions. We will in particular study the case of MDPs and consider a related problem that arises when performing model-checking for quantitative mu-calculi, which involves the computation of nested fixpoints. This is joint work with Paolo Baldan, Sebastian Gurke, Tommaso Padoan and Florian Wittbold.
Cite as

Barbara König. Approximating Fixpoints of Approximated Functions (Invited Talk). In 32nd EACSL Annual Conference on Computer Science Logic (CSL 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 288, p. 4:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{konig:LIPIcs.CSL.2024.4,
  author =	{K\"{o}nig, Barbara},
  title =	{{Approximating Fixpoints of Approximated Functions}},
  booktitle =	{32nd EACSL Annual Conference on Computer Science Logic (CSL 2024)},
  pages =	{4:1--4:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-310-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{288},
  editor =	{Murano, Aniello and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2024.4},
  URN =		{urn:nbn:de:0030-drops-196469},
  doi =		{10.4230/LIPIcs.CSL.2024.4},
  annote =	{Keywords: fixpoints, approximation, Markov decision processes}
}
Document
DOI: 10.4230/LIPIcs.WABI.2023.19
SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles

Authors: Mateo Gray, Sebastian Will, and Hosna Jabbari

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract
Motivation. Computational RNA secondary structure prediction by free energy minimization is indispensable for analyzing structural RNAs and their interactions. These methods find the structure with the minimum free energy (MFE) among exponentially many possible structures and have a restrictive time and space complexity (O(n³) time and O(n²) space for pseudoknot-free structures) for longer RNA sequences. Furthermore, accurate free energy calculations, including dangles contributions can be difficult and costly to implement, particularly when optimizing for time and space requirements. Results. Here we introduce a fast and efficient sparsified MFE pseudoknot-free structure prediction algorithm, SparseRNAFolD, that utilizes an accurate energy model that accounts for dangle contributions. While the sparsification technique was previously employed to improve the time and space complexity of a pseudoknot-free structure prediction method with a realistic energy model, SparseMFEFold, it was not extended to include dangle contributions due to the complexity of computation. This may come at the cost of prediction accuracy. In this work, we compare three different sparsified implementations for dangles contributions and provide pros and cons of each method. As well, we compare our algorithm to LinearFold, a linear time and space algorithm, where we find that in practice, SparseRNAFolD has lower memory consumption across all lengths of sequence and a faster time for lengths up to 1000 bases. Conclusion. Our SparseRNAFolD algorithm is an MFE-based algorithm that guarantees optimality of result and employs the most general energy model, including dangle contributions. We provide a basis for applying dangles to sparsified recursion in a pseudoknot-free model that has the ability to be extended to pseudoknots.
Cite as

Mateo Gray, Sebastian Will, and Hosna Jabbari. SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 19:1-19:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{gray_et_al:LIPIcs.WABI.2023.19,
  author =	{Gray, Mateo and Will, Sebastian and Jabbari, Hosna},
  title =	{{SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{19:1--19:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.19},
  URN =		{urn:nbn:de:0030-drops-186454},
  doi =		{10.4230/LIPIcs.WABI.2023.19},
  annote =	{Keywords: RNA, MFE, Secondary Structure Prediction, Dangle, Sparsification, Space Complexity, Time Complexity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.7
Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots

Authors: Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, and Yann Ponty

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
Despite being a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, RNA secondary structure prediction remains challenging whenever pseudoknots come into play. To circumvent the NP-hardness of energy minimization in realistic energy models, specialized algorithms have been proposed for restricted conformation classes that capture the most frequently observed configurations. While these methods rely on hand-crafted DP schemes, we generalize and fully automatize the design of DP pseudoknot prediction algorithms. We formalize the problem of designing DP algorithms for an (infinite) class of conformations, modeled by (a finite number of) fatgraphs, and automatically build DP schemes minimizing their algorithmic complexity. We propose an algorithm for the problem, based on the tree-decomposition of a well-chosen representative structure, which we simplify and reinterpret as a DP scheme. The algorithm is fixed-parameter tractable for the tree-width tw of the fatgraph, and its output represents a 𝒪(n^{tw+1}) algorithm for predicting the MFE folding of an RNA of length n. Our general framework supports general energy models, partition function computations, recursive substructures and partial folding, and could pave the way for algebraic dynamic programming beyond the context-free case.
Cite as

Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, and Yann Ponty. Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 7:1-7:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{marchand_et_al:LIPIcs.WABI.2022.7,
  author =	{Marchand, Bertrand and Will, Sebastian and Berkemer, Sarah J. and Bulteau, Laurent and Ponty, Yann},
  title =	{{Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{7:1--7:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.7},
  URN =		{urn:nbn:de:0030-drops-170414},
  doi =		{10.4230/LIPIcs.WABI.2022.7},
  annote =	{Keywords: RNA folding, treewidth, dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2022.29
Local Problems on Trees from the Perspectives of Distributed Algorithms, Finitary Factors, and Descriptive Combinatorics

Authors: Sebastian Brandt, Yi-Jun Chang, Jan Grebík, Christoph Grunau, Václav Rozhoň, and Zoltán Vidnyánszky

Published in: LIPIcs, Volume 215, 13th Innovations in Theoretical Computer Science Conference (ITCS 2022)

Abstract
We study connections between three different fields: distributed local algorithms, finitary factors of iid processes, and descriptive combinatorics. We focus on two central questions: Can we apply techniques from one of the areas to obtain results in another? Can we show that complexity classes coming from different areas contain precisely the same problems? We give an affirmative answer to both questions in the context of local problems on regular trees: 1) We extend the Borel determinacy technique of Marks [Marks - J. Am. Math. Soc. 2016] coming from descriptive combinatorics and adapt it to the area of distributed computing, thereby obtaining a more generally applicable lower bound technique in descriptive combinatorics and an entirely new lower bound technique for distributed algorithms. Using our new technique, we prove deterministic distributed Ω(log n)-round lower bounds for problems from a natural class of homomorphism problems. Interestingly, these lower bounds seem beyond the current reach of the powerful round elimination technique [Brandt - PODC 2019] responsible for all substantial locality lower bounds of the last years. Our key technical ingredient is a novel ID graph technique that we expect to be of independent interest; in fact, it has already played an important role in a new lower bound for the Lovász local lemma in the Local Computation Algorithms model from sequential computing [Brandt, Grunau, Rozhoň - PODC 2021]. 2) We prove that a local problem admits a Baire measurable coloring if and only if it admits a local algorithm with local complexity O(log n), extending the classification of Baire measurable colorings of Bernshteyn [Bernshteyn - personal communication]. A key ingredient of the proof is a new and simple characterization of local problems that can be solved in O(log n) rounds. We complement this result by showing separations between complexity classes from distributed computing, finitary factors, and descriptive combinatorics. Most notably, the class of problems that allow a distributed algorithm with sublogarithmic randomized local complexity is incomparable with the class of problems with a Borel solution. We hope that our treatment will help to view all three perspectives as part of a common theory of locality, in which we follow the insightful paper of [Bernshteyn - arXiv 2004.04905].
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Sebastian Brandt, Yi-Jun Chang, Jan Grebík, Christoph Grunau, Václav Rozhoň, and Zoltán Vidnyánszky. Local Problems on Trees from the Perspectives of Distributed Algorithms, Finitary Factors, and Descriptive Combinatorics. In 13th Innovations in Theoretical Computer Science Conference (ITCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 215, pp. 29:1-29:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{brandt_et_al:LIPIcs.ITCS.2022.29,
  author =	{Brandt, Sebastian and Chang, Yi-Jun and Greb{\'\i}k, Jan and Grunau, Christoph and Rozho\v{n}, V\'{a}clav and Vidny\'{a}nszky, Zolt\'{a}n},
  title =	{{Local Problems on Trees from the Perspectives of Distributed Algorithms, Finitary Factors, and Descriptive Combinatorics}},
  booktitle =	{13th Innovations in Theoretical Computer Science Conference (ITCS 2022)},
  pages =	{29:1--29:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-217-4},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{215},
  editor =	{Braverman, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2022.29},
  URN =		{urn:nbn:de:0030-drops-156259},
  doi =		{10.4230/LIPIcs.ITCS.2022.29},
  annote =	{Keywords: Distributed Algorithms, Descriptive Combinatorics}
}
Document
DOI: 10.4230/OASIcs.ASD.2020.3
Adaptable Demonstrator Platform for the Simulation of Distributed Agent-Based Automotive Systems

Authors: Philipp Weiss, Sebastian Nagel, Andreas Weichslgartner, and Sebastian Steinhorst

Published in: OASIcs, Volume 79, 2nd International Workshop on Autonomous Systems Design (ASD 2020)

Abstract
Future autonomous vehicles will no longer have a driver as a fallback solution in case of critical failure scenarios. However, it is costly to add hardware redundancy to achieve a fail-operational behaviour. Here, graceful degradation can be used by repurposing the allocated resources of non-critical applications for safety-critical applications. The degradation problem can be solved as a part of an application mapping problem. As future automotive software will be highly customizable to meet customers' demands, the mapping problem has to be solved for each individual configuration and the architecture has to be adaptable to frequent software changes. Thus, the mapping problem has to be solved at run-time as part of the software platform. In this paper we present an adaptable demonstrator platform consisting of a distributed simulation environment to evaluate such approaches. The platform can be easily configured to evaluate different hardware architectures. We discuss the advantages and limitations of this platform and present an exemplary demonstrator configuration running an agent-based graceful degradation approach.
Cite as

Philipp Weiss, Sebastian Nagel, Andreas Weichslgartner, and Sebastian Steinhorst. Adaptable Demonstrator Platform for the Simulation of Distributed Agent-Based Automotive Systems. In 2nd International Workshop on Autonomous Systems Design (ASD 2020). Open Access Series in Informatics (OASIcs), Volume 79, pp. 3:1-3:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{weiss_et_al:OASIcs.ASD.2020.3,
  author =	{Weiss, Philipp and Nagel, Sebastian and Weichslgartner, Andreas and Steinhorst, Sebastian},
  title =	{{Adaptable Demonstrator Platform for the Simulation of Distributed Agent-Based Automotive Systems}},
  booktitle =	{2nd International Workshop on Autonomous Systems Design (ASD 2020)},
  pages =	{3:1--3:6},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-141-2},
  ISSN =	{2190-6807},
  year =	{2020},
  volume =	{79},
  editor =	{Steinhorst, Sebastian and Deshmukh, Jyotirmoy V.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.ASD.2020.3},
  URN =		{urn:nbn:de:0030-drops-125974},
  doi =		{10.4230/OASIcs.ASD.2020.3},
  annote =	{Keywords: fail-operational, graceful degradation, agent-based mapping}
}
Document
Extended Abstract
DOI: 10.4230/OASIcs.ASD.2020.5
BreachFlows: Simulation-Based Design with Formal Requirements for Industrial CPS (Extended Abstract)

Authors: Alexandre Donzé

Published in: OASIcs, Volume 79, 2nd International Workshop on Autonomous Systems Design (ASD 2020)

Abstract
Cyber-Physical Systems (CPS) are computerized systems in interaction with their physical environment. They are notoriously difficult to design because their programming must take into account these interactions which are, by nature, a mix of discrete, continuous and real-time behaviors. As a consequence, formal verification is impossible but for the simplest CPS instances, and testing is used extensively but with little to no guarantee. Falsification is a type of approach that goes beyond testing in the direction of a more formal methodology. It has emerged in the recent years with some success. The idea is to generate input signals for the system, monitor the output for some requirements of interest, and use black-box optimization to guide the generation toward an input that will falsify, i.e., violate, those requirements. Breach is an open source Matlab/Simulink toolbox that implements this approach in a modular and extensible way. It is used in academia as well as for industrial applications, in particular in the automotive domain. Based on experience acquired during close collaborations between academia and industry, Decyphir is developing BreachFlows, and extension/front-end for Breach which implements features that are required or useful in an industrial context.
Cite as

