Volume
OASIcs, Volume 132
From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday
-
Part of:
Series:
Open Access Series in Informatics (OASIcs)
Conference: Roberto Grossi's Festschrift
Event
Grossi's Festschrift, July 25, 2025, Venice, ItalyEditors
Publication Details
- published at: 2025-08-11
- Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
- ISBN: 978-3-95977-391-1
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Document
Complete Volume
OASIcs, Volume 132, Grossi's Festschrift, Complete Volume
Abstract
OASIcs, Volume 132, Grossi's Festschrift, Complete Volume
Cite as
From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 1-312, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@Proceedings{conte_et_al:OASIcs.Grossi,
title = {{OASIcs, Volume 132, Grossi's Festschrift, Complete Volume}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {1--312},
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},
URN = {urn:nbn:de:0030-drops-243429},
doi = {10.4230/OASIcs.Grossi},
annote = {Keywords: OASIcs, Volume 132, Grossi's Festschrift, Complete Volume}
}
Document
Front Matter
Front Matter, Table of Contents, Preface, Conference Organization
Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as
From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 132, pp. 0:i-0:xxxii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{conte_et_al:OASIcs.Grossi.0,
author = {Conte, Alessio and Marino, Andrea and Rosone, Giovanna and Vitter, Jeffrey Scott},
title = {{Front Matter, Table of Contents, Preface, Conference Organization}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {0:i--0:xxxii},
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.0},
URN = {urn:nbn:de:0030-drops-239054},
doi = {10.4230/OASIcs.Grossi.0},
annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
Research
An Efficient Heuristic for Graph Edit Distance
Abstract
The graph edit distance (GED) is a flexible distance measure widely used in many applications. Existing GED computation methods are usually based upon the tree-based search algorithm that explores all possible vertex (or edge) mappings between two compared graphs. During this process, various GED lower bounds are adopted as heuristic estimations to accelerate the tree-based search algorithm. For the first time, we analyze the relationship among three state-of-the-art GED lower bounds, label edit distance (LED), Hausdorff edit distance (HED), and branch edit distance (BED). Specifically, we demonstrate that BED(G, Q) ≥ HED(G, Q) and BED(G, Q) ≥ LED(G, Q) for any two undirected graphs G and Q. Furthermore, for BED we propose an efficient heuristic BED^+ for improving the tree-based search algorithm. Extensive experiments on real and synthetic datasets confirm that BED^+ achieves smaller deviation and larger solvable ratios than LED, HED and BED when they are employed as heuristic estimations. The source code is available online.
Cite as
Xiaoyang Chen, Yujia Wang, Hongwei Huo, and Jeffrey Scott Vitter. An Efficient Heuristic for Graph Edit 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. 1:1-1:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{chen_et_al:OASIcs.Grossi.1,
author = {Chen, Xiaoyang and Wang, Yujia and Huo, Hongwei and Vitter, Jeffrey Scott},
title = {{An Efficient Heuristic for Graph Edit Distance}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {1:1--1:18},
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.1},
URN = {urn:nbn:de:0030-drops-238004},
doi = {10.4230/OASIcs.Grossi.1},
annote = {Keywords: Graph edit distance, Label edit distance, Hausdorff edit distance, Branch edit distance, Tree-based search, Heuristics}
}
Document
Research
On the Construction of Elastic Degenerate Strings
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)
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@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
Education
"Strutture Di Dati e Algoritmi. Progettazione, Analisi e Visualizzazione", a Book Beating Its Own Drum
Abstract
In this contribution, we discuss the innovative approach taken by Roberto Grossi and his co-authors in their book "Strutture di dati e algoritmi. Progettazione, analisi e visualizzazione," which aims to bridge the gap between the theoretical and practical aspects of algorithms. Unlike traditional texts that either focus on formal mathematical analysis or practical implementation, this book adopts an intermediate approach that emphasizes both programming skills and theoretical understanding. This contribution reflects our experience as instructors of the introductory algorithms course in the Computer Science degree program at the University of Pisa.
