106 Search Results for "Sadakane, Kunihiko"

Volume

LIPIcs, Volume 212

32nd International Symposium on Algorithms and Computation (ISAAC 2021)

ISAAC 2021, December 6-8, 2021, Fukuoka, Japan

Editors: Hee-Kap Ahn and Kunihiko Sadakane

Document
DOI: 10.4230/OASIcs.ATMOS.2024.2
Indexing Graphs for Shortest Beer Path Queries

Authors: David Coudert, Andrea D'Ascenzo, and Mattia D'Emidio

Published in: OASIcs, Volume 123, 24th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2024)

Abstract
A beer graph is an edge-weighted graph G = (V,E,ω) with beer vertices B ⊆ V. A beer path between two vertices s and t of a beer graph is a path that connects s and t and visits at least one vertex in B. The beer distance between two vertices is the weight of a shortest beer path, i.e. a beer path having minimum total weight. A graph indexing scheme is a two-phase method that constructs an index data structure by a one-time preprocessing of an input graph and then exploits it to compute (or accelerate the computation of) answers to queries on structures of the graph dataset. In the last decade, such indexing schemes have been designed to perform, effectively, many relevant types of queries, e.g. on reachability, and have gained significant popularity in essentially all data-intensive application domains where large number of queries have to be routinely answered (e.g. journey planners), since they have been shown, through many experimental studies, to offer extremely low query times at the price of limited preprocessing time and space overheads. In this paper, we showcase that an indexing scheme, to efficiently execute queries on beer distances or shortest beer paths for pairs of vertices of a beer graph, can be obtained by adapting the highway labeling, a recently introduced indexing method to accelerate the computation of classical shortest paths. We design a preprocessing algorithm to build a whl index, i.e. a weighted highway labeling of a beer graph, and show how it can be queried to compute beer distances and shortest beer paths. Through extensive experimentation on real networks, we empirically demonstrate its practical effectiveness and superiority, in terms of offered trade-off between preprocessing time, space overhead and query time, with respect to the state-of-the-art.
Cite as

David Coudert, Andrea D'Ascenzo, and Mattia D'Emidio. Indexing Graphs for Shortest Beer Path Queries. In 24th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2024). Open Access Series in Informatics (OASIcs), Volume 123, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{coudert_et_al:OASIcs.ATMOS.2024.2,
  author =	{Coudert, David and D'Ascenzo, Andrea and D'Emidio, Mattia},
  title =	{{Indexing Graphs for Shortest Beer Path Queries}},
  booktitle =	{24th Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2024)},
  pages =	{2:1--2:18},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-350-8},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{123},
  editor =	{Bouman, Paul C. and Kontogiannis, Spyros C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ATMOS.2024.2},
  URN =		{urn:nbn:de:0030-drops-211907},
  doi =		{10.4230/OASIcs.ATMOS.2024.2},
  annote =	{Keywords: Graph Algorithms, Indexing Schemes, Beer Distances, Algorithms Engineering}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.25
Graph Spanners for Group Steiner Distances

Authors: Davide Bilò, Luciano Gualà, Stefano Leucci, and Alessandro Straziota

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
A spanner is a sparse subgraph of a given graph G which preserves distances, measured w.r.t. some distance metric, up to a multiplicative stretch factor. This paper addresses the problem of constructing graph spanners w.r.t. the group Steiner metric, which generalizes the recently introduced beer distance metric. In such a metric we are given a collection of groups of required vertices, and we measure the distance between two vertices as the length of the shortest path between them that traverses at least one required vertex from each group. We discuss the relation between group Steiner spanners and classic spanners and we show that they exhibit strong ties with sourcewise spanners w.r.t. the shortest path metric. Nevertheless, group Steiner spanners capture several interesting scenarios that are not encompassed by existing spanners. This happens, e.g., for the singleton case, in which each group consists of a single required vertex, thus modeling the setting in which routes need to traverse certain points of interests (in any order). We provide several constructions of group Steiner spanners for both the all-pairs and single-source case, which exhibit various size-stretch trade-offs. Notably, we provide spanners with almost-optimal trade-offs for the singleton case. Moreover, some of our spanners also yield novel trade-offs for classical sourcewise spanners. Finally, we also investigate the query times that can be achieved when our spanners are turned into group Steiner distance oracles with the same size, stretch, and building time.
Cite as

Davide Bilò, Luciano Gualà, Stefano Leucci, and Alessandro Straziota. Graph Spanners for Group Steiner Distances. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 25:1-25:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bilo_et_al:LIPIcs.ESA.2024.25,
  author =	{Bil\`{o}, Davide and Gual\`{a}, Luciano and Leucci, Stefano and Straziota, Alessandro},
  title =	{{Graph Spanners for Group Steiner Distances}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{25:1--25:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.25},
  URN =		{urn:nbn:de:0030-drops-210968},
  doi =		{10.4230/LIPIcs.ESA.2024.25},
  annote =	{Keywords: Network sparsification, Graph spanners, Group Steiner tree, Distance oracles}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.64
A Simple Representation of Tree Covering Utilizing Balanced Parentheses and Efficient Implementation of Average-Case Optimal RMQs

Authors: Kou Hamada, Sankardeep Chakraborty, Seungbum Jo, Takuto Koriyama, Kunihiko Sadakane, and Srinivasa Rao Satti

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
Tree covering is a technique for decomposing a tree into smaller sized trees with desirable properties, and has been employed in various succinct data structures. However, significant hurdles stand in the way of a practical implementation of tree covering: a lot of pointers are used to maintain the tree-covering hierarchy and many indices for tree navigational queries consume theoretically negligible yet practically vast space. To tackle these problems, we propose a simple representation of tree covering using a balanced-parenthesis representation. The key to the proposal is the observation that every micro tree splits into at most two intervals on the BP representation. Utilizing the representation, we propose several data structures that represent a tree and its tree cover, which consequently allow micro tree compression with arbitrary coding and efficient tree navigational queries. We also applied our data structure to average-case optimal RMQ by Munro et al. [ESA 2021] and implemented the RMQ data structure. Our RMQ data structures spend less than 2n bits and process queries in a practical time on several settings of the performance evaluation, reducing the gap between theoretical space complexity and actual space consumption. For example, our implementation consumes 1.822n bits and processes queries in 5µs on average for random queries and in 13µs on average for the worst query widths. We also implement tree navigational operations while using the same amount of space as the RMQ data structures. We believe the representation can be widely utilized for designing practically memory-efficient data structures based on tree covering.
Cite as

Kou Hamada, Sankardeep Chakraborty, Seungbum Jo, Takuto Koriyama, Kunihiko Sadakane, and Srinivasa Rao Satti. A Simple Representation of Tree Covering Utilizing Balanced Parentheses and Efficient Implementation of Average-Case Optimal RMQs. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 64:1-64:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hamada_et_al:LIPIcs.ESA.2024.64,
  author =	{Hamada, Kou and Chakraborty, Sankardeep and Jo, Seungbum and Koriyama, Takuto and Sadakane, Kunihiko and Satti, Srinivasa Rao},
  title =	{{A Simple Representation of Tree Covering Utilizing Balanced Parentheses and Efficient Implementation of Average-Case Optimal RMQs}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{64:1--64:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.64},
  URN =		{urn:nbn:de:0030-drops-211359},
  doi =		{10.4230/LIPIcs.ESA.2024.64},
  annote =	{Keywords: Hypersuccinct trees, Succinct data structures, Range minimum queries, Binary trees}
}
Document
DOI: 10.4230/LIPIcs.ESA.2024.78
Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage

Authors: Justin Kim, Rahul Varki, Marco Oliva, and Christina Boucher

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
The RePair compression algorithm produces a context-free grammar by iteratively substituting the most frequently occurring pair of consecutive symbols with a new symbol until all consecutive pairs of symbols appear only once in the compressed text. It is widely used in the settings of bioinformatics, machine learning, and information retrieval where random access to the original input text is needed. For example, in pangenomics, RePair is used for random access to a population of genomes. BigRePair improves the scalability of the original RePair algorithm by using Prefix-Free Parsing (PFP) to preprocess the text prior to building the RePair grammar. Despite the efficiency of PFP on repetitive text, there is a scalability issue with the size of the parse which causes a memory bottleneck in BigRePair. In this paper, we design and implement recursive RePair (denoted as Re²Pair), which builds the RePair grammar using recursive PFP. Our novel algorithm faces the challenge of constructing the RePair grammar without direct access to the parse of text, relying solely on the dictionary of the text and the parse and dictionary of the parse of the text. We compare Re²Pair to BigRePair using SARS-CoV-2 haplotypes and haplotypes from the 1000 Genomes Project. We show that our method Re²Pair achieves over a 40% peak memory reduction and a speed up ranging between 12% to 79% compared to BigRePair when compressing the largest input texts in all experiments. Re²Pair is made publicly available under the GNU public license here: https://github.com/jkim210/Recursive-RePair
Cite as

Justin Kim, Rahul Varki, Marco Oliva, and Christina Boucher. Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 78:1-78:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kim_et_al:LIPIcs.ESA.2024.78,
  author =	{Kim, Justin and Varki, Rahul and Oliva, Marco and Boucher, Christina},
  title =	{{Re²Pair: Increasing the Scalability of RePair by Decreasing Memory Usage}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{78:1--78:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.78},
  URN =		{urn:nbn:de:0030-drops-211496},
  doi =		{10.4230/LIPIcs.ESA.2024.78},
  annote =	{Keywords: RePair, Compressed Data Structures, Prefix-free Parsing}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2024.12
Universal Optimization for Non-Clairvoyant Subadditive Joint Replenishment

Authors: Tomer Ezra, Stefano Leonardi, Michał Pawłowski, Matteo Russo, and Seeun William Umboh

Published in: LIPIcs, Volume 317, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)

Abstract
The online joint replenishment problem (JRP) is a fundamental problem in the area of online problems with delay. Over the last decade, several works have studied generalizations of JRP with different cost functions for servicing requests. Most prior works on JRP and its generalizations have focused on the clairvoyant setting. Recently, Touitou [Noam Touitou, 2023] developed a non-clairvoyant framework that provided an O(√{n log n}) upper bound for a wide class of generalized JRP, where n is the number of request types. We advance the study of non-clairvoyant algorithms by providing a simpler, modular framework that matches the competitive ratio established by Touitou for the same class of generalized JRP. Our key insight is to leverage universal algorithms for Set Cover to approximate arbitrary monotone subadditive functions using a simple class of functions termed disjoint. This allows us to reduce the problem to several independent instances of the TCP Acknowledgement problem, for which a simple 2-competitive non-clairvoyant algorithm is known. The modularity of our framework is a major advantage as it allows us to tailor the reduction to specific problems and obtain better competitive ratios. In particular, we obtain tight O(√n)-competitive algorithms for two significant problems: Multi-Level Aggregation and Weighted Symmetric Subadditive Joint Replenishment. We also show that, in contrast, Touitou’s algorithm is Ω(√{n log n})-competitive for both of these problems.
Cite as

