139 Search Results for "Pissis, Solon P."


Volume

LIPIcs, Volume 312

24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

WABI 2024, September 2-4, 2024, Royal Holloway, London, United Kingdom

Editors: Solon P. Pissis and Wing-Kin Sung

Volume

LIPIcs, Volume 128

30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)

CPM 2019, June 18-20, 2019, Pisa, Italy

Editors: Nadia Pisanti and Solon P. Pissis

Volume

LIPIcs, Volume 75

16th International Symposium on Experimental Algorithms (SEA 2017)

SEA 2017, June 21-23, 2017, London, UK

Editors: Costas S. Iliopoulos, Solon P. Pissis, Simon J. Puglisi, and Rajeev Raman

Document
Invited Talk
Simple (Invited Talk)

Authors: Eva Rotenberg

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


Abstract
Simplicity in algorithms has various aspects; interpretations and implications. One is the simplicity of the algorithmic solution itself: if an algorithm (or data structure) has a brief verbal description or can be written with few lines of pseudocode, this can lead to easier, more robust, and possibly more efficient implementations. Another aspect of simplicity relates to the proofs of correctness and efficiency of our algorithmic solutions. Here, we experience that algorithms and data structures with simpler proofs of statements about their properties can be easier to understand, easier to teach, and sometimes, easier to generalise. Simplification of proofs also receives attention in mathematics; here, too, simplification has benefits to clarity of exposition and possibility of generalisation. There are even examples of proof simplification leading to the design of new and more efficient algorithms. This talk will present examples illustrating these various aspects of simplicity. Examples where algorithmic simplification or proof simplification has led to improved performance of algorithms and data structures, in theory, in practice, or both. Finally, some of the most attractive questions in discrete mathematics and in theory of computing have a property in common: they are very simple to pose, but surprisingly, to our knowledge, not very simple to answer. The talk will include examples of such questions, which I leave as an open problem for the audience.

Cite as

Eva Rotenberg. Simple (Invited Talk). In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 2:1-2:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{rotenberg:LIPIcs.ESA.2024.2,
  author =	{Rotenberg, Eva},
  title =	{{Simple}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{2:1--2:2},
  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.2024.2},
  URN =		{urn:nbn:de:0030-drops-210739},
  doi =		{10.4230/LIPIcs.ESA.2024.2},
  annote =	{Keywords: Simplicity, graph algorithms, computational geometry, algorithmic simplification, data structures, combinatorics, proof simplification, dynamic graphs}
}
Document
Longest Common Substring with Gaps and Related Problems

Authors: Aranya Banerjee, Daniel Gibney, and Sharma V. Thankachan

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


Abstract
The longest common substring (also known as longest common factor) and longest common subsequence problems are two well-studied classical string problems. The former is solvable in optimal 𝒪(n) time for two strings of length m and n with m ≤ n, and the latter is solvable in 𝒪(nm) time, which is conditionally optimal under the Strong Exponential Time Hypothesis. In this work, we study the problem of longest common factor with gaps, that is, finding a set of at most k matching substrings obeying precedence conditions with maximum total length. For k = 1, this is equivalent to the longest common factor problem, and for k = m, this is equivalent to the longest common subsequence problem. Our work demonstrates that, for constant k, this problem can be solved in strongly subquadratic time, i.e., nm^{1 - Θ(1)}. Motivated by co-linear chaining applications in Computational Biology, we further demonstrate that the longest common factor with gaps results can be extended to the case where the matches are restricted to maximal exact matches (MEMs). To further demonstrate the applicability of our techniques, we show that a similar approach can be used for a restricted version of the episode matching problem where one seeks an ordered set of at most k matches whose concatenation equals a query pattern P and the length of the substring of T containing the matches is minimized. These solutions all run in strongly subquadratic time for constant k.

Cite as

Aranya Banerjee, Daniel Gibney, and Sharma V. Thankachan. Longest Common Substring with Gaps and Related Problems. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 16:1-16:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{banerjee_et_al:LIPIcs.ESA.2024.16,
  author =	{Banerjee, Aranya and Gibney, Daniel and Thankachan, Sharma V.},
  title =	{{Longest Common Substring with Gaps and Related Problems}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{16:1--16:18},
  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.2024.16},
  URN =		{urn:nbn:de:0030-drops-210877},
  doi =		{10.4230/LIPIcs.ESA.2024.16},
  annote =	{Keywords: Pattern Matching, Longest Common Subsequence, Episode Matching}
}
Document
Longest Common Extensions with Wildcards: Trade-Off and Applications

