16 Search Results for "Schmidt, Sebastian"

Artifact
Software
DOI: 10.4230/artifacts.22465
Practical Omnitigs

Authors: Sebastian Schmidt

Abstract
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Sebastian Schmidt. Practical Omnitigs (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@misc{dagstuhl-artifact-22465,
   title = {{Practical Omnitigs}}, 
   author = {Schmidt, Sebastian},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:rev:bb1de69873c6b48f183e51bca2f48d2a057b8b64;origin=https://github.com/algbio/practical-omnitigs;visit=swh:1:snp:04e6ac0423d201dfab2c8d8ebe834756a6f88de9}{\texttt{swh:1:rev:bb1de69873c6b48f183e51bca2f48d2a057b8b64}} (visited on 2024-11-28)},
   url = {https://github.com/algbio/practical-omnitigs},
   doi = {10.4230/artifacts.22465},
}
Document
DOI: 10.4230/OASIcs.DX.2024.7
Design Principles for Falsifiable, Replicable and Reproducible Empirical Machine Learning Research

Authors: Daniel Vranješ, Jonas Ehrhardt, René Heesch, Lukas Moddemann, Henrik Sebastian Steude, and Oliver Niggemann

Published in: OASIcs, Volume 125, 35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024)

Abstract
Machine learning is becoming increasingly important in the diagnosis and planning fields, where data-driven models and algorithms are being employed as alternatives to traditional first-principle approaches. Empirical research plays a fundamental role in the machine learning domain. At the heart of impactful empirical research lies the development of clear research hypotheses, which then shape the design of experiments. The execution of experiments must be carried out with precision to ensure reliable results, followed by statistical analysis to interpret these outcomes. This process is key to either supporting or refuting initial hypotheses. Despite its importance, there is a high variability in research practices across the machine learning community and no uniform understanding of quality criteria for empirical research. To address this gap, we propose a model for the empirical research process, accompanied by guidelines to uphold the validity of empirical research. By embracing these recommendations, greater consistency, enhanced reliability and increased impact can be achieved.
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Daniel Vranješ, Jonas Ehrhardt, René Heesch, Lukas Moddemann, Henrik Sebastian Steude, and Oliver Niggemann. Design Principles for Falsifiable, Replicable and Reproducible Empirical Machine Learning Research. In 35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024). Open Access Series in Informatics (OASIcs), Volume 125, pp. 7:1-7:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{vranjes_et_al:OASIcs.DX.2024.7,
  author =	{Vranje\v{s}, Daniel and Ehrhardt, Jonas and Heesch, Ren\'{e} and Moddemann, Lukas and Steude, Henrik Sebastian and Niggemann, Oliver},
  title =	{{Design Principles for Falsifiable, Replicable and Reproducible Empirical Machine Learning Research}},
  booktitle =	{35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024)},
  pages =	{7:1--7:13},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-356-0},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{125},
  editor =	{Pill, Ingo and Natan, Avraham and Wotawa, Franz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2024.7},
  URN =		{urn:nbn:de:0030-drops-220991},
  doi =		{10.4230/OASIcs.DX.2024.7},
  annote =	{Keywords: machine learning, hypothesis design, research design, experimental research, statistical testing, diagnosis, planning}
}
Document
DOI: 10.4230/OASIcs.ATMOS.2024.6
Two-Stage Weekly Shift Scheduling for Train Dispatchers

Authors: Tomas Lidén, Christiane Schmidt, and Rabii Zahir

Published in: OASIcs, Volume 123, 24th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2024)

Abstract
We consider the problem of creating weekly shift schedules for train dispatchers, which conform to a variety of operational constraints, in particular, several work and rest time restrictions. We create the schedules in a two-stage process. First, using a previously presented IP model, we create a set of feasible daily shifts, which takes care of minimum-rest and shift-length requirements, taskload bounds, and combinability of dispatching areas. We then formulate an IP model to combine these daily shifts into weekly schedules, enforcing that each daily shift is covered by some dispatcher every day of the week, while ensuring that the weekly schedules comply with various restrictions on working hours from a union agreement. With this approach, we aim to identify "good" sets of daily shifts for the longer schedules. We run experiments for real-world sized input and consider different distributions of the daily shifts w.r.t. shift length and ratio of night shifts. Daily shifts with shift-length variability, relatively few long shifts, and a low ratio of night shifts generally yield better weekly schedules. The runtime for the second stage with the best daily-shift pattern is below three hours, which - together with the runtime for stage 1 of ca. 2 hours per run - can be feasible for real-world use.
Cite as

