5 Search Results for "Chubet, Oliver A."

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)

Copy BibTex To Clipboard

@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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2025.88
Repetition Aware Text Indexing for Matching Patterns with Wildcards

Authors: Daniel Gibney, Jackson Huffstutler, Mano Prakash Parthasarathi, and Sharma V. Thankachan

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

Abstract
We study the problem of indexing a text T[1..n] to support pattern matching with wildcards. The input of a query is a pattern P[1..m] containing h ∈ [0, k] wildcard (a.k.a. don't care) characters and the output is the set of occurrences of P in T (i.e., starting positions of substrings of T that matches P), where k = o(log n) is fixed at index construction. A classic solution by Cole et al. [STOC 2004] provides an index with space complexity O(n ⋅ (clog n)^k/k!)) and query time O(m+2^h log log n+occ), where c > 1 is a constant, and occ denotes the number of occurrences of P in T. We introduce a new data structure that significantly reduces space usage for highly repetitive texts while maintaining efficient query processing. Its space (in words) and query time are as follows: O(δ log (n/δ)⋅ c^k (1+(log^k (δ log n))/k!)) and O((m+2^h +occ)log n)) The parameter δ, known as substring complexity, is a recently introduced measure of repetitiveness that serves as a unifying and lower-bounding metric for several popular measures, including the number of phrases in the LZ77 factorization (denoted by z) and the number of runs in the Burrows-Wheeler Transform (denoted by r). Moreover, O(δ log (n/δ)) represents the optimal space required to encode the data in terms of n and δ, helping us see how close our space is to the minimum required. In another trade-off, we match the query time of Cole et al.’s index using O(n+δ log (n/δ) ⋅ (clogδ)^{k+ε}/k!) space, where ε > 0 is an arbitrarily small constant. We also demonstrate how these techniques can be applied to a more general indexing problem, where the query pattern includes k-gaps (a gap can be interpreted as a contiguous sequence of wildcard characters).
Cite as

Daniel Gibney, Jackson Huffstutler, Mano Prakash Parthasarathi, and Sharma V. Thankachan. Repetition Aware Text Indexing for Matching Patterns with Wildcards. In 52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 334, pp. 88:1-88:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{gibney_et_al:LIPIcs.ICALP.2025.88,
  author =	{Gibney, Daniel and Huffstutler, Jackson and Parthasarathi, Mano Prakash and Thankachan, Sharma V.},
  title =	{{Repetition Aware Text Indexing for Matching Patterns with Wildcards}},
  booktitle =	{52nd International Colloquium on Automata, Languages, and Programming (ICALP 2025)},
  pages =	{88:1--88:20},
  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.2025.88},
  URN =		{urn:nbn:de:0030-drops-234656},
  doi =		{10.4230/LIPIcs.ICALP.2025.88},
  annote =	{Keywords: Pattern Matching, Text Indexing, Wildcard Matching}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.6
A Sparse Multicover Bifiltration of Linear Size

Authors: Ángel Javier Alonso

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
The k-cover of a point cloud X of ℝ^d at radius r is the set of all those points within distance r of at least k points of X. By varying r and k we obtain a two-parameter filtration known as the multicover bifiltration. This bifiltration has received attention recently due to being choice-free and robust to outliers. However, it is hard to compute: the smallest known equivalent simplicial bifiltration has O(|X|^{d+1}) simplices. In this paper we introduce a (1+ε)-approximation of the multicover bifiltration of linear size O(|X|), for fixed d and ε. The methods also apply to the subdivision Rips bifiltration on metric spaces of bounded doubling dimension yielding analogous results.
Cite as

Ángel Javier Alonso. A Sparse Multicover Bifiltration of Linear Size. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{alonso:LIPIcs.SoCG.2025.6,
  author =	{Alonso, \'{A}ngel Javier},
  title =	{{A Sparse Multicover Bifiltration of Linear Size}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{6:1--6:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.6},
  URN =		{urn:nbn:de:0030-drops-231587},
  doi =		{10.4230/LIPIcs.SoCG.2025.6},
  annote =	{Keywords: Multicover, Approximation, Sparsification, Multiparameter persistence}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.35
A Theory of Sub-Barcodes

Authors: Oliver A. Chubet, Kirk P. Gardner, and Donald R. Sheehy

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
The primary tool in topological data analysis (TDA) is persistent homology, which involves computing a barcode - often from point-cloud or scalar field data - that serves as a topological signature for the underlying function. In this work, we introduce sub-barcodes and show how they arise naturally from factorizations of persistence module homomorphisms. We show that, as a partial order induced by factorizations, the relation of being a sub-barcode is strictly stronger than the rank invariant, and we apply sub-barcode theory to the problem of inferring information about the barcode of an unknown Lipschitz function from samples. The advantage of this approach is that it permits strong guarantees - with no noise - while requiring no sampling assumptions, and the resulting barcode is guaranteed to be a sub-barcode of every Lipschitz function that agrees with the data. We also present an algorithmic theory that allows for the efficient approximation of sub-barcodes using filtered Delaunay triangulations for Euclidean inputs.
Cite as

Oliver A. Chubet, Kirk P. Gardner, and Donald R. Sheehy. A Theory of Sub-Barcodes. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 35:1-35:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{chubet_et_al:LIPIcs.SoCG.2025.35,
  author =	{Chubet, Oliver A. and Gardner, Kirk P. and Sheehy, Donald R.},
  title =	{{A Theory of Sub-Barcodes}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{35:1--35:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.35},
  URN =		{urn:nbn:de:0030-drops-231873},
  doi =		{10.4230/LIPIcs.SoCG.2025.35},
  annote =	{Keywords: Topology, Topological Data Analysis, Persistent Homology, Persistence Modules, Barcodes, Sub-barcodes, Factorizations, Lipschitz Extensions}
}
Document
Media Exposition
DOI: 10.4230/LIPIcs.SoCG.2023.64
Greedy Permutations and Finite Voronoi Diagrams (Media Exposition)

Authors: Oliver A. Chubet, Paul Macnichol, Parth Parikh, Donald R. Sheehy, and Siddharth S. Sheth

Published in: LIPIcs, Volume 258, 39th International Symposium on Computational Geometry (SoCG 2023)

Abstract
We illustrate the computation of a greedy permutation using finite Voronoi diagrams. We describe the neighbor graph, which is a sparse graph data structure that facilitates efficient point location to insert a new Voronoi cell. This data structure is not dependent on a Euclidean metric space. The greedy permutation is computed in O(nlog Δ) time for low-dimensional data using this method [Sariel Har-Peled and Manor Mendel, 2006; Donald R. Sheehy, 2020].
Cite as

Oliver A. Chubet, Paul Macnichol, Parth Parikh, Donald R. Sheehy, and Siddharth S. Sheth. Greedy Permutations and Finite Voronoi Diagrams (Media Exposition). In 39th International Symposium on Computational Geometry (SoCG 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 258, pp. 64:1-64:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{chubet_et_al:LIPIcs.SoCG.2023.64,
  author =	{Chubet, Oliver A. and Macnichol, Paul and Parikh, Parth and Sheehy, Donald R. and Sheth, Siddharth S.},
  title =	{{Greedy Permutations and Finite Voronoi Diagrams}},
  booktitle =	{39th International Symposium on Computational Geometry (SoCG 2023)},
  pages =	{64:1--64:5},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-273-0},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{258},
  editor =	{Chambers, Erin W. and Gudmundsson, Joachim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2023.64},
  URN =		{urn:nbn:de:0030-drops-179146},
  doi =		{10.4230/LIPIcs.SoCG.2023.64},
  annote =	{Keywords: greedy permutation, Voronoi diagrams}
}
  • Refine by Type
  • 5 Document/PDF
  • 4 Document/HTML

  • Refine by Publication Year
  • 1 2026
  • 3 2025
  • 1 2023

  • Refine by Author
  • 2 Chubet, Oliver A.
  • 2 Parthasarathi, Mano Prakash
  • 2 Sheehy, Donald R.
  • 2 Thankachan, Sharma V.
  • 1 Alonso, Ángel Javier
  • Show More...

  • Refine by Series/Journal
  • 5 LIPIcs

  • Refine by Classification
  • 3 Theory of computation → Computational geometry
  • 2 Theory of computation → Pattern matching
  • 1 Computing methodologies → Algebraic algorithms
  • 1 Mathematics of computing → Algebraic topology
  • 1 Mathematics of computing → Geometric topology
  • Show More...

  • Refine by Keyword
  • 2 Text Indexing
  • 1 Approximation
  • 1 Barcodes
  • 1 Data Structures
  • 1 Factorizations
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact