39 Search Results for "Faro, Simone"

Volume

LIPIcs, Volume 160

18th International Symposium on Experimental Algorithms (SEA 2020)

SEA 2020, June 16-18, 2020, Catania, Italy

Editors: Simone Faro and Domenico Cantone

Document
DOI: 10.4230/LIPIcs.FUN.2026.15
Spells for Quantum Programmers: Expressive High-Level Commands in Qutes

Authors: Simone Faro, Francesco Pio Marino, and Gabriele Messina

Published in: LIPIcs, Volume 366, 13th International Conference on Fun with Algorithms (FUN 2026)

Abstract
Classical computers are powerful but fundamentally mundane: they operate through explicit, step-by-step instructions that force programmers to think locally and procedurally. Quantum technologies, by contrast, resemble magical instruments, capable of acting on superpositions, correlations, and entire collections of states at once. Yet, despite their magical nature, quantum computers are still programmed as if they were ordinary machines, relying on long sequences of low-level operations that obscure the underlying algorithmic ideas. Magic, however, is not performed by improvisation alone: it requires a spellbook. In this paper we position Qutes as a book of spells for quantum programmers, providing high-level commands that capture complex quantum behaviour behind concise and expressive syntax. We focus on the manipulation of quantum arrays, which naturally arise in many algorithms but are notoriously cumbersome to manage at the circuit level. We introduce three new array-oriented spells in Qutes: global initialization, parallel pairwise comparison, and parallel (optionally controlled) swap. Individually, these spells encapsulate non-trivial quantum procedures; when combined, they enable programmers to express algorithms in a way that is immediate, readable, and surprisingly elegant. As a final demonstration, we show how these spells can be assembled to produce a remarkably compact implementation of Bubble Sort. While algorithmically simple, this example illustrates a broader message: when the right abstractions are available, quantum programming can feel less like engineering machinery and more like magic.
Cite as

Simone Faro, Francesco Pio Marino, and Gabriele Messina. Spells for Quantum Programmers: Expressive High-Level Commands in Qutes. In 13th International Conference on Fun with Algorithms (FUN 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 366, pp. 15:1-15:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{faro_et_al:LIPIcs.FUN.2026.15,
  author =	{Faro, Simone and Marino, Francesco Pio and Messina, Gabriele},
  title =	{{Spells for Quantum Programmers: Expressive High-Level Commands in Qutes}},
  booktitle =	{13th International Conference on Fun with Algorithms (FUN 2026)},
  pages =	{15:1--15:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-417-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{366},
  editor =	{Iacono, John},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2026.15},
  URN =		{urn:nbn:de:0030-drops-257349},
  doi =		{10.4230/LIPIcs.FUN.2026.15},
  annote =	{Keywords: Quantum programming languages, High-level abstractions, Quantum arrays}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.26
Approximate Cartesian Tree Matching with Substitutions

Authors: Panagiotis Charalampopoulos, Jonas Ellert, and Manal Mohamed

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

Abstract
The Cartesian tree of a sequence captures the relative order of the sequence’s elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a text T of length n and a pattern P of length m. In the exact Cartesian tree matching problem, the task is to find all length-m fragments of T whose Cartesian tree coincides with the Cartesian tree CT(P) of the pattern. Although the exact version of the problem can be solved in linear time [Park et al., TCS 2020], it remains rather restrictive; for example, it is not robust to outliers in the pattern. To overcome this limitation, we consider the approximate setting, where the goal is to identify all fragments of T that are close to some string whose Cartesian tree matches CT(P). In this work, we quantify closeness via the widely used Hamming distance metric. For a given integer parameter k > 0, we present an algorithm that computes all fragments of T that are at Hamming distance at most k from a string whose Cartesian tree matches CT(P). Our algorithm runs in time 𝒪(n √m ⋅ k^{2.5}) for k ≤ m^{1/5} and in time 𝒪(nk⁵) for k ≥ m^{1/5}, thereby improving upon the state-of-the-art 𝒪(nmk)-time algorithm of Kim and Han [TCS 2025] in the regime k = o(m^{1/4}). On the way to our solution, we develop a toolbox of independent interest. First, we introduce a new notion of periodicity in Cartesian trees. Then, we lift multiple well-known combinatorial and algorithmic results for string matching and periodicity in strings to Cartesian tree matching and periodicity in Cartesian trees.
Cite as