Cite as
Anna Bernasconi and Linda Pagli. "Strutture Di Dati e Algoritmi. Progettazione, Analisi e Visualizzazione", a Book Beating Its Own Drum. 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. 3:1-3:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{bernasconi_et_al:OASIcs.Grossi.3,
author = {Bernasconi, Anna and Pagli, Linda},
title = {{"Strutture Di Dati e Algoritmi. Progettazione, Analisi e Visualizzazione", a Book Beating Its Own Drum}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {3:1--3:5},
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.3},
URN = {urn:nbn:de:0030-drops-238028},
doi = {10.4230/OASIcs.Grossi.3},
annote = {Keywords: Algorithms, C-Programming, Basics of Computational Thinking}
}
Document
Research
On Graph Burning and Edge Burning
Abstract
Graph burning is a deterministic, discrete-time process that models how influence or contagion spreads in a graph. Initially, all vertices are unburned. At each round, one new vertex is chosen to burn. Once a vertex is burned, in the next round each of its unburned neighbors become burned. The process ends when all vertices are burned. The burning number of a graph is the minimum number of rounds needed for the process to end. Very recently, a variant called edge burning was introduced, where instead of vertices we burn edges: at each round one new edge is burned. Once an edge is burned, in the next round all its unburned incident edges become burned. The edge burning number is the minimum number of rounds that are needed to burn all the edges. In this paper, we present a systematic study of edge burning and provide some new results for graph burning. First, we show a tight relationship between the edge burning number and the burning number of a given graph: specifically, their absolute difference is at most 1. Moreover, we show that the edge burning number of a graph is equal to the graph burning number of its line graph. On the computation complexity side, we show that the edge burning problem is NP-complete, but can be solved in linear time on paths, split graphs, and cographs. Furthermore, we give an XP algorithm when the edge burning problem is parameterized by the diameter of the input graph and a linear kernel when parameterized by the neighborhood diversity. For the graph burning problem, we provide 2-approximation algorithms when either the solution is part of the input or forced to form a path.
Cite as
Giuseppe F. Italiano, Athanasios L. Konstantinidis, and Manas Jyoti Kashyop. On Graph Burning and Edge Burning. 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. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{italiano_et_al:OASIcs.Grossi.4,
author = {Italiano, Giuseppe F. and Konstantinidis, Athanasios L. and Kashyop, Manas Jyoti},
title = {{On Graph Burning and Edge Burning}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {4:1--4:18},
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.4},
URN = {urn:nbn:de:0030-drops-238039},
doi = {10.4230/OASIcs.Grossi.4},
annote = {Keywords: Burning Number, Graph Burning, Edge Burning, Approximation}
}
Document
Research
Generalized Fibonacci Cubes Based on Swap and Mismatch Distance
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
Research
Compact Data Structures for Collections of Sets
Abstract
We define a new entropy measure L(𝒮), called the containment entropy, for a set 𝒮 of sets, which considers the fact that some sets can be contained in others. We show how to represent 𝒮 within space close to L(𝒮) so that any element of any set can be retrieved in logarithmic time. We extend the result to predecessor and successor queries and show how some common set operations can be implemented efficiently.
Cite as
Jarno N. Alanko, Philip Bille, Inge Li Gørtz, Gonzalo Navarro, and Simon J. Puglisi. Compact Data Structures for Collections of Sets. 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. 6:1-6:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{alanko_et_al:OASIcs.Grossi.6,
author = {Alanko, Jarno N. and Bille, Philip and G{\o}rtz, Inge Li and Navarro, Gonzalo and Puglisi, Simon J.},
title = {{Compact Data Structures for Collections of Sets}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {6:1--6:7},
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.6},
URN = {urn:nbn:de:0030-drops-238051},
doi = {10.4230/OASIcs.Grossi.6},
annote = {Keywords: Compressed data structures, entropy of sets, data compression}
}
Document
Research
Conditional Lower Bounds for String Matching in Labelled Graphs
Abstract
The problem of String Matching in Labelled Graphs (SMLG) is one possible generalization of the classic problem of finding a string inside another of greater length. In its most general form, SMLG asks to find a match for a string into a graph, which can be directed or undirected. As for string matching, many different variations are possible. For example, the match could be exact or approximate, and the match could lie on a path or a walk. Some of these variations easily fall into the NP-hard realm, while other variants are solvable in polynomial time. For the latter ones, fine-grained complexity has been a game changer in proving quadratic conditional lower bounds, allowing to finally close the gap with those upper bounds that remained unmatched for almost two decades.
If the match is allowed to be approximate, SMLG enjoys the same conditional quadratic lower bounds shown for example for edit distance (Backurs and Indyk, STOC '15). The case that really requires ad hoc conditional lower bounds is the one of finding an exact match that lies on a walk. In this work, we focus on explaining various conditional lower bounds for this version of SMLG, with the goal of giving an overall perspective that could help understand which aspects of the problem make it quadratic. We will introduce the reader to the field of fine-grained complexity and show how it can successfully provide the exact type of lower bounds needed for polynomial problems such as SMLG.
Cite as
Massimo Equi. Conditional Lower Bounds for String Matching in Labelled Graphs. 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. 7:1-7:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{equi:OASIcs.Grossi.7,
author = {Equi, Massimo},
title = {{Conditional Lower Bounds for String Matching in Labelled Graphs}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {7:1--7:13},
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.7},
URN = {urn:nbn:de:0030-drops-238063},
doi = {10.4230/OASIcs.Grossi.7},
annote = {Keywords: conditional lower bounds, strong exponential time hypothesis, fine-grained complexity, string matching, graphs}
}
Document
Research
Enumeration of Ordered Trees with Leaf Restrictions
Abstract
An α-ary tree for a constant α ≥ 2 is a rooted tree in which each node has at most α children. A node having no children is called a leaf. For a given rooted tree and a node v, the number of edges from the root to v is called the depth of v. We call a vector w = (w_1,w_2,…, w_d) of nonnegative integers an (α-ary) distribution if there is an α-ary tree T such that the number of leaves at each depth i ∈ [1..d] in T is w_i. Although not every vector of nonnegative integers is a distribution, a distribution can be associated with many α-ary trees. In this paper, we present an algorithm to enumerate all α-ary trees for a given distribution. Our algorithm reports the first tree in O(d + ∑_{i = 1}^d w_i) time, and then each subsequent α-ary tree in O(max_{i = 1}^d w_i) time by representing each tree as the difference from the previous one. The algorithm can be restricted to computing all trees that are full, i.e., trees whose nodes have exactly α or no children.
Cite as
Yasuaki Kobayashi, Dominik Köppl, Yasuko Matsui, Hirotaka Ono, Toshiki Saitoh, and Yushi Uno. Enumeration of Ordered Trees with Leaf Restrictions. 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. 8:1-8:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{kobayashi_et_al:OASIcs.Grossi.8,
author = {Kobayashi, Yasuaki and K\"{o}ppl, Dominik and Matsui, Yasuko and Ono, Hirotaka and Saitoh, Toshiki and Uno, Yushi},
title = {{Enumeration of Ordered Trees with Leaf Restrictions}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {8:1--8:19},
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.8},
URN = {urn:nbn:de:0030-drops-238077},
doi = {10.4230/OASIcs.Grossi.8},
annote = {Keywords: binary trees, ordered trees, rooted trees, enumeration algorithm, constant-time delay}
}
Document
Research
On String and Graph Sanitization
Abstract
Data sanitization is a process that conceals sensitive patterns from a given dataset. A secondary goal is to not severely harm the utility of the underlying data along this process. We survey some recent advancements on two related data sanitization topics: string and graph sanitization. In particular, we highlight the important contributions of our friend Prof. Roberto Grossi along this journey.
Cite as
Giulia Bernardini, Huiping Chen, Grigorios Loukides, and Solon P. Pissis. On String and Graph Sanitization. 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. 9:1-9:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{bernardini_et_al:OASIcs.Grossi.9,
author = {Bernardini, Giulia and Chen, Huiping and Loukides, Grigorios and Pissis, Solon P.},
title = {{On String and Graph Sanitization}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {9:1--9:10},
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.9},
URN = {urn:nbn:de:0030-drops-238086},
doi = {10.4230/OASIcs.Grossi.9},
annote = {Keywords: data privacy, data sanitization, string algorithms, graph algorithms}
}
Document
Research
Faster Run-Length Compressed Suffix Arrays
Abstract
We first review how we can store a run-length compressed suffix array (RLCSA) for a text T of length n over an alphabet of size σ whose Burrows-Wheeler Transform (BWT) consists of r runs in O (r log (n / r) + r log σ + σ) bits such that later, given character a and the suffix-array (SA) interval for P, we can find the SA interval for a P in O (log r_a + log log n) time, where r_a is the number of runs of copies of a in the BWT. We then show how to modify the RLCSA such that we find the SA interval for a P in only O (log r_a) time, without increasing its asymptotic space bound. Our key idea is applying a result by Nishimoto and Tabei (ICALP 2021) and then replacing rank queries on sparse bitvectors by a constant number of select queries. We also review two-level indexing and discuss how our faster RLCSA may be useful in improving it. Finally, we briefly discuss how two-level indexing may speed up a recent heuristic for finding maximal exact matches of a pattern with respect to an indexed text.
Cite as
Nathaniel K. Brown, Travis Gagie, Giovanni Manzini, Gonzalo Navarro, and Marinella Sciortino. Faster Run-Length Compressed Suffix Arrays. 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. 10:1-10:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{brown_et_al:OASIcs.Grossi.10,
author = {Brown, Nathaniel K. and Gagie, Travis and Manzini, Giovanni and Navarro, Gonzalo and Sciortino, Marinella},
title = {{Faster Run-Length Compressed Suffix Arrays}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {10:1--10:15},
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.10},
URN = {urn:nbn:de:0030-drops-238095},
doi = {10.4230/OASIcs.Grossi.10},
annote = {Keywords: Run-length compressed suffix arrays, interpolative coding, two-level indexing}
}
Document
Education
Turing Arena Light: Enhancing Programming Education Through Competitive Environments
Abstract
Turing Arena light, the spiritual successor of Turing Arena, is a contest management system that is designed to be more geared towards the needs of classroom teaching, rather than competitive programming contests. It strives to be as simple as possible, while being very flexible and extensible.
The fundamental idea behind Turing Arena light is to have two programs that talk to each other through the standard input and output channels. One of the two programs is the problem manager, which is a program that interacts with a solution to give it the input and evaluate its output, and eventually give a verdict. The other program is the solution, which is the program written by the contestant that is meant to solve the problem.
In this paper we describe the architecture and the design of Turing Arena light.
Cite as
Giorgio Audrito, Luigi Laura, Alessio Orlandi, Dario Ostuni, Romeo Rizzi, and Luca Versari. Turing Arena Light: Enhancing Programming Education Through Competitive Environments. 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. 11:1-11:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{audrito_et_al:OASIcs.Grossi.11,
author = {Audrito, Giorgio and Laura, Luigi and Orlandi, Alessio and Ostuni, Dario and Rizzi, Romeo and Versari, Luca},
title = {{Turing Arena Light: Enhancing Programming Education Through Competitive Environments}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {11:1--11:14},
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.11},
URN = {urn:nbn:de:0030-drops-238108},
doi = {10.4230/OASIcs.Grossi.11},
annote = {Keywords: Competitive Programming, Contest Management Systems, Online Judges}
}
Document
Research
Encoding Data Structures for Range Queries on Arrays
Abstract
Efficiently processing range queries on arrays is a fundamental problem in computer science, with applications spanning diverse domains such as database management, computational biology, and geographic information systems. A range query retrieves information about a specific segment of an array, such as the sum, minimum, maximum, or median of elements within a given range. The challenge lies in designing data structures that allow such queries to be answered quickly, often in constant or logarithmic time, while keeping space overhead (and preprocessing time) small. Encoding data structures for range queries has emerged as a pivotal area of research due to the increasing demand for high-performance systems handling massive datasets. These structures consider the data together with the queries and aim to store only as much information about the data as is needed to answer the queries. The data structure does not need to access the original data to answer the queries. Encoding-based solutions often leverage techniques from succinct data structures, bit manipulation, and combinatorial optimization to achieve both space and time efficiency. By encoding the array in a manner that preserves critical information, these methods strike a balance between query time and space usage. In this survey article, we explore the landscape of encoding data structures for range queries on arrays, providing a comprehensive overview of some important results on space-efficient encodings for various types of range query.
Cite as
Seungbum Jo and Srinivasa Rao Satti. Encoding Data Structures for Range Queries on Arrays. 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. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{jo_et_al:OASIcs.Grossi.12,
author = {Jo, Seungbum and Satti, Srinivasa Rao},
title = {{Encoding Data Structures for Range Queries on Arrays}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {12:1--12:12},
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.12},
URN = {urn:nbn:de:0030-drops-238116},
doi = {10.4230/OASIcs.Grossi.12},
annote = {Keywords: range queries, RMQ, Cartesian tree, top-k queries, range median, range mode}
}
Document
Research
Secure Compressed Suffix Arrays
Abstract
This paper proposes a secure compressed suffix array, which is a data oblivious and compressed version of the suffix array used for finding substrings of a large string. Secure compressed suffix arrays can be used for indexing a large collection of strings containing personal information such as DNA data.
Cite as
Kunihiko Sadakane. Secure Compressed Suffix Arrays. 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. 13:1-13:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{sadakane:OASIcs.Grossi.13,
author = {Sadakane, Kunihiko},
title = {{Secure Compressed Suffix Arrays}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {13:1--13:8},
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.13},
URN = {urn:nbn:de:0030-drops-238122},
doi = {10.4230/OASIcs.Grossi.13},
annote = {Keywords: suffix array, compression, encryption, oblivious algorithm, secure computation}
}
Document
Research
Specific Patterns Against Reference Sequences
Abstract
We design alignment-free techniques for comparing a set of sequences or just a word, called a target, against another set of words, called a reference. This is done with the detection of factor patterns that distinguish the target from the reference. A target-specific factor of a target T against a reference R is then a factor w of a word in T that is not a factor of a word in R but whose proper factors of w are factors of a word in R. The strategy is based on the notion of minimal absent/forbidden words.
We first address the computation of the set of target-specific factors of a target T against a reference R, where T and R are finite sets of sequences. The result is the construction of an automaton accepting the set of all considered target-specific factors. The construction algorithm runs in linear time according to the size of T ∪ R.
The second result is the design of an algorithm to compute all the occurrences in a single sequence T of its target-specific factors against a reference R. The algorithm runs in real-time on the target sequence, independently of the number of occurrences of target-specific factors.
Cite as
Marie-Pierre Béal and Maxime Crochemore. Specific Patterns Against Reference Sequences. 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. 14:1-14:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{beal_et_al:OASIcs.Grossi.14,
author = {B\'{e}al, Marie-Pierre and Crochemore, Maxime},
title = {{Specific Patterns Against Reference Sequences}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {14:1--14:12},
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.14},
URN = {urn:nbn:de:0030-drops-238130},
doi = {10.4230/OASIcs.Grossi.14},
annote = {Keywords: Specific pattern, Minimal absent word, Minimal forbidden word, Directed Acyclic Word Graph (DAWG), Suffix automaton}
}
Document
Research
Wavelet Tree, Part I: A Brief History
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: one (this one) giving a brief history of Wavelet Trees, including its varieties and practical implementations, dedicated to this Festschrift’s honoree Roberto Grossi; the second part deals with Wavelet Tree-based text indexing and is included in the Festschrift dedicated to Giovanni Manzini [Ferragina et al., 2025].
Cite as
Paolo Ferragina, Raffaele Giancarlo, Giovanni Manzini, Giovanna Rosone, Rossano Venturini, and Jeffrey Scott Vitter. Wavelet Tree, Part I: A Brief History. 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. 15:1-15:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{ferragina_et_al:OASIcs.Grossi.15,
author = {Ferragina, Paolo and Giancarlo, Raffaele and Manzini, Giovanni and Rosone, Giovanna and Venturini, Rossano and Vitter, Jeffrey Scott},
title = {{Wavelet Tree, Part I: A Brief History}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {15:1--15:11},
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.15},
URN = {urn:nbn:de:0030-drops-238143},
doi = {10.4230/OASIcs.Grossi.15},
annote = {Keywords: Wavelet tree, data compression, text indexing, compressed suffix array, Burrows-Wheeler transform, rank and select}
}
Document
Research
Faster Range LCP Queries in Linear Space
Abstract
A range LCP query rlcp(α,β) on a text T[1 .. n] asks to return the length of the longest common prefix of any two suffixes of T with starting positions in a range [α,β]. In this paper we describe a data structure that uses O(n) space and supports range LCP queries in time O(log^ε n) for any constant ε > 0. Our result is the fastest currently known linear-space solution for this problem.
Cite as
Yakov Nekirch and Sharma V. Thankachan. Faster Range LCP Queries in Linear Space. 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. 16:1-16:6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{nekirch_et_al:OASIcs.Grossi.16,
author = {Nekirch, Yakov and Thankachan, Sharma V.},
title = {{Faster Range LCP Queries in Linear Space}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {16:1--16:6},
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.16},
URN = {urn:nbn:de:0030-drops-238158},
doi = {10.4230/OASIcs.Grossi.16},
annote = {Keywords: Data Structures, String Algorithms, Longest Common Prefix}
}
Document
Research
On Inverting the Burrows-Wheeler Transform
Abstract
We study the relationship between four fundamental problems: sorting, suffix sorting, element distinctness and BWT inversion. Our main contribution is an Ω(n log n) lower bound for BWT inversion in the comparison model. As a corollary, we obtain a new proof of the classical Ω(n log n) lower bound for sorting, which we believe to be of didactic interest for those who are not familiar with the Burrows-Wheeler transform.
Cite as
Nicola Cotumaccio. On Inverting the Burrows-Wheeler Transform. 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. 17:1-17:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{cotumaccio:OASIcs.Grossi.17,
author = {Cotumaccio, Nicola},
title = {{On Inverting the Burrows-Wheeler Transform}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {17:1--17:8},
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.17},
URN = {urn:nbn:de:0030-drops-238169},
doi = {10.4230/OASIcs.Grossi.17},
annote = {Keywords: Burrows-Wheeler transform, sorting, suffix array, element distinctness}
}
Document
Research
DNA Is a Puzzle Enthusiast
Abstract
This article presents a concise summary of research projects in which Roberto Grossi participated, yielding interesting results that were never previously published in research papers. At the time, these studies were deemed too limited and in need of further extensions and generalizations, which were never realized due to a lack of resources. The researches focused on methods for inferring possible three-dimensional DNA conformations based on nucleotide sequence characteristics. Specifically, two key approaches were investigated: the identification of structured motifs for detecting Transcription Factor Binding Sites (TFBS) and the study of nested permutations using PQ-trees. This article describes the obtained results in selected case studies, their potential implications, and the current state of the art in these research areas.
