7 Search Results for "Zhang, Louxin"

Document
DOI: 10.4230/LIPIcs.WABI.2024.2
On the Complexity of the Median and Closest Permutation Problems

Authors: Luís Cunha, Ignasi Sau, and Uéverton Souza

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

Abstract
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on genome rearrangement measures. Many pairwise rearrangement distances have been proposed, based on finding the minimum number of rearrangement events to transform one genome into the other, using some predefined operation. When more than two genomes are considered, we have the more challenging problem of rearrangement-based phylogeny reconstruction. Given a set of genomes and a distance notion, there are at least two natural ways to define the "target" genome. On the one hand, finding a genome that minimizes the sum of the distances from this to any other, called the median genome. On the other hand, finding a genome that minimizes the maximum distance to any other, called the closest genome. Considering genomes as permutations of distinct integers, some distance metrics have been extensively studied. We investigate the median and closest problems on permutations over the following metrics: breakpoint distance, swap distance, block-interchange distance, short-block-move distance, and transposition distance. In biological applications some values are usually very small, such as the solution value d or the number k of input permutations. For each of these metrics and parameters d or k, we analyze the closest and the median problems from the viewpoint of parameterized complexity. We obtain the following results: NP-hardness for finding the median/closest permutation regarding some metrics of distance, even for only k = 3 permutations; Polynomial kernels for the problems of finding the median permutation of all studied metrics, considering the target distance d as parameter; NP-hardness result for finding the closest permutation by short-block-moves; FPT algorithms and infeasibility of polynomial kernels for finding the closest permutation for some metrics when parameterized by the target distance d.
Cite as

Luís Cunha, Ignasi Sau, and Uéverton Souza. On the Complexity of the Median and Closest Permutation Problems. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cunha_et_al:LIPIcs.WABI.2024.2,
  author =	{Cunha, Lu{\'\i}s and Sau, Ignasi and Souza, U\'{e}verton},
  title =	{{On the Complexity of the Median and Closest Permutation Problems}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{2:1--2:23},
  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.2024.2},
  URN =		{urn:nbn:de:0030-drops-206468},
  doi =		{10.4230/LIPIcs.WABI.2024.2},
  annote =	{Keywords: Median problem, Closest problem, Genome rearrangements, Parameterized complexity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.3
An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree

Authors: Yao-ban Chan

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

Abstract
The phylogenies of species and the genes they contain are similar but distinct, due to evolutionary events that affect genes but do not create new species. These events include gene duplication and loss, but also paralog exchange (non-allelic homologous recombination), where duplicate copies of a gene recombine. To account for paralog exchange, the evolutionary history of the genes must be represented in the form of a phylogenetic network. We reconstruct the interlinked evolution of the genes and species with reconciliations, which map the gene network into the species tree by explicitly accounting for these events. In previous work, we proposed the problem of reconciling a gene network and a species tree, but did not find an efficient solution for a general gene network. In this paper, we develop such a solution, and prove that it solves the most parsimonious reconciliation problem. Our algorithm is exponential only in the level of the gene network (with a base of 2), and we demonstrate that it is a practical solution through simulations. This allows, for the first time, a fine-grained study of the paralogy/orthology relationship between genes along their sequences.
Cite as

Yao-ban Chan. An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chan:LIPIcs.WABI.2024.3,
  author =	{Chan, Yao-ban},
  title =	{{An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{3:1--3:17},
  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.2024.3},
  URN =		{urn:nbn:de:0030-drops-206472},
  doi =		{10.4230/LIPIcs.WABI.2024.3},
  annote =	{Keywords: Reconciliation, recombination, paralog exchange, phylogenetic network, gene duplication, gene loss}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.9
Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation

Authors: Tsuyoshi Urata, Manato Yokoyama, and Momoko Hayamizu

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

Abstract
The 𝒞-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired class 𝒞, and to find such an orientation if one exists. The problem can arise when visualising evolutionary data, for example, because popular phylogenetic network reconstruction methods such as Neighbor-Net are distance-based and thus inevitably produce undirected graphs. The complexity of 𝒞-Orientation remains open for many classes 𝒞, including binary tree-child networks, and practical methods are still lacking. In this paper, we propose an exponential but practically efficient FPT algorithm for 𝒞-Orientation, which is parameterised by the reticulation number and the maximum size of minimal basic cycles used in the computation. We also present a very fast heuristic for Tree-Child Orientation. To evaluate the empirical performance of the proposed methods, we compared their accuracy and execution time for Tree-Child Orientation with those of an exponential time 𝒞-orientation algorithm from the literature. Our experiments show that the proposed exact algorithm is significantly faster than the state-of-the-art exponential time algorithm. The proposed heuristic runs even faster but the accuracy decreases as the reticulation number increases.
Cite as

Tsuyoshi Urata, Manato Yokoyama, and Momoko Hayamizu. Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{urata_et_al:LIPIcs.WABI.2024.9,
  author =	{Urata, Tsuyoshi and Yokoyama, Manato and Hayamizu, Momoko},
  title =	{{Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{9:1--9:17},
  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.2024.9},
  URN =		{urn:nbn:de:0030-drops-206531},
  doi =		{10.4230/LIPIcs.WABI.2024.9},
  annote =	{Keywords: Phylogenetic Networks, Tree-Child Networks, Graph Orientation Algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.16
Finding Maximum Common Contractions Between Phylogenetic Networks

Authors: Bertrand Marchand, Nadia Tahiri, Olivier Tremblay-Savard, and Manuel Lafond

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

Abstract
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations connect the space of all phylogenetic networks on the same set of leaves, even if we forbid contractions that create cycles. This allows to define an operational distance on this space, as the minimum number of contractions and expansions required to transform one network into another. We highlight the difference between this distance and the computation of the maximum common contraction between two networks. Given its ability to outline a common structure between them, which can provide valuable biological insights, we study the algorithmic aspects of the latter. We first prove that computing a maximum common contraction between two networks is NP-hard, even when the maximum degree, the size of the common contraction, or the number of leaves is bounded. We also provide lower bounds to the problem based on the Exponential-Time Hypothesis. Nonetheless, we do provide a polynomial-time algorithm for weakly galled trees, a generalization of galled trees.
Cite as

Bertrand Marchand, Nadia Tahiri, Olivier Tremblay-Savard, and Manuel Lafond. Finding Maximum Common Contractions Between Phylogenetic Networks. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 16:1-16:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{marchand_et_al:LIPIcs.WABI.2024.16,
  author =	{Marchand, Bertrand and Tahiri, Nadia and Tremblay-Savard, Olivier and Lafond, Manuel},
  title =	{{Finding Maximum Common Contractions Between Phylogenetic Networks}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{16:1--16:24},
  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.2024.16},
  URN =		{urn:nbn:de:0030-drops-206606},
  doi =		{10.4230/LIPIcs.WABI.2024.16},
  annote =	{Keywords: Phylogenetic networks, contractions, algorithms, weakly galled trees}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.20
The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees

Authors: Alitzel López Sánchez, José Antonio Ramírez-Rafael, Alejandro Flores-Lamas, Maribel Hernández-Rosales, and Manuel Lafond

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

Abstract
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies differences in the topology of reconciled gene trees, but also considers discrepancies in predicted ancestral gene-species maps and speciation/duplication events, offering a refinement of existing metrics such as Robinson-Foulds (RF) and their labeled extensions LRF and ELRF. A tunable parameter α also allows users to adjust the balance between its species map and event labeling components. We show that PLR can be computed in linear time and that it is a semi-metric. We also discuss the diameters of reconciled gene tree measures, which are important in practice for normalization, and provide initial bounds on PLR, LRF, and ELRF. To validate PLR, we simulate reconciliations and perform comparisons with LRF and ELRF. The results show that PLR provides a more evenly distributed range of distances, making it less susceptible to overestimating differences in the presence of small topological changes, while at the same time being computationally efficient. Our findings suggest that the theoretical diameter is rarely reached in practice. The PLR measure advances phylogenetic reconciliation by combining theoretical rigor with practical applicability. Future research will refine its mathematical properties, explore its performance on different tree types, and integrate it with existing bioinformatics tools for large-scale evolutionary analyses. The open source code is available at: https://pypi.org/project/parle/.
Cite as