Panagiotis Charalampopoulos, Jonas Ellert, and Manal Mohamed. Approximate Cartesian Tree Matching with Substitutions. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 26:1-26:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{charalampopoulos_et_al:LIPIcs.STACS.2026.26,
  author =	{Charalampopoulos, Panagiotis and Ellert, Jonas and Mohamed, Manal},
  title =	{{Approximate Cartesian Tree Matching with Substitutions}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{26:1--26:21},
  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.2026.26},
  URN =		{urn:nbn:de:0030-drops-255151},
  doi =		{10.4230/LIPIcs.STACS.2026.26},
  annote =	{Keywords: Cartesian tree, Hamming distance, approximate pattern matching}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.68
Dynamic Pattern Matching with Wildcards

Authors: Arshia Ataee Naeini, Amir-Parsa Mobed, Masoud Seddighin, and Saeed Seddighin

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

Abstract
We study the fully dynamic pattern matching problem where the pattern may contain up to k wildcard symbols, each matching any symbol of the alphabet. Both the text and the pattern are subject to updates (insert, delete, change). We design an algorithm with 𝒪(n log² n) preprocessing and update/query time 𝒪̃(kn^{k/{k+1}} + k² log n). The bound is truly sublinear for a constant k, and sublinear when k = o(log n). We further complement our results with a conditional lower bound: assuming subquadratic preprocessing time, achieving truly sublinear update time for the case k = Ω(log n) would contradict the Strong Exponential Time Hypothesis (SETH). Finally, we develop sublinear algorithms for two special cases: - If the pattern contains w non-wildcard symbols, we give an algorithm with preprocessing time 𝒪(nw) and update time 𝒪(w + log n), which is truly sublinear whenever w is truly sublinear. - Using FFT technique combined with block decomposition, we design a deterministic truly sublinear algorithm with preprocessing time 𝒪(n^{1.8}) and update time 𝒪(n^{0.8} log n) for the case that there are at most two non-wildcards.
Cite as

Arshia Ataee Naeini, Amir-Parsa Mobed, Masoud Seddighin, and Saeed Seddighin. Dynamic Pattern Matching with Wildcards. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 68:1-68:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{naeini_et_al:LIPIcs.STACS.2026.68,
  author =	{Naeini, Arshia Ataee and Mobed, Amir-Parsa and Seddighin, Masoud and Seddighin, Saeed},
  title =	{{Dynamic Pattern Matching with Wildcards}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{68:1--68:20},
  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.2026.68},
  URN =		{urn:nbn:de:0030-drops-255579},
  doi =		{10.4230/LIPIcs.STACS.2026.68},
  annote =	{Keywords: pattern matching, wildcards, dynamic algorithms, string algorithms, data structures}
}
Document
Research
DOI: 10.4230/OASIcs.Grossi.5
Generalized Fibonacci Cubes Based on Swap and Mismatch Distance

Authors: Marcella Anselmo, Giuseppa Castiglione, Manuela Flores, Dora Giammarresi, Maria Madonia, and Sabrina Mantaci

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

Abstract
The hypercube of dimension n is the graph with 2ⁿ vertices associated to all binary words of length n and edges connecting pairs of vertices with Hamming distance equal to 1. Here, an edit distance based on swaps and mismatches is considered and referred to as tilde-distance. Accordingly, the tilde-hypercube is defined, with edges linking words having tilde-distance equal to 1. The focus is on the subgraphs of the tilde-hypercube obtained by removing all vertices having a given word as factor. If the word is 11, then the subgraph is called tilde-Fibonacci cube; in the case of a generic word, it is called generalized tilde-Fibonacci cube. The paper surveys recent results on the definition and characterization of those words that define generalized tilde-Fibonacci cubes that are isometric subgraphs of the tilde-hypercube. Finally, a special attention is given to the study of the tilde-Fibonacci cubes.
Cite as