Authors: Gabriel Bathie, Panagiotis Charalampopoulos, and Tatiana Starikovskaya

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


Abstract
We study the Longest Common Extension (LCE) problem in a string containing wildcards. Wildcards (also called "don't cares" or "holes") are special characters that match any other character in the alphabet, similar to the character "?" in Unix commands or "." in regular expression engines. We consider the problem parametrized by G, the number of maximal contiguous groups of wildcards in the input string. Our main contribution is a simple data structure for this problem that can be built in O(n (G/t) log n) time, occupies O(nG/t) space, and answers queries in O(t) time, for any t ∈ [1 .. G]. Up to the O(log n) factor, this interpolates smoothly between the data structure of Crochemore et al. [JDA 2015], which has O(nG) preprocessing time and space, and O(1) query time, and a simple solution based on the "kangaroo jumping" technique [Landau and Vishkin, STOC 1986], which has O(n) preprocessing time and space, and O(G) query time. By establishing a connection between this problem and Boolean matrix multiplication, we show that our solution is optimal up to subpolynomial factors when G = Ω(n) under a widely believed hypothesis. In addition, we develop a new simple, deterministic and combinatorial algorithm for sparse Boolean matrix multiplication. Finally, we show that our data structure can be used to obtain efficient algorithms for approximate pattern matching and structural analysis of strings with wildcards. First, we consider the problem of pattern matching with k errors (i.e., edit operations) in the setting where both the pattern and the text may contain wildcards. The "kangaroo jumping" technique can be adapted to yield an algorithm for this problem with runtime O(n(k+G)), where G is the total number of maximal contiguous groups of wildcards in the text and the pattern and n is the length of the text. By combining "kangaroo jumping" with a tailor-made data structure for LCE queries, Akutsu [IPL 1995] devised an O(n√{km} polylog m)-time algorithm. We improve on both algorithms when k ≪ G ≪ m by giving an algorithm with runtime O(n(k + √{Gk log n})). Secondly, we give O(n√G log n)-time and O(n)-space algorithms for computing the prefix array, as well as the quantum/deterministic border and period arrays of a string with wildcards. This is an improvement over the O(n√{nlog n})-time algorithms of Iliopoulos and Radoszewski [CPM 2016] when G = O(n / log n).

Cite as

Gabriel Bathie, Panagiotis Charalampopoulos, and Tatiana Starikovskaya. Longest Common Extensions with Wildcards: Trade-Off and Applications. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 19:1-19:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{bathie_et_al:LIPIcs.ESA.2024.19,
  author =	{Bathie, Gabriel and Charalampopoulos, Panagiotis and Starikovskaya, Tatiana},
  title =	{{Longest Common Extensions with Wildcards: Trade-Off and Applications}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{19:1--19:17},
  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.2024.19},
  URN =		{urn:nbn:de:0030-drops-210904},
  doi =		{10.4230/LIPIcs.ESA.2024.19},
  annote =	{Keywords: Longest common prefix, longest common extension, wildcards, Boolean matrix multiplication, approximate pattern matching, periodicity arrays}
}
Document
Pattern Matching with Mismatches and Wildcards

Authors: Gabriel Bathie, Panagiotis Charalampopoulos, and Tatiana Starikovskaya

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


Abstract
In this work, we address the problem of approximate pattern matching with wildcards. Given a pattern P of length m containing D wildcards, a text T of length n, and an integer k, our objective is to identify all fragments of T within Hamming distance k from P. Our primary contribution is an algorithm with runtime 𝒪(n + (D+k)(G+k)⋅ n/m) for this problem. Here, G ≤ D represents the number of maximal wildcard fragments in P. We derive this algorithm by elaborating in a non-trivial way on the ideas presented by [Charalampopoulos, Kociumaka, and Wellnitz, FOCS'20] for pattern matching with mismatches (without wildcards). Our algorithm improves over the state of the art when D, G, and k are small relative to n. For instance, if m = n/2, k = G = n^{2/5}, and D = n^{3/5}, our algorithm operates in 𝒪(n) time, surpassing the Ω(n^{6/5}) time requirement of all previously known algorithms. In the case of exact pattern matching with wildcards (k = 0), we present a much simpler algorithm with runtime 𝒪(n + DG ⋅ n/m) that clearly illustrates our main technical innovation: the utilisation of positions of P that do not belong to any fragment of P with a density of wildcards much larger than D/m as anchors for the sought (approximate) occurrences. Notably, our algorithm outperforms the best-known 𝒪(n log m)-time FFT-based algorithms of [Cole and Hariharan, STOC'02] and [Clifford and Clifford, IPL'04] if DG = o(m log m). We complement our algorithmic results with a structural characterization of the k-mismatch occurrences of P. We demonstrate that in a text of length 𝒪(m), these occurrences can be partitioned into 𝒪((D+k)(G+k)) arithmetic progressions. Additionally, we construct an infinite family of examples with Ω((D+k)k) arithmetic progressions of occurrences, leveraging a combinatorial result on progression-free sets [Elkin, SODA'10].

