32 Search Results for "El-Kebir, Mohammed"

Volume

LIPIcs, Volume 201

21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

WABI 2021, August 2-4, 2021, Virtual Conference

Editors: Alessandra Carbone and Mohammed El-Kebir

Document
DOI: 10.4230/LIPIcs.ESA.2025.55
Safe Sequences via Dominators in DAGs for Path-Covering Problems

Authors: Francisco Sena, Romeo Rizzi, and Alexandru I. Tomescu

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
A path-covering problem on a directed acyclic graph (DAG) requires finding a set of source-to-sink paths that cover all the nodes, all the arcs, or subsets thereof, and additionally they are optimal with respect to some function. In this paper we study safe sequences of nodes or arcs, namely sequences that appear in some path of every path cover of a DAG. We show that safe sequences admit a simple characterization via cutnodes. Moreover, we establish a connection between maximal safe sequences and leaf-to-root paths in the source- and sink-dominator trees of the DAG, which may be of independent interest in the extensive literature on dominators. With dominator trees, safe sequences admit an O(n)-size representation and a linear-time output-sensitive enumeration algorithm running in time O(m + o), where n and m are the number of nodes and arcs, respectively, and o is the total length of the maximal safe sequences. We then apply maximal safe sequences to simplify Integer Linear Programs (ILPs) for two path-covering problems, LeastSquares and MinPathError, which are at the core of RNA transcript assembly problems from bioinformatics. On various datasets, maximal safe sequences can be computed in under 0.1 seconds per graph, on average, and ILP solvers whose search space is reduced in this manner exhibit significant speed-ups. For example on graphs with a large width, average speed-ups are in the range 50-250× for MinPathError and in the range 80-350× for LeastSquares. Optimizing ILPs using safe sequences can thus become a fast building block of practical RNA transcript assembly tools, and more generally, of path-covering problems.
Cite as

Francisco Sena, Romeo Rizzi, and Alexandru I. Tomescu. Safe Sequences via Dominators in DAGs for Path-Covering Problems. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 55:1-55:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sena_et_al:LIPIcs.ESA.2025.55,
  author =	{Sena, Francisco and Rizzi, Romeo and Tomescu, Alexandru I.},
  title =	{{Safe Sequences via Dominators in DAGs for Path-Covering Problems}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{55:1--55:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.55},
  URN =		{urn:nbn:de:0030-drops-245230},
  doi =		{10.4230/LIPIcs.ESA.2025.55},
  annote =	{Keywords: directed acyclic graph, path cover, dominator tree, integer linear programming, least squares, minimum path error}
}
Artifact
Software
DOI: 10.4230/artifacts.24317
Dolphyin

Authors: Daniel W. Feng and Mohammed El-Kebir

Abstract
Cite as

Daniel W. Feng, Mohammed El-Kebir. Dolphyin (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@misc{dagstuhl-artifact-24317,
   title = {{Dolphyin}}, 
   author = {Feng, Daniel W. and El-Kebir, Mohammed},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:dir:61c0cd5f22da3a8e10cc6fdac70dd7d93ecb6be5;origin=https://github.com/elkebir-group/Dolphyin;visit=swh:1:snp:40995a37bef2ff3ba9886e82d6e8c8f3e0253b9a;anchor=swh:1:rev:fbf400f4100a33ee4aeb47286cefb957abd9b77d}{\texttt{swh:1:dir:61c0cd5f22da3a8e10cc6fdac70dd7d93ecb6be5}} (visited on 2025-08-15)},
   url = {https://github.com/elkebir-group/Dolphyin},
   doi = {10.4230/artifacts.24317},
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.9
Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer

Authors: Daniel W. Feng and Mohammed El-Kebir

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Several recent cancer phylogeny inference methods have used the k-Dollo evolutionary model for single-nucleotide variants. Specifically, in this problem one is given an m × n binary matrix B and seeks a rooted tree T with m leaves that correspond to the m rows of B, and each node of T is labeled by a binary state for each of the n characters subject to the restriction that each character is gained at most once (0-to-1 transition) and subsequently lost at most k times (1-to-0 transitions). The 1-Dollo variant, also known as the persistent perfect phylogeny where one is restricted to at most k = 1 losses per character, has been studied extensively, but its hardness remains an open question. Here, we prove that the 1-Dollo Linear Phylogeny (1DLP) problem, where we additionally require the resulting 1-Dollo phylogeny T to be linear, is equivalent to verifying whether the input matrix B adheres to the Consecutive Ones Property (C1P), which can be solved in polynomial time. Due to the equivalence, several known NP-hardness results for relevant variants of C1P carry over to 1DLP, including the minimization of false negatives (0-to-1 modifications to the input matrix B) or the allowance of 2 gains and 2 losses. We furthermore show how we can recursively decompose any, not necessarily linear, 1-Dollo phylogeny T into several 1-Dollo linear phylogenies, connected by matching branching points. We extend this characterization to matrices B that admit 1-Dollo phylogenies, giving necessary and sufficient conditions for the existence of a novel decomposition of B into several submatrices and corresponding branching points. This decomposition forms the basis of Dolphyin, a new exponential-time algorithm for inferring 1-Dollo phylogenies that efficiently leverages the determination of linear 1-Dollo phylogenies as a subroutine. Dolphyin can also be applied to input matrices B with false negatives. We demonstrate that Dolphyin is runtime-competitive with a previous integer linear programming based algorithm SPhyR on simulated datasets. We additionally analyze simulated datasets with false negative errors and find that in the median case, Dolphyin infers 1-Dollo phylogenies with inferred error rates at or below the ground truth rate. Finally, we apply Dolphyin to 99 acute myeloid leukemia single-cell sequencing datasets, finding that the majority of the cancers can be explained by 1-Dollo phylogenies with false negative error rates in line with the used sequencing technology. Availability. Dolphyin is available at: https://github.com/elkebir-group/Dolphyin.
Cite as

Daniel W. Feng and Mohammed El-Kebir. Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 9:1-9:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{feng_et_al:LIPIcs.WABI.2025.9,
  author =	{Feng, Daniel W. and El-Kebir, Mohammed},
  title =	{{Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{9:1--9:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.9},
  URN =		{urn:nbn:de:0030-drops-239356},
  doi =		{10.4230/LIPIcs.WABI.2025.9},
  annote =	{Keywords: Intra-tumor heterogeneity, persistent perfect phylogeny, consecutive ones property, combinatorics}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.5
Improved Algorithms for Bi-Partition Function Computation

Authors: John D. Bridgers, Jan Hoinka, S. Cenk Sahinalp, Salem Malikic, Teresa M. Przytycka, and Funda Ergun

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
The evolutionary history of a tumor, inferred from single-cell sequencing data, is typically represented as a tree in which each subtree corresponds to a clade of cells seeded by a specific set of mutations. Traditional methods typically identify a single most likely tree for downstream analyses, such as detecting driver mutations, studying mutation co-occurrence patterns and identifying common evolutionary trajectories. However, the reliability of such inferred trees, particularly their topology, clade composition, and mutational placements, often remains uncertain. To quantify this uncertainty, the concept of a Bi-partition Function was recently introduced, providing a probabilistic measure of how reliably a mutation seeds a given clade of cells. The single available algorithm for estimating the Bi-partition Function relies on simplifying assumptions and uses sampling for limited exploration of the tree-space. In this paper, we introduce the first exact algorithm for computing the Bi-partition Function. Our algorithm scales linearly with the number of mutations but exhibits super-exponential complexity with respect to the number of cells. Despite this complexity, it establishes crucial ground truth values, essential for accurately benchmarking and validating approximate methods. Additionally, we present a GPU-accelerated version of the available sampling-based algorithm, significantly boosting the computational performance through large-scale parallelization, enabling more accurate Bi-partition Function estimates via deeper exploration of the tree spaces. We compare our methods on synthetic datasets, demonstrating that especially when the number of mutations sufficiently exceed the number of cells, our GPU-accelerated sampling algorithm closely approximates the exact ground truth values.
Cite as

John D. Bridgers, Jan Hoinka, S. Cenk Sahinalp, Salem Malikic, Teresa M. Przytycka, and Funda Ergun. Improved Algorithms for Bi-Partition Function Computation. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 5:1-5:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bridgers_et_al:LIPIcs.WABI.2025.5,
  author =	{Bridgers, John D. and Hoinka, Jan and Sahinalp, S. Cenk and Malikic, Salem and Przytycka, Teresa M. and Ergun, Funda},
  title =	{{Improved Algorithms for Bi-Partition Function Computation}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{5:1--5:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.5},
  URN =		{urn:nbn:de:0030-drops-239318},
  doi =		{10.4230/LIPIcs.WABI.2025.5},
  annote =	{Keywords: Tumor Evolution, Bi-partition Function, Single-Cell Sequencing, Algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.7
Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees

Authors: Yuanyuan Qi and Mohammed El-Kebir

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

Abstract
Cancer phylogenies are key to understanding tumor evolution. There exist many important downstream analyses that take as input a single or a small number of trees. However, due to uncertainty, one typically infers many, equally-plausible phylogenies from bulk DNA sequencing data of tumors. We introduce Sapling, a heuristic method to solve the Backbone Tree Inference from Reads problem, which seeks a small set of backbone trees on a smaller subset of mutations that collectively summarize the entire solution space. Sapling also includes a greedy algorithm to solve the Backbone Tree Expansion from Reads problem, which aims to expand an inferred backbone tree into a full tree. We prove that both problems are NP-hard. On simulated and real data, we demonstrate that Sapling is capable of inferring high-quality backbone trees that adequately summarize the solution space and that can be expanded into full trees.
Cite as

Yuanyuan Qi and Mohammed El-Kebir. Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{qi_et_al:LIPIcs.WABI.2024.7,
  author =	{Qi, Yuanyuan and El-Kebir, Mohammed},
  title =	{{Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{7:1--7:19},
  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.2024.7},
  URN =		{urn:nbn:de:0030-drops-206518},
  doi =		{10.4230/LIPIcs.WABI.2024.7},
  annote =	{Keywords: Cancer, intra-tumor heterogeneity, consensus, maximum agreement}
}
Document
DOI: 10.4230/LIPIcs.WABI.2023.9
Inferring Temporally Consistent Migration Histories

Authors: Mrinmoy Saha Roddur, Sagi Snir, and Mohammed El-Kebir

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

Abstract
Not only do many biological populations undergo evolution, but population members may also migrate from one location to another. For example, tumor cells may migrate from the primary tumor and seed a new metastasis, and pathogens may migrate from one host to another. One may represent a population’s migration history by labeling the vertices of a given phylogeny T with locations such that an edge incident to vertices with distinct locations represents a migration. Additionally, in some biological populations, taxa from distinct lineages may comigrate from one location to another in a single event, a phenomenon known as a comigration. Here, we show that a previous problem statement for inferring migration histories that are parsimonious in terms of migrations and comigrations may lead to temporally inconsistent solutions. To remedy this deficiency, we introduce precise definitions of temporal consistency of comigrations in a phylogeny, leading to three successive problems. First, we formulate the Temporally Consistent Comigrations (TCC) problem to check if a set of comigrations is temporally consistent and provide a linear time algorithm for solving this problem. Second, we formulate the Parsimonious Consistent Comigration (PCC) problem, which aims to find comigrations given a location labeling of a phylogeny. We show that PCC is NP-hard. Third, we formulate the Parsimonious Consistent Comigration History (PCCH) problem, which infers the migration history given a phylogeny and locations of its extant vertices only. We show that PCCH is NP-hard as well. On the positive side, we propose integer linear programming models to solve the PCC and PCCH problems. We apply our approach to real and simulated data.
Cite as

Mrinmoy Saha Roddur, Sagi Snir, and Mohammed El-Kebir. Inferring Temporally Consistent Migration Histories. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 9:1-9:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{roddur_et_al:LIPIcs.WABI.2023.9,
  author =	{Roddur, Mrinmoy Saha and Snir, Sagi and El-Kebir, Mohammed},
  title =	{{Inferring Temporally Consistent Migration Histories}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{9:1--9:22},
  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.2023.9},
  URN =		{urn:nbn:de:0030-drops-186357},
  doi =		{10.4230/LIPIcs.WABI.2023.9},
  annote =	{Keywords: Metastasis, Migration, Integer Linear Programming, Maximum parsimony}
}
Document
DOI: 10.4230/LIPIcs.WABI.2023.21
Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design

Authors: Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir

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

Abstract
The problem of designing an RNA sequence v that encodes for a given target protein w plays an important role in messenger RNA (mRNA) vaccine design. Due to codon degeneracy, there exist exponentially many RNA sequences for a single target protein. These candidate RNA sequences may adopt different secondary structure conformations with varying minimum free energy (MFE), affecting their thermodynamic stability and consequently mRNA half-life. In addition, species-specific codon usage bias, as measured by the codon adaptation index (CAI), also plays an essential role in translation efficiency. While previous works have focused on optimizing either MFE or CAI, more recent works have shown the merits of optimizing both objectives. Importantly, there is a trade-off between MFE and CAI, i.e. optimizing one objective is at the expense of the other. Here, we formulate the Pareto Optimal RNA Design problem, seeking the set of Pareto optimal solutions for which no other solution exists that is better in terms of both MFE and CAI. We introduce DERNA (DEsign RNA), which uses the weighted sum method to enumerate the Pareto front by optimizing convex combinations of both objectives. DERNA uses dynamic programming to solve each convex combination in O(|w|³) time and O(|w|²) space. Compared to a previous approach that only optimizes MFE, we show on a benchmark dataset that DERNA obtains solutions with identical MFE but superior CAI. Additionally, we show that DERNA matches the performance in terms of solution quality of LinearDesign, a recent approach that similarly seeks to balance MFE and CAI. Finally, we demonstrate our method’s potential for mRNA vaccine design using SARS-CoV-2 spike as the target protein.
Cite as

Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir. Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 21:1-21:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{gu_et_al:LIPIcs.WABI.2023.21,
  author =	{Gu, Xinyu and Qi, Yuanyuan and El-Kebir, Mohammed},
  title =	{{Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{21:1--21:20},
  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.2023.21},
  URN =		{urn:nbn:de:0030-drops-186479},
  doi =		{10.4230/LIPIcs.WABI.2023.21},
  annote =	{Keywords: Multi-objective optimization, dynamic programming, RNA sequence design, reverse translation, mRNA vaccine design}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.WABI.2021
LIPIcs, Volume 201, WABI 2021, Complete Volume

Authors: Alessandra Carbone and Mohammed El-Kebir

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
LIPIcs, Volume 201, WABI 2021, Complete Volume
Cite as

21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 1-400, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@Proceedings{carbone_et_al:LIPIcs.WABI.2021,
  title =	{{LIPIcs, Volume 201, WABI 2021, Complete Volume}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{1--400},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021},
  URN =		{urn:nbn:de:0030-drops-143520},
  doi =		{10.4230/LIPIcs.WABI.2021},
  annote =	{Keywords: LIPIcs, Volume 201, WABI 2021, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.WABI.2021.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Alessandra Carbone and Mohammed El-Kebir

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

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

21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 0:i-0:x, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{carbone_et_al:LIPIcs.WABI.2021.0,
  author =	{Carbone, Alessandra and El-Kebir, Mohammed},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{0:i--0:x},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.0},
  URN =		{urn:nbn:de:0030-drops-143531},
  doi =		{10.4230/LIPIcs.WABI.2021.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.1
The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard

Authors: Matthew LeMay, Yi-Chieh Wu, and Ran Libeskind-Hadas

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics.
Cite as

Matthew LeMay, Yi-Chieh Wu, and Ran Libeskind-Hadas. The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 1:1-1:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{lemay_et_al:LIPIcs.WABI.2021.1,
  author =	{LeMay, Matthew and Wu, Yi-Chieh and Libeskind-Hadas, Ran},
  title =	{{The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{1:1--1:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.1},
  URN =		{urn:nbn:de:0030-drops-143546},
  doi =		{10.4230/LIPIcs.WABI.2021.1},
  annote =	{Keywords: phylogenetics, reconciliation, deep coalescence, hybridization, NP-hardness}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.2
Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence

Authors: Yoshiki Nakagawa, Satsuya Ohata, and Kana Shimizu

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
Finding a similar substring that commonly appears in query and database sequences is an essential task for genome data analysis. This study proposes a secure two-party variable-length string search protocol based on secret sharing. The unique feature of our protocol is that time, communication, and round complexities are not dependent on the database length N, after the query input. This property brings dramatic performance improvements in search time, since N is usually quite large in an actual genome database, and the same database is repeatedly used for many queries. Our concept hinges on a technique that efficiently applies the compressed full-text index (FOCS 2000) for a secret-sharing scheme. We conducted an experiment using a human genomic sequence with the length of 10 million as the database and a query with the length of 100 and found that the query response time of our protocol was at least three orders of magnitude faster than a well-designed baseline protocol under the realistic computation/network environment.
Cite as

Yoshiki Nakagawa, Satsuya Ohata, and Kana Shimizu. Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{nakagawa_et_al:LIPIcs.WABI.2021.2,
  author =	{Nakagawa, Yoshiki and Ohata, Satsuya and Shimizu, Kana},
  title =	{{Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{2:1--2:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.2},
  URN =		{urn:nbn:de:0030-drops-143552},
  doi =		{10.4230/LIPIcs.WABI.2021.2},
  annote =	{Keywords: Private Genome Sequence Search, Secure Multiparty Computation, Secret Sharing, FM-index, Suffix Tree, Maximal Exact Match}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.3
Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

Authors: Yishu Wang, Arnaud Mary, Marie-France Sagot, and Blerina Sinaimeri

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
Cophylogeny reconciliation is a powerful method for analyzing host-parasite (or host-symbiont) co-evolution. It models co-evolution as an optimization problem where the set of all optimal solutions may represent different biological scenarios which thus need to be analyzed separately. Despite the significant research done in the area, few approaches have addressed the problem of helping the biologist deal with the often huge space of optimal solutions. In this paper, we propose a new approach to tackle this problem. We introduce three different criteria under which two solutions may be considered biologically equivalent, and then we propose polynomial-delay algorithms that enumerate only one representative per equivalence class (without listing all the solutions). Our results are of both theoretical and practical importance. Indeed, as shown by the experiments, we are able to significantly reduce the space of optimal solutions while still maintaining important biological information about the whole space.
Cite as

Yishu Wang, Arnaud Mary, Marie-France Sagot, and Blerina Sinaimeri. Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{wang_et_al:LIPIcs.WABI.2021.3,
  author =	{Wang, Yishu and Mary, Arnaud and Sagot, Marie-France and Sinaimeri, Blerina},
  title =	{{Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{3:1--3:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.3},
  URN =		{urn:nbn:de:0030-drops-143564},
  doi =		{10.4230/LIPIcs.WABI.2021.3},
  annote =	{Keywords: Cophylogeny, Enumeration, Equivalence relation, Dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.4
Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth

Authors: Jason Fan, Skylar Chan, and Rob Patro

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
There has been rapid development of probabilistic models and inference methods for transcript abundance estimation from RNA-seq data. These models aim to accurately estimate transcript-level abundances, to account for different biases in the measurement process, and even to assess uncertainty in resulting estimates that can be propagated to subsequent analyses. The assumed accuracy of the estimates inferred by such methods underpin gene expression based analysis routinely carried out in the lab. Although hyperparameter selection is known to affect the distributions of inferred abundances (e.g. producing smooth versus sparse estimates), strategies for performing model selection in experimental data have been addressed informally at best. Thus, we derive perplexity for evaluating abundance estimates on fragment sets directly. We adapt perplexity from the analogous metric used to evaluate language and topic models and extend the metric to carefully account for corner cases unique to RNA-seq. In experimental data, estimates with the best perplexity also best correlate with qPCR measurements. In simulated data, perplexity is well behaved and concordant with genome-wide measurements against ground truth and differential expression analysis. To our knowledge, our study is the first to make possible model selection for transcript abundance estimation on experimental data in the absence of ground truth.
Cite as

Jason Fan, Skylar Chan, and Rob Patro. Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{fan_et_al:LIPIcs.WABI.2021.4,
  author =	{Fan, Jason and Chan, Skylar and Patro, Rob},
  title =	{{Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{4:1--4:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.4},
  URN =		{urn:nbn:de:0030-drops-143578},
  doi =		{10.4230/LIPIcs.WABI.2021.4},
  annote =	{Keywords: RNA-seq, transcript abundance estimation, model selection}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.5
The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet

Authors: Nicolas Boria, Laurent Gourvès, Vangelis Th. Paschos, and Jérôme Monnot

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
Given two strings A and B such that B is a permutation of A, the max duo-preservation string mapping (MPSM) problem asks to find a mapping π between them so as to preserve a maximum number of duos. A duo is any pair of consecutive characters in a string and it is preserved by π if its two consecutive characters in A are mapped to same two consecutive characters in B. This problem has received a growing attention in recent years, partly as an alternative way to produce approximation algorithms for its minimization counterpart, min common string partition, a widely studied problem due its applications in comparative genomics. Considering this favored field of application with short alphabet, it is surprising that MPSM^𝓁, the variant of MPSM with bounded alphabet, has received so little attention, with a single yet impressive work that provides a 2.67-approximation achieved in O(n) [Brubach, 2018], where n = |A| = |B|. Our work focuses on MPSM^𝓁, and our main contribution is the demonstration that this problem admits a Polynomial Time Approximation Scheme (PTAS) when 𝓁 = O(1). We also provide an alternate, somewhat simpler, proof of NP-hardness for this problem compared with the NP-hardness proof presented in [Haitao Jiang et al., 2012].
Cite as

Nicolas Boria, Laurent Gourvès, Vangelis Th. Paschos, and Jérôme Monnot. The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 5:1-5:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{boria_et_al:LIPIcs.WABI.2021.5,
  author =	{Boria, Nicolas and Gourv\`{e}s, Laurent and Paschos, Vangelis Th. and Monnot, J\'{e}r\^{o}me},
  title =	{{The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{5:1--5:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.5},
  URN =		{urn:nbn:de:0030-drops-143586},
  doi =		{10.4230/LIPIcs.WABI.2021.5},
  annote =	{Keywords: Maximum-Duo Preservation String Mapping, Bounded alphabet, Polynomial Time Approximation Scheme}
}
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