4 Search Results for "Bertram, Nico"

Document

DOI: 10.4230/LIPIcs.SEA.2024.1

Move-r: Optimizing the r-index

Authors: Nico Bertram, Johannes Fischer, and Lukas Nalbach

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

Abstract

We present a static text index called Move-r, which is a highly optimized version of the r-index ([Travis Gagie et al., 2020] Gagie et al., 2020) that encorporates recent theoretical developments of the move data structure ([Takaaki Nishimoto and Yasuo Tabei, 2021] Nishimoto and Tabei, 2021). The r-index is the method of choice for indexing highly repetitive texts, such as different versions of a text document or DNA from the same species, as it exploits the compressibilty of the underlying data. With Move-r, we can answer count- and locate queries 2-35 (typically 15) times as fast as with any other r-index supporting locate queries while being 0.8-2.5 (typically 2) times as large. A Move-r index can be constructed 0.9-2 (typically 2) times as fast while using 1/3-1 (typically 1/2) times as much space.

Cite as

Nico Bertram, Johannes Fischer, and Lukas Nalbach. Move-r: Optimizing the r-index. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 1:1-1:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bertram_et_al:LIPIcs.SEA.2024.1,
  author =	{Bertram, Nico and Fischer, Johannes and Nalbach, Lukas},
  title =	{{Move-r: Optimizing the r-index}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{1:1--1:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.1},
  URN =		{urn:nbn:de:0030-drops-203662},
  doi =		{10.4230/LIPIcs.SEA.2024.1},
  annote =	{Keywords: Compressed Text Index, Burrows-Wheeler Transform}
}

Document

Survey

DOI: 10.4230/TGDK.2.1.1

Towards Representing Processes and Reasoning with Process Descriptions on the Web

Authors: Andreas Harth, Tobias Käfer, Anisa Rula, Jean-Paul Calbimonte, Eduard Kamburjan, and Martin Giese

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

Abstract

We work towards a vocabulary to represent processes and temporal logic specifications as graph-structured data. Different fields use incompatible terminologies for describing essentially the same process-related concepts. In addition, processes can be represented from different perspectives and levels of abstraction: both state-centric and event-centric perspectives offer distinct insights into the underlying processes. In this work, we strive to unify the representation of processes and related concepts by leveraging the power of knowledge graphs. We survey approaches to representing processes and reasoning with process descriptions from different fields and provide a selection of scenarios to help inform the scope of a unified representation of processes. We focus on processes that can be executed and observed via web interfaces. We propose to provide a representation designed to combine state-centric and event-centric perspectives while incorporating temporal querying and reasoning capabilities on temporal logic specifications. A standardised vocabulary and representation for processes and temporal specifications would contribute towards bridging the gap between the terminologies from different fields and fostering the broader application of methods involving temporal logics, such as formal verification and program synthesis.

Cite as

Andreas Harth, Tobias Käfer, Anisa Rula, Jean-Paul Calbimonte, Eduard Kamburjan, and Martin Giese. Towards Representing Processes and Reasoning with Process Descriptions on the Web. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 1:1-1:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{harth_et_al:TGDK.2.1.1,
  author =	{Harth, Andreas and K\"{a}fer, Tobias and Rula, Anisa and Calbimonte, Jean-Paul and Kamburjan, Eduard and Giese, Martin},
  title =	{{Towards Representing Processes and Reasoning with Process Descriptions on the Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:32},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.1},
  URN =		{urn:nbn:de:0030-drops-198583},
  doi =		{10.4230/TGDK.2.1.1},
  annote =	{Keywords: Process modelling, Process ontology, Temporal logic, Web services}
}

Document

DOI: 10.4230/LIPIcs.SEA.2022.10

A Parallel Framework for Approximate Max-Dicut in Partitionable Graphs

Authors: Nico Bertram, Jonas Ellert, and Johannes Fischer

Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)

Abstract

Computing a maximum cut in undirected and weighted graphs is a well studied problem and has many practical solutions that also scale well in shared memory (despite its NP-completeness). For its counterpart in directed graphs, however, we are not aware of practical solutions that also utilize parallelism. We engineer a framework that computes a high quality approximate cut in directed and weighted graphs by using a graph partitioning approach. The general idea is to partition a graph into k subgraphs using a parallel partitioning algorithm of our choice (the first ingredient of our framework). Then, for each subgraph in parallel, we compute a cut using any polynomial time approximation algorithm (the second ingredient). In a final step, we merge the locally computed solutions using a high-quality or exact parallel Max-Dicut algorithm (the third ingredient). On graphs that can be partitioned well, the quality of the computed cut is significantly better than the best cut achieved by any linear time algorithm. This is particularly relevant for large graphs, where linear time algorithms used to be the only feasible option.

Cite as

Nico Bertram, Jonas Ellert, and Johannes Fischer. A Parallel Framework for Approximate Max-Dicut in Partitionable Graphs. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 10:1-10:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bertram_et_al:LIPIcs.SEA.2022.10,
  author =	{Bertram, Nico and Ellert, Jonas and Fischer, Johannes},
  title =	{{A Parallel Framework for Approximate Max-Dicut in Partitionable Graphs}},
  booktitle =	{20th International Symposium on Experimental Algorithms (SEA 2022)},
  pages =	{10:1--10:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-251-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{233},
  editor =	{Schulz, Christian and U\c{c}ar, Bora},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.10},
  URN =		{urn:nbn:de:0030-drops-165441},
  doi =		{10.4230/LIPIcs.SEA.2022.10},
  annote =	{Keywords: maximum directed cut, graph partitioning, algorithm engineering, approximation, parallel algorithms}
}

Document

DOI: 10.4230/LIPIcs.ESA.2021.15

Lyndon Words Accelerate Suffix Sorting

Authors: Nico Bertram, Jonas Ellert, and Johannes Fischer

Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)

Abstract

Suffix sorting is arguably the most fundamental building block in string algorithmics, like regular sorting in the broader field of algorithms. It is thus not surprising that the literature is full of algorithms for suffix sorting, in particular focusing on their practicality. However, the advances on practical suffix sorting stalled with the emergence of the DivSufSort algorithm more than 10 years ago, which, up to date, has remained the fastest suffix sorter. This article shows how properties of Lyndon words can be exploited algorithmically to accelerate suffix sorting again. Our new algorithm is 6-19% faster than DivSufSort on real-world texts, and up to three times as fast on artificial repetitive texts. It can also be parallelized, where similar speedups can be observed. Thus, we make the first advances in practical suffix sorting after more than a decade of standstill.

Cite as

Nico Bertram, Jonas Ellert, and Johannes Fischer. Lyndon Words Accelerate Suffix Sorting. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 15:1-15:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{bertram_et_al:LIPIcs.ESA.2021.15,
  author =	{Bertram, Nico and Ellert, Jonas and Fischer, Johannes},
  title =	{{Lyndon Words Accelerate Suffix Sorting}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{15:1--15:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-204-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{204},
  editor =	{Mutzel, Petra and Pagh, Rasmus 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.2021.15},
  URN =		{urn:nbn:de:0030-drops-145961},
  doi =		{10.4230/LIPIcs.ESA.2021.15},
  annote =	{Keywords: Suffix array, suffix sorting, Lyndon words, string algorithms}
}

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