34 Search Results for "López-Ortiz, Alejandro"

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

Authors: Jarno N. Alanko and Máximo Pérez-López

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

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

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

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@InProceedings{alanko_et_al:LIPIcs.CPM.2026.3,
  author =	{Alanko, Jarno N. and P\'{e}rez-L\'{o}pez, M\'{a}ximo},
  title =	{{Computing k-mers in Graphs}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{3:1--3:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.3},
  URN =		{urn:nbn:de:0030-drops-259294},
  doi =		{10.4230/LIPIcs.CPM.2026.3},
  annote =	{Keywords: Wheeler graph, Wheeler language, de Bruijn graph, graph, k-mer, q-gram, DFA, #P-hard}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.9
Indexing and Encoding Arrays for Element Distinctness Queries

Authors: Johannes Fischer and Filippo Lari

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

Abstract
We introduce the data structure variant of the well-known element distinctness problem. Given an array of n elements, the goal is to preprocess the array into a data structure that supports queries asking whether all elements within a given query range are distinct. This has applications in text indexing and possibly also in other algorithmic domains. In the indexing model (where access to the input array is allowed), we design a data structure using O((n log b)/b) bits and answering queries in the time needed to solve an online element distinctness instance of size O(b), for any b ≥ 1. As a concrete instantiation of this, there exists an index that answers queries in O(log log log n) time using O({n log²(log log log n)}/{log log log n}) bits of additional space. Moving to the encoding model (where access to the input array is not allowed), we begin by proving an information-theoretic lower bound for the space usage of 2n-O(log n) bits, and then design a matching encoding with O(1) time queries. We then consider the case in which the alphabet size σ is constant. In this setting, the lower bound can be refined to n log(r_σ) - 3 log(σ+2) + O(1) bits, where r_σ = 4cos²(π/(σ+2)). This lower bound is matched by an encoding with O(1) time queries.
Cite as

Johannes Fischer and Filippo Lari. Indexing and Encoding Arrays for Element Distinctness Queries. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{fischer_et_al:LIPIcs.CPM.2026.9,
  author =	{Fischer, Johannes and Lari, Filippo},
  title =	{{Indexing and Encoding Arrays for Element Distinctness Queries}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{9:1--9:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.9},
  URN =		{urn:nbn:de:0030-drops-259350},
  doi =		{10.4230/LIPIcs.CPM.2026.9},
  annote =	{Keywords: element distinctness, range queries, lower bounds, succinct data structures}
}
Document
DOI: 10.4230/LIPIcs.STACS.2026.62
Relative Compressed Reverse Suffix Array

Authors: Muhammed Oguzhan Kulekci, Mano Prakash Parthasarathi, Rahul Shah, and Sharma V. Thankachan

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

Abstract
Suffix trees and suffix arrays are two fundamental data structures in the field of string algorithms. For a string (a.k.a. text or sequence) of length n over an alphabet of size σ, these structures typically require O(nlog n) bits of space. The FM-index provides a compressed representation of the suffix array in ≈ nlog σ bits, allowing for efficient queries on both the suffix array and its inverse array in near logarithmic time. In certain applications, such as approximate pattern matching (i.e., with wildcards, mismatches, edits), there is a need to access the suffix array of a text, as well as the suffix array of text’s reverse. Motivated by this, we explore the possibility of encoding the suffix array of the reversed text in a compact form, assuming the availability of the FM-index for the original text. Our first solution is an O(n)-bit (relative) encoding of the suffix array of the reversed text, with the time for decoding an entry being only O(log^*n) times that of decoding an entry in the text’s suffix array using FM-index. We then demonstrate how to reduce the space to O(n/κ) bits for a parameter κ, while multiplicative factor in time becomes approximately O(κlog^*n+κ³). We can also support inverse suffix array and longest common extension queries on the reversed text. These results are achieved through some careful and non-trivial application of various succinct data structure techniques.
Cite as

Muhammed Oguzhan Kulekci, Mano Prakash Parthasarathi, Rahul Shah, and Sharma V. Thankachan. Relative Compressed Reverse Suffix Array. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 62:1-62:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kulekci_et_al:LIPIcs.STACS.2026.62,
  author =	{Kulekci, Muhammed Oguzhan and Parthasarathi, Mano Prakash and Shah, Rahul and Thankachan, Sharma V.},
  title =	{{Relative Compressed Reverse Suffix Array}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{62:1--62:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.62},
  URN =		{urn:nbn:de:0030-drops-255512},
  doi =		{10.4230/LIPIcs.STACS.2026.62},
  annote =	{Keywords: String Matching, Text Indexing, Data Structures, Suffix Trees}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.45
Fairness in the k-Server Problem

Authors: Mohammadreza Daneshvaramoli, Mohammad Hajiesmaili, Shahin Kamali, Helia Karisani, and Cameron Musco

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
We initiate a formal study of fairness for the k-server problem, where the objective is not only to minimize the total movement cost, but also to distribute the cost equitably among servers. We first define a general notion of (α,β)-fairness, where, for parameters α ≥ 1 and β ≥ 0, no server incurs more than an α/k-fraction of the total cost plus an additive term β. We then show that fairness can be achieved without a loss in competitiveness in both the offline and online settings. In the offline setting, we give a deterministic algorithm that, for any ε > 0, transforms any optimal solution into an (α,β)-fair solution for α = 1 + ε and β = O(diam ⋅ log k / ε), while increasing the cost of the solution by just an additive O(diam ⋅ k log k / ε) term. Here diam is the diameter of the underlying metric space. We give a similar result in the online setting, showing that any competitive algorithm can be transformed into a randomized online algorithm that is fair with high probability against an oblivious adversary and still competitive up to a small loss. The above results leave open a significant question: can fairness be achieved in the online setting, either with a deterministic algorithm or a randomized algorithm, against a fully adaptive adversary? We make progress towards answering this question, showing that the classic deterministic Double Coverage Algorithm (DCA) is fair on line metrics and on tree metrics when k = 2. However, we also show a negative result: DCA fails to be fair for any non-vacuous parameters on general tree metrics. We further show that on uniform metrics (i.e., the paging problem), the deterministic First-In First-Out (FIFO) algorithm is fair. We show that any "marking algorithm", including the Least Recently Used (LRU) algorithm, also satisfies a weaker, but still meaningful notion of fairness.
Cite as

Mohammadreza Daneshvaramoli, Mohammad Hajiesmaili, Shahin Kamali, Helia Karisani, and Cameron Musco. Fairness in the k-Server Problem. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 45:1-45:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{daneshvaramoli_et_al:LIPIcs.ITCS.2026.45,
  author =	{Daneshvaramoli, Mohammadreza and Hajiesmaili, Mohammad and Kamali, Shahin and Karisani, Helia and Musco, Cameron},
  title =	{{Fairness in the k-Server Problem}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{45:1--45:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.45},
  URN =		{urn:nbn:de:0030-drops-253328},
  doi =		{10.4230/LIPIcs.ITCS.2026.45},
  annote =	{Keywords: k-server problem, online algorithms, fairness, competitive analysis}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.87
Range Longest Increasing Subsequence and Its Relatives

Authors: Karthik C. S. and Saladi Rahul

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
Longest increasing subsequence (LIS) is a classical textbook problem which is still actively studied in various computational models. In this work, we present a few results for the range longest increasing subsequence problem (Range-LIS) and its variants. The input to Range-LIS is a sequence 𝒮 of n real numbers and a collection 𝒬 of m query ranges and for each query in 𝒬, the goal is to report the LIS of the sequence 𝒮 restricted to that query. Our two main results are for the following generalizations of the Range-LIS problem: 2D Range Queries: In this variant of the Range-LIS problem, each query is a pair of ranges, one of indices and the other of values, and we provide a randomized algorithm with running time Õ(mn^{1/2}+ n^{3/2})+O(k), where k is the cumulative length of the m output subsequences. This improves on the elementary Õ(mn) runtime algorithm when m = Ω(√n). Previously, the only known result breaking the quadratic barrier was of Tiskin [SODA'10] which could only handle 1D range queries (i.e., each query was a range of indices) and also just outputted the length of the LIS (instead of reporting the subsequence achieving that length). Subsequent to our paper, Gawrychowski, Gorbachev, and Kociumaka in a preprint have extended Tiskin’s approach to handle reporting 1D range queries in O(n(log n)³+m+k) time. Colored Sequences: In this variant of the Range-LIS problem, each element in 𝒮 is colored and for each query in 𝒬, the goal is to report a monochromatic LIS contained in the sequence 𝒮 restricted to that query. For 2D queries, we provide a randomized algorithm for this colored version with running time Õ(mn^{2/3}+ n^{5/3})+O(k). Moreover, for 1D queries, we provide an improved algorithm with running time Õ(mn^{1/2}+ n^{3/2})+O(k). Thus, we again improve on the elementary Õ(mn) runtime algorithm. Additionally, we prove that assuming the well-known Combinatorial Boolean Matrix Multiplication Hypothesis, that the runtime for 1D queries is essentially tight for combinatorial algorithms. Our algorithms combine several tools such as dynamic programming (to precompute increasing subsequences with some desirable properties), geometric data structures (to efficiently compute the dynamic programming entries), random sampling (to capture elements which are part of the LIS), classification of query ranges into large LIS and small LIS, and classification of colors into light and heavy. We believe that our techniques will be of interest to tackle other variants of LIS problem and other range-searching problems.
Cite as