Cite as

Gabriel Bathie, Panagiotis Charalampopoulos, and Tatiana Starikovskaya. Pattern Matching with Mismatches and Wildcards. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 20:1-20:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{bathie_et_al:LIPIcs.ESA.2024.20,
  author =	{Bathie, Gabriel and Charalampopoulos, Panagiotis and Starikovskaya, Tatiana},
  title =	{{Pattern Matching with Mismatches and Wildcards}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{20:1--20:15},
  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.2024.20},
  URN =		{urn:nbn:de:0030-drops-210910},
  doi =		{10.4230/LIPIcs.ESA.2024.20},
  annote =	{Keywords: pattern matching, wildcards, mismatches, Hamming distance}
}
Document
String 2-Covers with No Length Restrictions

Authors: Itai Boneh, Shay Golan, and Arseny Shur

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


Abstract
A λ-cover of a string S is a set of strings {C_i}₁^λ such that every index in S is contained in an occurrence of at least one string C_i. The existence of a 1-cover defines a well-known class of quasi-periodic strings. Quasi-periodicity can be decided in linear time, and all 1-covers of a string can be reported in linear time as well. Since in general it is NP-complete to decide whether a string has a λ-cover, the natural next step is the development of efficient algorithms for 2-covers. Radoszewski and Straszyński [ESA 2020] analysed the particular case where the strings in a 2-cover must be of the same length. They provided an algorithm that reports all such 2-covers of S in time near-linear in |S| and in the size of the output. In this work, we consider 2-covers in full generality. Since every length-n string has Ω(n²) trivial 2-covers (every prefix and suffix of total length at least n constitute such a 2-cover), we state the reporting problem as follows: given a string S and a number m, report all 2-covers {C₁,C₂} of S with length |C₁|+|C₂| upper bounded by m. We present an Õ(n + output) time algorithm solving this problem, with output being the size of the output. This algorithm admits a simpler modification that finds a 2-cover of minimum length. We also provide an Õ(n) time construction of a 2-cover oracle which, given two substrings C₁,C₂ of S, reports in poly-logarithmic time whether {C₁,C₂} is a 2-cover of S.

Cite as

Itai Boneh, Shay Golan, and Arseny Shur. String 2-Covers with No Length Restrictions. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 31:1-31:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{boneh_et_al:LIPIcs.ESA.2024.31,
  author =	{Boneh, Itai and Golan, Shay and Shur, Arseny},
  title =	{{String 2-Covers with No Length Restrictions}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{31:1--31:18},
  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.2024.31},
  URN =		{urn:nbn:de:0030-drops-211029},
  doi =		{10.4230/LIPIcs.ESA.2024.31},
  annote =	{Keywords: Quasi-periodicity, String cover, Range query, Range stabbing}
}
Document
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)


Copy BibTex To Clipboard

@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
A Textbook Solution for Dynamic Strings

Authors: Zsuzsanna Lipták, Francesco Masillo, and Gonzalo Navarro

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


Abstract
We consider the problem of maintaining a collection of strings while efficiently supporting splits and concatenations on them, as well as comparing two substrings, and computing the longest common prefix between two suffixes. This problem can be solved in optimal time O(log N) whp for the updates and O(1) worst-case time for the queries, where N is the total collection size [Gawrychowski et al., SODA 2018]. We present here a much simpler solution based on a forest of enhanced splay trees (FeST), where both the updates and the substring comparison take O(log n) amortized time, n being the lengths of the strings involved. The longest common prefix of length 𝓁 is computed in O(log n + log²𝓁) amortized time. Our query results are correct whp. Our simpler solution enables other more general updates in O(log n) amortized time, such as reversing a substring and/or mapping its symbols. We can also regard substrings as circular or as their omega extension.

