35 Search Results for "Chen, Jian-Jia"


Document
On the Equivalence of Maximum Reaction Time and Maximum Data Age for Cause-Effect Chains

Authors: Mario Günzel, Harun Teper, Kuan-Hsun Chen, Georg von der Brüggen, and Jian-Jia Chen

Published in: LIPIcs, Volume 262, 35th Euromicro Conference on Real-Time Systems (ECRTS 2023)


Abstract
Real-time systems require a formal guarantee of timing-constraints, not only for individual tasks but also for data-propagation. The timing behavior of data-propagation paths in a given system is typically described by its maximum reaction time and its maximum data age. This paper shows that they are equivalent. To reach this conclusion, partitioned job chains are introduced, which consist of one immediate forward and one immediate backward job chain. Such partitioned job chains are proven to describe maximum reaction time and maximum data age in a universal manner. This universal description does not only show the equivalence of maximum reaction time and maximum data age, but can also be exploited to speed up the computation of such significantly. In particular, the speed-up for synthesized task sets based on automotive benchmarks can be up to 1600. Since only very few non-restrictive assumptions are made, the equivalence of maximum data age and maximum reaction time holds for almost any scheduling mechanism and even for tasks which do not adhere to the typical periodic or sporadic task model. This observation is supported by a simulation of a ROS2 navigation system.

Cite as

Mario Günzel, Harun Teper, Kuan-Hsun Chen, Georg von der Brüggen, and Jian-Jia Chen. On the Equivalence of Maximum Reaction Time and Maximum Data Age for Cause-Effect Chains. In 35th Euromicro Conference on Real-Time Systems (ECRTS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 262, pp. 10:1-10:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{gunzel_et_al:LIPIcs.ECRTS.2023.10,
  author =	{G\"{u}nzel, Mario and Teper, Harun and Chen, Kuan-Hsun and von der Br\"{u}ggen, Georg and Chen, Jian-Jia},
  title =	{{On the Equivalence of Maximum Reaction Time and Maximum Data Age for Cause-Effect Chains}},
  booktitle =	{35th Euromicro Conference on Real-Time Systems (ECRTS 2023)},
  pages =	{10:1--10:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-280-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{262},
  editor =	{Papadopoulos, Alessandro V.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2023.10},
  URN =		{urn:nbn:de:0030-drops-180392},
  doi =		{10.4230/LIPIcs.ECRTS.2023.10},
  annote =	{Keywords: End-to-End, Timing Analysis, Maximum Data Age, Maximum Reaction Time, Cause-Effect Chain, Robot Operating Systems 2 (ROS2)}
}
Document
LLVMTA: An LLVM-Based WCET Analysis Tool

Authors: Sebastian Hahn, Michael Jacobs, Nils Hölscher, Kuan-Hsun Chen, Jian-Jia Chen, and Jan Reineke

Published in: OASIcs, Volume 103, 20th International Workshop on Worst-Case Execution Time Analysis (WCET 2022)


Abstract
We present llvmta, an academic WCET analysis tool based on the LLVM compiler infrastructure. It aims to enable the evaluation of novel WCET analysis approaches in a state-of-the-art analysis framework without dealing with the complexity of modeling real-world hardware architectures. We discuss the main design decisions and interfaces that allow to implement new analysis approaches. Finally, we highlight various existing research projects whose evaluation has been enabled by llvmta.

