9 Search Results for "Hoppenworth, Gary"

Document
DOI: 10.4230/LIPIcs.SEA.2026.4
Integer Programming Models for the Median of a 0-1 String Set Under Levenshtein Distance

Authors: Claudio Arbib, Andrea D'Ascenzo, Oya E. Karaşan, and Andrea Pizzuti

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
The Median String Problem calls for finding a string that minimizes the average distance from a given set of strings. Under the Levenshtein (or edit) metric, the problem is NP-hard even for binary strings. We devised two novel integer linear programming models for this case and tested them against the only formulation we are aware of in the literature. Our numerical experiments attest to the efficacy of the proposed approach.
Cite as

Claudio Arbib, Andrea D'Ascenzo, Oya E. Karaşan, and Andrea Pizzuti. Integer Programming Models for the Median of a 0-1 String Set Under Levenshtein Distance. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 4:1-4:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{arbib_et_al:LIPIcs.SEA.2026.4,
  author =	{Arbib, Claudio and D'Ascenzo, Andrea and Kara\c{s}an, Oya E. and Pizzuti, Andrea},
  title =	{{Integer Programming Models for the Median of a 0-1 String Set Under Levenshtein Distance}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{4:1--4:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.4},
  URN =		{urn:nbn:de:0030-drops-260081},
  doi =		{10.4230/LIPIcs.SEA.2026.4},
  annote =	{Keywords: Levenshtein Distance, Median String Problem, Integer Programming}
}
Document
DOI: 10.4230/LIPIcs.CPM.2026.14
Hardness Results on Characteristics for Elastic-Degenerate Strings

Authors: Dominik Köppl and Jannik Olbrich

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

Abstract
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores a character at each of its positions, generalizations consider a set of characters (indeterminate strings), a set of strings of equal length (generalized degenerate strings, or shortly GD strings), or a set of strings of arbitrary lengths (elastic-degenerate strings, or shortly ED strings). These generalizations are of importance to compactly represent such type of data, and find applications in bioinformatics for representing and maintaining a set of genetic sequences of the same taxonomy or a multiple sequence alignment. To be of use, attention has been drawn to answering various query types such as pattern matching or measuring similarity of ED strings by generalizing techniques known to plain strings. However, for some types of queries, it has been shown that a generalization of a polynomial-time solvable query on classic strings becomes NP-hard on ED strings, e.g. [Russo et al., 2022]. In that light, we wonder about other types of queries that are of particular interest to bioinformatics: unique substrings, absent words, anti-powers, longest previous factors, and Lempel-Ziv-like compression schemes. While we obtain a polynomial time algorithm for a variation of longest previous factors, we show that all other problems are NP-hard to compute, some of them even under the restriction that the input can be modeled as an indeterminate or GD string.
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Dominik Köppl and Jannik Olbrich. Hardness Results on Characteristics for Elastic-Degenerate Strings. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 14:1-14:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{koppl_et_al:LIPIcs.CPM.2026.14,
  author =	{K\"{o}ppl, Dominik and Olbrich, Jannik},
  title =	{{Hardness Results on Characteristics for Elastic-Degenerate Strings}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{14:1--14:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.14},
  URN =		{urn:nbn:de:0030-drops-259409},
  doi =		{10.4230/LIPIcs.CPM.2026.14},
  annote =	{Keywords: Elastic-degenerate strings, NP-hardness, longest common factor, minimal unique substring, minimal absent word, anti-power, longest previous factor}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.107
Length-Constrained Directed Expander Decomposition and Length-Constrained Vertex-Capacitated Flow Shortcuts

Authors: Bernhard Haeupler, Yaowei Long, Thatchaphol Saranurak, and Shengzhe Wang

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

Abstract
We show the existence of length-constrained expander decomposition in directed graphs and undirected vertex-capacitated graphs. Previously, its existence was shown only in undirected edge-capacitated graphs [Bernhard Haeupler et al., 2022; Haeupler et al., 2024]. Along the way, we prove the multi-commodity maxflow-mincut theorems for length-constrained expansion in both directed and undirected vertex-capacitated graphs. Based on our decomposition, we build a length-constrained flow shortcut for undirected vertex-capacitated graphs, which roughly speaking is a set of edges and vertices added to the graph so that every multi-commodity flow demand can be routed with approximately the same vertex-congestion and length, but all flow paths only contain few edges. This generalizes the shortcut for undirected edge-capacitated graphs from [Bernhard Haeupler et al., 2024]. Length-constrained expander decomposition and flow shortcuts have been crucial in the recent algorithms in undirected edge-capacitated graphs [Bernhard Haeupler et al., 2024; Haeupler et al., 2024]. Our work thus serves as a foundation to generalize these concepts to directed and vertex-capacitated graphs.
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Bernhard Haeupler, Yaowei Long, Thatchaphol Saranurak, and Shengzhe Wang. Length-Constrained Directed Expander Decomposition and Length-Constrained Vertex-Capacitated Flow Shortcuts. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 107:1-107:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{haeupler_et_al:LIPIcs.ESA.2025.107,
  author =	{Haeupler, Bernhard and Long, Yaowei and Saranurak, Thatchaphol and Wang, Shengzhe},
  title =	{{Length-Constrained Directed Expander Decomposition and Length-Constrained Vertex-Capacitated Flow Shortcuts}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{107:1--107:17},
  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.2025.107},
  URN =		{urn:nbn:de:0030-drops-245765},
  doi =		{10.4230/LIPIcs.ESA.2025.107},
  annote =	{Keywords: Length-Constrained Expander, Expander Decomposition, Shortcut}
}
Document
Research
DOI: 10.4230/OASIcs.Grossi.7
Conditional Lower Bounds for String Matching in Labelled Graphs

Authors: Massimo Equi

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

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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.69
Approximation Algorithms for Optimal Hopsets

Authors: Michael Dinitz, Ama Koranteng, and Yasamin Nazari

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

Abstract
For a given graph G, a hopset H with hopbound β and stretch α is a set of edges such that between every pair of vertices u and v, there is a path with at most β hops in G ∪ H that approximates the distance between u and v up to a multiplicative stretch of α. Hopsets have found a wide range of applications for distance-based problems in various computational models since the 90s. More recently, there has been significant interest in understanding these fundamental objects from an existential and structural perspective. But all of this work takes a worst-case (or existential) point of view: How many edges do we need to add to satisfy a given hopbound and stretch requirement for any input graph? We initiate the study of the natural optimization variant of this problem: given a specific graph instance, what is the minimum number of edges that satisfy the hopbound and stretch requirements? We give approximation algorithms for a generalized hopset problem which, when combined with known existential bounds, lead to different approximation guarantees for various regimes depending on hopbound, stretch, and directed vs. undirected inputs. We complement our upper bounds with a lower bound that implies Label Cover hardness for directed hopsets and shortcut sets with hopbound at least 3.
Cite as

Michael Dinitz, Ama Koranteng, and Yasamin Nazari. Approximation Algorithms for Optimal Hopsets. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 69:1-69:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dinitz_et_al:LIPIcs.ICALP.2025.69,
  author =	{Dinitz, Michael and Koranteng, Ama and Nazari, Yasamin},
  title =	{{Approximation Algorithms for Optimal Hopsets}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{69:1--69:20},
  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.2025.69},
  URN =		{urn:nbn:de:0030-drops-234464},
  doi =		{10.4230/LIPIcs.ICALP.2025.69},
  annote =	{Keywords: Hopsets, Approximation Algorithms}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.13
Low Sensitivity Hopsets

Authors: Vikrant Ashvinkumar, Aaron Bernstein, Chengyuan Deng, Jie Gao, and Nicole Wein

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract
Given a weighted graph G = (V,E,w), a (β, ε)-hopset H is an edge set such that for any s,t ∈ V, where s can reach t in G, there is a path from s to t in G ∪ H which uses at most β hops whose length is in the range [dist_G(s,t), (1+ε)dist_G(s,t)]. We break away from the traditional question that asks for a hopset H that achieves small |H| and small diameter β and instead study the sensitivity of H, a new quality measure. The sensitivity of a vertex (or edge) given a hopset H is, informally, the number of times a single hop in G ∪ H bypasses it; a bit more formally, assuming shortest paths in G are unique, it is the number of hopset edges (s,t) ∈ H such that the vertex (or edge) is contained in the unique st-path in G having length exactly dist_G(s,t). The sensitivity associated with H is then the maximum sensitivity over all vertices (or edges). The highlights of our results are: - A construction for (Õ(√n), 0)-hopsets on undirected graphs with O(log n) sensitivity, complemented with a lower bound showing that Õ(√n) is tight up to polylogarithmic factors for any construction with polylogarithmic sensitivity. - A construction for (n^o(1), ε)-hopsets on undirected graphs with n^o(1) sensitivity for any ε > 0 that is at least inverse polylogarithmic, complemented with a lower bound on the tradeoff between β, ε, and the sensitivity. - We define a notion of sensitivity for β-shortcut sets (which are the reachability analogues of hopsets) and give a construction for Õ(√n)-shortcut sets on directed graphs with O(log n) sensitivity, complemented with a lower bound showing that β = Ω̃(n^{1/3}) for any construction with polylogarithmic sensitivity. We believe hopset sensitivity is a natural measure in and of itself, and could potentially find use in a diverse range of contexts. More concretely, the notion of hopset sensitivity is also directly motivated by the Differentially Private All Sets Range Queries problem [Deng et al. WADS 23]. Our result for O(log n) sensitivity (Õ(√n), 0)-hopsets on undirected graphs immediately improves the current best-known upper bound on utility from Õ(n^{1/3}) to Õ(n^{1/4}) in the pure-DP setting, which is tight up to polylogarithmic factors.
Cite as

Vikrant Ashvinkumar, Aaron Bernstein, Chengyuan Deng, Jie Gao, and Nicole Wein. Low Sensitivity Hopsets. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 13:1-13:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ashvinkumar_et_al:LIPIcs.ITCS.2025.13,
  author =	{Ashvinkumar, Vikrant and Bernstein, Aaron and Deng, Chengyuan and Gao, Jie and Wein, Nicole},
  title =	{{Low Sensitivity Hopsets}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{13:1--13:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.13},
  URN =		{urn:nbn:de:0030-drops-226418},
  doi =		{10.4230/LIPIcs.ITCS.2025.13},
  annote =	{Keywords: Hopsets, Shortcuts, Sensitivity, Differential Privacy}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2024.27
The Discrepancy of Shortest Paths

Authors: Greg Bodwin, Chengyuan Deng, Jie Gao, Gary Hoppenworth, Jalaj Upadhyay, and Chen Wang

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)

Abstract
The hereditary discrepancy of a set system is a quantitative measure of the pseudorandom properties of the system. Roughly speaking, hereditary discrepancy measures how well one can 2-color the elements of the system so that each set contains approximately the same number of elements of each color. Hereditary discrepancy has numerous applications in computational geometry, communication complexity and derandomization. More recently, the hereditary discrepancy of the set system of shortest paths has found applications in differential privacy [Chen et al. SODA 23]. The contribution of this paper is to improve the upper and lower bounds on the hereditary discrepancy of set systems of unique shortest paths in graphs. In particular, we show that any system of unique shortest paths in an undirected weighted graph has hereditary discrepancy O(n^{1/4}), and we construct lower bound examples demonstrating that this bound is tight up to polylog n factors. Our lower bounds hold even for planar graphs and bipartite graphs, and improve a previous lower bound of Ω(n^{1/6}) obtained by applying the trace bound of Chazelle and Lvov [SoCG'00] to a classical point-line system of Erdős. As applications, we improve the lower bound on the additive error for differentially-private all pairs shortest distances from Ω(n^{1/6}) [Chen et al. SODA 23] to Ω̃(n^{1/4}), and we improve the lower bound on additive error for the differentially-private all sets range queries problem to Ω̃(n^{1/4}), which is tight up to polylog n factors [Deng et al. WADS 23].
Cite as

Greg Bodwin, Chengyuan Deng, Jie Gao, Gary Hoppenworth, Jalaj Upadhyay, and Chen Wang. The Discrepancy of Shortest Paths. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 27:1-27:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bodwin_et_al:LIPIcs.ICALP.2024.27,
  author =	{Bodwin, Greg and Deng, Chengyuan and Gao, Jie and Hoppenworth, Gary and Upadhyay, Jalaj and Wang, Chen},
  title =	{{The Discrepancy of Shortest Paths}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{27:1--27:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.27},
  URN =		{urn:nbn:de:0030-drops-201705},
  doi =		{10.4230/LIPIcs.ICALP.2024.27},
  annote =	{Keywords: Discrepancy, hereditary discrepancy, shortest paths, differential privacy}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2024.28
Additive Spanner Lower Bounds with Optimal Inner Graph Structure

Authors: Greg Bodwin, Gary Hoppenworth, Virginia Vassilevska Williams, Nicole Wein, and Zixuan Xu

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)

Abstract
We construct n-node graphs on which any O(n)-size spanner has additive error at least +Ω(n^{3/17}), improving on the previous best lower bound of Ω(n^{1/7}) [Bodwin-Hoppenworth FOCS '22]. Our construction completes the first two steps of a particular three-step research program, introduced in prior work and overviewed here, aimed at producing tight bounds for the problem by aligning aspects of the upper and lower bound constructions. More specifically, we develop techniques that enable the use of inner graphs in the lower bound framework whose technical properties are provably tight with the corresponding assumptions made in the upper bounds. As an additional application of our techniques, we improve the corresponding lower bound for O(n)-size additive emulators to +Ω(n^{1/14}).
Cite as

Greg Bodwin, Gary Hoppenworth, Virginia Vassilevska Williams, Nicole Wein, and Zixuan Xu. Additive Spanner Lower Bounds with Optimal Inner Graph Structure. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 28:1-28:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bodwin_et_al:LIPIcs.ICALP.2024.28,
  author =	{Bodwin, Greg and Hoppenworth, Gary and Vassilevska Williams, Virginia and Wein, Nicole and Xu, Zixuan},
  title =	{{Additive Spanner Lower Bounds with Optimal Inner Graph Structure}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{28:1--28:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.28},
  URN =		{urn:nbn:de:0030-drops-201715},
  doi =		{10.4230/LIPIcs.ICALP.2024.28},
  annote =	{Keywords: Additive Spanners, Graph Theory}
}
Document
DOI: 10.4230/LIPIcs.ESA.2020.61
The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance

Authors: Gary Hoppenworth, Jason W. Bentley, Daniel Gibney, and Sharma V. Thankachan

Published in: LIPIcs, Volume 173, 28th Annual European Symposium on Algorithms (ESA 2020)

Abstract
We present the first fine-grained complexity results on two classic problems on strings. The first one is the k-Median-Edit-Distance problem, where the input is a collection of k strings, each of length at most n, and the task is to find a new string that minimizes the sum of the edit distances from itself to all other strings in the input. Arising frequently in computational biology, this problem provides an important generalization of edit distance to multiple strings and is similar to the multiple sequence alignment problem in bioinformatics. We demonstrate that for any ε > 0 and k ≥ 2, an O(n^{k-ε}) time solution for the k-Median-Edit-Distance problem over an alphabet of size O(k) refutes the Strong Exponential Time Hypothesis (SETH). This provides the first matching conditional lower bound for the O(n^k) time algorithm established in 1975 by Sankoff. The second problem we study is the k-Center-Edit-Distance problem. Here also, the input is a collection of k strings, each of length at most n. The task is to find a new string that minimizes the maximum edit distance from itself to any other string in the input. We prove that the same conditional lower bound as before holds. Our results also imply new conditional lower bounds for the k-Tree-Alignment and the k-Bottleneck-Tree-Alignment problems studied in phylogenetics.
Cite as

Gary Hoppenworth, Jason W. Bentley, Daniel Gibney, and Sharma V. Thankachan. The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance. In 28th Annual European Symposium on Algorithms (ESA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 173, pp. 61:1-61:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{hoppenworth_et_al:LIPIcs.ESA.2020.61,
  author =	{Hoppenworth, Gary and Bentley, Jason W. and Gibney, Daniel and Thankachan, Sharma V.},
  title =	{{The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance}},
  booktitle =	{28th Annual European Symposium on Algorithms (ESA 2020)},
  pages =	{61:1--61:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-162-7},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{173},
  editor =	{Grandoni, Fabrizio and Herman, Grzegorz and Sanders, Peter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2020.61},
  URN =		{urn:nbn:de:0030-drops-129278},
  doi =		{10.4230/LIPIcs.ESA.2020.61},
  annote =	{Keywords: Edit Distance, Median String, Center String, SETH}
}
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