Alitzel López Sánchez, José Antonio Ramírez-Rafael, Alejandro Flores-Lamas, Maribel Hernández-Rosales, and Manuel Lafond. The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{lopezsanchez_et_al:LIPIcs.WABI.2024.20,
  author =	{L\'{o}pez S\'{a}nchez, Alitzel and Ram{\'\i}rez-Rafael, Jos\'{e} Antonio and Flores-Lamas, Alejandro and Hern\'{a}ndez-Rosales, Maribel and Lafond, Manuel},
  title =	{{The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{20:1--20:21},
  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.2024.20},
  URN =		{urn:nbn:de:0030-drops-206645},
  doi =		{10.4230/LIPIcs.WABI.2024.20},
  annote =	{Keywords: Reconciliation, gene trees, species trees, evolutionary scenarios}
}
Document
DOI: 10.4230/LIPIcs.AofA.2024.8
Galled Tree-Child Networks

Authors: Yu-Sheng Chang, Michael Fuchs, and Guan-Ru Yu

Published in: LIPIcs, Volume 302, 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)

Abstract
We propose the class of galled tree-child networks which is obtained as intersection of the classes of galled networks and tree-child networks. For the latter two classes, (asymptotic) counting results and stochastic results have been proved with very different methods. We show that a counting result for the class of galled tree-child networks follows with similar tools as used for galled networks, however, the result has a similar pattern as the one for tree-child networks. In addition, we also consider the (suitably scaled) numbers of reticulation nodes of random galled tree-child networks and show that they are asymptotically normal distributed. This is in contrast to the limit laws of the corresponding quantities for galled networks and tree-child networks which have been both shown to be discrete.
Cite as

Yu-Sheng Chang, Michael Fuchs, and Guan-Ru Yu. Galled Tree-Child Networks. In 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 302, pp. 8:1-8:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chang_et_al:LIPIcs.AofA.2024.8,
  author =	{Chang, Yu-Sheng and Fuchs, Michael and Yu, Guan-Ru},
  title =	{{Galled Tree-Child Networks}},
  booktitle =	{35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)},
  pages =	{8:1--8:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-329-4},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{302},
  editor =	{Mailler, C\'{e}cile and Wild, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AofA.2024.8},
  URN =		{urn:nbn:de:0030-drops-204439},
  doi =		{10.4230/LIPIcs.AofA.2024.8},
  annote =	{Keywords: Phylogenetic Network, galled Network, tree-child Network, asymptotic Enumeration, Limit Law, Lagrange Inversion}
}
Document
DOI: 10.4230/LIPIcs.WABI.2020.14
The Bourque Distances for Mutation Trees of Cancers

Authors: Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang

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

Abstract
Mutation trees are rooted trees of arbitrary node degree in which each node is labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutational history of tumours. Classical tree metrics such as the popular Robinson - Foulds distance are of limited use for the comparison of mutation trees. One reason is that mutation trees inferred with different methods or for different patients often contain different sets of mutation labels. Here, we generalize the Robinson - Foulds distance into a set of distance metrics called Bourque distances for comparing mutation trees. A connection between the Robinson - Foulds distance and the nearest neighbor interchange distance is also presented.
Cite as

Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang. The Bourque Distances for Mutation Trees of Cancers. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 14:1-14:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{jahn_et_al:LIPIcs.WABI.2020.14,
  author =	{Jahn, Katharina and Beerenwinkel, Niko and Zhang, Louxin},
  title =	{{The Bourque Distances for Mutation Trees of Cancers}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{14:1--14:22},
  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.2020.14},
  URN =		{urn:nbn:de:0030-drops-128039},
  doi =		{10.4230/LIPIcs.WABI.2020.14},
  annote =	{Keywords: mutation trees, clonal trees, tree distance, phylogenetic trees, tree metric, Robinson - Foulds distance, Bourque distance}
}
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