96 Search Results for "Li Gørtz, Inge"

Volume

LIPIcs, Volume 274

31st Annual European Symposium on Algorithms (ESA 2023)

ESA 2023, September 4-6, 2023, Amsterdam, The Netherlands

Editors: Inge Li Gørtz, Martin Farach-Colton, Simon J. Puglisi, and Grzegorz Herman

Volume

LIPIcs, Volume 161

31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)

CPM 2020, June 17-19, 2020, Copenhagen, Denmark

Editors: Inge Li Gørtz and Oren Weimann

Document
DOI: 10.4230/LIPIcs.SEA.2026.7
From Relative Compression to Hierarchical Compression

Authors: Philip Bille, Inge Li Gørtz, and Máximo Pérez-López

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
We introduce a framework to use any relative compression algorithm as a subroutine for hierarchical relative compression. In a dataset consisting of n sequences, it consists of constructing a rooted tree on the sequences, using hashing and similarity techniques, and compressing the children of a node relative to their parent. We build up on previous techniques [Bille et al., 2023], and optimize them further for computational efficiency. We test our framework with three existing relative compression algorithms on six genomic datasets, and we show that in datasets that contain heterogeneous data, hierarchical relative compression improves the compression ratio by a factor 2 or more, when compared to relative compression to a single sequence. Apart from compression ratio, we also explore the trade-offs with respect to compression speed, dataset decompression speed, and average sequence decompression speed. With two of the surveyed algorithms, dataset decompression becomes faster and sequence decompression remains practical, at the cost of compression time, which remains competitive for the datasets with highest variability.
Cite as

Philip Bille, Inge Li Gørtz, and Máximo Pérez-López. From Relative Compression to Hierarchical Compression. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 7:1-7:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{bille_et_al:LIPIcs.SEA.2026.7,
  author =	{Bille, Philip and G{\o}rtz, Inge Li and P\'{e}rez-L\'{o}pez, M\'{a}ximo},
  title =	{{From Relative Compression to Hierarchical Compression}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{7:1--7:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.7},
  URN =		{urn:nbn:de:0030-drops-260117},
  doi =		{10.4230/LIPIcs.SEA.2026.7},
  annote =	{Keywords: Relative compression, RLZ, string collections, compressed representation, data structures, efficient algorithms}
}
Document
DOI: 10.4230/LIPIcs.SEA.2026.10
Compressing Highly Repetitive Binary Trees with an Application to Range Minimum Queries

Authors: Gabriel Carmona and Filippo Lari

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
Tree compression is a well-studied area that aims at reducing the size of tree representations by exploiting different forms of repetition. While the underlying theory is well understood, there is still significant room for experimental investigation, particularly in the design of compressed representations that efficiently support navigational queries. In this work, we address the problem of designing, engineering, and experimentally evaluating a compression technique for unlabeled binary trees based on repeated subtrees, yielding the minimal Directed Acyclic Graph (DAG) of the input tree. We show how this representation can be computed in linear time and space directly from a succinct encoding of the tree, and how it can be augmented with compact auxiliary data structures to support Lowest Common Ancestor (LCA) queries. When the input tree is the Cartesian tree of an array, LCA queries can be used to answer Range Minimum Queries (RMQs) on the underlying array. This is particularly relevant in the encoding model, where the array is not accessible at query time, and a space lower bound of 2n-O(log n) bits is known. Given the numerous applications of RMQs, we use this problem as a case study for our experimental evaluation, testing our implementation on 11 real-world datasets. Our experiments show that, on almost every dataset, our implementation is the most space-efficient, using as few as 0.11n bits, while still delivering practical query times.
Cite as

Gabriel Carmona and Filippo Lari. Compressing Highly Repetitive Binary Trees with an Application to Range Minimum Queries. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{carmona_et_al:LIPIcs.SEA.2026.10,
  author =	{Carmona, Gabriel and Lari, Filippo},
  title =	{{Compressing Highly Repetitive Binary Trees with an Application to Range Minimum Queries}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{10:1--10:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.10},
  URN =		{urn:nbn:de:0030-drops-260140},
  doi =		{10.4230/LIPIcs.SEA.2026.10},
  annote =	{Keywords: tree compression, range minimum query, compact data structures, algorithm engineering, experimental evaluation}
}
Document
DOI: 10.4230/LIPIcs.SEA.2026.22
Engineering Fully Dynamic Convex Hulls

Authors: Ivor van der Hoog, Henrik Reinstädtler, and Eva Rotenberg

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
We present a new fully dynamic algorithm for maintaining convex hulls under insertions and deletions while supporting geometric queries. Our approach combines the logarithmic method with a deletion-only convex hull data structure, achieving amortised update times of O(log n log log n) and query times of O(log² n). We provide a robust and non-trivial implementation that supports point-location queries, a challenging and non-decomposable class of convex hull queries. We evaluate our implementation against the state of the art, including a new naive baseline that rebuilds the convex hull whenever an update affects it. On hulls that include polynomially many data points (e.g. Θ(n^ε) for some ε), such as the ones that often occur in practice, our method outperforms all other techniques. Update-heavy workloads strongly favour our approach, which is in line with our theoretical guarantees. Yet, our method remains competitive all the way down to when the update to query ratio is 1 to 10. Experiments on real-world data sets furthermore reveal that existing fully dynamic techniques suffer from significant robustness issues. In contrast, our implementation remains stable across all tested inputs.
Cite as

Ivor van der Hoog, Henrik Reinstädtler, and Eva Rotenberg. Engineering Fully Dynamic Convex Hulls. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 22:1-22:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{vanderhoog_et_al:LIPIcs.SEA.2026.22,
  author =	{van der Hoog, Ivor and Reinst\"{a}dtler, Henrik and Rotenberg, Eva},
  title =	{{Engineering Fully Dynamic Convex Hulls}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{22:1--22:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.22},
  URN =		{urn:nbn:de:0030-drops-260264},
  doi =		{10.4230/LIPIcs.SEA.2026.22},
  annote =	{Keywords: Convex hulls, fully-dynamic data structures, robustness}
}
Document
DOI: 10.4230/LIPIcs.SEA.2026.16
Efficient Large-Scale Text Precompression via Approximate LZ77 Parsings

Authors: Patrick Dinklage

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
The LZ77 [Lempel and Ziv, 1977] compression scheme is ubiquitous: it lies at the core of everyday general-purpose standard compressors such as gzip or zstd, but also behind the scenes of many applications such as the compression of payloads transmitted in networks. Computing the exact LZ77 parsing is largely solved in theory: it can be done in sublinear time and space, in compressed space and in external memory, to name but some scenarios. However, these approaches are often impractical for everyday use due to their intensive time or space requirements. Standard compressors tackle this issue by introducing heuristics that go hand in hand with sophisticated encoding schemes to achieve very good compression fast and in small space, however, they only have a local view (e.g., a sliding window) on the input, potentially missing out on long-range repetitions that may be located far apart from one another. In this work, we design and implement - in C++ and leveraging shared-memory parallelism - compression pipelines that first precompress the input using an approximate LZ77 parsing taking care of long-range repetitions. This then serves as an assist to standard compressors for producing a succinct encoding of the remaining short and local repetitions. Similar approaches have been considered by [Kosolobov et al., 2020] and [Nalbach, 2024], respectively using Relative Lempel Ziv [Kuruppu et al. 2010] or the string synchronizing set [Kempa & Kociumaka, 2019]. We fill a gap taking the route via the prefix-free parsing [Boucher et al., 2019], using an intermediate result of [Hong et al., 2023]. On large repetitive inputs of tens of gigabytes, our pipelines are orders of magnitudes faster than the state of the art for computing the exact LZ77 parsing, use space less than the input size and still - despite producing more phrases - achieve the best overall compression in comparison to related work.
Cite as

Patrick Dinklage. Efficient Large-Scale Text Precompression via Approximate LZ77 Parsings. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 16:1-16:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{dinklage:LIPIcs.SEA.2026.16,
  author =	{Dinklage, Patrick},
  title =	{{Efficient Large-Scale Text Precompression via Approximate LZ77 Parsings}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{16:1--16:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.16},
  URN =		{urn:nbn:de:0030-drops-260204},
  doi =		{10.4230/LIPIcs.SEA.2026.16},
  annote =	{Keywords: compression, algorithm engineering, parallel computation}
}
Artifact
Software
DOI: 10.4230/artifacts.26213
Hierarchical Relative Compression reference implementation

