46 Search Results for "Parida, Laxmi"

Volume

LIPIcs, Volume 113

18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

WABI 2018, August 20-22, 2018, Helsinki, Finland

Editors: Laxmi Parida and Esko Ukkonen

Document
DOI: 10.4230/OASIcs.Manzini.11
Circular Dictionary Matching Using Extended BWT

Authors: Wing-Kai Hon, Rahul Shah, and Sharma V. Thankachan

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The dictionary matching problem involves preprocessing a set of strings (patterns) into a data structure that efficiently identifies all occurrences of these patterns within a query string (text). In this work, we investigate a variation of this problem, termed circular dictionary matching, where the patterns are circular, meaning their cyclic shifts are also considered valid patterns. Such patterns naturally occur in areas such as bioinformatics and computational geometry. Based on the extended Burrows-Wheeler Transformation (eBWT), we design a space-efficient solution for this problem. Specifically, we show that a dictionary of d circular patterns of total length n can be indexed in nlog σ + O(n+dlog n+σ log n) bits of space and support circular dictionary matching on a query text T in O((|T|+occ)log n) time, where σ represents the size of the underlying alphabet and occ represents the output size.
Cite as

Wing-Kai Hon, Rahul Shah, and Sharma V. Thankachan. Circular Dictionary Matching Using Extended BWT. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 11:1-11:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hon_et_al:OASIcs.Manzini.11,
  author =	{Hon, Wing-Kai and Shah, Rahul and Thankachan, Sharma V.},
  title =	{{Circular Dictionary Matching Using Extended BWT}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{11:1--11:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.11},
  URN =		{urn:nbn:de:0030-drops-239195},
  doi =		{10.4230/OASIcs.Manzini.11},
  annote =	{Keywords: String algorithms, Burrows-Wheeler transformation, suffix trees, succinct data structures}
}
Document
DOI: 10.4230/OASIcs.Manzini.8
A Taxonomy of LCP-Array Construction Algorithms

Authors: Johannes Fischer and Enno Ohlebusch

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
The combination of the suffix array and the LCP-array can be used to solve many string processing problems efficiently. We review some of the most important sequential LCP-array construction algorithms in random access memory.
Cite as

Johannes Fischer and Enno Ohlebusch. A Taxonomy of LCP-Array Construction Algorithms. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 8:1-8:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fischer_et_al:OASIcs.Manzini.8,
  author =	{Fischer, Johannes and Ohlebusch, Enno},
  title =	{{A Taxonomy of LCP-Array Construction Algorithms}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{8:1--8:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.8},
  URN =		{urn:nbn:de:0030-drops-239166},
  doi =		{10.4230/OASIcs.Manzini.8},
  annote =	{Keywords: longest common prefix array, suffix array, Burrows-Wheeler transform}
}
Document
DOI: 10.4230/LIPIcs.CCC.2025.20
Counting Martingales for Measure and Dimension in Complexity Classes

Authors: John M. Hitchcock, Adewale Sekoni, and Hadi Shafei

Published in: LIPIcs, Volume 339, 40th Computational Complexity Conference (CCC 2025)

Abstract
This paper makes two primary contributions. First, we introduce the concept of counting martingales and use it to define counting measures and counting dimensions. Second, we apply these new tools to strengthen previous circuit lower bounds. Resource-bounded measure and dimension have traditionally focused on deterministic time and space bounds. We use counting complexity classes to develop resource-bounded counting measures and dimensions. Counting martingales are constructed using functions from the #𝖯, SpanP, and GapP complexity classes. We show that counting martingales capture many martingale constructions in complexity theory. The resulting counting measures and dimensions are intermediate in power between the standard time-bounded and space-bounded notions, enabling finer-grained analysis where space-bounded measures are known, but time-bounded measures remain open. For example, we show that BPP has #𝖯-dimension 0 and BQP has GapP-dimension 0, whereas the 𝖯-dimensions of these classes remain open. As our main application, we improve circuit-size lower bounds. Lutz (1992) strengthened Shannon’s classic (1-ε) 2ⁿ/n lower bound (1949) to PSPACE-measure, showing that almost all problems require circuits of size (2ⁿ/n)(1+(α log n)/n), for any α < 1. We extend this result to SpanP-measure, with a proof that uses a connection through the Minimum Circuit Size Problem (MCSP) to construct a counting martingale. Our results imply that the stronger lower bound holds within the third level of the exponential-time hierarchy, whereas previously, it was only known in ESPACE. Under a derandomization hypothesis, this lower bound holds within the second level of the exponential-time hierarchy, specifically in the class 𝖤^NP. We also study the #𝖯-dimension of classical circuit complexity classes and the GapP-dimension of quantum circuit complexity classes.
Cite as

