10 Search Results for "Schestag, Jannik"

Document
DOI: 10.4230/LIPIcs.SWAT.2026.25
Parameterized Critical Node Cut Revisited

Authors: Dušan Knop, Nikolaos Melissinos, and Manolis Vasilakis

Published in: LIPIcs, Volume 370, 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)

Abstract
We study how to sparsify connectivity in graphs under a tight deletion budget. Given a graph G and integers k,x ≥ 0, Critical Node Cut (CNC) asks whether we can delete at most k vertices so that the number of remaining unordered pairs of connected vertices is at most x. CNC generalizes Vertex Cover (the case x = 0) and models tasks in network design, epidemiology, and social network analysis. We comprehensively map the structural parameterized complexity landscape for Critical Node Cut. First, we prove W[1]-hardness for the combined parameter k + fes + Δ + pw, where fes is the feedback edge set number, Δ the maximum degree, and pw the pathwidth of the input graph, respectively. This significantly improves over the known W[1]-hardness for k+tw, where tw denotes the treewidth, and is tight in that tree-depth together with maximum degree trivially yields FPT. Second, we give new positive results. Specifically, we identify three structural parameters-max-leaf number, vertex integrity, and modular-width-that render the problem fixed-parameter tractable, and develop a polynomial-time algorithm for graphs of constant clique-width. Third, leveraging a technique introduced by Lampis [ICALP '14], we develop an FPT approximation scheme that, for any ε > 0, computes a (1+ε)-approximate solution in time (tw / ε)^{𝒪(tw)} n^{𝒪(1)}. Finally, we show that CNC admits no polynomial kernel when parameterized by vertex cover number, unless standard assumptions fail. Together, these results substantially sharpen the known complexity landscape for CNC.
Cite as

Dušan Knop, Nikolaos Melissinos, and Manolis Vasilakis. Parameterized Critical Node Cut Revisited. In 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 370, pp. 25:1-25:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

Copy BibTex To Clipboard

@InProceedings{knop_et_al:LIPIcs.SWAT.2026.25,
  author =	{Knop, Du\v{s}an and Melissinos, Nikolaos and Vasilakis, Manolis},
  title =	{{Parameterized Critical Node Cut Revisited}},
  booktitle =	{20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)},
  pages =	{25:1--25:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-421-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{370},
  editor =	{Fraigniaud, Pierre},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2026.25},
  URN =		{urn:nbn:de:0030-drops-260617},
  doi =		{10.4230/LIPIcs.SWAT.2026.25},
  annote =	{Keywords: Critical Node Cut, Parameterized Complexity, Treewidth}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2025.11
Parameterized Algorithms for Diversity of Networks with Ecological Dependencies

Authors: Mark Jones and Jannik Schestag

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be invested most efficiently. In recent years, efficient algorithms have been developed to find sets of taxa that maximize phylogenetic diversity either in a phylogenetic network or in a phylogenetic tree subject to ecological constraints, such as a food web. However, these aspects have mostly been studied independently. Since both factors are biologically important, it seems natural to consider them together. In this paper, we introduce decision problems where, given a phylogenetic network, a food web, and integers k, and D, the task is to find a set of k taxa with phylogenetic diversity of at least D under the maximize all paths measure, while also satisfying viability conditions within the food web. Here, we consider different definitions of viability, which all demand that a "sufficient" number of prey species survive to support surviving predators. We investigate the parameterized complexity of these problems and present several fixed-parameter tractable (FPT) algorithms. Specifically, we provide a complete complexity dichotomy characterizing which combinations of parameters - out of the size constraint k, the acceptable diversity loss D̄, the scanwidth of the food web sw_ℱ, the maximum in-degree δ in the network, and the network height h - lead to W[1]-hardness and which admit FPT algorithms. Our primary methodological contribution is a novel algorithmic framework for solving phylogenetic diversity problems in networks where dependencies (such as those from a food web) impose an order, using a color coding approach.
Cite as

Mark Jones and Jannik Schestag. Parameterized Algorithms for Diversity of Networks with Ecological Dependencies. In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 11:1-11:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{jones_et_al:LIPIcs.IPEC.2025.11,
  author =	{Jones, Mark and Schestag, Jannik},
  title =	{{Parameterized Algorithms for Diversity of Networks with Ecological Dependencies}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{11:1--11:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.11},
  URN =		{urn:nbn:de:0030-drops-251439},
  doi =		{10.4230/LIPIcs.IPEC.2025.11},
  annote =	{Keywords: Phylogenetic Diversity, Fixed-Parameter Tractability, Phylogenetic Networks, Food Webs, Color Coding}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.83
Fault-Tolerant Matroid Bases

Authors: Matthias Bentert, Fedor V. Fomin, Petr A. Golovach, and Laure Morelle

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

Abstract
We investigate the problem of constructing fault-tolerant bases in matroids. Given a matroid ℳ and a redundancy parameter k, a k-fault-tolerant basis is a minimum-size set of elements such that, even after the removal of any k elements, the remaining subset still spans the entire ground set. Since matroids generalize linear independence across structures such as vector spaces, graphs, and set systems, this problem unifies and extends several fault-tolerant concepts appearing in prior research. Our main contribution is a fixed-parameter tractable (FPT) algorithm for the k-fault-tolerant basis problem, parameterized by both k and the rank r of the matroid. This two-variable parameterization by k + r is shown to be tight in the following sense. On the one hand, the problem is already NP-hard for k = 1. On the other hand, it is Para-NP-hard for r ≥ 3 and polynomial-time solvable for r ≤ 2.
Cite as

Matthias Bentert, Fedor V. Fomin, Petr A. Golovach, and Laure Morelle. Fault-Tolerant Matroid Bases. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 83:1-83:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{bentert_et_al:LIPIcs.ESA.2025.83,
  author =	{Bentert, Matthias and Fomin, Fedor V. and Golovach, Petr A. and Morelle, Laure},
  title =	{{Fault-Tolerant Matroid Bases}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{83:1--83:14},
  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.2025.83},
  URN =		{urn:nbn:de:0030-drops-245511},
  doi =		{10.4230/LIPIcs.ESA.2025.83},
  annote =	{Keywords: Parameterized Complexity, matroids, robust bases}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.32
Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems

Authors: Niels Grüttemeier, Nils Morawietz, and Frank Sommer

Published in: LIPIcs, Volume 349, 19th International Symposium on Algorithms and Data Structures (WADS 2025)

Abstract
Parameterized local search combines classic local search heuristics with the paradigm of parameterized algorithmics. While most local search algorithms aim to improve given solutions by performing one single operation on a given solution, the parameterized approach aims to improve a solution by performing k simultaneous operations. Herein, k is a parameter called search radius for which the value can be chosen by a user. One major goal in the field of parameterized local search is to outline the trade-off between the size of k and the running time of the local search step. In this work, we introduce an abstract framework that generalizes natural parameterized local search approaches for a large class of partitioning problems: Given n items that are partitioned into b bins and a target function that evaluates the quality of the current partition, one asks whether it is possible to improve the solution by removing up to k items from their current bins and reassigning them to other bins. Among others, our framework applies for the local search versions of problems like Cluster Editing, Vector Bin Packing, and Nash Social Welfare. Motivated by a real-world application of the problem Vector Bin Packing, we introduce a parameter called number of types τ ≤ n and show that all problems fitting in our framework can be solved in τ^k ⋅ 2^𝒪(k) ⋅ |I|^𝒪(1) time, where |I| denotes the total input size. In case of Cluster Editing, the parameter τ generalizes the well-known parameter neighborhood diversity of the input graph. We complement these algorithms by showing that for all considered problems, an algorithm significantly improving over our algorithm with running time τ^k ⋅ 2^𝒪(k) ⋅ |I|^𝒪(1) would contradict the Exponential Time Hypothesis. Additionally, we show that even on very restricted instances, all considered problems are W[1]-hard when parameterized by the search radius k alone. In case of the local search version of Vector Bin Packing, we provide an even stronger W[1]-hardness result.
Cite as

Niels Grüttemeier, Nils Morawietz, and Frank Sommer. Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 32:1-32:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{gruttemeier_et_al:LIPIcs.WADS.2025.32,
  author =	{Gr\"{u}ttemeier, Niels and Morawietz, Nils and Sommer, Frank},
  title =	{{Fantastic Flips and Where to Find Them: A General Framework for Parameterized Local Search on Partitioning Problems}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{32:1--32:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-398-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{349},
  editor =	{Morin, Pat and Oh, Eunjin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WADS.2025.32},
  URN =		{urn:nbn:de:0030-drops-242631},
  doi =		{10.4230/LIPIcs.WADS.2025.32},
  annote =	{Keywords: Flip-Neighborhood, Cluster Editing, Vector Bin Packing, Vertex Cover, NP-hard problem, Max c-Cut}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.15
Average-Tree Phylogenetic Diversity of Networks

Authors: Leo van Iersel, Mark Jones, Jannik Schestag, Celine Scornavacca, and Mathias Weller