Cite as

Zsuzsanna Lipták, Francesco Masillo, and Gonzalo Navarro. A Textbook Solution for Dynamic Strings. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 86:1-86:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{liptak_et_al:LIPIcs.ESA.2024.86,
  author =	{Lipt\'{a}k, Zsuzsanna and Masillo, Francesco and Navarro, Gonzalo},
  title =	{{A Textbook Solution for Dynamic Strings}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{86:1--86:16},
  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.2024.86},
  URN =		{urn:nbn:de:0030-drops-211576},
  doi =		{10.4230/LIPIcs.ESA.2024.86},
  annote =	{Keywords: dynamic strings, splay trees, dynamic data structures, LCP, circular strings}
}
Document
Improved Space-Efficient Approximate Nearest Neighbor Search Using Function Inversion

Authors: Samuel McCauley

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


Abstract
Approximate nearest neighbor search (ANN) data structures have widespread applications in machine learning, computational biology, and text processing. The goal of ANN is to preprocess a set S so that, given a query q, we can find a point y whose distance from q approximates the smallest distance from q to any point in S. For most distance functions, the best-known ANN bounds for high-dimensional point sets are obtained using techniques based on locality-sensitive hashing (LSH). Unfortunately, space efficiency is a major challenge for LSH-based data structures. Classic LSH techniques require a very large amount of space, oftentimes polynomial in |S|. A long line of work has developed intricate techniques to reduce this space usage, but these techniques suffer from downsides: they must be hand tailored to each specific LSH, are often complicated, and their space reduction comes at the cost of significantly increased query times. In this paper we explore a new way to improve the space efficiency of LSH using function inversion techniques, originally developed in (Fiat and Naor 2000). We begin by describing how function inversion can be used to improve LSH data structures. This gives a fairly simple, black box method to reduce LSH space usage. Then, we give a data structure that leverages function inversion to improve the query time of the best known near-linear space data structure for approximate nearest neighbor search under Euclidean distance: the ALRW data structure of (Andoni, Laarhoven, Razenshteyn, and Waingarten 2017). ALRW was previously shown to be optimal among "list-of-points" data structures for both Euclidean and Manhattan ANN; thus, in addition to giving improved bounds, our results imply that list-of-points data structures are not optimal for Euclidean or Manhattan ANN .

Cite as

Samuel McCauley. Improved Space-Efficient Approximate Nearest Neighbor Search Using Function Inversion. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 88:1-88:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{mccauley:LIPIcs.ESA.2024.88,
  author =	{McCauley, Samuel},
  title =	{{Improved Space-Efficient Approximate Nearest Neighbor Search Using Function Inversion}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{88:1--88:19},
  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.2024.88},
  URN =		{urn:nbn:de:0030-drops-211590},
  doi =		{10.4230/LIPIcs.ESA.2024.88},
  annote =	{Keywords: similarity search, locality-sensitive hashing, randomized algorithms, data structures, space efficiency, function inversion}
}
Document
Complete Volume
LIPIcs, Volume 312, WABI 2024, Complete Volume

Authors: Solon P. Pissis and Wing-Kin Sung

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


Abstract
LIPIcs, Volume 312, WABI 2024, Complete Volume

Cite as

24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 1-454, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@Proceedings{pissis_et_al:LIPIcs.WABI.2024,
  title =	{{LIPIcs, Volume 312, WABI 2024, Complete Volume}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{1--454},
  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},
  URN =		{urn:nbn:de:0030-drops-206430},
  doi =		{10.4230/LIPIcs.WABI.2024},
  annote =	{Keywords: LIPIcs, Volume 312, WABI 2024, Complete Volume}
}
Document
Invited Talk
Bioinformatics of Pathogens (Invited Talk)

Authors: Tomáš Vinař

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


Abstract
Genomic sequencing has become an important tool in identification and surveillance of human pathogens. Compared to large organisms, where our goal is to obtain high-quality sequences for detailed analysis, in pathogen sequencing the emphasis is often on optimization of cost and time. Consequently, sequencing of pathogens creates interesting computational challenges and development of new methods has a potential to significantly enhance applicability of the results in epidemiology and clinical practice. In my talk, I will give two examples: plasmid identification in bacterial isolates and genomic surveillance of wastewater for SARS-CoV-2. In both cases, application of better algorithms and modeling helps to improve the quality of analysis of very noisy data.