Marcella Anselmo, Giuseppa Castiglione, Manuela Flores, Dora Giammarresi, Maria Madonia, and Sabrina Mantaci. Generalized Fibonacci Cubes Based on Swap and Mismatch Distance. 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. 5:1-5:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{anselmo_et_al:OASIcs.Grossi.5,
  author =	{Anselmo, Marcella and Castiglione, Giuseppa and Flores, Manuela and Giammarresi, Dora and Madonia, Maria and Mantaci, Sabrina},
  title =	{{Generalized Fibonacci Cubes Based on Swap and Mismatch Distance}},
  booktitle =	{From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
  pages =	{5:1--5:14},
  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.5},
  URN =		{urn:nbn:de:0030-drops-238044},
  doi =		{10.4230/OASIcs.Grossi.5},
  annote =	{Keywords: Swap and mismatch distance, Isometric words, Hypercube}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.9
Pattern Matching on Run-Length Grammar-Compressed Strings in Linear Time

Authors: Yuto Iguchi, Ryo Yoshinaka, and Ayumi Shinohara

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

Abstract
Run-length straight-line programs (RLSLPs) are a technique for grammar-based compression, allowing any string to be represented with optimal space for δ, the substring complexity of the string. We address the compressed pattern matching problem for RLSLPs: Given a compressed text in RLSLP format and an uncompressed pattern, determine if the pattern appears in the text. This paper proposes an algorithm that solves this problem in linear time with respect to the size of the grammar and the length of the pattern.
Cite as

Yuto Iguchi, Ryo Yoshinaka, and Ayumi Shinohara. Pattern Matching on Run-Length Grammar-Compressed Strings in Linear Time. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{iguchi_et_al:LIPIcs.CPM.2025.9,
  author =	{Iguchi, Yuto and Yoshinaka, Ryo and Shinohara, Ayumi},
  title =	{{Pattern Matching on Run-Length Grammar-Compressed Strings in Linear Time}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{9:1--9:16},
  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.2025.9},
  URN =		{urn:nbn:de:0030-drops-231034},
  doi =		{10.4230/LIPIcs.CPM.2025.9},
  annote =	{Keywords: pattern matching, run-length straight-line programs, compression, suffix tree}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.26
Extending the Burrows-Wheeler Transform for Cartesian Tree Matching and Constructing It

Authors: Eric M. Osterkamp and Dominik Köppl

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

Abstract
Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can be of interest for melody matching between musical scores. For the indexing problem, the state-of-the-art data structure is a Burrows-Wheeler transform based solution due to [Kim and Cho, CPM'21], which uses nearly succinct space and can count the number of substrings that Cartesian tree match with a pattern in time linear in the pattern length. The authors address the construction of their data structure with a straight-forward solution that, however, requires pointer-based data structures, resulting in O(n lg n) bits of space, where n is the text length [Kim and Cho, CPM'21, Section A.4]. We address this bottleneck by a construction that requires O(n lg σ) bits of space and has a time complexity of O(n (lg σ lg n)/(lg lg n)), where σ is alphabet size. Additionally, we can extend this index for indexing multiple circular texts in the spirit of the extended Burrows-Wheeler transform without sacrificing the time and space complexities. We present this index in a dynamic variant, where we pay a logarithmic slowdown and need space linear in the input texts in bits for the extra functionality that we can incrementally add texts. Our extended setting is of interest for finding repetitive motifs common in the aforementioned applications, independent of offsets and scaling.
Cite as