Authors: Philip Bille, Inge Li Gørtz, and Máximo Pérez-López

Abstract
Cite as

Philip Bille, Inge Li Gørtz, Máximo Pérez-López. Hierarchical Relative Compression reference implementation (Software, Source code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@misc{dagstuhl-artifact-26213,
   title = {{Hierarchical Relative Compression reference implementation}}, 
   author = {Bille, Philip and G{\o}rtz, Inge Li and P\'{e}rez-L\'{o}pez, M\'{a}ximo},
   note = {Software, version 1.0., Supported by Danish Research Council grant 10.46540/3105-00302B (visited on 2026-06-15)},
   url = {https://gitlab.gbar.dtu.dk/hierarchical-relative-compression/hrcimplementation},
   doi = {10.4230/artifacts.26213},
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.5
Efficient Grammar Compression via RLZ-Based RePair

Authors: Rahul Varki, Travis Gagie, and Christina Boucher

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
Among grammar-based compression techniques, RePair is a notable offline encoding scheme known for its simplicity and powerful combinatorial properties, producing compact grammars by repeatedly replacing the most frequent adjacent pairs of symbols, known as bigrams. However, RePair’s memory usage scales poorly with input size, as it loads the entire text into memory. In contrast, Relative Lempel-Ziv (RLZ) parsing offers a scalable and lightweight online encoding scheme that losslessly represents a text in terms of phrases that refer to a reference string, but it often fails to expose deeper structural patterns. We introduce an algorithm that produces a RePair grammar from the RLZ parse of the input, leveraging the strengths of both methods. Our method, RLZ-RePair, performs bigram replacements systematically, preserving the integrity of the RLZ phrases throughout the RePair iterations. When the reference is well chosen, our method achieves the same grammar as standard RePair while significantly reducing both memory usage and the number of bigram replacements. In particular, we show that RLZ-RePair can reduce memory usage by more than 80% while incurring only a modest runtime increase compared to RePair. To our knowledge, RLZ-RePair is one of the first scalable methods that constructs exact RePair grammars, resulting in a grammar-based compressor that is both practical for large datasets and faithful to the theoretical elegance of RePair.
Cite as

Rahul Varki, Travis Gagie, and Christina Boucher. Efficient Grammar Compression via RLZ-Based RePair. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 5:1-5:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{varki_et_al:LIPIcs.CPM.2026.5,
  author =	{Varki, Rahul and Gagie, Travis and Boucher, Christina},
  title =	{{Efficient Grammar Compression via RLZ-Based RePair}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{5:1--5:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.5},
  URN =		{urn:nbn:de:0030-drops-259310},
  doi =		{10.4230/LIPIcs.CPM.2026.5},
  annote =	{Keywords: RePair, RLZ, Grammar Compression}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.14
Hardness Results on Characteristics for Elastic-Degenerate Strings

Authors: Dominik Köppl and Jannik Olbrich

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores a character at each of its positions, generalizations consider a set of characters (indeterminate strings), a set of strings of equal length (generalized degenerate strings, or shortly GD strings), or a set of strings of arbitrary lengths (elastic-degenerate strings, or shortly ED strings). These generalizations are of importance to compactly represent such type of data, and find applications in bioinformatics for representing and maintaining a set of genetic sequences of the same taxonomy or a multiple sequence alignment. To be of use, attention has been drawn to answering various query types such as pattern matching or measuring similarity of ED strings by generalizing techniques known to plain strings. However, for some types of queries, it has been shown that a generalization of a polynomial-time solvable query on classic strings becomes NP-hard on ED strings, e.g. [Russo et al., 2022]. In that light, we wonder about other types of queries that are of particular interest to bioinformatics: unique substrings, absent words, anti-powers, longest previous factors, and Lempel-Ziv-like compression schemes. While we obtain a polynomial time algorithm for a variation of longest previous factors, we show that all other problems are NP-hard to compute, some of them even under the restriction that the input can be modeled as an indeterminate or GD string.
Cite as

Dominik Köppl and Jannik Olbrich. Hardness Results on Characteristics for Elastic-Degenerate Strings. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 14:1-14:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{koppl_et_al:LIPIcs.CPM.2026.14,
  author =	{K\"{o}ppl, Dominik and Olbrich, Jannik},
  title =	{{Hardness Results on Characteristics for Elastic-Degenerate Strings}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{14:1--14:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.14},
  URN =		{urn:nbn:de:0030-drops-259409},
  doi =		{10.4230/LIPIcs.CPM.2026.14},
  annote =	{Keywords: Elastic-degenerate strings, NP-hardness, longest common factor, minimal unique substring, minimal absent word, anti-power, longest previous factor}
}
Document
DOI: 10.4230/LIPIcs.SWAT.2026.13
Faster Algorithms for Shortest Unique or Absent Substrings

Authors: Panagiotis Charalampopoulos, Manal Mohamed, Solon P. Pissis, Hilde Verbeek, and Wiktor Zuba

Published in: LIPIcs, Volume 370, 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)

Abstract
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) in a string S of length n. Both problems admit folklore 𝒪(n)-time solutions using the suffix tree of S. However, for small alphabets, this complexity is not necessarily optimal in the word RAM model, where a string of length n over alphabet [0,σ) can be stored in 𝒪(n log σ/log n) space and read in 𝒪(n log σ/log n) time. We present an 𝒪(n log σ/√{log n})-time algorithm for computing a SUS in S. This algorithm decomposes the problem according to the length and the period of the sought substring and uses several tools and techniques, such as synchronizing sets, the analysis of runs, and wavelet trees, to reduce the computation of a SUS to a simple geometric problem. Further, we adapt this algorithm and combine it with an efficient construction of de Bruijn sequences in order to obtain an 𝒪(n log σ/√{log n})-time algorithm for computing a SAS in S.
Cite as

Panagiotis Charalampopoulos, Manal Mohamed, Solon P. Pissis, Hilde Verbeek, and Wiktor Zuba. Faster Algorithms for Shortest Unique or Absent Substrings. In 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 370, pp. 13:1-13:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{charalampopoulos_et_al:LIPIcs.SWAT.2026.13,
  author =	{Charalampopoulos, Panagiotis and Mohamed, Manal and Pissis, Solon P. and Verbeek, Hilde and Zuba, Wiktor},
  title =	{{Faster Algorithms for Shortest Unique or Absent Substrings}},
  booktitle =	{20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)},
  pages =	{13:1--13:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-421-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{370},
  editor =	{Fraigniaud, Pierre},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2026.13},
  URN =		{urn:nbn:de:0030-drops-260493},
  doi =		{10.4230/LIPIcs.SWAT.2026.13},
  annote =	{Keywords: string algorithms, unique substrings, absent substrings, absent words}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.27
Exploring the Gap Between LCS and LCStr

Authors: Shay Golan, Matan Kraus, Ely Porat, and B. Riva Shalom

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
The Longest Common Subsequence (LCS) problem and the Longest Common Substring (LCStr) problem are classical string problems with broad theoretical and practical significance. The former has a quadratic conditional lower bound [FOCS, 2015], while the latter admits a linear-time solution. In this paper, we study a natural variation of these problems, the Longest Common Subsequence-Substring (LCSS) problem. The LCSS problem seeks the longest string that is simultaneously a subsequence of one input string and a substring of the other. This variant bridges LCS and LCStr, raising intriguing algorithmic questions: Does the complexity of computing LCSS interpolate between the linear time of LCStr and the quadratic time of LCS? What about approximability? We also examine a natural extension of LCSS to multiple strings, parameterizing the balance between subsequence and substring requirements. Our results reveal several insights. First, under the SETH conjecture, the inherent complexity of LCSS is quadratic, similar to LCS. In contrast, we provide a linear-time approximation for LCSS. Finally, for the multi-string variant, unlike both problems, we design a quadratic-time algorithm, uncovering deeper structural properties of the problem. By studying the complexity of the LCSS problem, we aim to gain some understanding of what influences whether a variant of the LCS problem behaves more like the standard LCS or like LCStr. Our findings suggest that hybrid constraints can create computational "sweet spots," where problems become more tractable than their pure counterparts. This opens a broader research direction in constraint-mediated algorithm design. Beyond LCSS itself, our work highlights unexpected connections between subsequence and substring constraints, advancing the theoretical understanding of string problems and laying the foundation for new algorithmic techniques and complexity-theoretic insights in the rich space between classical string comparison paradigms.
Cite as

Shay Golan, Matan Kraus, Ely Porat, and B. Riva Shalom. Exploring the Gap Between LCS and LCStr. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 27:1-27:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{golan_et_al:LIPIcs.CPM.2026.27,
  author =	{Golan, Shay and Kraus, Matan and Porat, Ely and Shalom, B. Riva},
  title =	{{Exploring the Gap Between LCS and LCStr}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{27:1--27:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.27},
  URN =		{urn:nbn:de:0030-drops-259535},
  doi =		{10.4230/LIPIcs.CPM.2026.27},
  annote =	{Keywords: Longest Common Subsequence, Longest Common Substring, Conditional Lower Bound}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.29
The TAG Array of a Multiple Sequence Alignment

Authors: Jannik Olbrich and Enno Ohlebusch

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs, this has the advantage that efficient exact search via indexes based on the Burrows-Wheeler Transform (BWT) is possible, that no chimeric sequences are created, and that the results are not influenced by heuristics. However, such an index may report a match in thousands of positions even if these all correspond to the same locus, making downstream analysis unnecessarily more expensive. For sufficiently similar sequences (e.g. human chromosomes), a multiple sequence alignment (MSA) can be computed. Since an MSA tends to group similar strings in the same columns, it is likely that a string occurring thousands of times in the pangenome can be described by very few columns in the MSA. We describe a method to tag entries in the BWT with the corresponding column in the MSA and develop an index that can map matches in the BWT to columns in the MSA in time proportional to the output. As a by-product, we can project a match to a designated reference genome, a capability that current pangenome aligners lack.
Cite as

Jannik Olbrich and Enno Ohlebusch. The TAG Array of a Multiple Sequence Alignment. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 29:1-29:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{olbrich_et_al:LIPIcs.CPM.2026.29,
  author =	{Olbrich, Jannik and Ohlebusch, Enno},
  title =	{{The TAG Array of a Multiple Sequence Alignment}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{29:1--29:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.29},
  URN =		{urn:nbn:de:0030-drops-259555},
  doi =		{10.4230/LIPIcs.CPM.2026.29},
  annote =	{Keywords: Burrows-Wheeler Transform, pattern matching, index data structure, pangenomics}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.32
Balancing Two-Dimensional Straight-Line Programs

Authors: Itai Boneh, Estéban Gabory, Paweł Gawrychowski, and Adam Górkiewicz

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract
We consider building, given a straight-line program (SLP) consisting of g productions deriving a two-dimensional string T of size N× N, a structure capable of providing random access to any character of T. For one-dimensional strings, it is now known how to build a structure of size 𝒪(g) that provides random access in 𝒪(log N) time. In fact, it is known that this can be obtained by building an equivalent SLP of size 𝒪(g) and depth 𝒪(log N) [Ganardi, Jeż, Lohrey, JACM 2021]. We consider the analogous question for two-dimensional strings: can we build an equivalent SLP of roughly the same size and small depth? We show that the answer is negative: there exists an infinite family of two-dimensional strings of size N× N described by a 2D SLP of size g such that any 2D SLP of depth 𝒪(log N) describing the same string must be of size Ω(g⋅ N/log³N). We complement this with an upper bound showing how to construct such a 2D SLP of size 𝒪(g⋅ N). Next, we observe that one can naturally define a generalization of 2D SLP, which we call 2D SLP with holes. We show that a known general balancing theorem by [Ganardi, Jeż, Lohrey, JACM 2021] immediately implies that, given a 2D SLP of size g deriving a string of size N× N, we can construct a 2D SLP with holes of depth 𝒪(log N) and size 𝒪(g). This allows us to conclude that there is a structure of size 𝒪(g) providing random access in 𝒪(log N) time for such a 2D SLP. Further, this can be extended (analogously as for a 1D SLP) to obtain a structure of size 𝒪(g log^ε N) providing random access in 𝒪(log N/log log N) time, for any ε > 0. The same (optimal) random access time was very recently achieved by [De and Kempa, SODA 2026], but with a significantly larger structure of size 𝒪(g log^{2+ε} N).
Cite as