Tomer Ezra, Stefano Leonardi, Michał Pawłowski, Matteo Russo, and Seeun William Umboh. Universal Optimization for Non-Clairvoyant Subadditive Joint Replenishment. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 317, pp. 12:1-12:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ezra_et_al:LIPIcs.APPROX/RANDOM.2024.12,
  author =	{Ezra, Tomer and Leonardi, Stefano and Paw{\l}owski, Micha{\l} and Russo, Matteo and Umboh, Seeun William},
  title =	{{Universal Optimization for Non-Clairvoyant Subadditive Joint Replenishment}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)},
  pages =	{12:1--12:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-348-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{317},
  editor =	{Kumar, Amit and Ron-Zewi, Noga},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2024.12},
  URN =		{urn:nbn:de:0030-drops-210050},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2024.12},
  annote =	{Keywords: Set Cover, Joint Replenishment, TCP-Acknowledgment, Subadditive Function Approximation, Multi-Level Aggregation}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2024.62
Coboundary and Cosystolic Expansion Without Dependence on Dimension or Degree

Authors: Yotam Dikstein and Irit Dinur

Published in: LIPIcs, Volume 317, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)

Abstract
We give new bounds on the cosystolic expansion constants of several families of high dimensional expanders, and the known coboundary expansion constants of order complexes of homogeneous geometric lattices, including the spherical building of SL_n(𝔽_q). The improvement applies to the high dimensional expanders constructed by Lubotzky, Samuels and Vishne, and by Kaufman and Oppenheim. Our new expansion constants do not depend on the degree of the complex nor on its dimension, nor on the group of coefficients. This implies improved bounds on Gromov’s topological overlap constant, and on Dinur and Meshulam’s cover stability, which may have applications for agreement testing. In comparison, existing bounds decay exponentially with the ambient dimension (for spherical buildings) and in addition decay linearly with the degree (for all known bounded-degree high dimensional expanders). Our results are based on several new techniques: - We develop a new "color-restriction" technique which enables proving dimension-free expansion by restricting a multi-partite complex to small random subsets of its color classes. - We give a new "spectral" proof for Evra and Kaufman’s local-to-global theorem, deriving better bounds and getting rid of the dependence on the degree. This theorem bounds the cosystolic expansion of a complex using coboundary expansion and spectral expansion of the links. - We derive absolute bounds on the coboundary expansion of the spherical building (and any order complex of a homogeneous geometric lattice) by constructing a novel family of very short cones.
Cite as

Yotam Dikstein and Irit Dinur. Coboundary and Cosystolic Expansion Without Dependence on Dimension or Degree. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 317, pp. 62:1-62:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dikstein_et_al:LIPIcs.APPROX/RANDOM.2024.62,
  author =	{Dikstein, Yotam and Dinur, Irit},
  title =	{{Coboundary and Cosystolic Expansion Without Dependence on Dimension or Degree}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2024)},
  pages =	{62:1--62:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-348-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{317},
  editor =	{Kumar, Amit and Ron-Zewi, Noga},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2024.62},
  URN =		{urn:nbn:de:0030-drops-210556},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2024.62},
  annote =	{Keywords: High Dimensional Expanders, HDX, Spectral Expansion, Coboundary Expansion, Cocycle Expansion, Cosystolic Expansion}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.5
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.
Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.10
b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index

Authors: Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, and Jan Fostier

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Due to the increasing availability of high-quality genome sequences, pan-genomes are gradually replacing single consensus reference genomes in many bioinformatics pipelines to better capture genetic diversity. Traditional bioinformatics tools using the FM-index face memory limitations with such large genome collections. Recent advancements in run-length compressed indices like Gagie et al.’s r-index and Nishimoto and Tabei’s move structure, alleviate memory constraints but focus primarily on backward search for MEM-finding. Arakawa et al.’s br-index initiates complete approximate pattern matching using bidirectional search in run-length compressed space, but with significant computational overhead due to complex memory access patterns. We introduce b-move, a novel bidirectional extension of the move structure, enabling fast, cache-efficient bidirectional character extensions in run-length compressed space. It achieves bidirectional character extensions up to 8 times faster than the br-index, closing the performance gap with FM-index-based alternatives, while maintaining the br-index’s favorable memory characteristics. For example, all available complete E. coli genomes on NCBI’s RefSeq collection can be compiled into a b-move index that fits into the RAM of a typical laptop. Thus, b-move proves practical and scalable for pan-genome indexing and querying. We provide a C++ implementation of b-move, supporting efficient lossless approximate pattern matching including locate functionality, available at https://github.com/biointec/b-move under the AGPL-3.0 license.
Cite as

Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, and Jan Fostier. b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 10:1-10:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{depuydt_et_al:LIPIcs.WABI.2024.10,
  author =	{Depuydt, Lore and Renders, Luca and Van de Vyver, Simon and Veys, Lennart and Gagie, Travis and Fostier, Jan},
  title =	{{b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{10:1--10:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.10},
  URN =		{urn:nbn:de:0030-drops-206546},
  doi =		{10.4230/LIPIcs.WABI.2024.10},
  annote =	{Keywords: Pan-genomics, FM-index, r-index, Move Structure, Bidirectional Search, Approximate Pattern Matching, Lossless Alignment, Cache Efficiency}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.16
Finding Maximum Common Contractions Between Phylogenetic Networks

Authors: Bertrand Marchand, Nadia Tahiri, Olivier Tremblay-Savard, and Manuel Lafond

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations connect the space of all phylogenetic networks on the same set of leaves, even if we forbid contractions that create cycles. This allows to define an operational distance on this space, as the minimum number of contractions and expansions required to transform one network into another. We highlight the difference between this distance and the computation of the maximum common contraction between two networks. Given its ability to outline a common structure between them, which can provide valuable biological insights, we study the algorithmic aspects of the latter. We first prove that computing a maximum common contraction between two networks is NP-hard, even when the maximum degree, the size of the common contraction, or the number of leaves is bounded. We also provide lower bounds to the problem based on the Exponential-Time Hypothesis. Nonetheless, we do provide a polynomial-time algorithm for weakly galled trees, a generalization of galled trees.
Cite as

Bertrand Marchand, Nadia Tahiri, Olivier Tremblay-Savard, and Manuel Lafond. Finding Maximum Common Contractions Between Phylogenetic Networks. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 16:1-16:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{marchand_et_al:LIPIcs.WABI.2024.16,
  author =	{Marchand, Bertrand and Tahiri, Nadia and Tremblay-Savard, Olivier and Lafond, Manuel},
  title =	{{Finding Maximum Common Contractions Between Phylogenetic Networks}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{16:1--16:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.16},
  URN =		{urn:nbn:de:0030-drops-206606},
  doi =		{10.4230/LIPIcs.WABI.2024.16},
  annote =	{Keywords: Phylogenetic networks, contractions, algorithms, weakly galled trees}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.22
Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads

Authors: Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative of such anchor-enabled technology is LoopSeq Solo, a synthetic long read (SLR) sequencing protocol. LoopSeq Solo also achieves ultra-high sequencing depth and high purity of short reads covering the entire captured molecule. Despite the availability of many assembly methods, constructing full-length sequence from these anchor-enabled, ultra-high coverage sequencing data remains challenging due to the complexity of the underlying assembly graphs and the lack of specific algorithms leveraging anchors. We present Anchorage, a novel assembler that performs anchor-guided assembly for ultra-high-depth sequencing data. Anchorage starts with a kmer-based approach for precise estimation of molecule lengths. It then formulates the assembly problem as finding an optimal path that connects the two nodes determined by anchors in the underlying compact de Bruijn graph. The optimality is defined as maximizing the weight of the smallest node while matching the estimated sequence length. Anchorage uses a modified dynamic programming algorithm to efficiently find the optimal path. Through both simulations and real data, we show that Anchorage outperforms existing assembly methods, particularly in the presence of sequencing artifacts. Anchorage fills the gap in assembling anchor-enabled data. We anticipate its broad use as anchor-enabled sequencing technologies become prevalent. Anchorage is freely available at https://github.com/Shao-Group/anchorage; the scripts and documents that can reproduce all experiments in this manuscript are available at https://github.com/Shao-Group/anchorage-test.
Cite as

Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao. Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{zang_et_al:LIPIcs.WABI.2024.22,
  author =	{Zang, Xiaofei Carl and Li, Xiang and Metcalfe, Kyle and Ben-Yehezkel, Tuval and Kelley, Ryan and Shao, Mingfu},
  title =	{{Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{22:1--22:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.22},
  URN =		{urn:nbn:de:0030-drops-206660},
  doi =		{10.4230/LIPIcs.WABI.2024.22},
  annote =	{Keywords: Genome assembly, de Bruijn graph, synthetic long reads, anchor-guided assembly, LoopSeq}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.9
Quantum Algorithms for Hopcroft’s Problem

Authors: Vladimirs Andrejevs, Aleksandrs Belovs, and Jevgēnijs Vihrovs

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
In this work we study quantum algorithms for Hopcroft’s problem which is a fundamental problem in computational geometry. Given n points and n lines in the plane, the task is to determine whether there is a point-line incidence. The classical complexity of this problem is well-studied, with the best known algorithm running in O(n^{4/3}) time, with matching lower bounds in some restricted settings. Our results are two different quantum algorithms with time complexity Õ(n^{5/6}). The first algorithm is based on partition trees and the quantum backtracking algorithm. The second algorithm uses a quantum walk together with a history-independent dynamic data structure for storing line arrangement which supports efficient point location queries. In the setting where the number of points and lines differ, the quantum walk-based algorithm is asymptotically faster. The quantum speedups for the aforementioned data structures may be useful for other geometric problems.
Cite as

Vladimirs Andrejevs, Aleksandrs Belovs, and Jevgēnijs Vihrovs. Quantum Algorithms for Hopcroft’s Problem. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{andrejevs_et_al:LIPIcs.MFCS.2024.9,
  author =	{Andrejevs, Vladimirs and Belovs, Aleksandrs and Vihrovs, Jevg\={e}nijs},
  title =	{{Quantum Algorithms for Hopcroft’s Problem}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{9:1--9:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.9},
  URN =		{urn:nbn:de:0030-drops-205653},
  doi =		{10.4230/LIPIcs.MFCS.2024.9},
  annote =	{Keywords: Quantum algorithms, Quantum walks, Computational Geometry}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.45
Nearly-Tight Bounds for Flow Sparsifiers in Quasi-Bipartite Graphs

Authors: Syamantak Das, Nikhil Kumar, and Daniel Vaz

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
Flow sparsification is a classic graph compression technique which, given a capacitated graph G on k terminals, aims to construct another capacitated graph H, called a flow sparsifier, that preserves, either exactly or approximately, every multicommodity flow between terminals (ideally, with size as a small function of k). Cut sparsifiers are a restricted variant of flow sparsifiers which are only required to preserve maximum flows between bipartitions of the terminal set. It is known that exact cut sparsifiers require 2^Ω(k) many vertices [Krauthgamer and Rika, SODA 2013], with the hard instances being quasi-bipartite graphs, where there are no edges between non-terminals. On the other hand, it has been shown recently that exact (or even (1+ε)-approximate) flow sparsifiers on networks with just 6 terminals require unbounded size [Krauthgamer and Mosenzon, SODA 2023, Chen and Tan, SODA 2024]. In this paper, we construct exact flow sparsifiers of size 3^k³ and exact cut sparsifiers of size 2^k² for quasi-bipartite graphs. In particular, the flow sparsifiers are contraction-based, that is, they are obtained from the input graph by (vertex) contraction operations. Our main contribution is a new technique to construct sparsifiers that exploits connections to polyhedral geometry, and that can be generalized to graphs with a small separator that separates the graph into small components. We also give an improved reduction theorem for graphs of bounded treewidth [Andoni et al., SODA 2011], implying a flow sparsifier of size O(k⋅w) and quality O((log w)/log log w), where w is the treewidth.
Cite as

Syamantak Das, Nikhil Kumar, and Daniel Vaz. Nearly-Tight Bounds for Flow Sparsifiers in Quasi-Bipartite Graphs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 45:1-45:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{das_et_al:LIPIcs.MFCS.2024.45,
  author =	{Das, Syamantak and Kumar, Nikhil and Vaz, Daniel},
  title =	{{Nearly-Tight Bounds for Flow Sparsifiers in Quasi-Bipartite Graphs}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{45:1--45:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.45},
  URN =		{urn:nbn:de:0030-drops-206018},
  doi =		{10.4230/LIPIcs.MFCS.2024.45},
  annote =	{Keywords: Graph Sparsification, Cut Sparsifiers, Flow Sparsifiers, Quasi-bipartite Graphs, Bounded Treewidth}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.1
Move-r: Optimizing the r-index

Authors: Nico Bertram, Johannes Fischer, and Lukas Nalbach

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

Abstract
We present a static text index called Move-r, which is a highly optimized version of the r-index ([Travis Gagie et al., 2020] Gagie et al., 2020) that encorporates recent theoretical developments of the move data structure ([Takaaki Nishimoto and Yasuo Tabei, 2021] Nishimoto and Tabei, 2021). The r-index is the method of choice for indexing highly repetitive texts, such as different versions of a text document or DNA from the same species, as it exploits the compressibilty of the underlying data. With Move-r, we can answer count- and locate queries 2-35 (typically 15) times as fast as with any other r-index supporting locate queries while being 0.8-2.5 (typically 2) times as large. A Move-r index can be constructed 0.9-2 (typically 2) times as fast while using 1/3-1 (typically 1/2) times as much space.
Cite as

Nico Bertram, Johannes Fischer, and Lukas Nalbach. Move-r: Optimizing the r-index. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 1:1-1:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bertram_et_al:LIPIcs.SEA.2024.1,
  author =	{Bertram, Nico and Fischer, Johannes and Nalbach, Lukas},
  title =	{{Move-r: Optimizing the r-index}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{1:1--1:19},
  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.2024.1},
  URN =		{urn:nbn:de:0030-drops-203662},
  doi =		{10.4230/LIPIcs.SEA.2024.1},
  annote =	{Keywords: Compressed Text Index, Burrows-Wheeler Transform}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.2
Engineering Zuffix Arrays

Authors: Paolo Boldi, Stefano Marchini, and Sebastiano Vigna

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

Abstract
Searching patterns in long strings is a classical algorithmic problem with countless practical applications. Suffix trees and suffix arrays (and their variants) are a long-established solution that yields linear-time search (in the size of the pattern). In [Paolo Boldi and Sebastiano Vigna, 2018] it is shown that a z-map gadget can be attached to (enhanced) suffix arrays to improve their theoretical query time, obtaining a data structure called zuffix array. The main contribution of this paper is to show that a carefully engineered implementation of the z-map gadget does provide significant speedups with respect to enhanced suffix arrays on real-world datasets, albeit doubling the required space. In particular, for large alphabets we observe a sevenfold improvement in query time with respect to enhanced suffix arrays; even in the worst case (small alphabets), the query time is almost halved. Thus, zuffix arrays provide a very interesting new point in the space-time tradeoff spectrum.
Cite as

Paolo Boldi, Stefano Marchini, and Sebastiano Vigna. Engineering Zuffix Arrays. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boldi_et_al:LIPIcs.SEA.2024.2,
  author =	{Boldi, Paolo and Marchini, Stefano and Vigna, Sebastiano},
  title =	{{Engineering Zuffix Arrays}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{2:1--2:18},
  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.2024.2},
  URN =		{urn:nbn:de:0030-drops-203677},
  doi =		{10.4230/LIPIcs.SEA.2024.2},
  annote =	{Keywords: Suffix trees, suffix arrays, z-fast tries}
}
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