4 Search Results for "El-Mabrouk, Nadia"

Document
DOI: 10.4230/LIPIcs.STACS.2025.64
Cluster Editing on Cographs and Related Classes

Authors: Manuel Lafond, Alitzel López Sánchez, and Weidong Luo

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
In the Cluster Editing problem, sometimes known as (unweighted) Correlation Clustering, we must insert and delete a minimum number of edges to achieve a graph in which every connected component is a clique. Owing to its applications in computational biology, social network analysis, machine learning, and others, this problem has been widely studied for decades and is still undergoing active research. There exist several parameterized algorithms for general graphs, but little is known about the complexity of the problem on specific classes of graphs. Among the few important results in this direction, if only deletions are allowed, the problem can be solved in polynomial time on cographs, which are the P₄-free graphs. However, the complexity of the broader editing problem on cographs is still open. We show that even on a very restricted subclass of cographs, the problem is NP-hard, W[1]-hard when parameterized by the number p of desired clusters, and that time n^o(p/log p) is forbidden under the ETH. This shows that the editing variant is substantially harder than the deletion-only case, and that hardness holds for the many superclasses of cographs (including graphs of clique-width at most 2, perfect graphs, circle graphs, permutation graphs). On the other hand, we provide an almost tight upper bound of time n^O(p), which is a consequence of a more general n^O(cw⋅p) time algorithm, where cw is the clique-width. Given that forbidding P₄s maintains NP-hardness, we look at {P₄, C₄}-free graphs, also known as trivially perfect graphs, and provide a cubic-time algorithm for this class.
Cite as

Manuel Lafond, Alitzel López Sánchez, and Weidong Luo. Cluster Editing on Cographs and Related Classes. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 64:1-64:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lafond_et_al:LIPIcs.STACS.2025.64,
  author =	{Lafond, Manuel and L\'{o}pez S\'{a}nchez, Alitzel and Luo, Weidong},
  title =	{{Cluster Editing on Cographs and Related Classes}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{64:1--64:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2025.64},
  URN =		{urn:nbn:de:0030-drops-228895},
  doi =		{10.4230/LIPIcs.STACS.2025.64},
  annote =	{Keywords: Cluster editing, cographs, parameterized algorithms, clique-width, trivially perfect graphs}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.5
Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer

Authors: Mathieu Gascon and Nadia El-Mabrouk

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
Gene transfer between the mitochondrial and nuclear genome of the same species, called endosymbiotic gene transfer (EGT), is a mechanism which has largely shaped gene contents in eukaryotes since a unique ancestral endosymbiotic event know to be at the origin of all mitochondria. The gene tree-species tree reconciliation model has been recently extended to account for EGTs: given a binary gene tree and a binary species tree, the EndoRex software outputs an optimal DLE-Reconciliation, that is an embedding of the gene tree into the species tree inducing a most parsimonious history of Duplications, Losses and EGT events. Here, we provide the first algorithmic study for DLE-Reconciliation in the case of a multifurcated (non-binary) gene tree. We present a general two-steps method: first, ignoring the mitochondrial-nuclear (or 0-1) labeling of leaves, output a binary resolution minimizing the DL-Reconciliation and, for each resolution, assign a known number of 0s and 1s to the leaves in a way minimizing EGT events. While Step 1 corresponds to the well studied non-binary DL-Reconciliation problem, the complexity of the formal label assignment problem related to Step 2 is unknown. Here, we show it is NP-complete even for a single polytomy (non-binary node). We then provide a heuristic which is exact for the unitary cost of operations, and a polynomial-time algorithm for solving a polytomy in the special case where genes are specific to a single genome (mitochondrial or nuclear) in all but one species.
Cite as

