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DOI: 10.4230/LIPIcs.WABI.2023.5

Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem

Authors: Junyan Dai, Tobias Rubel, Yunheng Han, and Erin K. Molloy

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract

The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for classic parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem in polynomial time for the Dollo criterion score. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. Thus, we implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility in the context of species phylogenetics using both simulated and real data sets. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony.

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Junyan Dai, Tobias Rubel, Yunheng Han, and Erin K. Molloy. Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{dai_et_al:LIPIcs.WABI.2023.5,
  author =	{Dai, Junyan and Rubel, Tobias and Han, Yunheng and Molloy, Erin K.},
  title =	{{Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{5:1--5:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.5},
  URN =		{urn:nbn:de:0030-drops-186312},
  doi =		{10.4230/LIPIcs.WABI.2023.5},
  annote =	{Keywords: phylogenetics, parsimony, Dollo, Camin-Sokal, dynamic programming, constraints}
}

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DOI: 10.4230/LIPIcs.WABI.2023.16

Fast, Parallel, and Cache-Friendly Suffix Array Construction

Authors: Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin Molloy, and Rob Patro

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract

String indexes such as the suffix array (SA) and the closely related longest common prefix (LCP) array are fundamental objects in bioinformatics and have a wide variety of applications. Despite their importance in practice, few scalable parallel algorithms for constructing these are known, and the existing algorithms can be highly non-trivial to implement and parallelize. In this paper we present CaPS-SA, a simple and scalable parallel algorithm for constructing these string indexes inspired by samplesort. Due to its design, CaPS-SA has excellent memory-locality and thus incurs fewer cache misses and achieves strong performance on modern multicore systems with deep cache hierarchies. We show that despite its simple design, CaPS-SA outperforms existing state-of-the-art parallel SA and LCP-array construction algorithms on modern hardware. Finally, motivated by applications in modern aligners where the query strings have bounded lengths, we introduce the notion of a bounded-context SA and show that CaPS-SA can easily be extended to exploit this structure to obtain further speedups.

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Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin Molloy, and Rob Patro. Fast, Parallel, and Cache-Friendly Suffix Array Construction. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 16:1-16:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{khan_et_al:LIPIcs.WABI.2023.16,
  author =	{Khan, Jamshed and Rubel, Tobias and Dhulipala, Laxman and Molloy, Erin and Patro, Rob},
  title =	{{Fast, Parallel, and Cache-Friendly Suffix Array Construction}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{16:1--16:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.16},
  URN =		{urn:nbn:de:0030-drops-186424},
  doi =		{10.4230/LIPIcs.WABI.2023.16},
  annote =	{Keywords: Suffix Array, Longest Common Prefix, Data Structures, Indexing, Parallel Algorithms}
}

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Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem

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Fast, Parallel, and Cache-Friendly Suffix Array Construction

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