21 Search Results for "Kuhnle, Alan"

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}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.3
Computing k-mers in Graphs

Authors: Jarno N. Alanko and Máximo Pérez-López

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

Abstract
We initiate the study of computational problems on k-mers (strings of length k) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct k-mers found on the walks of a graph. We establish that this is #P-hard, even on connected deterministic DAGs. However, in the class of deterministic Wheeler graphs (Gagie, Manzini, and Sirén, TCS 2017), we show that distinct k-mers of such a graph W = (V, E) can be counted using O(|W|k) or O(n⁴ log k) arithmetic operations, where n = |V|, m = |E| and |W| = n+m. The latter result uses a new generalization of the technique of prefix doubling to Wheeler graphs. To generalize our results beyond Wheeler graphs, we discuss ways to transform a graph into a Wheeler graph in a manner that preserves the k-mers. As an application of our k-mer counting algorithms, we construct a representation of the de Bruijn graph of the k-mers that occupies O(n_k + |W|k log(max_{1 ≤ 𝓁 ≤ k} n_𝓁) + σlog m) bits of space, where n_𝓁 is the number of distinct 𝓁-mers in the Wheeler graph, and σ is the size of the alphabet. We show how to construct it in the same time complexity. Given that the Wheeler graph can be exponentially smaller than the de Bruijn graph, for large k this provides a theoretical improvement over previous de Bruijn graph construction methods from graphs, which must spend Ω(k) time per k-mer in the graph.
Cite as

Jarno N. Alanko and Máximo Pérez-López. Computing k-mers in Graphs. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{alanko_et_al:LIPIcs.CPM.2026.3,
  author =	{Alanko, Jarno N. and P\'{e}rez-L\'{o}pez, M\'{a}ximo},
  title =	{{Computing k-mers in Graphs}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{3:1--3:17},
  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.2026.3},
  URN =		{urn:nbn:de:0030-drops-259294},
  doi =		{10.4230/LIPIcs.CPM.2026.3},
  annote =	{Keywords: Wheeler graph, Wheeler language, de Bruijn graph, graph, k-mer, q-gram, DFA, #P-hard}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.16
Merging RLBWTs Adaptively

Authors: Travis Gagie

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

Abstract
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in O (r) space and O ((r + L) log (m + n)) time, where m and n are the lengths of the uncompressed strings, r is the number of runs in the final eBWT and L is the sum of its irreducible LCP values.
Cite as

Travis Gagie. Merging RLBWTs Adaptively. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 16:1-16:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{gagie:LIPIcs.CPM.2026.16,
  author =	{Gagie, Travis},
  title =	{{Merging RLBWTs Adaptively}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{16:1--16:15},
  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.2026.16},
  URN =		{urn:nbn:de:0030-drops-259420},
  doi =		{10.4230/LIPIcs.CPM.2026.16},
  annote =	{Keywords: Burrows-Wheeler Transform, run-length compression, RLBWT, construction, merging}
}
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.2026.30
Constructing Suffixient Arrays Revisited

Authors: Paola Bonizzoni, Younan Gao, and Brian Riccardi

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

Abstract
Recently, Cenzato et al. proposed a new text index, called the suffixient array, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random access to the input text T[1..n] is available. They show that, given the suffix array, the longest common prefix array, and the Burrows-Wheeler transform (BWT) of the reverse of T[1..n] over an alphabet {1,…,σ}, a suffixient array can be constructed in linear time. However, their construction algorithms require multiple scans of these arrays. When restricted to a single pass over the arrays, they present an alternative construction algorithm running in O(n + r log σ) time, where r is the number of runs in the BWT of the reversed text. In this paper, we present a new one-pass algorithm that constructs a suffixient array in linear time under the standard RAM model.
Cite as

Paola Bonizzoni, Younan Gao, and Brian Riccardi. Constructing Suffixient Arrays Revisited. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 30:1-30:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{bonizzoni_et_al:LIPIcs.CPM.2026.30,
  author =	{Bonizzoni, Paola and Gao, Younan and Riccardi, Brian},
  title =	{{Constructing Suffixient Arrays Revisited}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{30:1--30:18},
  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.2026.30},
  URN =		{urn:nbn:de:0030-drops-259564},
  doi =		{10.4230/LIPIcs.CPM.2026.30},
  annote =	{Keywords: Suffixient set, suffixient array, right-maximal substring, linear-time algorithm}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.36
Time-Optimal Construction of String Synchronizing Sets

Authors: Jonas Ellert and Tomasz Kociumaka

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract
A powerful design principle behind many modern string algorithms is local consistency: breaking the symmetry between string positions based on their small contexts so that matching fragments are handled consistently. Among the most influential instantiations of this principle are string synchronizing sets [Kempa & Kociumaka; STOC 2019]. A τ-synchronizing set of a string of length n is a set of O(n/τ) string positions, chosen using their length-2τ contexts, such that (outside of highly periodic regions) every block of τ consecutive positions contains at least one element of the set. Synchronizing sets have found dozens of applications in diverse settings, from quantum and dynamic algorithms to fully compressed computation. In the classic word RAM model, particularly for strings over small alphabets, they enabled faster solutions to core problems in data compression, text indexing, and string similarity. In this work, we show that any string T ∈ [0 .. σ)ⁿ can be preprocessed in O(n log σ / log n) time so that, for any given integer τ ∈ [1 .. n], a τ-synchronizing set of T can be constructed in O((n log τ)/(τ log n)) time. Both bounds are optimal in the word RAM model with machine word size w = Θ(log n), matching the information-theoretic minimum for the input and output sizes, respectively. Previously, constructing a τ-synchronizing set required O(n/τ) time after an O(n)-time preprocessing [Kociumaka, Radoszewski, Rytter, and Waleń; SICOMP 2024], or, in the restricted regime of τ < 0.2 log_σ n, without any preprocessing needed [Kempa & Kociumaka; STOC 2019]. A simple instantiation of our method outputs the synchronizing set as a sorted list in O(n/τ) time, or as a bitmask in O(n/log n) time. Our optimal construction produces a compact fully indexable dictionary, supporting select queries in O(1) time and rank queries in O(log ((log τ)/(log log n))) time. The latter complexity matches known unconditional cell-probe lower bounds for τ ≤ n^{1-Ω(1)}. To achieve this, we introduce a general framework for efficiently processing sparse integer sequences via a custom variable-length encoding. We also augment the optimal variant of van Emde Boas trees [Pătraşcu & Thorup; STOC 2006] with a deterministic linear-time construction. When the set is represented as a bitmask under our sparse encoding, the same guarantees for select and rank queries hold after preprocessing in time proportional to the size of our encoding (in words).
Cite as

Jonas Ellert and Tomasz Kociumaka. Time-Optimal Construction of String Synchronizing Sets. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 36:1-36:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ellert_et_al:LIPIcs.STACS.2026.36,
  author =	{Ellert, Jonas and Kociumaka, Tomasz},
  title =	{{Time-Optimal Construction of String Synchronizing Sets}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{36:1--36:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.36},
  URN =		{urn:nbn:de:0030-drops-255258},
  doi =		{10.4230/LIPIcs.STACS.2026.36},
  annote =	{Keywords: synchronizing sets, local consistency, packed strings}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.100
Cut-Query Algorithms with Few Rounds

Authors: Yotam Kenneth-Mordoch and Robert Krauthgamer

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

Abstract
In the cut-query model, the algorithm can access the input graph G = (V,E) only via cut queries that report, given a set S ⊆ V, the total weight of edges crossing the cut between S and V⧵ S. This model was introduced by Rubinstein, Schramm and Weinberg [ITCS'18] and its investigation has so far focused on the number of queries needed to solve optimization problems, such as global minimum cut. We turn attention to the round complexity of cut-query algorithms, and show that several classical problems can be solved in this model with only a constant number of rounds. Our main results are algorithms for finding a minimum cut in a graph, that offer different tradeoffs between round complexity and query complexity, where n = |V| and δ(G) denotes the minimum degree of G: (i) Õ(n^{4/3}) cut queries in two rounds in unweighted graphs; (ii) Õ(rn^{1+1/r}/δ(G)^{1/r}) queries in 2r+1 rounds for any integer r ≥ 1 again in unweighted graphs; and (iii) Õ(rn^{1+(1+log_n W)/r}) queries in 4r+3 rounds for any r ≥ 1 in weighted graphs. We also provide algorithms that find a minimum (s,t)-cut and approximate the maximum cut in a few rounds.
Cite as

Yotam Kenneth-Mordoch and Robert Krauthgamer. Cut-Query Algorithms with Few Rounds. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 100:1-100:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kennethmordoch_et_al:LIPIcs.ESA.2025.100,
  author =	{Kenneth-Mordoch, Yotam and Krauthgamer, Robert},
  title =	{{Cut-Query Algorithms with Few Rounds}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{100:1--100:14},
  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.2025.100},
  URN =		{urn:nbn:de:0030-drops-245692},
  doi =		{10.4230/LIPIcs.ESA.2025.100},
  annote =	{Keywords: Cut Queries, Round Complexity, Submodular Optimization}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.60
Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars

Authors: Jannik Olbrich

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

Abstract
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the entire dataset in main memory. Fortunately, such large datasets are often highly repetitive. It can thus be beneficial to compute the BWT from a compressed representation. We propose an algorithm for computing the BWT via the Lyndon straight-line program, a grammar based on the standard factorization of Lyndon words. Our algorithm can also be used to compute the extended BWT (eBWT) of a multiset of sequences. We empirically evaluate our implementation and find that we can compute the BWT and eBWT of very large datasets faster and/or with less memory than competing methods.
Cite as

Jannik Olbrich. Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 60:1-60:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{olbrich:LIPIcs.ESA.2025.60,
  author =	{Olbrich, Jannik},
  title =	{{Fast and Memory-Efficient BWT Construction of Repetitive Texts Using Lyndon Grammars}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{60:1--60:19},
  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.2025.60},
  URN =		{urn:nbn:de:0030-drops-245286},
  doi =		{10.4230/LIPIcs.ESA.2025.60},
  annote =	{Keywords: Burrows-Wheeler Transform, Grammar compression}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.9
MorphisHash: Improving Space Efficiency of ShockHash for Minimal Perfect Hashing

Authors: Stefan Hermann

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

Abstract
A minimal perfect hash function (MPHF) maps a set of n keys to unique positions {1, …, n}. Representing an MPHF requires at least log₂(e)≈ 1.443 bits per key. ShockHash is a technique to construct an MPHF and requires just slightly more space. It gives each key two random candidate positions. If each key can be mapped to one of its two candidate positions such that there is exactly one key mapped to each position, then an MPHF is found. If not, ShockHash repeats the process with a new set of random candidate positions. ShockHash has to store how many repetitions were required and for each key to which of the two candidate positions it is mapped. However, when a given set of candidate positions can be used as MPHF then there is not only one but multiple ways of mapping the keys to one of their candidate positions such that the mapping results in an MPHF. This redundancy makes up for the majority of the remaining space overhead in ShockHash. In this paper, we present MorphisHash which almost completely eliminates this redundancy. Our theoretical result is that MorphisHash saves Θ(ln(n)) bits in expectation compared to ShockHash. This corresponds to a factor of 20 less space overhead in practice. Just like ShockHash, MorphisHash can be used as a building block within RecSplit to obtain MorphisHash-RS. When compared for same space consumption, MorphisHash-RS can be constructed up to 21 times faster than ShockHash-RS. The technique to accomplish this might be of a more general interest to compress data structures.
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Stefan Hermann. MorphisHash: Improving Space Efficiency of ShockHash for Minimal Perfect Hashing. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hermann:LIPIcs.ESA.2025.9,
  author =	{Hermann, Stefan},
  title =	{{MorphisHash: Improving Space Efficiency of ShockHash for Minimal Perfect Hashing}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{9:1--9:16},
  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.2025.9},
  URN =		{urn:nbn:de:0030-drops-244779},
  doi =		{10.4230/LIPIcs.ESA.2025.9},
  annote =	{Keywords: compressed data structure, perfect hashing, random graph, pseudoforest, component}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.WABI.2025.1
Recursive Parsing and Grammar Compression in the Era of Pangenomics (Invited Talk)