Eric M. Osterkamp and Dominik Köppl. Extending the Burrows-Wheeler Transform for Cartesian Tree Matching and Constructing It. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 26:1-26:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{osterkamp_et_al:LIPIcs.CPM.2025.26,
  author =	{Osterkamp, Eric M. and K\"{o}ppl, Dominik},
  title =	{{Extending the Burrows-Wheeler Transform for Cartesian Tree Matching and Constructing It}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{26:1--26:17},
  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.2025.26},
  URN =		{urn:nbn:de:0030-drops-231201},
  doi =		{10.4230/LIPIcs.CPM.2025.26},
  annote =	{Keywords: Cartesian tree matching, extended Burrows-Wheeler transform, construction algorithm, generalized pattern matching}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.24
Efficient Exact Online String Matching Through Linked Weak Factors

Authors: Matthew N. Palmer, Simone Faro, and Stefano Scafiti

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

Abstract
Online exact string matching is a fundamental computational problem in computer science, involving the sequential search for a pattern within a large text without prior access to the entire text. Its significance is underscored by its diverse applications in data compression, data mining, text editing, and bioinformatics, just to cite a few, where efficient substring matching is crucial. While the problem has been a subject of study for years, recent decades have witnessed a heightened focus on experimental solutions, employing various techniques to achieve superior performance. Notably, approaches centered around weak factor recognition have emerged as leaders in experimental settings, gaining increasing attention. This paper introduces Hash Chain, a novel algorithm founded on a robust weak factor recognition approach that links adjacent factors through hashing. Building upon the efficacy of weak recognition techniques, the proposed algorithm incorporates innovative strategies for organizing data structures and optimizations to enhance performance. Despite its quadratic worst-case time complexity, the new proposed algorithm demonstrates sublinear behavior in practice, outperforming currently known algorithms in the literature.
Cite as

Matthew N. Palmer, Simone Faro, and Stefano Scafiti. Efficient Exact Online String Matching Through Linked Weak Factors. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{palmer_et_al:LIPIcs.SEA.2024.24,
  author =	{Palmer, Matthew N. and Faro, Simone and Scafiti, Stefano},
  title =	{{Efficient Exact Online String Matching Through Linked Weak Factors}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{24:1--24:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.24},
  URN =		{urn:nbn:de:0030-drops-203896},
  doi =		{10.4230/LIPIcs.SEA.2024.24},
  annote =	{Keywords: String matching, text processing, weak recognition, hashing, experimental algorithms, design and analysis of algorithms}
}
Document
DOI: 10.4230/LIPIcs.FUN.2024.13
The Great Textual Hoax: Boosting Sampled String Matching with Fake Samples

Authors: Simone Faro, Francesco Pio Marino, Andrea Moschetto, Arianna Pavone, and Antonio Scardace

Published in: LIPIcs, Volume 291, 12th International Conference on Fun with Algorithms (FUN 2024)

Abstract
Sampled String Matching is presented as an efficient solution to the string matching problem, aiming to tackle the space constraints of indexed string matching while purportedly reducing search times for online solutions. Despite the problem’s inception dating back to 1991, practical solutions have only recently emerged. These purportedly accelerate online searches by up to 35 times compared to conventional methods, achieved through a partial index occupying a mere 5% of the text size. This paper delves into the intricacies of one of the latest and most effective text sampling techniques, character distance sampling, which revolves around sampling distances between characters of a selected alphabet within the text. Specifically, we introduce fake samples while remaining honest! In other words, the study reveals that, interestingly, strategically introducing fake samples within the sampled sequence slashes the required index space by almost half, just avoid compromising the algorithm’s correctness. Additionally, since efficiency is everything, this approach, in turn, purportedly enhances the algorithm’s efficiency under specific conditions.
Cite as

Simone Faro, Francesco Pio Marino, Andrea Moschetto, Arianna Pavone, and Antonio Scardace. The Great Textual Hoax: Boosting Sampled String Matching with Fake Samples. In 12th International Conference on Fun with Algorithms (FUN 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 291, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{faro_et_al:LIPIcs.FUN.2024.13,
  author =	{Faro, Simone and Marino, Francesco Pio and Moschetto, Andrea and Pavone, Arianna and Scardace, Antonio},
  title =	{{The Great Textual Hoax: Boosting Sampled String Matching with Fake Samples}},
  booktitle =	{12th International Conference on Fun with Algorithms (FUN 2024)},
  pages =	{13:1--13:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-314-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{291},
  editor =	{Broder, Andrei Z. and Tamir, Tami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FUN.2024.13},
  URN =		{urn:nbn:de:0030-drops-199211},
  doi =		{10.4230/LIPIcs.FUN.2024.13},
  annote =	{Keywords: string matching, sampling}
}
Document
DOI: 10.4230/LIPIcs.WABI.2020.19
Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations

Authors: Domenico Cantone, Simone Faro, and Arianna Pavone

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

Abstract
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in genomic sequence analysis, little attention has been devoted to the problem of matching sequences allowing for this kind of chromosomal alteration. In this paper we investigate the approximate string matching problem when the edit operations are non-overlapping unbalanced translocations of adjacent factors. In particular, we first present a 𝒪(nm³)-time and 𝒪(m²)-space algorithm based on the dynamic-programming approach. Then we improve our first result by designing a second solution which makes use of the Directed Acyclic Word Graph of the pattern. In particular, we show that under the assumptions of equiprobability and independence of characters, our algorithm has a 𝒪(nlog²_{σ} m) average time complexity, for an alphabet of size σ, still maintaining the 𝒪(nm³)-time and the 𝒪(m²)-space complexity in the worst case. To the best of our knowledge this is the first solution in literature for the approximate string matching problem allowing for unbalanced translocations of factors.
Cite as

Domenico Cantone, Simone Faro, and Arianna Pavone. Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 19:1-19:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{cantone_et_al:LIPIcs.WABI.2020.19,
  author =	{Cantone, Domenico and Faro, Simone and Pavone, Arianna},
  title =	{{Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{19:1--19:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.19},
  URN =		{urn:nbn:de:0030-drops-128086},
  doi =		{10.4230/LIPIcs.WABI.2020.19},
  annote =	{Keywords: Text processing, approximate matching, inversions, sequence matching}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.SEA.2020
LIPIcs, Volume 160, SEA 2020, Complete Volume

Authors: Simone Faro and Domenico Cantone

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

Abstract
LIPIcs, Volume 160, SEA 2020, Complete Volume
Cite as

18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 1-366, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@Proceedings{faro_et_al:LIPIcs.SEA.2020,
  title =	{{LIPIcs, Volume 160, SEA 2020, Complete Volume}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{1--366},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020},
  URN =		{urn:nbn:de:0030-drops-120730},
  doi =		{10.4230/LIPIcs.SEA.2020},
  annote =	{Keywords: LIPIcs, Volume 160, SEA 2020, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.SEA.2020.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Simone Faro and Domenico Cantone

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as

18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{faro_et_al:LIPIcs.SEA.2020.0,
  author =	{Faro, Simone and Cantone, Domenico},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{0:i--0:xii},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.0},
  URN =		{urn:nbn:de:0030-drops-120741},
  doi =		{10.4230/LIPIcs.SEA.2020.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.SEA.2020.1
Algorithm Engineering for High-Dimensional Similarity Search Problems (Invited Talk)

Authors: Martin Aumüller

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

Abstract
Similarity search problems in high-dimensional data arise in many areas of computer science such as data bases, image analysis, machine learning, and natural language processing. One of the most prominent problems is finding the k nearest neighbors of a data point q ∈ ℝ^d in a large set of data points S ⊂ ℝ^d, under same distance measure such as Euclidean distance. In contrast to lower dimensional settings, we do not know of worst-case efficient data structures for such search problems in high-dimensional data, i.e., data structures that are faster than a linear scan through the data set. However, there is a rich body of (often heuristic) approaches that solve nearest neighbor search problems much faster than such a scan on many real-world data sets. As a necessity, the term solve means that these approaches give approximate results that are close to the true k-nearest neighbors. In this talk, we survey recent approaches to nearest neighbor search and related problems. The talk consists of three parts: (1) What makes nearest neighbor search difficult? (2) How do current state-of-the-art algorithms work? (3) What are recent advances regarding similarity search on GPUs, in distributed settings, or in external memory?
Cite as

