2 Search Results for "Cook, James"

Document
DOI: 10.4230/LIPIcs.WABI.2024.23
AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors: Adam Cicherski, Anna Lisiecka, and Norbert Dojer

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

Abstract
The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.
Cite as

Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23,
  author =	{Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert},
  title =	{{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{23:1--23:18},
  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.2024.23},
  URN =		{urn:nbn:de:0030-drops-206673},
  doi =		{10.4230/LIPIcs.WABI.2024.23},
  annote =	{Keywords: pangenome, variation graph, genome alignment, population genomics}
}
Document
DOI: 10.4230/LIPIcs.CCC.2022.8
Trading Time and Space in Catalytic Branching Programs

Authors: James Cook and Ian Mertz

Published in: LIPIcs, Volume 234, 37th Computational Complexity Conference (CCC 2022)

Abstract
An m-catalytic branching program (Girard, Koucký, McKenzie 2015) is a set of m distinct branching programs for f which are permitted to share internal (i.e. non-source non-sink) nodes. While originally introduced as a non-uniform analogue to catalytic space, this also gives a natural notion of amortized non-uniform space complexity for f, namely the smallest value |G|/m for an m-catalytic branching program G for f (Potechin 2017). Potechin (2017) showed that every function f has amortized size O(n), witnessed by an m-catalytic branching program where m = 2^(2ⁿ-1). We recreate this result by defining a catalytic algorithm for evaluating polynomials using a large amount of space but O(n) time. This allows us to balance this with previously known algorithms which are efficient with respect to space at the cost of time (Cook, Mertz 2020, 2021). We show that for any ε ≥ 2n^(-1), every function f has an m-catalytic branching program of size O_ε(mn), where m = 2^(2^(ε n)). We similarly recreate an improved result due to Robere and Zuiddam (2021), and show that for d ≤ n and ε ≥ 2d^(-1), the same result holds for m = 2^binom(n, ≤ ε d) as long as f is a degree-d polynomial over 𝔽₂. We also show that for certain classes of functions, m can be reduced to 2^(poly n) while still maintaining linear or quasi-linear amortized size. In the other direction, we bound the necessary length, and by extension the amortized size, of any permutation branching program for an arbitrary function between 3n and 4n-4.
Cite as

James Cook and Ian Mertz. Trading Time and Space in Catalytic Branching Programs. In 37th Computational Complexity Conference (CCC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 234, pp. 8:1-8:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{cook_et_al:LIPIcs.CCC.2022.8,
  author =	{Cook, James and Mertz, Ian},
  title =	{{Trading Time and Space in Catalytic Branching Programs}},
  booktitle =	{37th Computational Complexity Conference (CCC 2022)},
  pages =	{8:1--8:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-241-9},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{234},
  editor =	{Lovett, Shachar},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2022.8},
  URN =		{urn:nbn:de:0030-drops-165708},
  doi =		{10.4230/LIPIcs.CCC.2022.8},
  annote =	{Keywords: complexity theory, branching programs, amortized, space complexity, catalytic computation}
}
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