Tomas Lidén, Christiane Schmidt, and Rabii Zahir. Two-Stage Weekly Shift Scheduling for Train Dispatchers. In 24th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2024). Open Access Series in Informatics (OASIcs), Volume 123, pp. 6:1-6:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{liden_et_al:OASIcs.ATMOS.2024.6,
  author =	{Lid\'{e}n, Tomas and Schmidt, Christiane and Zahir, Rabii},
  title =	{{Two-Stage Weekly Shift Scheduling for Train Dispatchers}},
  booktitle =	{24th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2024)},
  pages =	{6:1--6:16},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-350-8},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{123},
  editor =	{Bouman, Paul C. and Kontogiannis, Spyros C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ATMOS.2024.6},
  URN =		{urn:nbn:de:0030-drops-211944},
  doi =		{10.4230/OASIcs.ATMOS.2024.6},
  annote =	{Keywords: shift scheduling, IP, train dispatcher shift scheduling}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.11
How to Reduce Temporal Cliques to Find Sparse Spanners

Authors: Sebastian Angrick, Ben Bals, Tobias Friedrich, Hans Gawendowicz, Niko Hastrich, Nicolas Klodt, Pascal Lenzner, Jonas Schmidt, George Skretas, and Armin Wells

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
Many real-world networks, such as transportation or trade networks, are dynamic in the sense that the edge-set may change over time, but these changes are known in advance. This behavior is captured by the temporal graphs model, which has recently become a trending topic in theoretical computer science. A core open problem in the field is to prove the existence of linear-size temporal spanners in temporal cliques, i.e., sparse subgraphs of complete temporal graphs that ensure all-pairs reachability via temporal paths. So far, the best known result is the existence of temporal spanners with 𝒪(nlog n) many edges. We present significant progress towards proving whether linear-size temporal spanners exist in all temporal cliques. We adapt techniques used in previous works and heavily expand and generalize them. This allows us to show that the existence of a linear spanner in cliques and bi-cliques is equivalent and using this, we provide a simpler and more intuitive proof of the 𝒪(nlog n) bound by giving an efficient algorithm for finding linearithmic spanners. Moreover, we use our novel and efficiently computable approach to show that a large class of temporal cliques, called edge-pivotable graphs, admit linear-size temporal spanners. To contrast this, we investigate other classes of temporal cliques that do not belong to the class of edge-pivotable graphs. We introduce two such graph classes and we develop novel algorithmic techniques for establishing the existence of linear temporal spanners in these graph classes as well.
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Sebastian Angrick, Ben Bals, Tobias Friedrich, Hans Gawendowicz, Niko Hastrich, Nicolas Klodt, Pascal Lenzner, Jonas Schmidt, George Skretas, and Armin Wells. How to Reduce Temporal Cliques to Find Sparse Spanners. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 11:1-11:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{angrick_et_al:LIPIcs.ESA.2024.11,
  author =	{Angrick, Sebastian and Bals, Ben and Friedrich, Tobias and Gawendowicz, Hans and Hastrich, Niko and Klodt, Nicolas and Lenzner, Pascal and Schmidt, Jonas and Skretas, George and Wells, Armin},
  title =	{{How to Reduce Temporal Cliques to Find Sparse Spanners}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{11:1--11:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.11},
  URN =		{urn:nbn:de:0030-drops-210822},
  doi =		{10.4230/LIPIcs.ESA.2024.11},
  annote =	{Keywords: Temporal Graphs, temporal Clique, temporal Spanner, Reachability, Graph Connectivity, Graph Sparsification}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.8
Applying the Safe-And-Complete Framework to Practical Genome Assembly

Authors: Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the omnitig algorithm, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (simple omnitigs), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the D. melanogaster and the C. elegans genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies.
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Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu. Applying the Safe-And-Complete Framework to Practical Genome Assembly. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{schmidt_et_al:LIPIcs.WABI.2024.8,
  author =	{Schmidt, Sebastian and Toivonen, Santeri and Medvedev, Paul and Tomescu, Alexandru I.},
  title =	{{Applying the Safe-And-Complete Framework to Practical Genome Assembly}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{8:1--8:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.8},
  URN =		{urn:nbn:de:0030-drops-206520},
  doi =		{10.4230/LIPIcs.WABI.2024.8},
  annote =	{Keywords: Genome assembly, Omnitigs, Safe-and-complete framework, graph algorithm, HiFi sequencing data, Assembly evaluation}
}
Document
DOI: 10.4230/DagMan.10.1.1
Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282)

Authors: James P. Delgrande, Birte Glimm, Thomas Meyer, Miroslaw Truszczynski, and Frank Wolter

Published in: Dagstuhl Manifestos, Volume 10, Issue 1 (2024)

Abstract
Knowledge Representation and Reasoning is a central, longstanding, and active area of Artificial Intelligence. Over the years it has evolved significantly; more recently it has been challenged and complemented by research in areas such as machine learning and reasoning under uncertainty. In July 2022,sser a Dagstuhl Perspectives workshop was held on Knowledge Representation and Reasoning. The goal of the workshop was to describe the state of the art in the field, including its relation with other areas, its shortcomings and strengths, together with recommendations for future progress. We developed this manifesto based on the presentations, panels, working groups, and discussions that took place at the Dagstuhl Workshop. It is a declaration of our views on Knowledge Representation: its origins, goals, milestones, and current foci; its relation to other disciplines, especially to Artificial Intelligence; and on its challenges, along with key priorities for the next decade.
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James P. Delgrande, Birte Glimm, Thomas Meyer, Miroslaw Truszczynski, and Frank Wolter. Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282). In Dagstuhl Manifestos, Volume 10, Issue 1, pp. 1-61, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{delgrande_et_al:DagMan.10.1.1,
  author =	{Delgrande, James P. and Glimm, Birte and Meyer, Thomas and Truszczynski, Miroslaw and Wolter, Frank},
  title =	{{Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282)}},
  pages =	{1--61},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2024},
  volume =	{10},
  number =	{1},
  editor =	{Delgrande, James P. and Glimm, Birte and Meyer, Thomas and Truszczynski, Miroslaw and Wolter, Frank},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.10.1.1},
  URN =		{urn:nbn:de:0030-drops-201403},
  doi =		{10.4230/DagMan.10.1.1},
  annote =	{Keywords: Knowledge representation and reasoning, Applications of logics, Declarative representations, Formal logic}
}
Document
DOI: 10.4230/LIPIcs.SEA.2023.10
Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover

Authors: Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt

Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)

Abstract
In the Directed Feedback Vertex Set (DFVS) problem, one is given a directed graph G = (V,E) and wants to find a minimum cardinality set S ⊆ V such that G-S is acyclic. DFVS is a fundamental problem in computer science and finds applications in areas such as deadlock detection. The problem was the subject of the 2022 PACE coding challenge. We develop a novel exact algorithm for the problem that is tailored to perform well on instances that are mostly bi-directed. For such instances, we adapt techniques from the well-researched vertex cover problem. Our core idea is an iterative reduction to vertex cover. To this end, we also develop a new reduction rule that reduces the number of not bi-directed edges. With the resulting algorithm, we were able to win third place in the exact track of the PACE challenge. We perform computational experiments and compare the running time to other exact algorithms, in particular to the winning algorithm in PACE. Our experiments show that we outpace the other algorithms on instances that have a low density of uni-directed edges.
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Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt. Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{angrick_et_al:LIPIcs.SEA.2023.10,
  author =	{Angrick, Sebastian and Bals, Ben and Casel, Katrin and Cohen, Sarel and Friedrich, Tobias and Hastrich, Niko and Hradilak, Theresa and Issac, Davis and Ki{\ss}ig, Otto and Schmidt, Jonas and Wendt, Leo},
  title =	{{Solving Directed Feedback Vertex Set by Iterative Reduction to Vertex Cover}},
  booktitle =	{21st International Symposium on Experimental Algorithms (SEA 2023)},
  pages =	{10:1--10:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-279-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{265},
  editor =	{Georgiadis, Loukas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.10},
  URN =		{urn:nbn:de:0030-drops-183602},
  doi =		{10.4230/LIPIcs.SEA.2023.10},
  annote =	{Keywords: directed feedback vertex set, vertex cover, reduction rules}
}
Document
DOI: 10.4230/LIPIcs.STACS.2023.17
Cut Paths and Their Remainder Structure, with Applications

Authors: Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, and Elia C. Zirondelli

Published in: LIPIcs, Volume 254, 40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023)

Abstract
In a strongly connected graph G = (V,E), a cut arc (also called strong bridge) is an arc e ∈ E whose removal makes the graph no longer strongly connected. Equivalently, there exist u,v ∈ V, such that all u-v walks contain e. Cut arcs are a fundamental graph-theoretic notion, with countless applications, especially in reachability problems. In this paper we initiate the study of cut paths, as a generalisation of cut arcs, which we naturally define as those paths P for which there exist u,v ∈ V, such that all u-v walks contain P as subwalk. We first prove various properties of cut paths and define their remainder structures, which we use to present a simple O(m)-time verification algorithm for a cut path (|V| = n, |E| = m). Secondly, we apply cut paths and their remainder structures to improve several reachability problems from bioinformatics, as follows. A walk is called safe if it is a subwalk of every node-covering closed walk of a strongly connected graph. Multi-safety is defined analogously, by considering node-covering sets of closed walks instead. We show that cut paths provide simple O(m)-time algorithms verifying if a walk is safe or multi-safe. For multi-safety, we present the first linear time algorithm, while for safety, we present a simple algorithm where the state-of-the-art employed complex data structures. Finally we show that the simultaneous computation of remainder structures of all subwalks of a cut path can be performed in linear time, since they are related in a structured way. These properties yield an O(mn)-time algorithm outputting all maximal multi-safe walks, improving over the state-of-the-art algorithm running in time O(m²+n³). The results of this paper only scratch the surface in the study of cut paths, and we believe a rich structure of a graph can be revealed, considering the perspective of a path, instead of just an arc.
Cite as

Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, and Elia C. Zirondelli. Cut Paths and Their Remainder Structure, with Applications. In 40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 254, pp. 17:1-17:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{cairo_et_al:LIPIcs.STACS.2023.17,
  author =	{Cairo, Massimo and Khan, Shahbaz and Rizzi, Romeo and Schmidt, Sebastian and Tomescu, Alexandru I. and Zirondelli, Elia C.},
  title =	{{Cut Paths and Their Remainder Structure, with Applications}},
  booktitle =	{40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023)},
  pages =	{17:1--17:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-266-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{254},
  editor =	{Berenbrink, Petra and Bouyer, Patricia and Dawar, Anuj and Kant\'{e}, Mamadou Moustapha},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2023.17},
  URN =		{urn:nbn:de:0030-drops-176690},
  doi =		{10.4230/LIPIcs.STACS.2023.17},
  annote =	{Keywords: reachability, cut arc, strong bridge, covering walk, safety, persistence, essentiality, genome assembly}
}
Document
PACE Solver Description
DOI: 10.4230/LIPIcs.IPEC.2022.28
PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set

Authors: Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt

Published in: LIPIcs, Volume 249, 17th International Symposium on Parameterized and Exact Computation (IPEC 2022)

Abstract
In this document we describe the techniques we used and implemented for our submission to the Parameterized Algorithms and Computational Experiments Challenge (PACE) 2022. The given problem is Directed Feedback Vertex Set (DFVS), where one is given a directed graph G = (V,E) and wants to find a minimum S ⊆ V such that G-S is acyclic. We approach this problem by first exhaustively applying a set of reduction rules. In order to find a minimum DFVS on the remaining instance, we create and solve a series of Vertex Cover instances.
Cite as

Sebastian Angrick, Ben Bals, Katrin Casel, Sarel Cohen, Tobias Friedrich, Niko Hastrich, Theresa Hradilak, Davis Issac, Otto Kißig, Jonas Schmidt, and Leo Wendt. PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set. In 17th International Symposium on Parameterized and Exact Computation (IPEC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 249, pp. 28:1-28:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{angrick_et_al:LIPIcs.IPEC.2022.28,
  author =	{Angrick, Sebastian and Bals, Ben and Casel, Katrin and Cohen, Sarel and Friedrich, Tobias and Hastrich, Niko and Hradilak, Theresa and Issac, Davis and Ki{\ss}ig, Otto and Schmidt, Jonas and Wendt, Leo},
  title =	{{PACE Solver Description: Mount Doom - An Exact Solver for Directed Feedback Vertex Set}},
  booktitle =	{17th International Symposium on Parameterized and Exact Computation (IPEC 2022)},
  pages =	{28:1--28:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-260-0},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{249},
  editor =	{Dell, Holger and Nederlof, Jesper},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2022.28},
  URN =		{urn:nbn:de:0030-drops-173847},
  doi =		{10.4230/LIPIcs.IPEC.2022.28},
  annote =	{Keywords: directed feedback vertex set, vertex cover, reduction rules}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.2
Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time