Authors: Christina Boucher

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Prefix-Free Parsing (PFP) and its recursive variant (RPFP) provide a scalable framework for compressing and indexing large genomic datasets. By enabling efficient construction of succinct data structures, these methods support fast and memory-efficient read alignment across thousands of genomes. Their deterministic and modular design makes them especially well-suited for pangenomics and large-scale sequence analysis.
Cite as

Christina Boucher. Recursive Parsing and Grammar Compression in the Era of Pangenomics (Invited Talk). In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 1:1-1:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{boucher:LIPIcs.WABI.2025.1,
  author =	{Boucher, Christina},
  title =	{{Recursive Parsing and Grammar Compression in the Era of Pangenomics}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{1:1--1:2},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.1},
  URN =		{urn:nbn:de:0030-drops-239278},
  doi =		{10.4230/LIPIcs.WABI.2025.1},
  annote =	{Keywords: Prefix-Free Parsing, Recursive Prefix-Free Parsing, Grammar-Based Compression, Succinct Data Structures, RePair Compression}
}
Document
Extended Abstract
DOI: 10.4230/LIPIcs.WABI.2025.23
Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract)

Authors: Vikram S. Shivakumar and Ben Langmead

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Pangenome collections continue to grow and proliferate to hundreds of high-quality genomes, for example, the expanded v2 version of the Human Pangenome Reference Consortium (HPRC) dataset spanning 474 human haplotypes [Liao et al., 2023]. As the size and complexity of these collections grow, it is increasingly important that our methods for studying and indexing pangenomes be scalable and updateable. Maximal Unique Matches (multi-MUMs), exact substring matches present exactly once in all sequences in a pangenome collection, represent conserved anchor sequences that can comprise a common coordinate system. We previously proposed a framework and tool called Mumemto for rapidly identifying multi-MUMs during construction of a compressed pangenome index [Shivakumar and Langmead, 2025]. Using prefix-free parsing (PFP) [Boucher et al., 2019], a compressed-space method for computing full-text indexes, Mumemto outperforms existing methods for identifying multi-MUMs. However, one drawback remains updateability and scalability. Mumemto can become memory-intensive for large pangenomes (> 300 human genomes), and as newly assembled genomes are added to a pangenome collection, Mumemto requires re-running on the entire updated collection. To address this, we developed a partition-merging approach to compute multi-MUMs with Mumemto. We introduce two strategies for merging of multi-MUMs computed across different collections (see Figure 1), enabling parallelization across partitions and simple computation of multi-MUMs for incrementally-updated collections. The first strategy requires a common sequence in each partition (which we call "anchor-based merging"), which serves as a coordinate system to identify multi-MUM overlaps between partitions. By tracking the next longest match for all multi-MUMs and unique matches (UMs) in an auxiliary data structure, intersections between matches can be filtered out if no longer unique in the union collection. The second strategy identifies overlaps directly from the multi-MUM substrings (called "string-based merging"). The overlaps are identified by running Mumemto over the extracted multi-MUM sequences and are similarly filtered out if they are too short to considered unique. Lastly, we propose an extension to anchor-based merging to enable the computation of partial multi-MUMs, present in only a subset of sequences in the union set. The partition-merging framework introduces a tradeoff space in Mumemto between running time and memory, depending on partition size and the number of threads. Running parallel, per-partition Mumemto processes and merging the results reduces the running time but increases the peak memory footprint, while running a single Mumemto thread over each partition serially yields longer running time but a smaller memory footprint. To evaluate this tradeoff, we computed multi-MUMs across 474 haplotypes of chr19 from the HPRC v2 dataset [Liao et al., 2023] and 69 assemblies of A. thaliana [Lian et al., 2024] (Table 1). The string-based method also enables merging multi-MUMs between disjoint collections, for example subclades in a phylogenetic tree. By merging multi-MUMs along the shape of the tree, we can compute matches at internal nodes of the tree along with the root, revealing clade-specific conservation and structural variation. Multi-MUM merging also enables interspecific match computation, which was previously infeasible with Mumemto due to high memory usage for highly-diverse input sequence collections. We use partition-merging to compute multi-MUMs across 29 primate assemblies, and found a correspondence to ultraconserved elements previously found across mammalian genomes [Cummins et al., 2024]. We show that a partitioned Mumemto enables scalability to growing pangenome collections and expands the applicability of Mumemto to larger, more diverse datasets. As a result, Mumemto is the only method capable of computing exact matches across the entire HPRC v2 dataset (474 haplotypes [Liao et al., 2023]), and can easily incorporate future releases of assemblies without recomputation. This increases the scope for exploration of genomic conservation and variation and highlights the potential for Mumemto as a core method for future pangenomics and comparative genomics research. The partitioned Mumemto framework is implemented in v1.3.0 and is available open-source at https://github.com/vikshiv/mumemto.
Cite as

Vikram S. Shivakumar and Ben Langmead. Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract). In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 23:1-23:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{shivakumar_et_al:LIPIcs.WABI.2025.23,
  author =	{Shivakumar, Vikram S. and Langmead, Ben},
  title =	{{Partitioned Multi-MUM Finding for Scalable Pangenomics}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{23:1--23:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.23},
  URN =		{urn:nbn:de:0030-drops-239490},
  doi =		{10.4230/LIPIcs.WABI.2025.23},
  annote =	{Keywords: Pangenomics, Comparative genomics, Compressed indexing}
}
Document
DOI: 10.4230/OASIcs.Manzini.3
BWT for String Collections

Authors: Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipták, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT variants and give a categorization of publicly available tools for computing the BWT of string collections. We show how the specific method used impacts on the resulting transform, including the number of runs, and on the dynamicity of the transform with respect to adding or removing strings from the collection. We then focus on the number of runs of these BWT variants and present the optimal BWT introduced in [Cenzato et al., DCC 2023], which implements an algorithm originally proposed by [Bentley et al., ESA 2020] to minimize the number of BWT-runs. We also discuss several recent heuristics and study their impact on the compression of biological sequences. We conclude with an overview of the applications and the impact of the BWT of string collections in bioinformatics.
Cite as

Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, and Marinella Sciortino. BWT for String Collections. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 3:1-3:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cenzato_et_al:OASIcs.Manzini.3,
  author =	{Cenzato, Davide and Lipt\'{a}k, Zsuzsanna and Pisanti, Nadia and Rosone, Giovanna and Sciortino, Marinella},
  title =	{{BWT for String Collections}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{3:1--3:29},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.3},
  URN =		{urn:nbn:de:0030-drops-239113},
  doi =		{10.4230/OASIcs.Manzini.3},
  annote =	{Keywords: Burrows-Wheeler transform, Extended Burrows-Wheeler transform, compressed text indexes, text compression, string collections, bioinformatics}
}
Document
DOI: 10.4230/OASIcs.Manzini.1
BWT and Combinatorics on Words

Authors: Gabriele Fici, Sabrina Mantaci, Antonio Restivo, Giuseppe Romana, Giovanna Rosone, and Marinella Sciortino

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Burrows-Wheeler Transform (BWT) is a reversible transformation on words (strings) introduced in 1994 in the context of data compression, which is a permutation of the characters in the word. Its clustering effect, i.e., the remarkable property of grouping identical characters (BWT runs) when they share common contexts, has made it a powerful tool for boosting compression performances and enabling efficient pattern searching in highly repetitive string collections. In this chapter, we analyze the Burrows-Wheeler transform under the combinatorial point of view, and we survey known properties and connections with different aspects of combinatorics on words. In particular, we focus on the properties of words in relation to the number of their BWT runs. The value r, which counts the number of BWT runs, impacts both compression performance and indexing efficiency, and is considered a measure to evaluate the above-mentioned clustering effect and, consequently, the repetitiveness of a word. We give an overview of the results relating r to other combinatorial repetitiveness measures related to the factor complexity. The chapter also explores extremal cases of the clustering effect. Finally, some results on the sensitivity of the measure r are considered, where the effects of combinatorial operations are studied, such as reversal, edits, and the application of morphisms.
Cite as

Gabriele Fici, Sabrina Mantaci, Antonio Restivo, Giuseppe Romana, Giovanna Rosone, and Marinella Sciortino. BWT and Combinatorics on Words. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 1:1-1:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fici_et_al:OASIcs.Manzini.1,
  author =	{Fici, Gabriele and Mantaci, Sabrina and Restivo, Antonio and Romana, Giuseppe and Rosone, Giovanna and Sciortino, Marinella},
  title =	{{BWT and Combinatorics on Words}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{1:1--1:23},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.1},
  URN =		{urn:nbn:de:0030-drops-239090},
  doi =		{10.4230/OASIcs.Manzini.1},
  annote =	{Keywords: Burrows-Wheeler Transform, Combinatorics on Words, Clustering Effect, BWT Runs}
}
Document
DOI: 10.4230/OASIcs.Manzini.6
Optimizing the Performance of the FM-Index for Large-Scale Data

Authors: Eddie Ferro and Christina Boucher

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The FM-index is a fundamental data structure used in bioinformatics to efficiently search for strings and index genomes. However, the FM-index can pose computational challenges, particularly in the context of large-scale genomic datasets, due to the complexity of its underlying components and data encodings. In this paper, we present a comprehensive review of efficient variants of the FM-index and the encoding strategies used to improve performance. We examine hardware-accelerated techniques, such as memory-efficient data layouts and cache-aware structures, as well as software-level innovations, including algorithmic refinements and compact representations. The reviewed work demonstrates substantial gains in both speed and scalability, making methods that use the FM-index more practical for high-throughput genomic applications. By analyzing the trade-offs and design choices of these variants, we highlight how combining hardware-aware and software-centric strategies enables more efficient FM-index construction and usage across a range of bioinformatics tasks.
Cite as

Eddie Ferro and Christina Boucher. Optimizing the Performance of the FM-Index for Large-Scale Data. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ferro_et_al:OASIcs.Manzini.6,
  author =	{Ferro, Eddie and Boucher, Christina},
  title =	{{Optimizing the Performance of the FM-Index for Large-Scale Data}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{6:1--6:21},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.6},
  URN =		{urn:nbn:de:0030-drops-239140},
  doi =		{10.4230/OASIcs.Manzini.6},
  annote =	{Keywords: FM-Index Acceleration, Run-Length Encoding, Suffix Array Optimization, Burrows-Wheeler Transform, Efficient Backward Search}
}
Document
DOI: 10.4230/OASIcs.Manzini.4
Wavelet Tree, Part II: Text Indexing

Authors: Paolo Ferragina, Raffaele Giancarlo, Roberto Grossi, Giovanna Rosone, Rossano Venturini, and Jeffrey Scott Vitter

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The Wavelet Tree data structure introduced in Grossi, Gupta, and Vitter [Grossi et al., 2003] is a space-efficient technique for rank and select queries that generalizes from binary symbols to an arbitrary multisymbol alphabet. Over the last two decades, it has become a pivotal tool in modern full-text indexing and data compression because of its properties and capabilities in compressing and indexing data, with many applications to information retrieval, genome analysis, data mining, and web search. In this paper, we survey the fascinating history and impact of Wavelet Trees; no doubt many more developments are yet to come. Our survey borrows some content from the authors' earlier works. This paper is divided into two parts: The first part gives a brief history of Wavelet Trees, including its varieties and practical implementations, which appears in the Festschrift dedicated to Roberto Grossi; the second part (this one) deals with Wavelet Tree-based text indexing and is included in the Festschrift dedicated to Giovanni Manzini.
Cite as

Paolo Ferragina, Raffaele Giancarlo, Roberto Grossi, Giovanna Rosone, Rossano Venturini, and Jeffrey Scott Vitter. Wavelet Tree, Part II: Text Indexing. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 4:1-4:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ferragina_et_al:OASIcs.Manzini.4,
  author =	{Ferragina, Paolo and Giancarlo, Raffaele and Grossi, Roberto and Rosone, Giovanna and Venturini, Rossano and Vitter, Jeffrey Scott},
  title =	{{Wavelet Tree, Part II: Text Indexing}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{4:1--4:10},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.4},
  URN =		{urn:nbn:de:0030-drops-239127},
  doi =		{10.4230/OASIcs.Manzini.4},
  annote =	{Keywords: Wavelet tree, data compression, text indexing, compressed suffix array, Burrows-Wheeler transform, rank and select}
}
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