Alexandre Donzé. BreachFlows: Simulation-Based Design with Formal Requirements for Industrial CPS (Extended Abstract). In 2nd International Workshop on Autonomous Systems Design (ASD 2020). Open Access Series in Informatics (OASIcs), Volume 79, pp. 5:1-5:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{donze:OASIcs.ASD.2020.5,
  author =	{Donz\'{e}, Alexandre},
  title =	{{BreachFlows: Simulation-Based Design with Formal Requirements for Industrial CPS}},
  booktitle =	{2nd International Workshop on Autonomous Systems Design (ASD 2020)},
  pages =	{5:1--5:5},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-141-2},
  ISSN =	{2190-6807},
  year =	{2020},
  volume =	{79},
  editor =	{Steinhorst, Sebastian and Deshmukh, Jyotirmoy V.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.ASD.2020.5},
  URN =		{urn:nbn:de:0030-drops-125995},
  doi =		{10.4230/OASIcs.ASD.2020.5},
  annote =	{Keywords: Cyber Physical Systems, Verification and Validation, Test, Model-Based Design, Formal Requirements, Falsification}
}
Document
DOI: 10.4230/LIPIcs.WABI.2019.14
Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs

Authors: Milad Miladi, Martin Raden, Sebastian Will, and Rolf Backofen

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)

Abstract
Motivation: Simultaneous alignment and folding (SA&F) of RNAs is the indispensable gold standard for inferring the structure of non-coding RNAs and their general analysis. The original algorithm, proposed by Sankoff, solves the theoretical problem exactly with a complexity of O(n^6) in the full energy model. Over the last two decades, several variants and improvements of the Sankoff algorithm have been proposed to reduce its extreme complexity by proposing simplified energy models or imposing restrictions on the predicted alignments. Results: Here we introduce a novel variant of Sankoff’s algorithm that reconciles the simplifications of PMcomp, namely moving from the full energy model to a simpler base pair-based model, with the accuracy of the loop-based full energy model. Instead of estimating pseudo-energies from unconditional base pair probabilities, our model calculates energies from conditional base pair probabilities that allow to accurately capture structure probabilities, which obey a conditional dependency. Supporting modifications with surgical precision, this model gives rise to the fast and highly accurate novel algorithm Pankov (Probabilistic Sankoff-like simultaneous alignment and folding of RNAs inspired by Markov chains). Pankov benefits from the speed-up of excluding unreliable base-pairing without compromising the loop-based free energy model of the Sankoff’s algorithm. We show that Pankov outperforms its predecessors LocARNA and SPARSE in folding quality and is faster than LocARNA. Pankov is developed as a branch of the LocARNA package and available at https://github.com/mmiladi/Pankov.
Cite as

Milad Miladi, Martin Raden, Sebastian Will, and Rolf Backofen. Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 14:1-14:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{miladi_et_al:LIPIcs.WABI.2019.14,
  author =	{Miladi, Milad and Raden, Martin and Will, Sebastian and Backofen, Rolf},
  title =	{{Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{14:1--14:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.14},
  URN =		{urn:nbn:de:0030-drops-110446},
  doi =		{10.4230/LIPIcs.WABI.2019.14},
  annote =	{Keywords: RNA secondary structure, Structural bioinformatics, Alignment, Algorithms}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2018.5
A Measurement-Based Model for Parallel Real-Time Tasks

Authors: Kunal Agrawal and Sanjoy Baruah

Published in: LIPIcs, Volume 106, 30th Euromicro Conference on Real-Time Systems (ECRTS 2018)

Abstract
Under the federated paradigm of multiprocessor scheduling, a set of processors is reserved for the exclusive use of each real-time task. If tasks are characterized very conservatively (as is typical in safety-critical systems), it is likely that most invocations of the task will have computational demand far below the worst-case characterization, and could have been scheduled correctly upon far fewer processors than were assigned to it assuming the worst-case characterization of its run-time behavior. Provided we could safely determine during run-time when all the processors are going to be needed, for the rest of the time the unneeded processors could be idled in low-energy "sleep" mode, or used for executing non-real time work in the background. In this paper we propose a model for representing parallelizable real-time tasks in a manner that permits us to do so. Our model does not require us to have fine-grained knowledge of the internal structure of the code represented by the task; rather, it characterizes each task by a few parameters that are obtained by repeatedly executing the code under different conditions and measuring the run-times.
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Kunal Agrawal and Sanjoy Baruah. A Measurement-Based Model for Parallel Real-Time Tasks. In 30th Euromicro Conference on Real-Time Systems (ECRTS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 106, pp. 5:1-5:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{agrawal_et_al:LIPIcs.ECRTS.2018.5,
  author =	{Agrawal, Kunal and Baruah, Sanjoy},
  title =	{{A Measurement-Based Model for Parallel Real-Time Tasks}},
  booktitle =	{30th Euromicro Conference on Real-Time Systems (ECRTS 2018)},
  pages =	{5:1--5:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-075-0},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{106},
  editor =	{Altmeyer, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2018.5},
  URN =		{urn:nbn:de:0030-drops-89999},
  doi =		{10.4230/LIPIcs.ECRTS.2018.5},
  annote =	{Keywords: multiprocessor federated scheduling, parallel tasks, work and span, mixed criticality}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2018.13
Virtual Timing Isolation for Mixed-Criticality Systems

Authors: Johannes Freitag, Sascha Uhrig, and Theo Ungerer

Published in: LIPIcs, Volume 106, 30th Euromicro Conference on Real-Time Systems (ECRTS 2018)

Abstract
Commercial of the shelf multicore processors suffer from timing interferences between cores which complicates applying them in hard real-time systems like avionic applications. This paper proposes a virtual timing isolation of one main application running on one core from all other cores. The proposed technique is based on hardware external to the multicore processor and completely transparent to the main application i.e., no modifications of the software including the operating system are necessary. The basic idea is to apply a single-core execution based Worst Case Execution Time analysis and to accept a predefined slowdown during multicore execution. If the slowdown exceeds the acceptable bounds, interferences will be reduced by controlling the behavior of low-critical cores to keep the main application's progress inside the given bounds. Apart from the main goal of isolating the timing of the critical application a subgoal is also to efficiently use the other cores. For that purpose, three different mechanisms for controlling the non-critical cores are compared regarding efficient usage of the complete processor. Measuring the progress of the main application is performed by tracking the application's Fingerprint. This technology quantifies online any slowdown of execution compared to a given baseline (single-core execution). Several countermeasures to compensate unacceptable slowdowns are proposed and evaluated in this paper, together with an accuracy evaluation of the Fingerprinting. Our evaluations using the TACLeBench benchmark suite show that we can meet a given acceptable timing bound of 4 percent slowdown with a resulting real slowdown of only 3.27 percent in case of a pulse width modulated control and of 4.44 percent in the case of a frequency scaling control.
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Johannes Freitag, Sascha Uhrig, and Theo Ungerer. Virtual Timing Isolation for Mixed-Criticality Systems. In 30th Euromicro Conference on Real-Time Systems (ECRTS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 106, pp. 13:1-13:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{freitag_et_al:LIPIcs.ECRTS.2018.13,
  author =	{Freitag, Johannes and Uhrig, Sascha and Ungerer, Theo},
  title =	{{Virtual Timing Isolation for Mixed-Criticality Systems}},
  booktitle =	{30th Euromicro Conference on Real-Time Systems (ECRTS 2018)},
  pages =	{13:1--13:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-075-0},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{106},
  editor =	{Altmeyer, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2018.13},
  URN =		{urn:nbn:de:0030-drops-89904},
  doi =		{10.4230/LIPIcs.ECRTS.2018.13},
  annote =	{Keywords: multicore, hard real-time systems, timing isolation, safety-critical systems, mixed-criticality design and assurance}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2018.17
Camera Networks Dimensioning and Scheduling with Quasi Worst-Case Transmission Time

Authors: Viktor Edpalm, Alexandre Martins, Karl-Erik Årzén, and Martina Maggio

Published in: LIPIcs, Volume 106, 30th Euromicro Conference on Real-Time Systems (ECRTS 2018)

Abstract
This paper describes a method to compute frame size estimates to be used in quasi Worst-Case Transmission Times (qWCTT) for cameras that transmit frames over IP-based communication networks. The precise determination of qWCTT allows us to model the network access scheduling problem as a multiframe problem and to re-use theoretical results for network scheduling. The paper presents a set of experiments, conducted in an industrial testbed, that validate the qWCTT estimation. We believe that a more precise estimation will lead to savings for network infrastructure and to better network utilization.
Cite as

Viktor Edpalm, Alexandre Martins, Karl-Erik Årzén, and Martina Maggio. Camera Networks Dimensioning and Scheduling with Quasi Worst-Case Transmission Time. In 30th Euromicro Conference on Real-Time Systems (ECRTS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 106, pp. 17:1-17:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{edpalm_et_al:LIPIcs.ECRTS.2018.17,
  author =	{Edpalm, Viktor and Martins, Alexandre and \r{A}rz\'{e}n, Karl-Erik and Maggio, Martina},
  title =	{{Camera Networks Dimensioning and Scheduling with Quasi Worst-Case Transmission Time}},
  booktitle =	{30th Euromicro Conference on Real-Time Systems (ECRTS 2018)},
  pages =	{17:1--17:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-075-0},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{106},
  editor =	{Altmeyer, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2018.17},
  URN =		{urn:nbn:de:0030-drops-89869},
  doi =		{10.4230/LIPIcs.ECRTS.2018.17},
  annote =	{Keywords: worst-case transmission time, H.264, bandwidth estimation, video compression, network access scheduling, multiframe model, camera network}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2018.25
Using Lock Servers to Scale Real-Time Locking Protocols: Chasing Ever-Increasing Core Counts

Authors: Catherine E. Nemitz, Tanya Amert, and James H. Anderson

Published in: LIPIcs, Volume 106, 30th Euromicro Conference on Real-Time Systems (ECRTS 2018)

Abstract
During the past decade, parallelism-related issues have been at the forefront of real-time systems research due to the advent of multicore technologies. In the coming years, such issues will loom ever larger due to increasing core counts. Having more cores means a greater potential exists for platform capacity loss when the available parallelism cannot be fully exploited. In this paper, such capacity loss is considered in the context of real-time locking protocols. In this context, lock nesting becomes a key concern as it can result in transitive blocking chains that force tasks to execute sequentially unnecessarily. Such chains can be quite long on a larger machine. Contention-sensitive real-time locking protocols have been proposed as a means of "breaking" transitive blocking chains, but such protocols tend to have high overhead due to more complicated lock/unlock logic. To ease such overhead, the usage of lock servers is considered herein. In particular, four specific lock-server paradigms are proposed and many nuances concerning their deployment are explored. Experiments are presented that show that, by executing cache hot, lock servers can enable reductions in lock/unlock overhead of up to 86%. Such reductions make contention-sensitive protocols a viable approach in practice.
Cite as

Catherine E. Nemitz, Tanya Amert, and James H. Anderson. Using Lock Servers to Scale Real-Time Locking Protocols: Chasing Ever-Increasing Core Counts. In 30th Euromicro Conference on Real-Time Systems (ECRTS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 106, pp. 25:1-25:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{nemitz_et_al:LIPIcs.ECRTS.2018.25,
  author =	{Nemitz, Catherine E. and Amert, Tanya and Anderson, James H.},
  title =	{{Using Lock Servers to Scale Real-Time Locking Protocols: Chasing Ever-Increasing Core Counts}},
  booktitle =	{30th Euromicro Conference on Real-Time Systems (ECRTS 2018)},
  pages =	{25:1--25:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-075-0},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{106},
  editor =	{Altmeyer, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2018.25},
  URN =		{urn:nbn:de:0030-drops-89789},
  doi =		{10.4230/LIPIcs.ECRTS.2018.25},
  annote =	{Keywords: multiprocess locking protocols, nested locks, priority-inversion blocking, reader/writer locks, real-time locking protocols}
}
Document
DOI: 10.4230/DagMan.7.1.30
QoE Vadis? (Dagstuhl Perspectives Workshop 16472)

Authors: Markus Fiedler, Sebastian Möller, Peter Reichl, and Min Xie

Published in: Dagstuhl Manifestos, Volume 7, Issue 1 (2018)

Abstract
The goal of the Dagstuhl Perspectives Workshop 16472 has been to discuss and outline the strategic evolution of Quality of Experience as a key topic for future Internet research. The resulting manifesto, which is presented here, reviews the state of the art in the Quality of Experience (QoE) domain, along with a SWOT analysis. Based on those, it discusses how the QoE research area might develop in the future, and how QoE research will lead to innovative and improved products and services. It closes by providing a set of recommendations for the scientific community and industry, as well as for future funding of QoE-related activities.
Cite as

Markus Fiedler, Sebastian Möller, Peter Reichl, and Min Xie. QoE Vadis? (Dagstuhl Perspectives Workshop 16472). In Dagstuhl Manifestos, Volume 7, Issue 1, pp. 30-51, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@Article{fiedler_et_al:DagMan.7.1.30,
  author =	{Fiedler, Markus and M\"{o}ller, Sebastian and Reichl, Peter and Xie, Min},
  title =	{{QoE Vadis? (Dagstuhl Perspectives Workshop 16472)}},
  pages =	{30--51},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2018},
  volume =	{7},
  number =	{1},
  editor =	{Fiedler, Markus and M\"{o}ller, Sebastian and Reichl, Peter and Xie, Min},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagMan.7.1.30},
  URN =		{urn:nbn:de:0030-drops-86830},
  doi =		{10.4230/DagMan.7.1.30},
  annote =	{Keywords: multimedia, network and application management, network quality monitoring and measurement, quality of experience, socio-economic and business aspects}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.12
Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice

Authors: Hosna Jabbari, Ian Wark, Carlo Montemagno, and Sebastian Will

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
While computational RNA secondary structure prediction is an important tool in RNA research, it is still fundamentally limited to pseudoknot-free structures (or at best very simple pseudoknots) in practice. Here, we make the prediction of complex pseudoknots - including kissing hairpin structures - practically applicable by reducing the originally high space consumption. For this aim, we apply the technique of sparsification and other space-saving modifications to the recurrences of the pseudoknot prediction algorithm by Chen, Condon and Jabbari (CCJ algorithm). Thus, the theoretical space complexity of free energy minimization is reduced to Theta(n^3+Z), in the sequence length n and the number of non-optimally decomposable fragments ("candidates") Z. The sparsified CCJ algorithm, sparseCCJ, is presented in detail. Moreover, we provide and compare three generations of CCJ implementations, which continuously improve the space requirements: the original CCJ implementation, our first modified implementation, and our final sparsified implementation. The two latest implementations implement the established HotKnots DP09 energy model. In our experiments, using 244GB of RAM, the original CCJ implementation failed to handle sequences longer than 195 bases; sparseCCJ handles our pseudoknot data set (up to about length 400 bases) in this space limit. All three CCJ implementations are available at https://github.com/HosnaJabbari/CCJ.
Cite as

Hosna Jabbari, Ian Wark, Carlo Montemagno, and Sebastian Will. Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 12:1-12:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{jabbari_et_al:LIPIcs.WABI.2017.12,
  author =	{Jabbari, Hosna and Wark, Ian and Montemagno, Carlo and Will, Sebastian},
  title =	{{Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{12:1--12:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.12},
  URN =		{urn:nbn:de:0030-drops-76408},
  doi =		{10.4230/LIPIcs.WABI.2017.12},
  annote =	{Keywords: RNA, secondary structure prediction, pseudoknots, space efficiency, sparsification}
}
Document
DOI: 10.4230/DagRep.6.10.1
Programming Language Techniques for Incremental and Reactive Computing (Dagstuhl Seminar 16402)

Authors: Camil Demetrescu, Sebastian Erdweg, Matthew A. Hammer, and Shriram Krishnamurthi

Published in: Dagstuhl Reports, Volume 6, Issue 10 (2017)

Abstract
Incremental computations are those that process input changes faster than naive computation that runs from scratch, and reactive computations consist of interactive behavior that varies over time. Due to the importance and prevalence of incremental, reactive systems, ad hoc variants of incremental and reactive computation are ubiquitous in modern software systems. In response to this reality, the PL research community has worked for several decades to advance new languages for systems that interface with a dynamically-changing environment. In this space, researchers propose new general-purpose languages and algorithms to express and implement efficient, dynamic behavior, in the form of incremental and reactive language systems. While these research lines continue to develop successfully, this work lacks a shared community that synthesizes a collective discussion about common motivations, alternative techniques, current results and future challenges. To overcome this lack of community, this seminar will work towards building one, by strengthening existing research connections and by forging new ones. Developing a shared culture is critical to the future advancement of incremental and reactive computing in modern PL research, and in turn, this PL research is critical to developing the efficient, understandable interactive systems of the future.
Cite as

Camil Demetrescu, Sebastian Erdweg, Matthew A. Hammer, and Shriram Krishnamurthi. Programming Language Techniques for Incremental and Reactive Computing (Dagstuhl Seminar 16402). In Dagstuhl Reports, Volume 6, Issue 10, pp. 1-12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@Article{demetrescu_et_al:DagRep.6.10.1,
  author =	{Demetrescu, Camil and Erdweg, Sebastian and Hammer, Matthew A. and Krishnamurthi, Shriram},
  title =	{{Programming Language Techniques for Incremental and Reactive Computing (Dagstuhl Seminar 16402)}},
  pages =	{1--12},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2017},
  volume =	{6},
  number =	{10},
  editor =	{Demetrescu, Camil and Erdweg, Sebastian and Hammer, Matthew A. and Krishnamurthi, Shriram},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.6.10.1},
  URN =		{urn:nbn:de:0030-drops-69491},
  doi =		{10.4230/DagRep.6.10.1},
  annote =	{Keywords: Incremental computing, reactive programming, memoization, change propagation, dynamic dependency graph, dataflow programming, live programming}
}
Document
DOI: 10.4230/LIPIcs.APPROX-RANDOM.2014.356
Robust Appointment Scheduling

Authors: Shashi Mittal, Andreas S. Schulz, and Sebastian Stiller

Published in: LIPIcs, Volume 28, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014)

Abstract
Health care providers are under tremendous pressure to reduce costs and increase quality of their services. It has long been recognized that well-designed appointment systems have the potential to improve utilization of expensive personnel and medical equipment and to reduce waiting times for patients. In a widely influential survey on outpatient scheduling, Cayirli and Veral (2003) concluded that the "biggest challenge for future research will be to develop easy-to-use heuristics." We analyze the appointment scheduling problem from a robust-optimization perspective, and we establish the existence of a closed-form optimal solution--arguably the simplest and best `heuristic' possible. In case the order of patients is changeable, the robust optimization approach yields a novel formulation of the appointment scheduling problem as that of minimizing a concave function over a supermodular polyhedron. We devise the first constant-factor approximation algorithm for this case.
Cite as

Shashi Mittal, Andreas S. Schulz, and Sebastian Stiller. Robust Appointment Scheduling. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014). Leibniz International Proceedings in Informatics (LIPIcs), Volume 28, pp. 356-370, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)

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@InProceedings{mittal_et_al:LIPIcs.APPROX-RANDOM.2014.356,
  author =	{Mittal, Shashi and Schulz, Andreas S. and Stiller, Sebastian},
  title =	{{Robust Appointment Scheduling}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2014)},
  pages =	{356--370},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-74-3},
  ISSN =	{1868-8969},
  year =	{2014},
  volume =	{28},
  editor =	{Jansen, Klaus and Rolim, Jos\'{e} and Devanur, Nikhil R. and Moore, Cristopher},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX-RANDOM.2014.356},
  URN =		{urn:nbn:de:0030-drops-47089},
  doi =		{10.4230/LIPIcs.APPROX-RANDOM.2014.356},
  annote =	{Keywords: Robust Optimization, Health Care Scheduling, Approximation Algorithms}
}
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