Algorithms and Complexity on Indexing Founder Graphs

We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICAL...

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Vydané v:	Algorithmica Ročník 85; číslo 6; s. 1586 - 1623
Hlavní autori:	Equi, Massimo, Norri, Tuukka, Alanko, Jarno, Cazaux, Bastien, Tomescu, Alexandru I., Mäkinen, Veli
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	New York Springer US 01.06.2023 Springer Nature B.V Springer Verlag
Predmet:	Algorithm Analysis and Problem Complexity Algorithms Burrows-Wheeler transform Computer Science Computer Systems Organization and Communication Networks Data Structures and Information Theory Graphs Indexing Lower bounds Mathematics of Computing Polynomials Special Issue on Algorithms and Computation (ISAAC 2021) String matching Theory of Computation Compressed data structures Multiple sequence alignment String matching Segmentation algorithms Graph algorithms Computational complexity Pangenomics
ISSN:	0178-4617, 1432-0541
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Abstract	We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICALP 2019, SOFSEM 2021). These conditional lower-bounds cover even deterministic graphs with binary alphabet, but there naturally exist also graph classes that are easy to index: For example, Wheeler graphs (Gagie et al. Theor. Comp. Sci. 2017) cover graphs admitting a Burrows-Wheeler transform -based indexing scheme. However, it is NP-complete to recognize if a graph is a Wheeler graph (Gibney, Thankachan, ESA 2019). We propose an approach to alleviate the construction bottleneck of Wheeler graphs. Rather than starting from an arbitrary graph, we study graphs induced from multiple sequence alignments (MSAs). Elastic degenerate strings (Bernadini et al. SPIRE 2017, ICALP 2019) can be seen as such graphs, and we introduce here their generalization: elastic founder graphs . We first prove that even such induced graphs are hard to index under OVH. Then we introduce two subclasses, repeat-free and semi-repeat-free graphs, that are easy to index. We give a linear time algorithm to construct a repeat-free (non-elastic) founder graph from a gapless MSA, and (parameterized) near-linear time algorithms to construct a semi-repeat-free (repeat-free, respectively) elastic founder graph from general MSA. Finally, we show that repeat-free founder graphs admit a reduction to Wheeler graphs in polynomial time.
AbstractList	We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICALP 2019, SOFSEM 2021). These conditional lower-bounds cover even deterministic graphs with binary alphabet, but there naturally exist also graph classes that are easy to index: For example, Wheeler graphs (Gagie et al. Theor. Comp. Sci. 2017) cover graphs admitting a Burrows-Wheeler transform -based indexing scheme. However, it is NP-complete to recognize if a graph is a Wheeler graph (Gibney, Thankachan, ESA 2019). We propose an approach to alleviate the construction bottleneck of Wheeler graphs. Rather than starting from an arbitrary graph, we study graphs induced from multiple sequence alignments (MSAs). Elastic degenerate strings (Bernadini et al. SPIRE 2017, ICALP 2019) can be seen as such graphs, and we introduce here their generalization: elastic founder graphs . We first prove that even such induced graphs are hard to index under OVH. Then we introduce two subclasses, repeat-free and semi-repeat-free graphs, that are easy to index. We give a linear time algorithm to construct a repeat-free (non-elastic) founder graph from a gapless MSA, and (parameterized) near-linear time algorithms to construct a semi-repeat-free (repeat-free, respectively) elastic founder graph from general MSA. Finally, we show that repeat-free founder graphs admit a reduction to Wheeler graphs in polynomial time. We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICALP 2019, SOFSEM 2021). These conditional lower-bounds cover even deterministic graphs with binary alphabet, but there naturally exist also graph classes that are easy to index: For example, Wheeler graphs (Gagie et al. Theor. Comp. Sci. 2017) cover graphs admitting a Burrows-Wheeler transform -based indexing scheme. However, it is NP-complete to recognize if a graph is a Wheeler graph (Gibney, Thankachan, ESA 2019). We propose an approach to alleviate the construction bottleneck of Wheeler graphs. Rather than starting from an arbitrary graph, we study graphs induced from multiple sequence alignments (MSAs). Elastic degenerate strings (Bernadini et al. SPIRE 2017, ICALP 2019) can be seen as such graphs, and we introduce here their generalization: elastic founder graphs. We first prove that even such induced graphs are hard to index under OVH. Then we introduce two subclasses, repeat-free and semi-repeat-free graphs, that are easy to index. We give a linear time algorithm to construct a repeat-free (non-elastic) founder