Cite as

Sebastian Hahn, Michael Jacobs, Nils Hölscher, Kuan-Hsun Chen, Jian-Jia Chen, and Jan Reineke. LLVMTA: An LLVM-Based WCET Analysis Tool. In 20th International Workshop on Worst-Case Execution Time Analysis (WCET 2022). Open Access Series in Informatics (OASIcs), Volume 103, pp. 2:1-2:17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@InProceedings{hahn_et_al:OASIcs.WCET.2022.2,
  author =	{Hahn, Sebastian and Jacobs, Michael and H\"{o}lscher, Nils and Chen, Kuan-Hsun and Chen, Jian-Jia and Reineke, Jan},
  title =	{{LLVMTA: An LLVM-Based WCET Analysis Tool}},
  booktitle =	{20th International Workshop on Worst-Case Execution Time Analysis (WCET 2022)},
  pages =	{2:1--2:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-244-0},
  ISSN =	{2190-6807},
  year =	{2022},
  volume =	{103},
  editor =	{Ballabriga, Cl\'{e}ment},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.WCET.2022.2},
  URN =		{urn:nbn:de:0030-drops-166242},
  doi =		{10.4230/OASIcs.WCET.2022.2},
  annote =	{Keywords: WCET analysis, low-level analysis, LLVM}
}
Document
Artifact
Unikernel-Based Real-Time Virtualization Under Deferrable Servers: Analysis and Realization (Artifact)

Authors: Kuan-Hsun Chen, Mario Günzel, Boguslaw Jablkowski, Markus Buschhoff, and Jian-Jia Chen

Published in: DARTS, Volume 8, Issue 1, Special Issue of the 34th Euromicro Conference on Real-Time Systems (ECRTS 2022)


Abstract
This artifact provides the source code to validate and reproduce the numerical results of the associated paper "Unikernel-Based Real-Time Virtualization under Deferrable Servers: Analysis and Realization". Due to the nature of a close-source project with the company, i.e., EMVICORE GmbH, the source code of the case study in Section 6.2 is not included in this artifact.

Cite as

Kuan-Hsun Chen, Mario Günzel, Boguslaw Jablkowski, Markus Buschhoff, and Jian-Jia Chen. Unikernel-Based Real-Time Virtualization Under Deferrable Servers: Analysis and Realization (Artifact). In Special Issue of the 34th Euromicro Conference on Real-Time Systems (ECRTS 2022). Dagstuhl Artifacts Series (DARTS), Volume 8, Issue 1, pp. 2:1-2:2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@Article{chen_et_al:DARTS.8.1.2,
  author =	{Chen, Kuan-Hsun and G\"{u}nzel, Mario and Jablkowski, Boguslaw and Buschhoff, Markus and Chen, Jian-Jia},
  title =	{{Unikernel-Based Real-Time Virtualization Under Deferrable Servers: Analysis and Realization (Artifact)}},
  pages =	{2:1--2:2},
  journal =	{Dagstuhl Artifacts Series},
  ISSN =	{2509-8195},
  year =	{2022},
  volume =	{8},
  number =	{1},
  editor =	{Chen, Kuan-Hsun and G\"{u}nzel, Mario and Jablkowski, Boguslaw and Buschhoff, Markus and Chen, Jian-Jia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DARTS.8.1.2},
  URN =		{urn:nbn:de:0030-drops-164987},
  doi =		{10.4230/DARTS.8.1.2},
  annote =	{Keywords: Unikernel, Virtualization, Reservation Servers, Deferrable Servers, Cyber-Physical Systems, Real-Time Systems}
}
Document
Unikernel-Based Real-Time Virtualization Under Deferrable Servers: Analysis and Realization

Authors: Kuan-Hsun Chen, Mario Günzel, Boguslaw Jablkowski, Markus Buschhoff, and Jian-Jia Chen

Published in: LIPIcs, Volume 231, 34th Euromicro Conference on Real-Time Systems (ECRTS 2022)


Abstract
For cyber-physical systems, real-time virtualization optimizes the hardware utilization by consolidating multiple systems into the same platform, while satisfying the timing constraints of their real-time tasks. This paper considers virtualization based on unikernels, i.e., single address space kernels usually constructed by using library operating systems. Each unikernel is a guest operating system in the virtualization and hosts a single real-time task. We consider deferrable servers in the virtualization platform to schedule the unikernel-based guest operating systems and analyze the worst-case response time of a sporadic real-time task under such a virtualization architecture. Throughout synthesized tasksets, we empirically show that our analysis outperforms the restated analysis derived from the state-of-the-art, which is based on Real-Time Calculus. Furthermore, we provide insights on implementation-specific issues and offer evidence that the proposed scheduling architecture can be effectively implemented on top of the Xen hypervisor while incurring acceptable overhead.