Karthik C. S. and Saladi Rahul. Range Longest Increasing Subsequence and Its Relatives. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 87:1-87:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{karthikc.s._et_al:LIPIcs.ITCS.2026.87,
  author =	{Karthik C. S. and Rahul, Saladi},
  title =	{{Range Longest Increasing Subsequence and Its Relatives}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{87:1--87:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.87},
  URN =		{urn:nbn:de:0030-drops-253740},
  doi =		{10.4230/LIPIcs.ITCS.2026.87},
  annote =	{Keywords: Longest Increasing Subsequence, Range Query, Fine-Grained Complexity}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2025.13
A General Input-Dependent Colorless Computability Theorem and Applications to Core-Dependent Adversaries

Authors: Yannis Coutouly and Emmanuel Godard

Published in: LIPIcs, Volume 361, 29th International Conference on Principles of Distributed Systems (OPODIS 2025)

Abstract
Distributed computing tasks can be presented with a triple (ℐ,𝒪,Δ). The solvability of a colorless task on the Iterated Immediate Snapshot model (IIS) has been characterized by the Colorless Computability Theorem [Maurice Herlihy et al., 2013]. A recent paper [Yannis Coutouly and Emmanuel Godard, 2024] generalizes this theorem for any message adversaries ℳ ⊆ IIS by geometric methods. In 2001, Mostéfaoui, Rajsbaum, Raynal, and Roy [Achour Mostéfaoui et al., 2002] introduced condition-based adversaries. This setting considers a particular adversary that will be applied only to a subset of input configurations. In this setting, they studied the k-set agreement task with condition-based t-resilient adversaries and obtained a sufficient condition on the conditions that make k-Set Agreement solvable. In this paper we have three contributions: 1) We generalize the characterization of [Yannis Coutouly and Emmanuel Godard, 2024] to input-dependent adversaries, which means that the adversaries can change depending on the input configuration. 2) We show that core-resilient adversaries of IIS_n have the same computability power as the core-resilient adversaries of IIS_n where crashes only happen at the start. 3) Using the two previous contributions, we provide a necessary and sufficient characterization of the condition-based, core-dependent adversaries that can solve k-Set Agreement. We also distinguish four settings that may appear when presenting a distributed task as (ℐ,𝒪,Δ). Finally, in a later section, we present structural properties on the carrier map Δ. Such properties allow simpler proof, without changing the computability power of the task. Most of the proofs in this article leverage the topological framework used in distributed computing by using simple geometric constructions.
Cite as

Yannis Coutouly and Emmanuel Godard. A General Input-Dependent Colorless Computability Theorem and Applications to Core-Dependent Adversaries. In 29th International Conference on Principles of Distributed Systems (OPODIS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 361, pp. 13:1-13:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{coutouly_et_al:LIPIcs.OPODIS.2025.13,
  author =	{Coutouly, Yannis and Godard, Emmanuel},
  title =	{{A General Input-Dependent Colorless Computability Theorem and Applications to Core-Dependent Adversaries}},
  booktitle =	{29th International Conference on Principles of Distributed Systems (OPODIS 2025)},
  pages =	{13:1--13:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-409-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{361},
  editor =	{Arusoaie, Andrei and Onica, Emanuel and Spear, Michael and Tucci-Piergiovanni, Sara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2025.13},
  URN =		{urn:nbn:de:0030-drops-251862},
  doi =		{10.4230/LIPIcs.OPODIS.2025.13},
  annote =	{Keywords: colorless task, topological methods, geometric simplicial complex, k-set-agreement, t-resilient model, condition-based computability}
}
Document
Research
DOI: 10.4230/TGDK.3.3.4
Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web

Authors: Florian Ruosch, Cristina Sarasua, and Abraham Bernstein

Published in: TGDK, Volume 3, Issue 3 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 3

Abstract
In Argument Mining, predicting argumentative relations between texts (or spans) remains one of the most challenging aspects, even more so in the cross-document setting. This paper makes three key contributions to advance research in this domain. We first extend an existing dataset, the Sci-Arg corpus, by annotating it with explicit inter-document argumentative relations, thereby allowing arguments to be distributed over several documents forming an Argument Web; these new annotations are published using Semantic Web technologies (RDF, OWL). Second, we explore and evaluate three automated approaches for predicting these inter-document argumentative relations, establishing critical baselines on the new dataset. We find that a simple classifier based on discourse indicators with access to context outperforms neural methods. Third, we conduct a comparative analysis of these approaches for both intra- and inter-document settings, identifying statistically significant differences in results that indicate the necessity of distinguishing between these two scenarios. Our findings highlight significant challenges in this complex domain and open crucial avenues for future research on the Argument Web of Science, particularly for those interested in leveraging Semantic Web technologies and knowledge graphs to understand scholarly discourse. With this, we provide the first stepping stones in the form of a benchmark dataset, three baseline methods, and an initial analysis for a systematic exploration of this field relevant to the Web of Data and Science.
Cite as

Florian Ruosch, Cristina Sarasua, and Abraham Bernstein. Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 3, pp. 4:1-4:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{ruosch_et_al:TGDK.3.3.4,
  author =	{Ruosch, Florian and Sarasua, Cristina and Bernstein, Abraham},
  title =	{{Mining Inter-Document Argument Structures in Scientific Papers for an Argument Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:33},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{3},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.3.4},
  URN =		{urn:nbn:de:0030-drops-252159},
  doi =		{10.4230/TGDK.3.3.4},
  annote =	{Keywords: Argument Mining, Large Language Models, Knowledge Graphs, Link Prediction}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.5
External-Memory Priority Queues with Optimal Insertions

Authors: Gerth Stølting Brodal, Michael T. Goodrich, John Iacono, Jared Lo, Ulrich Meyer, Victor Pagan, Nodari Sitchinava, and Rolf Svenning

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

Abstract
We present an external-memory priority queue structure supporting Insert and DeleteMin with amortized 𝒪(1) and 𝒪(lg N) comparisons, respectively, and amortized 𝒪(1/B) and 𝒪(1/B log_{M/B} N/B) I/Os, respectively. Here, M is the size of the internal memory, B is the block size of I/Os between internal and external memory, and N is the number of elements in the priority queue just before an operation is performed. Previous external-memory priority queues required amortized 𝒪(lg N) comparisons and 𝒪(1/B log_{M/B} N/B) I/Os for both Insert and DeleteMin. The construction requires the minimal assumption M ≥ 2B.
Cite as

Gerth Stølting Brodal, Michael T. Goodrich, John Iacono, Jared Lo, Ulrich Meyer, Victor Pagan, Nodari Sitchinava, and Rolf Svenning. External-Memory Priority Queues with Optimal Insertions. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 5:1-5:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{brodal_et_al:LIPIcs.ESA.2025.5,
  author =	{Brodal, Gerth St{\o}lting and Goodrich, Michael T. and Iacono, John and Lo, Jared and Meyer, Ulrich and Pagan, Victor and Sitchinava, Nodari and Svenning, Rolf},
  title =	{{External-Memory Priority Queues with Optimal Insertions}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{5:1--5:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.5},
  URN =		{urn:nbn:de:0030-drops-244734},
  doi =		{10.4230/LIPIcs.ESA.2025.5},
  annote =	{Keywords: priority queues, external memory, cache aware, amortized complexity}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.76
A 3.3904-Competitive Online Algorithm for List Update with Uniform Costs