graph from a gapless MSA, and (parameterized) near-linear time algorithms to construct a semi-repeat-free (repeat-free, respectively) elastic founder graph from general MSA. Finally, we show that repeat-free founder graphs admit a reduction to Wheeler graphs in polynomial time. Abstract We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICALP 2019, SOFSEM 2021). These conditional lower-bounds cover even deterministic graphs with binary alphabet, but there naturally exist also graph classes that are easy to index: For example, Wheeler graphs (Gagie et al. Theor. Comp. Sci. 2017) cover graphs admitting a Burrows-Wheeler transform -based indexing scheme. However, it is NP-complete to recognize if a graph is a Wheeler graph (Gibney, Thankachan, ESA 2019). We propose an approach to alleviate the construction bottleneck of Wheeler graphs. Rather than starting from an arbitrary graph, we study graphs induced from multiple sequence alignments (). Elastic degenerate strings (Bernadini et al. SPIRE 2017, ICALP 2019) can be seen as such graphs, and we introduce here their generalization: elastic founder graphs . We first prove that even such induced graphs are hard to index under OVH. Then we introduce two subclasses, repeat-free and semi-repeat-free graphs, that are easy to index. We give a linear time algorithm to construct a repeat-free (non-elastic) founder graph from a gapless , and (parameterized) near-linear time algorithms to construct a semi-repeat-free (repeat-free, respectively) elastic founder graph from general . Finally, we show that repeat-free founder graphs admit a reduction to Wheeler graphs in polynomial time. We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial time to answer queries efficiently (Equi et al. ICALP 2019, SOFSEM 2021). These conditional lower-bounds cover even deterministic graphs with binary alphabet, but there naturally exist also graph classes that are easy to index: For example, Wheeler graphs (Gagie et al. Theor. Comp. Sci. 2017) cover graphs admitting a Burrows-Wheeler transform -based indexing scheme. However, it is NP-complete to recognize if a graph is a Wheeler graph (Gibney, Thankachan, ESA 2019). We propose an approach to alleviate the construction bottleneck of Wheeler graphs. Rather than starting from an arbitrary graph, we study graphs induced from multiple sequence alignments (). Elastic degenerate strings (Bernadini et al. SPIRE 2017, ICALP 2019) can be seen as such graphs, and we introduce here their generalization: elastic founder graphs . We first prove that even such induced graphs are hard to index under OVH. Then we introduce two subclasses, repeat-free and semi-repeat-free graphs, that are easy to index. We give a linear time algorithm to construct a repeat-free (non-elastic) founder graph from a gapless , and (parameterized) near-linear time algorithms to construct a semi-repeat-free (repeat-free, respectively) elastic founder graph from general . Finally, we show that repeat-free founder graphs admit a reduction to Wheeler graphs in polynomial time.
Author	Norri, Tuukka Cazaux, Bastien Mäkinen, Veli Equi, Massimo Alanko, Jarno Tomescu, Alexandru I.
Author_xml	– sequence: 1 givenname: Massimo surname: Equi fullname: Equi, Massimo organization: Department of Computer Science, University of Helsinki – sequence: 2 givenname: Tuukka surname: Norri fullname: Norri, Tuukka organization: Department of Computer Science, University of Helsinki – sequence: 3 givenname: Jarno surname: Alanko fullname: Alanko, Jarno organization: Department of Computer Science, University of Helsinki, Faculty of Computer Science, Dalhousie University – sequence: 4 givenname: Bastien surname: Cazaux fullname: Cazaux, Bastien organization: LIRMM, Univ. Montpellier, CNRS – sequence: 5 givenname: Alexandru I. surname: Tomescu fullname: Tomescu, Alexandru I. organization: Department of Computer Science, University of Helsinki – sequence: 6 givenname: Veli orcidid: 0000-0003-4454-1493 surname: Mäkinen fullname: Mäkinen, Veli email: veli.makinen@helsinki.fi organization: Department of Computer Science, University of Helsinki
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Snippet	We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one... We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one... Abstract We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is...
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SubjectTerms	Algorithm Analysis and Problem Complexity Algorithms Burrows-Wheeler transform Computer Science Computer Systems Organization and Communication Networks Data Structures and Information Theory Graphs Indexing Lower bounds Mathematics of Computing Polynomials Special Issue on Algorithms and Computation (ISAAC 2021) String matching Theory of Computation
Title	Algorithms and Complexity on Indexing Founder Graphs
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