John M. Hitchcock, Adewale Sekoni, and Hadi Shafei. Counting Martingales for Measure and Dimension in Complexity Classes. In 40th Computational Complexity Conference (CCC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 339, pp. 20:1-20:35, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hitchcock_et_al:LIPIcs.CCC.2025.20,
  author =	{Hitchcock, John M. and Sekoni, Adewale and Shafei, Hadi},
  title =	{{Counting Martingales for Measure and Dimension in Complexity Classes}},
  booktitle =	{40th Computational Complexity Conference (CCC 2025)},
  pages =	{20:1--20:35},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-379-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{339},
  editor =	{Srinivasan, Srikanth},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2025.20},
  URN =		{urn:nbn:de:0030-drops-237145},
  doi =		{10.4230/LIPIcs.CCC.2025.20},
  annote =	{Keywords: resource-bounded measure, resource-bounded dimension, counting martingales, counting complexity, circuit complexity, Kolmogorov complexity, quantum complexity, Minimum Circuit Size Problem}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.58
Tracking the Persistence of Harmonic Chains: Barcode and Stability

Authors: Tao Hou, Salman Parsa, and Bei Wang

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
The persistence barcode is a topological descriptor of data that plays a fundamental role in topological data analysis. Given a filtration of data, the persistence barcode tracks the evolution of its homology groups. In this paper, we introduce a new type of barcode, called the harmonic chain barcode, which tracks the evolution of harmonic chains. In addition, we show that the harmonic chain barcode is stable. Given a filtration of a simplicial complex of size m, we present an algorithm to compute its harmonic chain barcode in O(m³) time. Consequently, the harmonic chain barcode can enrich the family of topological descriptors in applications where a persistence barcode is applicable, such as feature vectorization and machine learning.
Cite as

Tao Hou, Salman Parsa, and Bei Wang. Tracking the Persistence of Harmonic Chains: Barcode and Stability. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 58:1-58:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{hou_et_al:LIPIcs.SoCG.2025.58,
  author =	{Hou, Tao and Parsa, Salman and Wang, Bei},
  title =	{{Tracking the Persistence of Harmonic Chains: Barcode and Stability}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{58:1--58:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.58},
  URN =		{urn:nbn:de:0030-drops-232100},
  doi =		{10.4230/LIPIcs.SoCG.2025.58},
  annote =	{Keywords: Persistent homology, harmonic chains, topological data analysis}
}
Document
Media Exposition
DOI: 10.4230/LIPIcs.SoCG.2025.84
Incremental and Interactive PQ- and PC-Trees (Media Exposition)

Authors: Simon D. Fink and Dominik Peters

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
PQ-trees [Booth, 1975; Kellogg S. Booth and George S. Lueker, 1976] (and their more general variant PC-trees [Hsu and McConnell, 2003; Wei-Kuan and Wen-Lian, 1999]) are a well-known data structure for representing the set of linear (or for PC-trees, circular) orders respecting a given set of consecutivity constraints. Each such constraint is specified by a set of elements and requires that these elements appear consecutively in the linear (or circular) order; thus, they disallow the set to be interleaved with its complement. The main operation supported by these data structures is thus the so-called update, which takes as input a set that forms an additional constraint, and in response changes the tree in order to restrict the represented orders to those satisfying the new constraint. Interpreting a given tree is straightforward: leaves represent the underlying elements, while inner nodes either allow the order of their subtrees to be reversed (Q/C-nodes) or to be arbitrarily permuted (P-nodes). However, the way this structure and the set of represented orders change under updates is less intuitive. We present an interactive web app that allows users to specify sets of consecutivity constraints in the form of a 0/1-matrix and then calculates and visualizes the corresponding PQ- or PC-tree. The constraints can then be changed dynamically while observing how this changes the structure of the tree and the set of represented orders. Through this interactive exploration, we hope to make PQ- and PC-trees more accessible to a wider audience.
Cite as