Authors: Mateusz Basiak, Marcin Bienkowski, Martin Böhm, Marek Chrobak, Łukasz Jeż, Jiří Sgall, and Agnieszka Tatarczuk

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

Abstract
We consider the List Update problem where the cost of each swap is assumed to be 1. This is in contrast to the "standard" model, in which an algorithm is allowed to swap the requested item with previous items for free. We construct an online algorithm Full-Or-Partial-Move (FPM), whose competitive ratio is at most 3.3904, improving over the previous best known bound of 4.
Cite as

Mateusz Basiak, Marcin Bienkowski, Martin Böhm, Marek Chrobak, Łukasz Jeż, Jiří Sgall, and Agnieszka Tatarczuk. A 3.3904-Competitive Online Algorithm for List Update with Uniform Costs. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 76:1-76:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{basiak_et_al:LIPIcs.ESA.2025.76,
  author =	{Basiak, Mateusz and Bienkowski, Marcin and B\"{o}hm, Martin and Chrobak, Marek and Je\.{z}, {\L}ukasz and Sgall, Ji\v{r}{\'\i} and Tatarczuk, Agnieszka},
  title =	{{A 3.3904-Competitive Online Algorithm for List Update with Uniform Costs}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{76:1--76:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.76},
  URN =		{urn:nbn:de:0030-drops-245442},
  doi =		{10.4230/LIPIcs.ESA.2025.76},
  annote =	{Keywords: List update, work functions, amortized analysis, online algorithms, competitive analysis}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.6
Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs

Authors: Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro

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

Abstract
Motivation. Indexes for the colored de Bruijn graph (c-dBG) play a crucial role in computational biology by facilitating complex tasks such as read mapping and assembly. These indexes map k-mers (substrings of length k) appearing in a large collection of reference strings to the set of identifiers of the strings where they appear. These sets, colloquially referred to as color sets, tend to occupy large quantities of memory, especially for large pangenomes. Our previous work thus focused on leveraging the repetitiveness of the color sets to improve the space effectiveness of the resulting index. As a matter of fact, repetition-aware indexes can be up to one order of magnitude smaller on large pangenomes compared to indexes that do not exploit such repetitiveness. Such improved space effectiveness, on the other hand, imposes an overhead at query time when performing tasks such as pseudoalignment that require the collection and processing of multiple related color sets. Methods. In this paper, we show how to avoid this overhead. We devise novel query algorithms tailored for the specific repetition-aware representations adopted by the Fulgor index, a state-of-the-art c-dBG index, to significantly improve its pseudoalignment efficiency and without consuming additional space. Results. Our results indicate that with increasing redundancy in the pangenomes, the compression factor provided by the Fulgor index increases, while the relative query time actually reduces. For example, while the space of the Fulgor index improves by 2.5× with repetition-aware compression and its query time improves by 1.6× on a collection of 5,000 Salmonella Enterica genomes, these factors become (6.1×,2.8×) and (11.2×,3.2×) for 50,000 and 150,000 genomes respectively. For an even larger collection of 300,000 genomes, we obtained an index that is 22.3× smaller and 2.2× faster.
Cite as

Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro. Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{campanelli_et_al:LIPIcs.WABI.2025.6,
  author =	{Campanelli, Alessio and Pibiri, Giulio Ermanno and Patro, Rob},
  title =	{{Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{6:1--6:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.6},
  URN =		{urn:nbn:de:0030-drops-239327},
  doi =		{10.4230/LIPIcs.WABI.2025.6},
  annote =	{Keywords: Colored de Bruijn graphs, Pseudoalignment, Repetition-aware compression}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.23
On the Instance Optimality of Detecting Collisions and Subgraphs