Itai Boneh, Estéban Gabory, Paweł Gawrychowski, and Adam Górkiewicz. Balancing Two-Dimensional Straight-Line Programs. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 32:1-32:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{boneh_et_al:LIPIcs.CPM.2026.32,
  author =	{Boneh, Itai and Gabory, Est\'{e}ban and Gawrychowski, Pawe{\l} and G\'{o}rkiewicz, Adam},
  title =	{{Balancing Two-Dimensional Straight-Line Programs}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{32:1--32:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.32},
  URN =		{urn:nbn:de:0030-drops-259582},
  doi =		{10.4230/LIPIcs.CPM.2026.32},
  annote =	{Keywords: Two-dimensional string, straight-line program, random access}
}
Document
DOI: 10.4230/LIPIcs.FORC.2026.9
Serving Clients Fairly: On Facility Location and k-Median with Fair Outliers

Authors: Rajni Dabas, Samir Khuller, and Emilie Rivkin

Published in: LIPIcs, Volume 368, 7th Symposium on Foundations of Responsible Computing (FORC 2026)

Abstract
Classical clustering problems such as Facility Location and k-Median aim to efficiently serve a set of clients from a subset of facilities - minimizing the total cost of facility openings and client assignments in Facility Location, and minimizing assignment (service) cost under a facility count constraint in k-Median. These problems are highly sensitive to outliers, and therefore researchers have studied variants that allow excluding a small number of clients as outliers to reduce cost. However, in many real-world settings, clients belong to different demographic or functional groups, and unconstrained outlier removal can disproportionately exclude certain groups, raising fairness concerns, especially when the facilities correspond to critically needed facilities for emergencies such as fire stations, hospitals and other emergency services. We study Facility Location with Fair Outliers, where each group is allowed a specified number of outliers, and the objective is to minimize total cost while respecting group-wise fairness constraints. We present a bicriteria approximation with a O(1/ε) approximation factor and (1+ 2ε) factor violation in outliers per group. For k-Median with Fair Outliers, we design a bicriteria approximation with a 4(1+ω/ε) approximation factor and (ω + ε) violation in outliers per group improving on prior work by avoiding dependence on k in outlier violations. We also prove that the problems are W[1]-hard parameterized by ω. We complement our algorithmic contributions with a detailed empirical analysis, demonstrating that fairness can be achieved with negligible increase in cost and that the integrality gap of the standard LP is small in practice.
Cite as

Rajni Dabas, Samir Khuller, and Emilie Rivkin. Serving Clients Fairly: On Facility Location and k-Median with Fair Outliers. In 7th Symposium on Foundations of Responsible Computing (FORC 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 368, pp. 9:1-9:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{dabas_et_al:LIPIcs.FORC.2026.9,
  author =	{Dabas, Rajni and Khuller, Samir and Rivkin, Emilie},
  title =	{{Serving Clients Fairly: On Facility Location and k-Median with Fair Outliers}},
  booktitle =	{7th Symposium on Foundations of Responsible Computing (FORC 2026)},
  pages =	{9:1--9:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-419-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{368},
  editor =	{Lin, Huijia (Rachel)},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FORC.2026.9},
  URN =		{urn:nbn:de:0030-drops-259812},
  doi =		{10.4230/LIPIcs.FORC.2026.9},
  annote =	{Keywords: Approximation algorithms, fairness}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.48
FPT Approximations for Capacitated Sum of Radii and Diameters

Authors: Arnold Filtser and Ameet Gadekar

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
The Capacitated Sum of Radii problem involves partitioning a set of points P, where each point p ∈ P has capacity U_p, into k clusters that minimize the sum of cluster radii, such that the number of points in the cluster centered at point p is at most U_p. We begin by showing that the problem is APX-hard, and that under gap-ETH there is no parameterized approximation scheme (FPT-AS). We then construct a ≈5.83-approximation algorithm in FPT time (improving a previous ≈7.61 approximation in FPT time). Our results also hold when the objective is a general monotone symmetric norm of radii. We also improve the approximation factors for the uniform capacity case, and for the closely related problem of Capacitated Sum of Diameters.
Cite as

Arnold Filtser and Ameet Gadekar. FPT Approximations for Capacitated Sum of Radii and Diameters. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 48:1-48:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{filtser_et_al:LIPIcs.SoCG.2026.48,
  author =	{Filtser, Arnold and Gadekar, Ameet},
  title =	{{FPT Approximations for Capacitated Sum of Radii and Diameters}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{48:1--48:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.48},
  URN =		{urn:nbn:de:0030-drops-258545},
  doi =		{10.4230/LIPIcs.SoCG.2026.48},
  annote =	{Keywords: clustering, sum of radii, sum of diameter, capacitated clustering, fpt}
}
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