Simon D. Fink and Dominik Peters. Incremental and Interactive PQ- and PC-Trees (Media Exposition). In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 84:1-84:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fink_et_al:LIPIcs.SoCG.2025.84,
  author =	{Fink, Simon D. and Peters, Dominik},
  title =	{{Incremental and Interactive PQ- and PC-Trees}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{84:1--84:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.84},
  URN =		{urn:nbn:de:0030-drops-232365},
  doi =		{10.4230/LIPIcs.SoCG.2025.84},
  annote =	{Keywords: PQ trees, PC trees, planarity, consecutive ones problem, interactive exploration}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.18
Improved Circular Dictionary Matching

Authors: Nicola Cotumaccio

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)

Abstract
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back to its first character. The circular dictionary matching problem is motivated by applications in bioinformatics and computational geometry. In 2011, Hon et al. [ISAAC 2011] showed how to efficiently solve circular dictionary matching queries within compressed space by building on Mantaci et al.’s eBWT and Sadakane’s compressed suffix tree. The proposed solution is based on the assumption that the strings in the dictionary are all distinct and non-periodic, no string is a circular rotation of some other string, and the strings in the dictionary have similar lengths. In this paper, we consider arbitrary dictionaries, and we show how to solve circular dictionary matching queries in O((m + occ) log n) time within compressed space using n log σ (1 + o(1)) + O(n) + O(d log n) bits, where n is the total length of the dictionary, m is the length of the pattern, occ is the number of occurrences, d is the number of strings in the dictionary and σ is the size of the alphabet. Our solution is based on an extension of the suffix array to arbitrary dictionaries and a sampling mechanism for the LCP array of a dictionary inspired by recent results in graph indexing and compression.
Cite as

Nicola Cotumaccio. Improved Circular Dictionary Matching. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 18:1-18:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cotumaccio:LIPIcs.CPM.2025.18,
  author =	{Cotumaccio, Nicola},
  title =	{{Improved Circular Dictionary Matching}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{18:1--18:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.18},
  URN =		{urn:nbn:de:0030-drops-231122},
  doi =		{10.4230/LIPIcs.CPM.2025.18},
  annote =	{Keywords: Circular pattern matching, dictionary matching, suffix tree, compressed suffix tree, suffix array, LCP array, Burrows-Wheeler Transform, FM-index}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.58
The Computational Complexity of Factored Graphs

Authors: Shreya Gupta, Boyang Huang, Russell Impagliazzo, Stanley Woo, and Christopher Ye

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract
While graphs and abstract data structures can be large and complex, practical instances are often regular or highly structured. If the instance has sufficient structure, we might hope to compress the object into a more succinct representation. An efficient algorithm (with respect to the compressed input size) could then lead to more efficient computations than algorithms taking the explicit, uncompressed object as input. This leads to a natural question: when does knowing the input instance has a more succinct representation make computation easier? We initiate the study of the computational complexity of problems on factored graphs: graphs that are given as a formula of products and unions on smaller graphs. For any graph problem, we define a parameterized version that takes factored graphs as input, parameterized by the number of (smaller) ordinary graphs used to construct the factored graph. In this setting, we characterize the parameterized complexity of several natural graph problems, exhibiting a variety of complexities. We show that a decision version of lexicographically first maximal independent set is XP-complete, and therefore unconditionally not fixed-parameter tractable (FPT). On the other hand, we show that clique counting is FPT. Finally, we show that reachability is XNL-complete. Moreover, XNL is contained in FPT if and only if NL is contained in some fixed polynomial time.
Cite as