Mathieu Gascon and Nadia El-Mabrouk. Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{gascon_et_al:LIPIcs.WABI.2022.5,
  author =	{Gascon, Mathieu and El-Mabrouk, Nadia},
  title =	{{Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{5:1--5:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.5},
  URN =		{urn:nbn:de:0030-drops-170390},
  doi =		{10.4230/LIPIcs.WABI.2022.5},
  annote =	{Keywords: Reconciliation, Duplication, Endosymbiotic gene transfer, Multifurcated gene tree, Polytomy}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.8
A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation

Authors: Nadia El-Mabrouk and Aïda Ouangraoua

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Due to the key role played by gene trees and species phylogenies in biological studies, it is essential to have as much confidence as possible on the available trees. As phylogenetic tools are error-prone, it is a common task to use a correction method for improving an initial tree. Various correction methods exist. In this paper we focus on those based on the Duplication-Loss reconciliation model. The polytomy resolution approach consists in contracting weakly supported branches and then refining the obtained non-binary tree in a way minimizing a reconciliation distance with the given species tree. On the other hand, the supertree approach takes as input a set of separated subtrees, either obtained for separared orthology groups or by removing the upper branches of an initial tree to a certain level, and amalgamating them in an optimal way preserving the topology of the initial trees. The two classes of problems have always been considered as two separate fields, based on apparently different models. In this paper we give a unifying view showing that these two classes of problems are in fact special cases of a more general problem that we call LabelGTC, whose input includes a 0-1 edge-labelled gene tree to be corrected. Considering a tree as a set of triplets, we also formulate the TripletGTC Problem whose input includes a set of gene triplets that should be preserved in the corrected tree. These two general models allow to unify, understand and compare the principles of the duplication-loss reconciliation-based tree correction approaches. We show that LabelGTC is a special case of TripletGTC. We then develop appropriate algorithms allowing to handle these two general correction problems.
Cite as

Nadia El-Mabrouk and Aïda Ouangraoua. A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 8:1-8:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{elmabrouk_et_al:LIPIcs.WABI.2017.8,
  author =	{El-Mabrouk, Nadia and Ouangraoua, A\"{i}da},
  title =	{{A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{8:1--8:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.8},
  URN =		{urn:nbn:de:0030-drops-76565},
  doi =		{10.4230/LIPIcs.WABI.2017.8},
  annote =	{Keywords: Gene tree correction, Supertree, Polytomy, Reconciliation, Phylogeny}
}
Document
DOI: 10.4230/LIPIcs.CPM.2016.14
Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost

Authors: Manuel Lafond, Emmanuel Noutahi, and Nadia El-Mabrouk

Published in: LIPIcs, Volume 54, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)

Abstract
Polytomies in gene trees are multifurcated nodes corresponding to unresolved parts of the tree, usually due to insufficient differentiation between sequences of homologous gene copies. Apart from gene sequences, other information such as that contained in the species tree can be used to resolve such intricate parts of a gene tree. The problem of resolving a multifurcated tree has been considered by many authors, the objective function often being the number of duplications and losses reflected by the reconciliation of the resolved gene tree with the species tree. Here, we present PolytomySolver, an algorithm accounting for a more general model allowing different costs for duplications and losses per species. The time complexity of this algorithm is linear for the unit cost and is quadratic for the general cost, which outperforms the best known solutions so far by a linear factor. We show on simulated trees that the gain in theoretical complexity has a real practical impact on running times.
Cite as

Manuel Lafond, Emmanuel Noutahi, and Nadia El-Mabrouk. Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 14:1-14:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

Copy BibTex To Clipboard

@InProceedings{lafond_et_al:LIPIcs.CPM.2016.14,
  author =	{Lafond, Manuel and Noutahi, Emmanuel and El-Mabrouk, Nadia},
  title =	{{Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{14:1--14:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Grossi, Roberto and Lewenstein, Moshe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2016.14},
  URN =		{urn:nbn:de:0030-drops-60907},
  doi =		{10.4230/LIPIcs.CPM.2016.14},
  annote =	{Keywords: gene tree, polytomy, reconciliation, resolution, weighted cost, phylogeny}
}
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