Cite as
Roberto Marangoni. DNA Is a Puzzle Enthusiast. 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. 18:1-18:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{marangoni:OASIcs.Grossi.18,
author = {Marangoni, Roberto},
title = {{DNA Is a Puzzle Enthusiast}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {18:1--18:8},
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.18},
URN = {urn:nbn:de:0030-drops-238172},
doi = {10.4230/OASIcs.Grossi.18},
annote = {Keywords: DNA, 3D structure, PQ trees, structural motifs}
}
Document
Research
Designing Output Sensitive Algorithms for Subgraph Enumeration
Abstract
The enumeration of all subgraphs respecting some structural property is a fundamental task in theoretical computer science, with practical applications in many branches of data mining and network analysis. It is often of interest to only consider solutions (subgraphs) that are maximal under inclusion, and to achieve output-sensitive complexity, i.e., bounding the running time with respect to the number of subgraphs produced. In this paper, we provide a survey of techniques for designing output-sensitive algorithms for subgraph enumeration, including partition-based approaches such as flashlight search, solution-graph traversal methods such as reverse search, and cost amortization strategies such as push-out amortization. We also briefly discuss classes of efficiency, hardness of enumeration, and variants such as approximate enumeration. The paper is meant as an accessible handbook for learning the basics of the field and as a practical reference for selecting state-of-the-art subgraph enumeration strategies fitting to one’s needs.
Cite as
Alessio Conte, Kazuhiro Kurita, Andrea Marino, Giulia Punzi, Takeaki Uno, and Kunihiro Wasa. Designing Output Sensitive Algorithms for Subgraph Enumeration. 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. 19:1-19:40, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{conte_et_al:OASIcs.Grossi.19,
author = {Conte, Alessio and Kurita, Kazuhiro and Marino, Andrea and Punzi, Giulia and Uno, Takeaki and Wasa, Kunihiro},
title = {{Designing Output Sensitive Algorithms for Subgraph Enumeration}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {19:1--19:40},
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.19},
URN = {urn:nbn:de:0030-drops-238180},
doi = {10.4230/OASIcs.Grossi.19},
annote = {Keywords: Graph algorithms, Graph enumeration, Output sensitive enumeration}
}
Document
Research
Subsequence-Based Indices for Genome Sequence Analysis
Abstract
Compact indices are a fundamental tool in string analysis, even more so in bioinformatics, where genomic sequences can reach billions in length. This paper presents some recent results in which Roberto Grossi has been involved, showing how some of these indices do more than just efficiently represent data, but rather are able to bring out salient information within it, which can be exploited for their downstream analysis. Specifically, we first review a recently-introduced method [Guerrini et al., 2023] that employs the Burrows-Wheeler Transform to build reasonably accurate phylogenetic trees in an assembly-free scenario. We then describe a recent practical tool [Buzzega et al., 2025] for indexing Maximal Common Subsequences between strings, which can enable analysis of genomic sequence similarity. Experimentally, we show that the results produced by the one index are consistent with the expectations about the results of the other index.
Cite as
Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, and Lorenzo Tattini. Subsequence-Based Indices for Genome Sequence Analysis. 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. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
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@InProceedings{buzzega_et_al:OASIcs.Grossi.20,
author = {Buzzega, Giovanni and Conte, Alessio and Guerrini, Veronica and Punzi, Giulia and Rosone, Giovanna and Tattini, Lorenzo},
title = {{Subsequence-Based Indices for Genome Sequence Analysis}},
booktitle = {From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday},
pages = {20:1--20:21},
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.20},
URN = {urn:nbn:de:0030-drops-238199},
doi = {10.4230/OASIcs.Grossi.20},
annote = {Keywords: String Indices, Burrows-Wheeler Transform, Maximal Common Subsequences, Sequence Analysis, Phylogeny}
}