Shreya Gupta, Boyang Huang, Russell Impagliazzo, Stanley Woo, and Christopher Ye. The Computational Complexity of Factored Graphs. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 58:1-58:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gupta_et_al:LIPIcs.ITCS.2025.58,
  author =	{Gupta, Shreya and Huang, Boyang and Impagliazzo, Russell and Woo, Stanley and Ye, Christopher},
  title =	{{The Computational Complexity of Factored Graphs}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{58:1--58:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.58},
  URN =		{urn:nbn:de:0030-drops-226865},
  doi =		{10.4230/LIPIcs.ITCS.2025.58},
  annote =	{Keywords: Parameterized Complexity, Fine-grained complexity, Fixed-parameter tractability, Graph algorithms}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.WABI.2018
LIPIcs, Volume 113, WABI'18, Complete Volume

Authors: Laxmi Parida and Esko Ukkonen

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
LIPIcs, Volume 113, WABI'18, Complete Volume
Cite as

18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@Proceedings{parida_et_al:LIPIcs.WABI.2018,
  title =	{{LIPIcs, Volume 113, WABI'18, Complete Volume}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018},
  URN =		{urn:nbn:de:0030-drops-97246},
  doi =		{10.4230/LIPIcs.WABI.2018},
  annote =	{Keywords: Applied computing, Bioinformatics, Theory of computation, Design and analysis of algorithms, Mathematics of computing, Probabilistic inference problem}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.WABI.2018.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Laxmi Parida and Esko Ukkonen

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as

18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{parida_et_al:LIPIcs.WABI.2018.0,
  author =	{Parida, Laxmi and Ukkonen, Esko},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{0:i--0:xvi},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.0},
  URN =		{urn:nbn:de:0030-drops-93028},
  doi =		{10.4230/LIPIcs.WABI.2018.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.1
A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models

Authors: Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
Elemental balance, the property of having the same number of each type of atom on both sides of the equation, is a fundamental feature of chemical reactions. In metabolic network models, this property is typically verified on a reaction-by-reaction basis. In this paper we show how violations of elemental balance can be efficiently detected in an entire network, without the need for specifying the chemical formula of each of the metabolites, which enhances a modeler's ability to automatically verify that their model satisfies elemental balance. Our method makes use of duality theory, linear programming, and mixed integer linear programming, and runs efficiently on genome-scale metabolic networks (GSMNs). We detect elemental balance violations in 40 out of 84 metabolic network models in the BiGG database. We also identify a short list of reactions that are candidates for being elementally imbalanced. Out of these candidates, nearly half turn out to be truly imbalanced reactions, and the rest can be seen as witnesses of elemental balance violations elsewhere in the network. The majority of these violations involve a proton imbalance, a known challenge of metabolic network reconstruction. Our approach is efficient, easy to use and powerful. It can be helpful to metabolic network modelers during model verification. Our methods are fully integrated into the MONGOOSE software suite and are available at https://github.com/WGS-TB/MongooseGUI3.
Cite as

Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch. A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 1:1-1:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{zabeti_et_al:LIPIcs.WABI.2018.1,
  author =	{Zabeti, Hooman and Stephen, Tamon and Berger, Bonnie and Chindelevitch, Leonid},
  title =	{{A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{1:1--1:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.1},
  URN =		{urn:nbn:de:0030-drops-93034},
  doi =		{10.4230/LIPIcs.WABI.2018.1},
  annote =	{Keywords: Metabolic network analysis, elemental imbalance, linear programming, model verification}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.2
Prefix-Free Parsing for Building Big BWTs

Authors: Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such indexes is a challenge. Fortunately, many of these genomic databases are highly-repetitive - a characteristic that can be exploited and enable the computation of the Burrows-Wheeler Transform (BWT), which underlies many popular indexes. In this paper, we introduce a preprocessing algorithm, referred to as prefix-free parsing, that takes a text T as input, and in one-pass generates a dictionary D and a parse P of T with the property that the BWT of T can be constructed from D and P using workspace proportional to their total size and O(|T|)-time. Our experiments show that D and P are significantly smaller than T in practice, and thus, can fit in a reasonable internal memory even when T is very large. Therefore, prefix-free parsing eases BWT construction, which is pertinent to many bioinformatics applications.
Cite as

Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 2:1-2:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{boucher_et_al:LIPIcs.WABI.2018.2,
  author =	{Boucher, Christina and Gagie, Travis and Kuhnle, Alan and Manzini, Giovanni},
  title =	{{Prefix-Free Parsing for Building Big BWTs}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{2:1--2:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.2},
  URN =		{urn:nbn:de:0030-drops-93044},
  doi =		{10.4230/LIPIcs.WABI.2018.2},
  annote =	{Keywords: Burrows-Wheeler Transform, prefix-free parsing, compression-aware algorithms, genomic databases}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.3
Detecting Mutations by eBWT

Authors: Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts how many copies of any nucleotide are expected inside each such cluster, and how an elegant and precise LCP array based procedure can locate these clusters in the eBWT. Our findings are very general and can be applied to a wide range of different problems. In this paper, we consider the case of alignment-free and reference-free SNPs discovery in multiple collections of reads. We note that, in accordance with our theoretical results, SNPs are clustered in the eBWT of the reads collection, and we develop a tool finding SNPs with a simple scan of the eBWT and LCP arrays. Preliminary results show that our method requires much less coverage than state-of-the-art tools while drastically improving precision and sensitivity.
Cite as

Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone. Detecting Mutations by eBWT. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 3:1-3:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{prezza_et_al:LIPIcs.WABI.2018.3,
  author =	{Prezza, Nicola and Pisanti, Nadia and Sciortino, Marinella and Rosone, Giovanna},
  title =	{{Detecting Mutations by eBWT}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{3:1--3:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.3},
  URN =		{urn:nbn:de:0030-drops-93051},
  doi =		{10.4230/LIPIcs.WABI.2018.3},
  annote =	{Keywords: BWT, LCP Array, SNPs, Reference-free, Assembly-free}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.4
Haplotype-aware graph indexes

Authors: Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information to identify which paths are more likely to be correct. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by indexing the 1000 Genomes Project haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.
Cite as

Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin. Haplotype-aware graph indexes. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 4:1-4:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{siren_et_al:LIPIcs.WABI.2018.4,
  author =	{Sir\'{e}n, Jouni and Garrison, Erik and Novak, Adam M. and Paten, Benedict J. and Durbin, Richard},
  title =	{{Haplotype-aware graph indexes}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{4:1--4:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.4},
  URN =		{urn:nbn:de:0030-drops-93060},
  doi =		{10.4230/LIPIcs.WABI.2018.4},
  annote =	{Keywords: FM-indexes, variation graphs, haplotypes}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.5
Reconciling Multiple Genes Trees via Segmental Duplications and Losses

Authors: Riccardo Dondi, Manuel Lafond, and Celine Scornavacca

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost delta and lambda, respectively. We show that the problem is polynomial-time solvable when delta <= lambda (via LCA-mapping), while if delta > lambda the problem is NP-hard, even when lambda = 0 and a single gene tree is given, solving a long standing open problem on the complexity of the reconciliation problem. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are delta/lambda and the number d of segmental duplications, of time complexity O(ceil[delta/lambda]^d * n * delta/lambda). Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or refute hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.
Cite as

Riccardo Dondi, Manuel Lafond, and Celine Scornavacca. Reconciling Multiple Genes Trees via Segmental Duplications and Losses. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{dondi_et_al:LIPIcs.WABI.2018.5,
  author =	{Dondi, Riccardo and Lafond, Manuel and Scornavacca, Celine},
  title =	{{Reconciling Multiple Genes Trees via Segmental Duplications and Losses}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{5:1--5:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.5},
  URN =		{urn:nbn:de:0030-drops-93079},
  doi =		{10.4230/LIPIcs.WABI.2018.5},
  annote =	{Keywords: Gene trees/species tree reconciliation, phylogenetics, computational complexity, fixed-parameter algorithms}
}
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