Cite as

Tomáš Vinař. Bioinformatics of Pathogens (Invited Talk). In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 1:1-1:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{vinar:LIPIcs.WABI.2024.1,
  author =	{Vina\v{r}, Tom\'{a}\v{s}},
  title =	{{Bioinformatics of Pathogens}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{1:1--1:2},
  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.2024.1},
  URN =		{urn:nbn:de:0030-drops-206455},
  doi =		{10.4230/LIPIcs.WABI.2024.1},
  annote =	{Keywords: sequence analysis, genome assembly, neural networks, probabilistic modeling}
}
Document
On the Complexity of the Median and Closest Permutation Problems

Authors: Luís Cunha, Ignasi Sau, and Uéverton Souza

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


Abstract
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on genome rearrangement measures. Many pairwise rearrangement distances have been proposed, based on finding the minimum number of rearrangement events to transform one genome into the other, using some predefined operation. When more than two genomes are considered, we have the more challenging problem of rearrangement-based phylogeny reconstruction. Given a set of genomes and a distance notion, there are at least two natural ways to define the "target" genome. On the one hand, finding a genome that minimizes the sum of the distances from this to any other, called the median genome. On the other hand, finding a genome that minimizes the maximum distance to any other, called the closest genome. Considering genomes as permutations of distinct integers, some distance metrics have been extensively studied. We investigate the median and closest problems on permutations over the following metrics: breakpoint distance, swap distance, block-interchange distance, short-block-move distance, and transposition distance. In biological applications some values are usually very small, such as the solution value d or the number k of input permutations. For each of these metrics and parameters d or k, we analyze the closest and the median problems from the viewpoint of parameterized complexity. We obtain the following results: NP-hardness for finding the median/closest permutation regarding some metrics of distance, even for only k = 3 permutations; Polynomial kernels for the problems of finding the median permutation of all studied metrics, considering the target distance d as parameter; NP-hardness result for finding the closest permutation by short-block-moves; FPT algorithms and infeasibility of polynomial kernels for finding the closest permutation for some metrics when parameterized by the target distance d.

Cite as

Luís Cunha, Ignasi Sau, and Uéverton Souza. On the Complexity of the Median and Closest Permutation Problems. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{cunha_et_al:LIPIcs.WABI.2024.2,
  author =	{Cunha, Lu{\'\i}s and Sau, Ignasi and Souza, U\'{e}verton},
  title =	{{On the Complexity of the Median and Closest Permutation Problems}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{2:1--2:23},
  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.2024.2},
  URN =		{urn:nbn:de:0030-drops-206468},
  doi =		{10.4230/LIPIcs.WABI.2024.2},
  annote =	{Keywords: Median problem, Closest problem, Genome rearrangements, Parameterized complexity}
}
Document
An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree

Authors: Yao-ban Chan

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


Abstract
The phylogenies of species and the genes they contain are similar but distinct, due to evolutionary events that affect genes but do not create new species. These events include gene duplication and loss, but also paralog exchange (non-allelic homologous recombination), where duplicate copies of a gene recombine. To account for paralog exchange, the evolutionary history of the genes must be represented in the form of a phylogenetic network. We reconstruct the interlinked evolution of the genes and species with reconciliations, which map the gene network into the species tree by explicitly accounting for these events. In previous work, we proposed the problem of reconciling a gene network and a species tree, but did not find an efficient solution for a general gene network. In this paper, we develop such a solution, and prove that it solves the most parsimonious reconciliation problem. Our algorithm is exponential only in the level of the gene network (with a base of 2), and we demonstrate that it is a practical solution through simulations. This allows, for the first time, a fine-grained study of the paralogy/orthology relationship between genes along their sequences.

Cite as

Yao-ban Chan. An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


Copy BibTex To Clipboard

@InProceedings{chan:LIPIcs.WABI.2024.3,
  author =	{Chan, Yao-ban},
  title =	{{An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{3:1--3:17},
  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.2024.3},
  URN =		{urn:nbn:de:0030-drops-206472},
  doi =		{10.4230/LIPIcs.WABI.2024.3},
  annote =	{Keywords: Reconciliation, recombination, paralog exchange, phylogenetic network, gene duplication, gene loss}
}
  • Refine by Author
  • 36 Pissis, Solon P.
  • 14 Charalampopoulos, Panagiotis
  • 13 Radoszewski, Jakub
  • 10 Bernardini, Giulia
  • 9 Loukides, Grigorios
  • Show More...

  • Refine by Classification
  • 42 Theory of computation → Pattern matching
  • 12 Applied computing → Bioinformatics
  • 12 Theory of computation → Design and analysis of algorithms
  • 11 Applied computing → Computational biology
  • 7 Theory of computation → Data compression
  • Show More...

  • Refine by Keyword
  • 11 string algorithms
  • 7 Hamming distance
  • 6 de Bruijn graph
  • 5 edit distance
  • 5 pattern matching
  • Show More...

  • Refine by Type
  • 136 document
  • 3 volume

  • Refine by Publication Year
  • 42 2024
  • 39 2017
  • 37 2019
  • 6 2021
  • 4 2018
  • Show More...

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail