8 Search Results for "Mwaniki, Moses Njagi"

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)

Copy BibTex To Clipboard

@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.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

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

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  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.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.14
Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

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

Abstract
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz, a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al. and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip, gbz, and sequitur. sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al.. When combined with bgzip, sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.
Cite as

Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}
Document
Research
DOI: 10.4230/OASIcs.Grossi.2
On the Construction of Elastic Degenerate Strings

Authors: Nicola Rizzo, Veli Mäkinen, and Nadia Pisanti

Published in: OASIcs, Volume 132, From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday (2025)

Abstract
An elastic degenerate string (EDS) is a sequence of sets of strings. In the context of bioinformatics, EDSes can be used to represent the variations observed in a population from its consensus genome. Pattern matching and comparison problems on EDSes have been widely studied in the literature, but their construction has been largely omitted. We fill this gap by showing how algorithms originally developed for related problems of founder reconstruction can be adapted to minimize the total cardinality of the EDS sets and total length of the EDS strings in linear time, given suitable multiple alignments representing the input data.
Cite as

Nicola Rizzo, Veli Mäkinen, and Nadia Pisanti. On the Construction of Elastic Degenerate Strings. In From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 2:1-2:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{rizzo_et_al:OASIcs.Grossi.2,
  author =	{Rizzo, Nicola and M\"{a}kinen, Veli and Pisanti, Nadia},
  title =	{{On the Construction of Elastic Degenerate Strings}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{2:1--2:13},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-391-1},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{132},
  editor =	{Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Grossi.2},
  URN =		{urn:nbn:de:0030-drops-238014},
  doi =		{10.4230/OASIcs.Grossi.2},
  annote =	{Keywords: multiple sequence alignment, pattern matching, data structures, segmentation algorithms, founder reconstruction, dynamic programming, semi-dynamic range minimum queries, positional Burrows-Wheeler transform}
}
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)

Copy BibTex To Clipboard

@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/LIPIcs.CPM.2025.28
Faster Approximate Elastic-Degenerate String Matching - Part A

Authors: Solon P. Pissis, Jakub Radoszewski, and Wiktor Zuba

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)

Abstract
An elastic-degenerate (ED) string 𝐓 is a sequence 𝐓 = 𝐓[1] ⋯ 𝐓[n] of n finite sets of strings. The cardinality m of 𝐓 is the total number of strings in 𝐓[i], for all i ∈ [1..n]. The size N of 𝐓 is the total length of all m strings of 𝐓. ED strings have been introduced to represent a set of closely-related DNA sequences. Let P = P[1..p] be a pattern of length p and k > 0 be an integer. We consider the problem of k-Approximate ED String Matching (EDSM): searching k-approximate occurrences of P in the language of 𝐓. We call k-Approximate EDSM under the Hamming distance, k-Mismatch EDSM; and we call k-Approximate EDSM under edit distance, k-Edit EDSM. Bernardini et al. (Theoretical Computer Science, 2020) showed a simple 𝒪(k m p + kN)-time algorithm for k-Mismatch EDSM and an 𝒪(k² m p + kN)-time algorithm for k-Edit EDSM. We improve the dependency on k in both results, obtaining an Õ(k^{2/3}mp+√kN)-time algorithm for k-Mismatch EDSM and an Õ(kmp+ kN)-time algorithm for k-Edit EDSM. Bernardini et al. (Theory of Computing Systems, 2024) presented several algorithms for 1-Approximate EDSM working in Õ(np²+N) time. They have also left the possibility to generalize these solutions for k > 1 as an open problem. We improve the runtime of their solution for 1-Mismatch and 1-Edit EDSM from Õ(np²+N) to 𝒪(np²+N). We further show algorithms for k-Approximate EDSM for the Hamming and edit distances working in Õ(np² + N) time, for any constant k > 0. Finally, we show how our techniques can be applied to improve upon the complexity of the k-Approximate ED String Intersection and k-Approximate Doubly EDSM problems that were introduced very recently by Gabory et al. (Information and Computation, 2025).
Cite as

Solon P. Pissis, Jakub Radoszewski, and Wiktor Zuba. Faster Approximate Elastic-Degenerate String Matching - Part A. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 28:1-28:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{pissis_et_al:LIPIcs.CPM.2025.28,
  author =	{Pissis, Solon P. and Radoszewski, Jakub and Zuba, Wiktor},
  title =	{{Faster Approximate Elastic-Degenerate String Matching - Part A}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{28:1--28:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.28},
  URN =		{urn:nbn:de:0030-drops-231227},
  doi =		{10.4230/LIPIcs.CPM.2025.28},
  annote =	{Keywords: ED string, approximate string matching, Hamming distance, edit distance}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.29
Faster Approximate Elastic-Degenerate String Matching - Part B

Authors: Paweł Gawrychowski, Adam Górkiewicz, Pola Marciniak, Solon P. Pissis, and Karol Pokorski

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)

Abstract
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of n finite sets of strings of total length N, and compactly describes a collection of strings obtained by first choosing exactly one string in every set, and then concatenating them together. This is motivated by the need of storing a collection of highly similar DNA sequences. The basic algorithmic question on elastic-degenerate strings is pattern matching: given such an elastic-degenerate string and a standard pattern of length m, check if the pattern occurs in one of the strings in the described collection. Bernardini et al. [SICOMP 2022] showed how to leverage fast matrix multiplication to obtain an Õ(nm^{ω-1})+𝒪(N)-time complexity for this problem, where ω is the matrix multiplication exponent. However, from the point of view of possible applications, it is more desirable to work with approximate pattern matching, where we seek approximate occurrences of the pattern. This generalization has been considered in a few papers already, but the best result so far for occurrences with k mismatches, where k is a constant, is the Õ(nm²+N)-time algorithm presented in Part A [CPM 2025]. This brings the question whether increasing the dependency on m from m^{ω-1} to quadratic is necessary when moving from k = 0 to larger (but still constant) k. We design an Õ(nm^{1.5}+N)-time algorithm for pattern matching with k mismatches in an elastic-degenerate string, for any constant k. To obtain this time bound, we leverage the structural characterization of occurrences with k mismatches of Charalampopoulos, Kociumaka, and Wellnitz [FOCS 2020] together with fast Fourier transform. We need to work with multiple patterns at the same time, instead of a single pattern, which requires refining the original characterization. This might be of independent interest.
Cite as

Paweł Gawrychowski, Adam Górkiewicz, Pola Marciniak, Solon P. Pissis, and Karol Pokorski. Faster Approximate Elastic-Degenerate String Matching - Part B. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 29:1-29:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{gawrychowski_et_al:LIPIcs.CPM.2025.29,
  author =	{Gawrychowski, Pawe{\l} and G\'{o}rkiewicz, Adam and Marciniak, Pola and Pissis, Solon P. and Pokorski, Karol},
  title =	{{Faster Approximate Elastic-Degenerate String Matching - Part B}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{29:1--29:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.29},
  URN =		{urn:nbn:de:0030-drops-231236},
  doi =		{10.4230/LIPIcs.CPM.2025.29},
  annote =	{Keywords: ED string, approximate pattern matching, Hamming distance, k mismatches}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.11
Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications

Authors: Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, and Wiktor Zuba

Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)

Abstract
An elastic-degenerate (ED) string T is a sequence of n sets T[1],…,T[n] containing m strings in total whose cumulative length is N. We call n, m, and N the length, the cardinality and the size of T, respectively. The language of T is defined as ℒ(T) = {S_1 ⋯ S_n : S_i ∈ T[i] for all i ∈ [1,n]}. ED strings have been introduced to represent a set of closely-related DNA sequences, also known as a pangenome. The basic question we investigate here is: Given two ED strings, how fast can we check whether the two languages they represent have a nonempty intersection? We call the underlying problem the ED String Intersection (EDSI) problem. For two ED strings T₁ and T₂ of lengths n₁ and n₂, cardinalities m₁ and m₂, and sizes N₁ and N₂, respectively, we show the following: - There is no 𝒪((N₁N₂)^{1-ε})-time algorithm, thus no 𝒪((N₁m₂+N₂m₁)^{1-ε})-time algorithm and no 𝒪((N₁n₂+N₂n₁)^{1-ε})-time algorithm, for any constant ε > 0, for EDSI even when T₁ and T₂ are over a binary alphabet, unless the Strong Exponential-Time Hypothesis is false. - There is no combinatorial 𝒪((N₁+N₂)^{1.2-ε}f(n₁,n₂))-time algorithm, for any constant ε > 0 and any function f, for EDSI even when T₁ and T₂ are over a binary alphabet, unless the Boolean Matrix Multiplication conjecture is false. - An 𝒪(N₁log N₁log n₁+N₂log N₂log n₂)-time algorithm for outputting a compact (RLE) representation of the intersection language of two unary ED strings. In the case when T₁ and T₂ are given in a compact representation, we show that the problem is NP-complete. - An 𝒪(N₁m₂+N₂m₁)-time algorithm for EDSI. - An Õ(N₁^{ω-1}n₂+N₂^{ω-1}n₁)-time algorithm for EDSI, where ω is the exponent of matrix multiplication; the Õ notation suppresses factors that are polylogarithmic in the input size. We also show that the techniques we develop have applications outside of ED string comparison.
Cite as

Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, and Wiktor Zuba. Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 11:1-11:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{gabory_et_al:LIPIcs.CPM.2023.11,
  author =	{Gabory, Esteban and Mwaniki, Moses Njagi and Pisanti, Nadia and Pissis, Solon P. and Radoszewski, Jakub and Sweering, Michelle and Zuba, Wiktor},
  title =	{{Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{11:1--11:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-276-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{259},
  editor =	{Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.11},
  URN =		{urn:nbn:de:0030-drops-179650},
  doi =		{10.4230/LIPIcs.CPM.2023.11},
  annote =	{Keywords: elastic-degenerate string, sequence comparison, languages intersection, pangenome, acronym identification}
}
  • Refine by Type
  • 8 Document/PDF
  • 7 Document/HTML

  • Refine by Publication Year
  • 1 2026
  • 6 2025
  • 1 2023

  • Refine by Author
  • 3 Pisanti, Nadia
  • 3 Pissis, Solon P.
  • 2 Radoszewski, Jakub
  • 2 Zuba, Wiktor
  • 1 Cenzato, Davide
  • Show More...

  • Refine by Series/Journal
  • 6 LIPIcs
  • 2 OASIcs

  • Refine by Classification
  • 4 Theory of computation → Pattern matching
  • 1 Applied computing → Bioinformatics
  • 1 Applied computing → Computational genomics
  • 1 Applied computing → Genomics
  • 1 Mathematics of computing → Graph algorithms
  • Show More...

  • Refine by Keyword
  • 2 ED string
  • 2 Hamming distance
  • 1 Burrows-Wheeler transform
  • 1 Elastic-degenerate strings
  • 1 Extended Burrows-Wheeler transform
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact