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Documents authored by Rossi, Massimiliano


Document
RLBWT Tricks

Authors: Nathaniel K. Brown, Travis Gagie, and Massimiliano Rossi

Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)


Abstract
Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit lower bounds from predecessor queries. At ICALP '21, however, Nishimoto and Tabei described a new, simple and constant-time implementation. For a permutation π, it stores an O (r)-space table - where r is the number of positions i where either i = 0 or π (i + 1) ≠ π (i) + 1 - that enables the computation of successive values of π(i) by table look-ups and linear scans. Nishimoto and Tabei showed how to increase the number of rows in the table to bound the length of the linear scans such that the query time for computing π(i) is constant while maintaining O (r)-space. In this paper we refine Nishimoto and Tabei’s approach, including a time-space tradeoff, and experimentally evaluate different implementations demonstrating the practicality of part of their result. We show that even without adding rows to the table, in practice we almost always scan only a few entries during queries. We propose a decomposition scheme of the permutation π corresponding to the LF-mapping that allows an improved compression of the data structure, while limiting the query time. We tested our implementation on real-world genomic datasets and found that without compression of the table, backward-stepping is drastically faster than with sparse bitvector implementations but, unfortunately, also uses drastically more space. After compression, backward-stepping is competitive both in time and space with the best existing implementations.

Cite as

Nathaniel K. Brown, Travis Gagie, and Massimiliano Rossi. RLBWT Tricks. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 16:1-16:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@InProceedings{brown_et_al:LIPIcs.SEA.2022.16,
  author =	{Brown, Nathaniel K. and Gagie, Travis and Rossi, Massimiliano},
  title =	{{RLBWT Tricks}},
  booktitle =	{20th International Symposium on Experimental Algorithms (SEA 2022)},
  pages =	{16:1--16:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-251-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{233},
  editor =	{Schulz, Christian and U\c{c}ar, Bora},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.16},
  URN =		{urn:nbn:de:0030-drops-165500},
  doi =		{10.4230/LIPIcs.SEA.2022.16},
  annote =	{Keywords: Compressed String Indexes, Repetitive Text Collections, Burrows-Wheeler Transform}
}
Document
Computing Maximal Unique Matches with the r-Index

Authors: Sara Giuliani, Giuseppe Romana, and Massimiliano Rossi

Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)


Abstract
In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique Matches (MUMs) have proven themselves to be useful in multiple bioinformatic contexts, for example short-read alignment and multiple-genome alignment. However, standard techniques using suffix trees and FM-indexes do not scale to a pangenomic level. Recently, Gagie et al. [JACM 20] introduced the r-index that is a Burrows-Wheeler Transform (BWT)-based index able to handle hundreds of human genomes. Later, Rossi et al. [JCB 22] enabled the computation of MEMs using the r-index, and Boucher et al. [DCC 21] showed how to compute them in a streaming fashion. In this paper, we show how to augment Boucher et al.’s approach to enable the computation of MUMs on the r-index, while preserving the space and time bounds. We add additional O(r) samples of the longest common prefix (LCP) array, where r is the number of equal-letter runs of the BWT, that permits the computation of the second longest match of the pattern suffix with respect to the input text, which in turn allows the computation of candidate MUMs. We implemented a proof-of-concept of our approach, that we call MUM-PHINDER, and tested on real-world datasets. We compared our approach with competing methods that are able to compute MUMs. We observe that our method is up to 8 times smaller, while up to 19 times slower when the dataset is not highly repetitive, while on highly repetitive data, our method is up to 6.5 times slower and uses up to 25 times less memory.

Cite as

Sara Giuliani, Giuseppe Romana, and Massimiliano Rossi. Computing Maximal Unique Matches with the r-Index. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 22:1-22:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@InProceedings{giuliani_et_al:LIPIcs.SEA.2022.22,
  author =	{Giuliani, Sara and Romana, Giuseppe and Rossi, Massimiliano},
  title =	{{Computing Maximal Unique Matches with the r-Index}},
  booktitle =	{20th International Symposium on Experimental Algorithms (SEA 2022)},
  pages =	{22:1--22:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-251-8},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{233},
  editor =	{Schulz, Christian and U\c{c}ar, Bora},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.22},
  URN =		{urn:nbn:de:0030-drops-165568},
  doi =		{10.4230/LIPIcs.SEA.2022.22},
  annote =	{Keywords: Burrows-Wheeler Transform, r-index, maximal unique matches, bioinformatics, pangenomics}
}
Document
Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph

Authors: Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, and Christina Boucher

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)


Abstract
Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there exists very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary method that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics' Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as rmapper, and compare its performance against the assembler of Valouev et al. (2006) and Solve by Bionano Genomics on data from three genomes - E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was the only one able to successfully run on all three genomes. The method of Valouev et al. (2006) only successfully ran on E. coli and Bionano Solve successfully ran on E. coli and human but not on the fish genome. Moreover, on the human genome rmapper was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies.

Cite as

Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, and Christina Boucher. Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 9:1-9:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


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@InProceedings{mukherjee_et_al:LIPIcs.WABI.2020.9,
  author =	{Mukherjee, Kingshuk and Rossi, Massimiliano and Salmela, Leena and Boucher, Christina},
  title =	{{Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{9:1--9:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.9},
  URN =		{urn:nbn:de:0030-drops-127982},
  doi =		{10.4230/LIPIcs.WABI.2020.9},
  annote =	{Keywords: optical maps, de Bruijn graph, assembly}
}
Document
Pattern Discovery in Colored Strings

Authors: Zsuzsanna Lipták, Simon J. Puglisi, and Massimiliano Rossi

Published in: LIPIcs, Volume 160, 18th International Symposium on Experimental Algorithms (SEA 2020)


Abstract
We consider the problem of identifying patterns of interest in colored strings. A colored string is a string in which each position is colored with one of a finite set of colors. Our task is to find substrings that always occur followed by the same color at the same distance. The problem is motivated by applications in embedded systems verification, in particular, assertion mining. The goal there is to automatically infer properties of the embedded system from the analysis of its simulation traces. We show that the number of interesting patterns is upper-bounded by 𝒪(n²) where n is the length of the string. We introduce a baseline algorithm with 𝒪(n²) running time which identifies all interesting patterns for all colors in the string satisfying certain minimality conditions. When one is interested in patterns related to only one color, we provide an algorithm that identifies patterns in 𝒪(n²log n) time, but is faster than the first algorithm in practice, both on simulated and on real-world patterns.

Cite as

Zsuzsanna Lipták, Simon J. Puglisi, and Massimiliano Rossi. Pattern Discovery in Colored Strings. In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 12:1-12:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


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@InProceedings{liptak_et_al:LIPIcs.SEA.2020.12,
  author =	{Lipt\'{a}k, Zsuzsanna and Puglisi, Simon J. and Rossi, Massimiliano},
  title =	{{Pattern Discovery in Colored Strings}},
  booktitle =	{18th International Symposium on Experimental Algorithms (SEA 2020)},
  pages =	{12:1--12:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-148-1},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{160},
  editor =	{Faro, Simone and Cantone, Domenico},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.12},
  URN =		{urn:nbn:de:0030-drops-120862},
  doi =		{10.4230/LIPIcs.SEA.2020.12},
  annote =	{Keywords: property testing, suffix tree, pattern mining}
}
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