Cite as

Kuan-Hsun Chen, Mario Günzel, Boguslaw Jablkowski, Markus Buschhoff, and Jian-Jia Chen. Unikernel-Based Real-Time Virtualization Under Deferrable Servers: Analysis and Realization. In 34th Euromicro Conference on Real-Time Systems (ECRTS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 231, pp. 6:1-6:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@InProceedings{chen_et_al:LIPIcs.ECRTS.2022.6,
  author =	{Chen, Kuan-Hsun and G\"{u}nzel, Mario and Jablkowski, Boguslaw and Buschhoff, Markus and Chen, Jian-Jia},
  title =	{{Unikernel-Based Real-Time Virtualization Under Deferrable Servers: Analysis and Realization}},
  booktitle =	{34th Euromicro Conference on Real-Time Systems (ECRTS 2022)},
  pages =	{6:1--6:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-239-6},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{231},
  editor =	{Maggio, Martina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2022.6},
  URN =		{urn:nbn:de:0030-drops-163239},
  doi =		{10.4230/LIPIcs.ECRTS.2022.6},
  annote =	{Keywords: Unikernel, Virtualization, Reservation Servers, Deferrable Servers, Cyber-Physical Systems, Real-Time Systems}
}
Document
Using Markov’s Inequality with Power-Of-k Function for Probabilistic WCET Estimation

Authors: Sergi Vilardell, Isabel Serra, Enrico Mezzetti, Jaume Abella, Francisco J. Cazorla, and Joan del Castillo

Published in: LIPIcs, Volume 231, 34th Euromicro Conference on Real-Time Systems (ECRTS 2022)


Abstract
Deriving WCET estimates for software programs with probabilistic means (a.k.a. pWCET estimation) has received significant attention during last years as a way to deal with the increased complexity of the processors used in real-time systems. Many works build on Extreme Value Theory (EVT) that is fed with a sample of the collected data (execution times). In its application, EVT carries two sources of uncertainty: the first one that is intrinsic to the EVT model and relates to determining the subset of the sample that belongs to the (upper) tail, and hence, is actually used by EVT for prediction; and the second one that is induced by the sampling process and hence is inherent to all sample-based methods. In this work, we show that Markov’s inequality can be used to obtain provable trustworthy probabilistic bounds to the tail of a distribution without incurring any model-intrinsic uncertainty. Yet, it produces pessimistic estimates that we shave substantially by proposing the use of a power-of-k function instead of the default identity function used by Markov’s inequality. Lastly, we propose a method to deal with sampling uncertainty for Markov’s inequality that consistently improves EVT estimates on synthetic and real data obtained from a railway application.

Cite as

Sergi Vilardell, Isabel Serra, Enrico Mezzetti, Jaume Abella, Francisco J. Cazorla, and Joan del Castillo. Using Markov’s Inequality with Power-Of-k Function for Probabilistic WCET Estimation. In 34th Euromicro Conference on Real-Time Systems (ECRTS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 231, pp. 20:1-20:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)


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@InProceedings{vilardell_et_al:LIPIcs.ECRTS.2022.20,
  author =	{Vilardell, Sergi and Serra, Isabel and Mezzetti, Enrico and Abella, Jaume and Cazorla, Francisco J. and del Castillo, Joan},
  title =	{{Using Markov’s Inequality with Power-Of-k Function for Probabilistic WCET Estimation}},
  booktitle =	{34th Euromicro Conference on Real-Time Systems (ECRTS 2022)},
  pages =	{20:1--20:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-239-6},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{231},
  editor =	{Maggio, Martina},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2022.20},
  URN =		{urn:nbn:de:0030-drops-163377},
  doi =		{10.4230/LIPIcs.ECRTS.2022.20},
  annote =	{Keywords: Markov’s inequality, probabilistic time estimates, probabilistic WCET, Extreme Value Theory}
}
Document
Hard Real-Time Stationary GANG-Scheduling

