2 Search Results for "Thibodeau, David"

Document
DOI: 10.4230/LIPIcs.WABI.2025.17
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT

Authors: Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang

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

Abstract
String matching problems in bioinformatics are typically for finding exact substring matches between a query and a reference text. Previous formulations often focus on maximum exact matches (MEMs). However, multiple occurrences of substrings of the query in the text that are long enough but not maximal may not be captured by MEMs. Such long matches can be informative, especially when the text is a collection of similar sequences such as genomes. In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount of LEMs, so we only consider those above some length threshold ℒ. These are referred to as long LEMs. The purpose of long LEMs is to capture substring matches between a query and a text that are not necessarily maximal in the pattern but still long enough to be important. Therefore efficient long LEMs finding algorithms are desired for these datasets. However, these datasets are too large to query on traditional string indexes. Fortunately, these datasets are very repetitive. Recently, compressed string indexes that take advantage of the redundancy in the data but retain efficient querying capability have been proposed as a solution. We therefore give an efficient algorithm for computing all the long LEMs of a query and a text in a BWT runs compressed string index. We describe an O(m+occ) expected time algorithm that relies on an O(r) words space string index for outputting all long LEMs of a pattern with respect to a text given the matching statistics of the pattern with respect to the text. Here m is the length of the query, occ is the number of long LEMs outputted, and r is the number of runs in the BWT of the text. The O(r) space string index we describe relies on an adaptation of the move data structure by Nishimoto and Tabei. We are able to support LCP[i] queries in constant time given SA[i]. In other words, we answer PLCP[i] queries in constant time. These PLCP queries enable the efficient long LEM query. Long LEMs may provide useful similarity information between a pattern and a text that MEMs may ignore. This information is particularly useful in pangenome and biobank scale haplotype panel contexts.
Cite as

Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{sanaullah_et_al:LIPIcs.WABI.2025.17,
  author =	{Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaojie},
  title =	{{An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{17:1--17:25},
  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.2025.17},
  URN =		{urn:nbn:de:0030-drops-239433},
  doi =		{10.4230/LIPIcs.WABI.2025.17},
  annote =	{Keywords: BWT, LEM, Long LEM, MEM, Run Length Compressed BWT, Move Data Structure, Pangenome}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2018.19
Index-Stratified Types

Authors: Rohan Jacob-Rao, Brigitte Pientka, and David Thibodeau

Published in: LIPIcs, Volume 108, 3rd International Conference on Formal Structures for Computation and Deduction (FSCD 2018)

Abstract
We present Tores, a core language for encoding metatheoretic proofs. The novel features we introduce are well-founded Mendler-style (co)recursion over indexed data types and a form of recursion over objects in the index language to build new types. The latter, which we call index-stratified types, are analogue to the concept of large elimination in dependently typed languages. These features combined allow us to encode sophisticated case studies such as normalization for lambda calculi and normalization by evaluation. We prove the soundness of Tores as a programming and proof language via the key theorems of subject reduction and termination.
Cite as

Rohan Jacob-Rao, Brigitte Pientka, and David Thibodeau. Index-Stratified Types. In 3rd International Conference on Formal Structures for Computation and Deduction (FSCD 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 108, pp. 19:1-19:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

@InProceedings{jacobrao_et_al:LIPIcs.FSCD.2018.19,
  author =	{Jacob-Rao, Rohan and Pientka, Brigitte and Thibodeau, David},
  title =	{{Index-Stratified Types}},
  booktitle =	{3rd International Conference on Formal Structures for Computation and Deduction (FSCD 2018)},
  pages =	{19:1--19:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-077-4},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{108},
  editor =	{Kirchner, H\'{e}l\`{e}ne},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2018.19},
  URN =		{urn:nbn:de:0030-drops-91891},
  doi =		{10.4230/LIPIcs.FSCD.2018.19},
  annote =	{Keywords: Indexed types, (co)recursive types, logical relations}
}
  • Refine by Type
  • 2 Document/PDF
  • 1 Document/HTML

  • Refine by Publication Year
  • 1 2025
  • 1 2018

  • Refine by Author
  • 1 Jacob-Rao, Rohan
  • 1 Pientka, Brigitte
  • 1 Sanaullah, Ahsan
  • 1 Thibodeau, David
  • 1 Zhang, Shaojie
  • Show More...

  • Refine by Series/Journal
  • 2 LIPIcs

  • Refine by Classification
  • 1 Theory of computation → Data compression
  • 1 Theory of computation → Logic and verification
  • 1 Theory of computation → Pattern matching
  • 1 Theory of computation → Type theory

  • Refine by Keyword
  • 1 (co)recursive types
  • 1 BWT
  • 1 Indexed types
  • 1 LEM
  • 1 Long LEM
  • 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
© 2023-2025 Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact