6 Search Results for "Giegerich, Robert"

Document
DOI: 10.4230/LIPIcs.ESA.2025.94
Faster Algorithm for Bounded Tree Edit Distance in the Low-Distance Regime

Authors: Tomasz Kociumaka and Ali Shahali

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet Σ. It is defined as the minimum number of node edits - insertions, deletions, and relabelings - required to transform one tree into the other. The weighted variant assigns costs ≥ 1 to edits (based on node labels), minimizing total cost rather than edit count. The unweighted tree edit distance between two trees of total size n can be computed in 𝒪(n^{2.6857}) time; in contrast, determining the weighted tree edit distance is fine-grained equivalent to the All-Pairs Shortest Paths (APSP) problem and requires n³/2^Ω(√{log n}) time [Nogler, Polak, Saha, Vassilevska Williams, Xu, Ye; STOC'25]. These impractical super-quadratic times for large, similar trees motivate the bounded version, parameterizing runtime by the distance k to enable faster algorithms for k ≪ n. Prior algorithms for bounded unweighted edit distance achieve 𝒪(nk²log n) [Akmal & Jin; ICALP’21] and 𝒪(n + k⁷log k) [Das, Gilbert, Hajiaghayi, Kociumaka, Saha; STOC'23]. For weighted, only 𝒪(n + k^{15}) is known [Das, Gilbert, Hajiaghayi, Kociumaka, Saha; STOC'23]. We present an 𝒪(n + k⁶ log k)-time algorithm for bounded tree edit distance in both weighted/unweighted settings. First, we devise a simpler weighted 𝒪(nk² log n)-time algorithm. Next, we exploit periodic structures in input trees via an optimized universal kernel: modifying prior 𝒪(n)-time 𝒪(k⁵)-size kernels to generate such structured instances, enabling efficient analysis.
Cite as

Tomasz Kociumaka and Ali Shahali. Faster Algorithm for Bounded Tree Edit Distance in the Low-Distance Regime. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 94:1-94:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kociumaka_et_al:LIPIcs.ESA.2025.94,
  author =	{Kociumaka, Tomasz and Shahali, Ali},
  title =	{{Faster Algorithm for Bounded Tree Edit Distance in the Low-Distance Regime}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{94:1--94:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.94},
  URN =		{urn:nbn:de:0030-drops-245634},
  doi =		{10.4230/LIPIcs.ESA.2025.94},
  annote =	{Keywords: tree edit distance, edit distance, kernelization, dynamic programming}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.130
An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands

Authors: Ahmed Shalaby and Damien Woods

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
The information-encoding molecules RNA and DNA bind via base pairing to form an exponentially large set of secondary structures. Practitioners need algorithms to predict the most favoured structures, called minimum free energy (MFE) structures, or to compute a partition function that allows assigning a probability to any structure. MFE prediction is NP-hard in the presence pseudoknots - base pairings that violate a restricted planarity condition. However, for single-stranded unpseudoknotted structures, there are polynomial time dynamic programming algorithms. For multiple strands, the problem is significantly more complicated: Codon, Hajiaghayi and Thachuk [DNA27, 2021] proved it NP-hard for N bases and 𝒪(N) strands. Dirks, Bois, Schaeffer, Winfree and Pierce [SIAM Review, 2007] gave a polynomial time partition function algorithm for multiple (𝒪(1)) strands, now widely-used, however their technique did not generalise to MFE which they left open. We give an 𝒪(N⁴) time algorithm for unpseudoknotted multiple (𝒪(1)) strand MFE prediction, answering the open problem from Dirks et al. The challenge lies in considering the rotational symmetry of secondary structures, a global feature not immediately amenable to local subproblem decomposition used in dynamic programming. Our proof has two main technical contributions: First, a characterisation of symmetric secondary structures implying only quadratically many need to be considered when computing the rotational symmetry penalty. Second, that bound is leveraged by a backtracking algorithm to efficiently find the MFE in an exponential space of contenders.
Cite as

Ahmed Shalaby and Damien Woods. An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 130:1-130:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{shalaby_et_al:LIPIcs.ICALP.2025.130,
  author =	{Shalaby, Ahmed and Woods, Damien},
  title =	{{An Efficient Algorithm to Compute the Minimum Free Energy of Interacting Nucleic Acid Strands}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{130:1--130:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.130},
  URN =		{urn:nbn:de:0030-drops-235071},
  doi =		{10.4230/LIPIcs.ICALP.2025.130},
  annote =	{Keywords: Minimum free energy, MFE, partition function, nucleic acid, DNA, RNA, secondary structure, computational complexity, algorithm analysis and design, dynamic programming}
}
Document
DOI: 10.4230/LITES-v004-i001-a004
How Is Your Satellite Doing? Battery Kinetics with Recharging and Uncertainty

Authors: Holger Hermanns, Jan Krčál, and Gilles Nies

Published in: LITES, Volume 4, Issue 1 (2017). Leibniz Transactions on Embedded Systems, Volume 4, Issue 1

Abstract
The kinetic battery model is a popular model of the dynamic behaviour of a conventional battery, useful to predict or optimize the time until battery depletion. The model however lacks certain obvious aspects of batteries in-the-wild, especially with respect to the effects of random influences and the behaviour when charging up to capacity limits.This paper considers the kinetic battery model with limited capacity in the context of piecewise constant yet random charging and discharging. We provide exact representations of the battery behaviour wherever possible, and otherwise develop safe approximations that bound the probability distribution of the battery state from above and below. The resulting model enables the time-dependent evaluation of the risk of battery depletion. This is demonstrated in an extensive dependability study of a nano satellite currently orbiting the earth.
Cite as

Holger Hermanns, Jan Krčál, and Gilles Nies. How Is Your Satellite Doing? Battery Kinetics with Recharging and Uncertainty. In LITES, Volume 4, Issue 1 (2017). Leibniz Transactions on Embedded Systems, Volume 4, Issue 1, pp. 04:1-04:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@Article{hermanns_et_al:LITES-v004-i001-a004,
  author =	{Hermanns, Holger and Kr\v{c}\'{a}l, Jan and Nies, Gilles},
  title =	{{How Is Your Satellite Doing? Battery Kinetics with Recharging and Uncertainty}},
  journal =	{Leibniz Transactions on Embedded Systems},
  pages =	{04:1--04:28},
  ISSN =	{2199-2002},
  year =	{2017},
  volume =	{4},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES-v004-i001-a004},
  URN =		{urn:nbn:de:0030-drops-192655},
  doi =		{10.4230/LITES-v004-i001-a004},
  annote =	{Keywords: Battery Power, Depletion Risk, Bounded Charging and Discharging, Stochastic Load, Distribution Bounds}
}
Document
DOI: 10.4230/OASIcs.GCB.2013.110
Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment

Authors: Benedikt Löwes and Robert Giegerich

Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013

Abstract
Several algorithms have been suggested for minisatellite alignment. Their time complexity is high -- close to O(n^3) -- due to the necessary reconstruction of duplication histories. We investigate the uniqueness of optimal alignments computed under the common single-copy duplication model. To this extent, it is necessary to avoid ambiguity in the algorithm employed. We re-code the ARLEM algorithm in the form of a grammar, and apply a disambiguation technique which uses a mapping to a canonical representation of minisatellite alignments. Having arrived at a non-ambiguous algorithm this way, we demonstrate that the underlying model -- independent of the algorithm -- gives rise to an exorbitant number of different, co-optimal alignments when applied to real-world data. We conclude that alignment-free methods should be considered for minisatellite comparison.
Cite as

Benedikt Löwes and Robert Giegerich. Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 110-124, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{lowes_et_al:OASIcs.GCB.2013.110,
  author =	{L\"{o}wes, Benedikt and Giegerich, Robert},
  title =	{{Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{110--124},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-59-0},
  ISSN =	{2190-6807},
  year =	{2013},
  volume =	{34},
  editor =	{Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.110},
  URN =		{urn:nbn:de:0030-drops-42285},
  doi =		{10.4230/OASIcs.GCB.2013.110},
  annote =	{Keywords: minisatellite alignment, dynamic programming, ambiguity}
}
Document
DOI: 10.4230/DagSemRep.89
Functional Programming in the Real World (Dagstuhl Seminar 9420)

Authors: Robert Giegerich and John Hughes

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
Cite as

Robert Giegerich and John Hughes. Functional Programming in the Real World (Dagstuhl Seminar 9420). Dagstuhl Seminar Report 89, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1994)

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@TechReport{giegerich_et_al:DagSemRep.89,
  author =	{Giegerich, Robert and Hughes, John},
  title =	{{Functional Programming in the Real World (Dagstuhl Seminar 9420)}},
  pages =	{1--22},
  ISSN =	{1619-0203},
  year =	{1994},
  type = 	{Dagstuhl Seminar Report},
  number =	{89},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.89},
  URN =		{urn:nbn:de:0030-drops-149776},
  doi =		{10.4230/DagSemRep.89},
}
Document
DOI: 10.4230/DagSemRep.13
Code Generation - Concepts, Tools, Techniques (Dagstuhl Seminar 9121)

Authors: Robert Giegerich and Susan L. Graham

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
Cite as

Robert Giegerich and Susan L. Graham. Code Generation - Concepts, Tools, Techniques (Dagstuhl Seminar 9121). Dagstuhl Seminar Report 13, pp. 1-31, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1991)

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@TechReport{giegerich_et_al:DagSemRep.13,
  author =	{Giegerich, Robert and Graham, Susan L.},
  title =	{{Code Generation - Concepts, Tools, Techniques (Dagstuhl Seminar 9121)}},
  pages =	{1--31},
  ISSN =	{1619-0203},
  year =	{1991},
  type = 	{Dagstuhl Seminar Report},
  number =	{13},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemRep.13},
  URN =		{urn:nbn:de:0030-drops-149011},
  doi =		{10.4230/DagSemRep.13},
}
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