Authors: Omri Ben-Eliezer, Tomer Grossman, and Moni Naor

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
Suppose you are given a function f: [n] → [n] via (black-box) query access to the function. You are looking to find something local, like a collision (a pair x ≠ y s.t. f(x) = f(y)). The question is whether knowing the "shape" of the function helps you or not (by shape we mean that some permutation of the function is known). Formally, we investigate the unlabeled instance optimality of substructure detection problems in graphs and functions. A problem is g(n)-instance optimal if it admits an algorithm A satisfying that for any possible input, the (randomized) query complexity of A is at most g(n) times larger than the query complexity of any algorithm A' which solves the same problem while holding an unlabeled copy of the input (i.e., any A' that "knows the structure of the input"). Our results point to a trichotomy of unlabeled instance optimality among substructure detection problems in graphs and functions: - A few very simple properties have an O(1)-instance optimal algorithm. - Most properties of graphs and functions, with examples such as containing a fixed point or a 3-collision in functions, or a triangle in graphs, are n^{c}-far from instance optimal for some constant c > 0. - The problems of collision detection in functions and finding a claw in a graph serve as a middle ground between the two regimes. We show that these two properties are not Ω(log n)-instance optimal, and conjecture that this bound is tight. We provide evidence towards this conjecture, by proving that finding a claw in a graph is O(log(n))-instance optimal among all input graphs for which the query complexity of an algorithm holding an unlabeled certificate is O(√{n/(log n)}).
Cite as

Omri Ben-Eliezer, Tomer Grossman, and Moni Naor. On the Instance Optimality of Detecting Collisions and Subgraphs. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 23:1-23:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{beneliezer_et_al:LIPIcs.ICALP.2025.23,
  author =	{Ben-Eliezer, Omri and Grossman, Tomer and Naor, Moni},
  title =	{{On the Instance Optimality of Detecting Collisions and Subgraphs}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{23:1--23:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.23},
  URN =		{urn:nbn:de:0030-drops-234002},
  doi =		{10.4230/LIPIcs.ICALP.2025.23},
  annote =	{Keywords: instance optimality, instance complexity, unlabeled certificate, subgraph detection, collision detection}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.75
Tight Bounds for Heavy-Hitters and Moment Estimation in the Sliding Window Model

Authors: Shiyuan Feng, William Swartworth, and David Woodruff

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
We consider the heavy-hitters and F_p moment estimation problems in the sliding window model. For F_p moment estimation with 1 < p ≤ 2, we show that it is possible to give a (1± ε) multiplicative approximation to the F_p moment with 2/3 probability on any given window of size n using Õ(1/(ε^p)log² n + 1/(ε²)log n) bits of space. We complement this result with a lower bound showing that our algorithm gives tight bounds up to factors of log log n and log1/(ε). As a consequence of our F₂ moment estimation algorithm, we show that the heavy-hitters problem can be solved on an arbitrary window using O(1/(ε²)log² n) space which is tight.
Cite as

Shiyuan Feng, William Swartworth, and David Woodruff. Tight Bounds for Heavy-Hitters and Moment Estimation in the Sliding Window Model. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 75:1-75:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{feng_et_al:LIPIcs.ICALP.2025.75,
  author =	{Feng, Shiyuan and Swartworth, William and Woodruff, David},
  title =	{{Tight Bounds for Heavy-Hitters and Moment Estimation in the Sliding Window Model}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{75:1--75:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.75},
  URN =		{urn:nbn:de:0030-drops-234524},
  doi =		{10.4230/LIPIcs.ICALP.2025.75},
  annote =	{Keywords: sketching, streaming, heavy hitters, sliding window, moment estimation}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.123
New and Improved Bounds for Markov Paging

Authors: Chirag Pabbaraju and Ali Vakilian

Published in: LIPIcs, Volume 334, 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)

Abstract
In the Markov paging model, one assumes that page requests are drawn from a Markov chain over the pages in memory, and the goal is to maintain a fast cache that suffers few page faults in expectation. While computing the optimal online algorithm (OPT) for this problem naively takes time exponential in the size of the cache, the best-known polynomial-time approximation algorithm is the dominating distribution algorithm due to Lund, Phillips and Reingold (FOCS 1994), who showed that the algorithm is 4-competitive against OPT. We substantially improve their analysis and show that the dominating distribution algorithm is in fact 2-competitive against OPT. We also show a lower bound of 1.5907-competitiveness for this algorithm - to the best of our knowledge, no such lower bound was previously known.
Cite as

Chirag Pabbaraju and Ali Vakilian. New and Improved Bounds for Markov Paging. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 123:1-123:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{pabbaraju_et_al:LIPIcs.ICALP.2025.123,
  author =	{Pabbaraju, Chirag and Vakilian, Ali},
  title =	{{New and Improved Bounds for Markov Paging}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{123:1--123:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-372-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{334},
  editor =	{Censor-Hillel, Keren and Grandoni, Fabrizio and Ouaknine, Jo\"{e}l and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2025.123},
  URN =		{urn:nbn:de:0030-drops-235005},
  doi =		{10.4230/LIPIcs.ICALP.2025.123},
  annote =	{Keywords: Beyond Worst-case Analyis, Online Paging, Markov Paging}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.27
Succinct Data Structures for Segments

Authors: Philip Bille, Inge Li Gørtz, and Simon R. Tarnow

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

Abstract
We consider succinct data structures for representing a set of n horizontal line segments in the plane given in rank space to support segment access, segment selection, and segment rank queries. A segment access query finds the segment (x₁, x₂, y) given its y-coordinate (y-coordinates of the segments are distinct), a segment selection query finds the jth smallest segment (the segment with the jth smallest y-coordinate) among the segments crossing the vertical line for a given x-coordinate, and a segment rank query finds the number of segments crossing the vertical line through x-coordinate i with y-coordinate at most y, for a given x and y. This problem is a central component in compressed data structures for persistent strings supporting random access. Our main result is a data structure using 2n lg n + O(n lg n / lg lg n) bits of space and O(lg n / lg lg n) query time for all operations. We show that this space bound is optimal up to lower-order terms. We will also show that the query time for segment rank is optimal. The query time for segment selection is also optimal by a previous bound. To obtain our results, we present a novel segment wavelet tree data structure of independent interest. This structure is inspired by and extends the classic wavelet tree for sequences. This leads to a simple, succinct solution with O(log n) query times. We then extend this solution to obtain optimal query time. Our space lower bound follows from a simple counting argument, and our lower bound for segment rank is obtained by a reduction from 2-dimensional counting.
Cite as

Philip Bille, Inge Li Gørtz, and Simon R. Tarnow. Succinct Data Structures for Segments. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 27:1-27:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bille_et_al:LIPIcs.CPM.2025.27,
  author =	{Bille, Philip and G{\o}rtz, Inge Li and Tarnow, Simon R.},
  title =	{{Succinct Data Structures for Segments}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{27:1--27:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.27},
  URN =		{urn:nbn:de:0030-drops-231218},
  doi =		{10.4230/LIPIcs.CPM.2025.27},
  annote =	{Keywords: Succinct, Data structures, Selection}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.24
Sorted Consecutive Occurrence Queries in Substrings

Authors: Waseem Akram and Takuya Mieno

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

Abstract
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for preprocessing and a pattern P of length m as a query, the goal is to report all occurrences of P as substrings of T. Navarro and Thankachan [CPM 2015, Theor. Comput. Sci. 2016] introduced a variant of this problem called the gap-bounded consecutive occurrence query, which reports pairs of consecutive occurrences of P in T such that their gaps (i.e., the distances between them) lie within a query-specified range [g₁, g₂]. Recently, Bille et al. [FSTTCS 2020, Theor. Comput. Sci. 2022] proposed the top-k close consecutive occurrence query, which reports the k closest consecutive occurrences of P in T, sorted in non-decreasing order of distance. Both problems are optimally solved in query time with O(n log n)-space data structures. In this paper, we generalize these problems to the range query model, which focuses only on occurrences of P in a specified substring T[a.. b] of T. Our contributions are as follows: - We propose an O(n log² n)-space data structure that answers the range top-k consecutive occurrence query in O(|P| + log log n + k) time. - We propose an O(n log^{2+ε} n)-space data structure that answers the range gap-bounded consecutive occurrence query in O(|P| + log log n + output) time, where ε is a positive constant and output denotes the number of outputs. Additionally, as by-products, we present algorithms for geometric problems involving weighted horizontal segments in a 2D plane, which are of independent interest.
Cite as

Waseem Akram and Takuya Mieno. Sorted Consecutive Occurrence Queries in Substrings. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 24:1-24:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{akram_et_al:LIPIcs.CPM.2025.24,
  author =	{Akram, Waseem and Mieno, Takuya},
  title =	{{Sorted Consecutive Occurrence Queries in Substrings}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{24:1--24:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.24},
  URN =		{urn:nbn:de:0030-drops-231187},
  doi =		{10.4230/LIPIcs.CPM.2025.24},
  annote =	{Keywords: string algorithm, consecutive occurrences, suffix tree}
}
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