Authors: Niklas Ueter, Mario Günzel, Georg von der Brüggen, and Jian-Jia Chen

Published in: LIPIcs, Volume 196, 33rd Euromicro Conference on Real-Time Systems (ECRTS 2021)


Abstract
The scheduling of parallel real-time tasks enables the efficient utilization of modern multiprocessor platforms for systems with real-time constrains. In this situation, the gang task model, in which each parallel sub-job has to be executed simultaneously, has shown significant performance benefits due to reduced context switches and more efficient intra-task synchronization. In this paper, we provide the first schedulability analysis for sporadic constrained-deadline gang task systems and propose a novel stationary gang scheduling algorithm. We show that the schedulability problem of gang task sets can be reduced to the uniprocessor self-suspension schedulability problem. Furthermore, we provide a class of partitioning algorithms to find a stationary gang assignment and show that it bounds the worst-case interference of each task. To demonstrate the effectiveness of our proposed approach, we evaluate it for implicit-deadline systems using randomized task sets under different settings, showing that our approach outperforms the state-of-the-art.

Cite as

Niklas Ueter, Mario Günzel, Georg von der Brüggen, and Jian-Jia Chen. Hard Real-Time Stationary GANG-Scheduling. In 33rd Euromicro Conference on Real-Time Systems (ECRTS 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 196, pp. 10:1-10:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)


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@InProceedings{ueter_et_al:LIPIcs.ECRTS.2021.10,
  author =	{Ueter, Niklas and G\"{u}nzel, Mario and von der Br\"{u}ggen, Georg and Chen, Jian-Jia},
  title =	{{Hard Real-Time Stationary GANG-Scheduling}},
  booktitle =	{33rd Euromicro Conference on Real-Time Systems (ECRTS 2021)},
  pages =	{10:1--10:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-192-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{196},
  editor =	{Brandenburg, Bj\"{o}rn B.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2021.10},
  URN =		{urn:nbn:de:0030-drops-139410},
  doi =		{10.4230/LIPIcs.ECRTS.2021.10},
  annote =	{Keywords: Real-Time Systems, Gang Scheduling, Parallel Computing, Scheduling Algorithms}
}
Document
Offloading Safety- and Mission-Critical Tasks via Unreliable Connections

Authors: Lea Schönberger, Georg von der Brüggen, Kuan-Hsun Chen, Benjamin Sliwa, Hazem Youssef, Aswin Karthik Ramachandran Venkatapathy, Christian Wietfeld, Michael ten Hompel, and Jian-Jia Chen

Published in: LIPIcs, Volume 165, 32nd Euromicro Conference on Real-Time Systems (ECRTS 2020)


Abstract
For many cyber-physical systems, e.g., IoT systems and autonomous vehicles, offloading workload to auxiliary processing units has become crucial. However, since this approach highly depends on network connectivity and responsiveness, typically only non-critical tasks are offloaded, which have less strict timing requirements than critical tasks. In this work, we provide two protocols allowing to offload critical and non-critical tasks likewise, while providing different service levels for non-critical tasks in the event of an unsuccessful offloading operation, depending on the respective system requirements. We analyze the worst-case timing behavior of the local cyber-physical system and, based on these analyses, we provide a sufficient schedulability test for each of the proposed protocols. In the course of comprehensive experiments, we show that our protocols have reasonable acceptance ratios under the provided schedulability tests. Moreover, we demonstrate that the system behavior under our proposed protocols is strongly dependent on probability of unsuccessful offloading operations, the percentage of critical tasks in the system, and the amount of offloaded workload.