Martin Aumüller. Algorithm Engineering for High-Dimensional Similarity Search Problems (Invited Talk). In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 1:1-1:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{aumuller:LIPIcs.SEA.2020.1,
  author =	{Aum\"{u}ller, Martin},
  title =	{{Algorithm Engineering for High-Dimensional Similarity Search Problems}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{1:1--1:3},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.1},
  URN =		{urn:nbn:de:0030-drops-120751},
  doi =		{10.4230/LIPIcs.SEA.2020.1},
  annote =	{Keywords: Nearest neighbor search, Benchmarking}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.SEA.2020.2
Algorithm Engineering for Sorting and Searching, and All That (Invited Talk)

Authors: Stefan Edelkamp

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

Abstract
We look at several proposals to engineer the set of fundamental searching and sorting algorithms. Aspects are improving locality of disk access and cache access, the efficiency tuning by reducing the number of branch mispredictions, and reducing at leading factors hidden in the Big-Oh notation. These studies in algorithm engineering, in turn, lead to exiting new algorithm designs. On the practical side, we will establish that efficient sorting and searching algorithms are in tight collaboration, as sorting is used for finding duplicates in disk-based search, and heap structures designed for efficient graph search can be exploited in classical and adaptive sorting. We indicate the effects of engineered sorting and searching for combined task and motion planning.
Cite as

Stefan Edelkamp. Algorithm Engineering for Sorting and Searching, and All That (Invited Talk). In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 2:1-2:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{edelkamp:LIPIcs.SEA.2020.2,
  author =	{Edelkamp, Stefan},
  title =	{{Algorithm Engineering for Sorting and Searching, and All That}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{2:1--2:3},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.2},
  URN =		{urn:nbn:de:0030-drops-120766},
  doi =		{10.4230/LIPIcs.SEA.2020.2},
  annote =	{Keywords: Sorting, Searching, Algorithm Engineering}
}
Document
Invited Talk
DOI: 10.4230/LIPIcs.SEA.2020.3
Indexing Compressed Text: A Tale of Time and Space (Invited Talk)

Authors: Nicola Prezza

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)

Abstract
Text indexing is a classical algorithmic problem that has been studied for over four decades. The earliest optimal-time solution to the problem, the suffix tree [Weiner, 1973], dates back to 1973 and requires up to two orders of magnitude more space than the text to be stored. In the year 2000, two breakthrough works [Grossi and Vitter, 2000; Ferragina and Manzini, 2000] showed that this space overhead is not necessary: both the index and the text can be stored in a space proportional to the text’s entropy. These contributions had an enormous impact in bioinformatics: nowadays, the two most widely-used DNA aligners employ compressed indexes [Li and Durbin, 2009; Langmead et al., 2009]. In recent years, it became apparent that entropy had reached its limits: modern datasets (for example, collections of thousands of human genomes) are extremely large but very repetitive and, by its very definition, entropy cannot compress repetitive texts [S. Kreft and G. Navarro, 2013]. To overcome this problem, a new generation of indexes based on dictionary compressors (for example, LZ77 and run-length BWT) emerged [S. Kreft and G. Navarro, 2013; Gagie et al., 2020; F. Claude and G. Navarro, 2012], together with generalizations of the indexing problem to labeled graphs [Ferragina et al., 2009; Sirén et al., 2014; Travis Gagie et al., 2017]. This talk is a short and friendly survey of the landmarks of this fascinating path that took us from suffix trees to the most modern compressed indexes on labeled graphs.
Cite as

Nicola Prezza. Indexing Compressed Text: A Tale of Time and Space (Invited Talk). In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 3:1-3:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{prezza:LIPIcs.SEA.2020.3,
  author =	{Prezza, Nicola},
  title =	{{Indexing Compressed Text: A Tale of Time and Space}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{3:1--3:2},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.3},
  URN =		{urn:nbn:de:0030-drops-120772},
  doi =		{10.4230/LIPIcs.SEA.2020.3},
  annote =	{Keywords: Compressed Text Indexing}
}
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