Authors: Sebastian Schmidt and Jarno N. Alanko

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

Abstract
A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy and efficient to use (i.e. without k-mer repetitions and in plain text). Recently, heuristics were presented to compute a near-minimum such representation. We present an algorithm to compute a minimum representation in optimal (linear) time and use it to evaluate the existing heuristics. For that, we present a formalisation of arc-centric bidirected de Bruijn graphs and carefully prove that it accurately models the k-mer spectrum of the input. Our algorithm first constructs the de Bruijn graph in linear time in the length of the input strings (for a fixed-size alphabet). Then it uses a Eulerian-cycle-based algorithm to compute the minimum representation, in time linear in the size of the output.
Cite as

Sebastian Schmidt and Jarno N. Alanko. Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 2:1-2:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{schmidt_et_al:LIPIcs.WABI.2022.2,
  author =	{Schmidt, Sebastian and Alanko, Jarno N.},
  title =	{{Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{2:1--2:21},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.2},
  URN =		{urn:nbn:de:0030-drops-170361},
  doi =		{10.4230/LIPIcs.WABI.2022.2},
  annote =	{Keywords: Spectrum preserving string sets, Eulerian cycle, Suffix tree, Bidirected arc-centric de Bruijn graph, k-mer based methods}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2021.43
Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time

Authors: Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, and Elia C. Zirondelli

Published in: LIPIcs, Volume 198, 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)

Abstract
Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from practical issues (size and errors of real data), and from the fact that problem formulations inherently admit multiple solutions. Given these, at their core, most state-of-the-art assemblers are based on finding non-branching paths (unitigs) in an assembly graph. While such paths constitute only partial assemblies, they are likely to be correct. More precisely, if one defines a genome assembly solution as a closed arc-covering walk of the graph, then unitigs appear in all solutions, being thus safe partial solutions. Until recently, it was open what are all the safe walks of an assembly graph. Tomescu and Medvedev (RECOMB 2016) characterized all such safe walks (omnitigs), thus giving the first safe and complete genome assembly algorithm. Even though omnitig finding was later improved to quadratic time, it remained open whether the crucial linear-time feature of finding unitigs can be attained with omnitigs. We answer this question affirmatively, by describing a surprising O(m)-time algorithm to identify all maximal omnitigs of a graph with n nodes and m arcs, notwithstanding the existence of families of graphs with Θ(mn) total maximal omnitig size. This is based on the discovery of a family of walks (macrotigs) with the property that all the non-trivial omnitigs are univocal extensions of subwalks of a macrotig. This has two consequences: (1) A linear-time output-sensitive algorithm enumerating all maximal omnitigs. (2) A compact O(m) representation of all maximal omnitigs, which allows, e.g., for O(m)-time computation of various statistics on them. Our results close a long-standing theoretical question inspired by practical genome assemblers, originating with the use of unitigs in 1995. We envision our results to be at the core of a reverse transfer from theory to practical and complete genome assembly programs, as has been the case for other key Bioinformatics problems.
Cite as

Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, and Elia C. Zirondelli. Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time. In 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 198, pp. 43:1-43:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{cairo_et_al:LIPIcs.ICALP.2021.43,
  author =	{Cairo, Massimo and Rizzi, Romeo and Tomescu, Alexandru I. and Zirondelli, Elia C.},
  title =	{{Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time}},
  booktitle =	{48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)},
  pages =	{43:1--43:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-195-5},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{198},
  editor =	{Bansal, Nikhil and Merelli, Emanuela and Worrell, James},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2021.43},
  URN =		{urn:nbn:de:0030-drops-141122},
  doi =		{10.4230/LIPIcs.ICALP.2021.43},
  annote =	{Keywords: Graph algorithm, strong connectivity, reachability under failures}
}
Document
Media Exposition
DOI: 10.4230/LIPIcs.SoCG.2021.62
Can You Walk This? Eulerian Tours and IDEA Instructions (Media Exposition)

Authors: Aaron T. Becker, Sándor P. Fekete, Matthias Konitzny, Sebastian Morr, and Arne Schmidt

Published in: LIPIcs, Volume 189, 37th International Symposium on Computational Geometry (SoCG 2021)

Abstract
We illustrate and animate the classic problem of deciding whether a given graph has an Eulerian path. Starting with a collection of instances of increasing difficulty, we present a set of pictorial instructions, and show how they can be used to solve all instances. These IDEA instructions ("A series of nonverbal algorithm assembly instructions") have proven to be both entertaining for experts and enlightening for novices. We (w)rap up with a song and dance to Euler’s original instance.
Cite as

Aaron T. Becker, Sándor P. Fekete, Matthias Konitzny, Sebastian Morr, and Arne Schmidt. Can You Walk This? Eulerian Tours and IDEA Instructions (Media Exposition). In 37th International Symposium on Computational Geometry (SoCG 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 189, pp. 62:1-62:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{becker_et_al:LIPIcs.SoCG.2021.62,
  author =	{Becker, Aaron T. and Fekete, S\'{a}ndor P. and Konitzny, Matthias and Morr, Sebastian and Schmidt, Arne},
  title =	{{Can You Walk This? Eulerian Tours and IDEA Instructions}},
  booktitle =	{37th International Symposium on Computational Geometry (SoCG 2021)},
  pages =	{62:1--62:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-184-9},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{189},
  editor =	{Buchin, Kevin and Colin de Verdi\`{e}re, \'{E}ric},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2021.62},
  URN =		{urn:nbn:de:0030-drops-138616},
  doi =		{10.4230/LIPIcs.SoCG.2021.62},
  annote =	{Keywords: Eulerian tours, algorithms, education, IDEA instructions}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2020.42
Worst-Case Optimal Covering of Rectangles by Disks

Authors: Sándor P. Fekete, Utkarsh Gupta, Phillip Keldenich, Christian Scheffer, and Sahil Shah

Published in: LIPIcs, Volume 164, 36th International Symposium on Computational Geometry (SoCG 2020)

Abstract
We provide the solution for a fundamental problem of geometric optimization by giving a complete characterization of worst-case optimal disk coverings of rectangles: For any λ ≥ 1, the critical covering area A^*(λ) is the minimum value for which any set of disks with total area at least A^*(λ) can cover a rectangle of dimensions λ× 1. We show that there is a threshold value λ₂ = √{√7/2 - 1/4} ≈ 1.035797…, such that for λ < λ₂ the critical covering area A^*(λ) is A^*(λ) = 3π(λ²/16 + 5/32 + 9/(256λ²)), and for λ ≥ λ₂, the critical area is A^*(λ)=π(λ²+2)/4; these values are tight. For the special case λ=1, i.e., for covering a unit square, the critical covering area is 195π/256 ≈ 2.39301…. The proof uses a careful combination of manual and automatic analysis, demonstrating the power of the employed interval arithmetic technique.
Cite as

Sándor P. Fekete, Utkarsh Gupta, Phillip Keldenich, Christian Scheffer, and Sahil Shah. Worst-Case Optimal Covering of Rectangles by Disks. In 36th International Symposium on Computational Geometry (SoCG 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 164, pp. 42:1-42:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{fekete_et_al:LIPIcs.SoCG.2020.42,
  author =	{Fekete, S\'{a}ndor P. and Gupta, Utkarsh and Keldenich, Phillip and Scheffer, Christian and Shah, Sahil},
  title =	{{Worst-Case Optimal Covering of Rectangles by Disks}},
  booktitle =	{36th International Symposium on Computational Geometry (SoCG 2020)},
  pages =	{42:1--42:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-143-6},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{164},
  editor =	{Cabello, Sergio and Chen, Danny Z.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2020.42},
  URN =		{urn:nbn:de:0030-drops-122003},
  doi =		{10.4230/LIPIcs.SoCG.2020.42},
  annote =	{Keywords: Disk covering, critical density, covering coefficient, tight worst-case bound, interval arithmetic, approximation}
}
Document
DOI: 10.4230/OASIcs.ATMOS.2019.7
Vehicle Capacity-Aware Rerouting of Passengers in Delay Management

Authors: Matthias Müller-Hannemann, Ralf Rückert, and Sebastian S. Schmidt

Published in: OASIcs, Volume 75, 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019)

Abstract
Due to the significant growth in passenger numbers, higher vehicle load factors and crowding become more and more of an issue in public transport. For safety reasons and because of an unsatisfactory discomfort, standing of passengers is rather limited in high-speed long-distance trains. In case of delays and (partially) cancelled trains, many passengers have to be rerouted. State-of-the-art rerouting merely focuses on minimizing delay at the destination of affected passengers but neglects limited vehicle capacities and crowding. Not considering capacities allows using highly efficient shortest path algorithms like RAPTOR or the connection scan algorithm (CSA). In this paper, we study the more complicated scenario where passengers compete for scarce capacities. This can be modeled as a piece-wise linear, convex cost multi-source multi-commodity unsplittable flow problem where each passenger group which has to be rerouted corresponds to a commodity. We compare a path-based integer linear programming (ILP) model with a heuristic greedy approach. In experiments with instances from German long-distance train traffic, we quantify the importance of considering vehicle capacities in case of train cancellations. We observe a tradeoff: The ILP approach slightly outperforms the greedy approach and both are much better than capacity unaware rerouting in quality, while the greedy algorithm runs more than three times faster.
Cite as

Matthias Müller-Hannemann, Ralf Rückert, and Sebastian S. Schmidt. Vehicle Capacity-Aware Rerouting of Passengers in Delay Management. In 19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019). Open Access Series in Informatics (OASIcs), Volume 75, pp. 7:1-7:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{mullerhannemann_et_al:OASIcs.ATMOS.2019.7,
  author =	{M\"{u}ller-Hannemann, Matthias and R\"{u}ckert, Ralf and Schmidt, Sebastian S.},
  title =	{{Vehicle Capacity-Aware Rerouting of Passengers in Delay Management}},
  booktitle =	{19th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2019)},
  pages =	{7:1--7:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-128-3},
  ISSN =	{2190-6807},
  year =	{2019},
  volume =	{75},
  editor =	{Cacchiani, Valentina and Marchetti-Spaccamela, Alberto},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ATMOS.2019.7},
  URN =		{urn:nbn:de:0030-drops-114192},
  doi =		{10.4230/OASIcs.ATMOS.2019.7},
  annote =	{Keywords: Delay management, passenger flows, vehicle capacities, rerouting}
}
Document
DOI: 10.4230/OASIcs.ATMOS.2013.1
Recoverable Robust Timetable Information

Authors: Marc Goerigk, Sacha Heße, Matthias Müller-Hannemann, Marie Schmidt, and Anita Schöbel

Published in: OASIcs, Volume 33, 13th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (2013)

Abstract
Timetable information is the process of determining a suitable travel route for a passenger. Due to delays in the original timetable, in practice it often happens that the travel route cannot be used as originally planned. For a passenger being already en route, it would hence be useful to know about alternatives that ensure that his/her destination can be reached. In this work we propose a recoverable robust approach to timetable information; i.e., we aim at finding travel routes that can easily be updated when delays occur during the journey. We present polynomial-time algorithms for this problem and evaluate the performance of the routes obtained this way on schedule data of the German train network of 2013 and simulated delay scenarios.
Cite as

Marc Goerigk, Sacha Heße, Matthias Müller-Hannemann, Marie Schmidt, and Anita Schöbel. Recoverable Robust Timetable Information. In 13th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems. Open Access Series in Informatics (OASIcs), Volume 33, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{goerigk_et_al:OASIcs.ATMOS.2013.1,
  author =	{Goerigk, Marc and He{\ss}e, Sacha and M\"{u}ller-Hannemann, Matthias and Schmidt, Marie and Sch\"{o}bel, Anita},
  title =	{{Recoverable Robust Timetable Information}},
  booktitle =	{13th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems},
  pages =	{1--14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-58-3},
  ISSN =	{2190-6807},
  year =	{2013},
  volume =	{33},
  editor =	{Frigioni, Daniele and Stiller, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ATMOS.2013.1},
  URN =		{urn:nbn:de:0030-drops-42407},
  doi =		{10.4230/OASIcs.ATMOS.2013.1},
  annote =	{Keywords: timetable information, recoverable robustness, delay scenarios}
}
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