Cite as

Lea Schönberger, Georg von der Brüggen, Kuan-Hsun Chen, Benjamin Sliwa, Hazem Youssef, Aswin Karthik Ramachandran Venkatapathy, Christian Wietfeld, Michael ten Hompel, and Jian-Jia Chen. Offloading Safety- and Mission-Critical Tasks via Unreliable Connections. In 32nd Euromicro Conference on Real-Time Systems (ECRTS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 165, pp. 18:1-18:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


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@InProceedings{schonberger_et_al:LIPIcs.ECRTS.2020.18,
  author =	{Sch\"{o}nberger, Lea and von der Br\"{u}ggen, Georg and Chen, Kuan-Hsun and Sliwa, Benjamin and Youssef, Hazem and Ramachandran Venkatapathy, Aswin Karthik and Wietfeld, Christian and ten Hompel, Michael and Chen, Jian-Jia},
  title =	{{Offloading Safety- and Mission-Critical Tasks via Unreliable Connections}},
  booktitle =	{32nd Euromicro Conference on Real-Time Systems (ECRTS 2020)},
  pages =	{18:1--18:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-152-8},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{165},
  editor =	{V\"{o}lp, Marcus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2020.18},
  URN =		{urn:nbn:de:0030-drops-123811},
  doi =		{10.4230/LIPIcs.ECRTS.2020.18},
  annote =	{Keywords: internet of things, cyber-physical systems, real-time, mixed-criticality, self-suspension, computation offloading, scheduling, communication}
}
Document
Short Paper
Smartphone Usability for Emergency Evacuation Applications (Short Paper)

Authors: David Amores, Maria Vasardani, and Egemen Tanin

Published in: LIPIcs, Volume 142, 14th International Conference on Spatial Information Theory (COSIT 2019)


Abstract
Mobile phone ubiquity has allowed the implementation of a number of emergency-related evacuation aids. Yet, these applications still face a number of challenges in human-mobile interaction, namely: (1) lack of widely accepted mobile usability guidelines, (2) people’s limited cognitive capacity when using mobile phones under stress, and (3) difficulty recreating emergency scenarios as experiments for usability testing. This study is intended as an initial view into smartphone usability under emergency evacuations by compiling a list of experimental observations and setting the ground for future research in cognitively-informed spatial algorithms and app design.

Cite as

David Amores, Maria Vasardani, and Egemen Tanin. Smartphone Usability for Emergency Evacuation Applications (Short Paper). In 14th International Conference on Spatial Information Theory (COSIT 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 142, pp. 2:1-2:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{amores_et_al:LIPIcs.COSIT.2019.2,
  author =	{Amores, David and Vasardani, Maria and Tanin, Egemen},
  title =	{{Smartphone Usability for Emergency Evacuation Applications}},
  booktitle =	{14th International Conference on Spatial Information Theory (COSIT 2019)},
  pages =	{2:1--2:7},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-115-3},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{142},
  editor =	{Timpf, Sabine and Schlieder, Christoph and Kattenbeck, Markus and Ludwig, Bernd and Stewart, Kathleen},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2019.2},
  URN =		{urn:nbn:de:0030-drops-110947},
  doi =		{10.4230/LIPIcs.COSIT.2019.2},
  annote =	{Keywords: cognitive load, smartphone usability, ecological validity, emergency evacuation}
}
Document
A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference

Authors: Mohammadamin Edrisi, Hamim Zafar, and Luay Nakhleh

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


Abstract
Single-cell sequencing provides a powerful approach for elucidating intratumor heterogeneity by resolving cell-to-cell variability. However, it also poses additional challenges including elevated error rates, allelic dropout and non-uniform coverage. A recently introduced single-cell-specific mutation detection algorithm leverages the evolutionary relationship between cells for denoising the data. However, due to its probabilistic nature, this method does not scale well with the number of cells. Here, we develop a novel combinatorial approach for utilizing the genealogical relationship of cells in detecting mutations from noisy single-cell sequencing data. Our method, called scVILP, jointly detects mutations in individual cells and reconstructs a perfect phylogeny among these cells. We employ a novel Integer Linear Program algorithm for deterministically and efficiently solving the joint inference problem. We show that scVILP achieves similar or better accuracy but significantly better runtime over existing methods on simulated data. We also applied scVILP to an empirical human cancer dataset from a high grade serous ovarian cancer patient.

Cite as

Mohammadamin Edrisi, Hamim Zafar, and Luay Nakhleh. A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 22:1-22:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{edrisi_et_al:LIPIcs.WABI.2019.22,
  author =	{Edrisi, Mohammadamin and Zafar, Hamim and Nakhleh, Luay},
  title =	{{A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{22:1--22:13},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.22},
  URN =		{urn:nbn:de:0030-drops-110525},
  doi =		{10.4230/LIPIcs.WABI.2019.22},
  annote =	{Keywords: Mutation calling, Single-cell sequencing, Integer linear programming, Perfect phylogeny}
}
Document
Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation

Authors: Natalie Sauerwald, Yihang Shen, and Carl Kingsford

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


Abstract
Topological data analysis (TDA) is a mathematically well-founded set of methods to derive robust information about the structure and topology of data. It has been applied successfully in several biological contexts. Derived primarily from algebraic topology, TDA rigorously identifies persistent features in complex data, making it well-suited to better understand the key features of three-dimensional chromosome structure. Chromosome structure has a significant influence in many diverse genomic processes and has recently been shown to relate to cellular differentiation. While there exist many methods to study specific substructures of chromosomes, we are still missing a global view of all geometric features of chromosomes. By applying TDA to the study of chromosome structure through differentiation across three cell lines, we provide insight into principles of chromosome folding and looping. We identify persistent connected components and one-dimensional topological features of chromosomes and characterize them across cell types and stages of differentiation. Availability: Scripts to reproduce the results from this study can be found at https://github.com/Kingsford-Group/hictda

Cite as

Natalie Sauerwald, Yihang Shen, and Carl Kingsford. Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 23:1-23:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{sauerwald_et_al:LIPIcs.WABI.2019.23,
  author =	{Sauerwald, Natalie and Shen, Yihang and Kingsford, Carl},
  title =	{{Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{23:1--23:16},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.23},
  URN =		{urn:nbn:de:0030-drops-110537},
  doi =		{10.4230/LIPIcs.WABI.2019.23},
  annote =	{Keywords: topological data analysis, chromosome structure, Hi-C, topologically associating domains}
}
Document
Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem

Authors: Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford

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


Abstract
Transcriptomic structural variants (TSVs) - large-scale transcriptome sequence change due to structural variation - are common, especially in cancer. Detecting TSVs is a challenging computational problem. Sample heterogeneity (including differences between alleles in diploid organisms) is a critical confounding factor when identifying TSVs. To improve TSV detection in heterogeneous RNA-seq samples, we introduce the Multiple Compatible Arrangement Problem (MCAP), which seeks k genome rearrangements to maximize the number of reads that are concordant with at least one rearrangement. This directly models the situation of a heterogeneous or diploid sample. We prove that MCAP is NP-hard and provide a 1/4-approximation algorithm for k=1 and a 3/4-approximation algorithm for the diploid case (k=2) assuming an oracle for k=1. Combining these, we obtain a 3/16-approximation algorithm for MCAP when k=2 (without an oracle). We also present an integer linear programming formulation for general k. We characterize the graph structures that require k>1 to satisfy all edges and show such structures are prevalent in cancer samples. We evaluate our algorithms on 381 TCGA samples and 2 cancer cell lines and show improved performance compared to the state-of-the-art TSV-calling tool, SQUID.

Cite as

Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford. Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 18:1-18:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{qiu_et_al:LIPIcs.WABI.2019.18,
  author =	{Qiu, Yutong and Ma, Cong and Xie, Han and Kingsford, Carl},
  title =	{{Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{18:1--18:5},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.18},
  URN =		{urn:nbn:de:0030-drops-110483},
  doi =		{10.4230/LIPIcs.WABI.2019.18},
  annote =	{Keywords: transcriptomic structural variation, integer linear programming, heterogeneity}
}
Document
Short Paper
Towards Modeling Geographical Processes with Generative Adversarial Networks (GANs) (Short Paper)

Authors: David Jonietz and Michael Kopp

Published in: LIPIcs, Volume 142, 14th International Conference on Spatial Information Theory (COSIT 2019)


Abstract
Recently, Generative Adversarial Networks (GANs) have demonstrated great potential for a range of Machine Learning tasks, including synthetic video generation, but have so far not been applied to the domain of modeling geographical processes. In this study, we align these two problems and - motivated by the potential advantages of GANs compared to traditional geosimulation methods - test the capability of GANs to learn a set of underlying rules which determine a geographical process. For this purpose, we turn to Conway’s well-known Game of Life (GoL) as a source for spatio-temporal training data, and further argue for its (and simple variants of it) usefulness as a potential standard training data set for benchmarking generative geographical process models.

Cite as

David Jonietz and Michael Kopp. Towards Modeling Geographical Processes with Generative Adversarial Networks (GANs) (Short Paper). In 14th International Conference on Spatial Information Theory (COSIT 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 142, pp. 27:1-27:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{jonietz_et_al:LIPIcs.COSIT.2019.27,
  author =	{Jonietz, David and Kopp, Michael},
  title =	{{Towards Modeling Geographical Processes with Generative Adversarial Networks (GANs)}},
  booktitle =	{14th International Conference on Spatial Information Theory (COSIT 2019)},
  pages =	{27:1--27:9},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-115-3},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{142},
  editor =	{Timpf, Sabine and Schlieder, Christoph and Kattenbeck, Markus and Ludwig, Bernd and Stewart, Kathleen},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2019.27},
  URN =		{urn:nbn:de:0030-drops-111193},
  doi =		{10.4230/LIPIcs.COSIT.2019.27},
  annote =	{Keywords: GAN, generative modeling, deep learning, geosimulation, game of life}
}
Document
RLE Edit Distance in Near Optimal Time

Authors: Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
We show that the edit distance between two run-length encoded strings of compressed lengths m and n respectively, can be computed in O(mn log(mn)) time. This improves the previous record by a factor of O(n/log(mn)). The running time of our algorithm is within subpolynomial factors of being optimal, subject to the standard SETH-hardness assumption. This effectively closes a line of algorithmic research first started in 1993.

Cite as

Raphaël Clifford, Paweł Gawrychowski, Tomasz Kociumaka, Daniel P. Martin, and Przemysław Uznański. RLE Edit Distance in Near Optimal Time. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 66:1-66:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{clifford_et_al:LIPIcs.MFCS.2019.66,
  author =	{Clifford, Rapha\"{e}l and Gawrychowski, Pawe{\l} and Kociumaka, Tomasz and Martin, Daniel P. and Uzna\'{n}ski, Przemys{\l}aw},
  title =	{{RLE Edit Distance in Near Optimal Time}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{66:1--66:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.66},
  URN =		{urn:nbn:de:0030-drops-110109},
  doi =		{10.4230/LIPIcs.MFCS.2019.66},
  annote =	{Keywords: String algorithms, Compression, Pattern matching, Run-length encoding}
}
Document
Computing Probabilistic Bisimilarity Distances for Probabilistic Automata

Authors: Giorgio Bacci, Giovanni Bacci, Kim G. Larsen, Radu Mardare, Qiyi Tang, and Franck van Breugel

Published in: LIPIcs, Volume 140, 30th International Conference on Concurrency Theory (CONCUR 2019)


Abstract
The probabilistic bisimilarity distance of Deng et al. has been proposed as a robust quantitative generalization of Segala and Lynch’s probabilistic bisimilarity for probabilistic automata. In this paper, we present a novel characterization of the bisimilarity distance as the solution of a simple stochastic game. The characterization gives us an algorithm to compute the distances by applying Condon’s simple policy iteration on these games. The correctness of Condon’s approach, however, relies on the assumption that the games are stopping. Our games may be non-stopping in general, yet we are able to prove termination for this extended class of games. Already other algorithms have been proposed in the literature to compute these distances, with complexity in UP cap coUP and PPAD. Despite the theoretical relevance, these algorithms are inefficient in practice. To the best of our knowledge, our algorithm is the first practical solution. In the proofs of all the above-mentioned results, an alternative presentation of the Hausdorff distance due to Mémoli plays a central rôle.

Cite as

Giorgio Bacci, Giovanni Bacci, Kim G. Larsen, Radu Mardare, Qiyi Tang, and Franck van Breugel. Computing Probabilistic Bisimilarity Distances for Probabilistic Automata. In 30th International Conference on Concurrency Theory (CONCUR 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 140, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{bacci_et_al:LIPIcs.CONCUR.2019.9,
  author =	{Bacci, Giorgio and Bacci, Giovanni and Larsen, Kim G. and Mardare, Radu and Tang, Qiyi and van Breugel, Franck},
  title =	{{Computing Probabilistic Bisimilarity Distances for Probabilistic Automata}},
  booktitle =	{30th International Conference on Concurrency Theory (CONCUR 2019)},
  pages =	{9:1--9:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-121-4},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{140},
  editor =	{Fokkink, Wan and van Glabbeek, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2019.9},
  URN =		{urn:nbn:de:0030-drops-109119},
  doi =		{10.4230/LIPIcs.CONCUR.2019.9},
  annote =	{Keywords: Probabilistic automata, Behavioural metrics, Simple stochastic games, Simple policy iteration algorithm}
}
Document
Overparameterization: A Connection Between Software 1.0 and Software 2.0

Authors: Michael Carbin

Published in: LIPIcs, Volume 136, 3rd Summit on Advances in Programming Languages (SNAPL 2019)


Abstract
A new ecosystem of machine-learning driven applications, titled Software 2.0, has arisen that integrates neural networks into a variety of computational tasks. Such applications include image recognition, natural language processing, and other traditional machine learning tasks. However, these techniques have also grown to include other structured domains, such as program analysis and program optimization for which novel, domain-specific insights mate with model design. In this paper, we connect the world of Software 2.0 with that of traditional software - Software 1.0 - through overparameterization: a program may provide more computational capacity and precision than is necessary for the task at hand. In Software 2.0, overparamterization - when a machine learning model has more parameters than datapoints in the dataset - arises as a contemporary understanding of the ability for modern, gradient-based learning methods to learn models over complex datasets with high-accuracy. Specifically, the more parameters a model has, the better it learns. In Software 1.0, the results of the approximate computing community show that traditional software is also overparameterized in that software often simply computes results that are more precise than is required by the user. Approximate computing exploits this overparameterization to improve performance by eliminating unnecessary, excess computation. For example, one - of many techniques - is to reduce the precision of arithmetic in the application. In this paper, we argue that the gap between available precision and that that is required for either Software 1.0 or Software 2.0 is a fundamental aspect of software design that illustrates the balance between software designed for general-purposes and domain-adapted solutions. A general-purpose solution is easier to develop and maintain versus a domain-adapted solution. However, that ease comes at the expense of performance. We show that the approximate computing community and the machine learning community have developed overlapping techniques to improve performance by reducing overparameterization. We also show that because of these shared techniques, questions, concerns, and answers on how to construct software can translate from one software variant to the other.

Cite as

Michael Carbin. Overparameterization: A Connection Between Software 1.0 and Software 2.0. In 3rd Summit on Advances in Programming Languages (SNAPL 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 136, pp. 1:1-1:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{carbin:LIPIcs.SNAPL.2019.1,
  author =	{Carbin, Michael},
  title =	{{Overparameterization: A Connection Between Software 1.0 and Software 2.0}},
  booktitle =	{3rd Summit on Advances in Programming Languages (SNAPL 2019)},
  pages =	{1:1--1:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-113-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{136},
  editor =	{Lerner, Benjamin S. and Bod{\'\i}k, Rastislav and Krishnamurthi, Shriram},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SNAPL.2019.1},
  URN =		{urn:nbn:de:0030-drops-105440},
  doi =		{10.4230/LIPIcs.SNAPL.2019.1},
  annote =	{Keywords: Approximate Computing, Machine Learning, Software 2.0}
}
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