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

Abstract
Phylogenetic diversity is a measure used to quantify the biodiversity of a set of species. Here, we introduce the "average-tree" phylogenetic diversity score in rooted binary phylogenetic networks and consider algorithms for computing and maximizing the score on a given network. Basically, the score is the weighted average of the phylogenetic diversity scores in all trees displayed by the network, with the weights determined by the inheritance probabilities on the reticulation edges used in the embeddings. We show that computing the score of a given set of taxa in a given network is #P-hard, directly implying #P-hardness of finding a subset of k taxa achieving maximum diversity score and, thereby, ruling out polynomial-time algorithms for these problems unless the polynomial hierarchy collapses. However, we show that both problems can be solved efficiently if the input network is close to being a tree in the sense that its reticulation number is small. More precisely, we prove that we can solve the optimization problem in networks with n leaves and r reticulations in 2^{𝒪(r)}⋅ n⋅ k time. Using experiments on data produced by simulating a reticulate-evolution process, we show that our algorithm runs efficiently on networks with hundreds of taxa and tens of reticulations.
Cite as

Leo van Iersel, Mark Jones, Jannik Schestag, Celine Scornavacca, and Mathias Weller. Average-Tree Phylogenetic Diversity of Networks. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 15:1-15:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{vaniersel_et_al:LIPIcs.WABI.2025.15,
  author =	{van Iersel, Leo and Jones, Mark and Schestag, Jannik and Scornavacca, Celine and Weller, Mathias},
  title =	{{Average-Tree Phylogenetic Diversity of Networks}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{15:1--15:20},
  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.2025.15},
  URN =		{urn:nbn:de:0030-drops-239405},
  doi =		{10.4230/LIPIcs.WABI.2025.15},
  annote =	{Keywords: phylogenetic diversity, phylogenetic networks, network phylogenetic diversity, algorithms, computational complexity}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2024.28
Maximizing Phylogenetic Diversity Under Ecological Constraints: A Parameterized Complexity Study

Authors: Christian Komusiewicz and Jannik Schestag

Published in: LIPIcs, Volume 323, 44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2024)

Abstract
In the NP-hard Optimizing Phylogenetic Diversity with Dependencies(PDD) problem, the input consists of a phylogenetic tree 𝒯 over a set of taxa X, a food-web that describes the prey-predator relationships in X, and integers k and D. The task is to find a set S of k species that is viable in the food-web such that the subtree of 𝒯 obtained by retaining only the vertices of S has total edge weight at least D. Herein, viable means that for every predator taxon of S, the set S contains at least one prey taxon. We provide the first systematic analysis of PDD and its special case with star trees, s-PDD, from a parameterized complexity perspective. For solution-size related parameters, we show that PDD is fixed-parameter tractable (FPT) with respect to D and with respect to k plus the height of the phylogenetic tree. Moreover, we consider structural parameterizations of the food-web. For example, we show an FPT-algorithm for the parameter that measures the vertex deletion distance to graphs where every connected component is a complete graph. Finally, we show that s-PDD admits an FPT-algorithm for the treewidth of the food-web. This disproves, unless P = NP, a conjecture of Faller et al. [Annals of Combinatorics, 2011] who conjectured that s-PDD is NP-hard even when the food-web is a tree.
Cite as

Christian Komusiewicz and Jannik Schestag. Maximizing Phylogenetic Diversity Under Ecological Constraints: A Parameterized Complexity Study. In 44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 323, pp. 28:1-28:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

Copy BibTex To Clipboard

@InProceedings{komusiewicz_et_al:LIPIcs.FSTTCS.2024.28,
  author =	{Komusiewicz, Christian and Schestag, Jannik},
  title =	{{Maximizing Phylogenetic Diversity Under Ecological Constraints: A Parameterized Complexity Study}},
  booktitle =	{44th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2024)},
  pages =	{28:1--28:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-355-3},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{323},
  editor =	{Barman, Siddharth and Lasota, S{\l}awomir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2024.28},
  URN =		{urn:nbn:de:0030-drops-222175},
  doi =		{10.4230/LIPIcs.FSTTCS.2024.28},
  annote =	{Keywords: phylogenetic diversity, food-webs, structural parameterization, color-coding, dynamic programming}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2023.4
On the Complexity of Finding a Sparse Connected Spanning Subgraph in a Non-Uniform Failure Model

Authors: Matthias Bentert, Jannik Schestag, and Frank Sommer

Published in: LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)

Abstract
We study a generalization of the classic Spanning Tree problem that allows for a non-uniform failure model. More precisely, edges are either safe or unsafe and we assume that failures only affect unsafe edges. In Unweighted Flexible Graph Connectivity we are given an undirected graph G = (V,E) in which the edge set E is partitioned into a set S of safe edges and a set U of unsafe edges and the task is to find a set T of at most k edges such that T - {u} is connected and spans V for any unsafe edge u ∈ T. Unweighted Flexible Graph Connectivity generalizes both Spanning Tree and Hamiltonian Cycle. We study Unweighted Flexible Graph Connectivity in terms of fixed-parameter tractability (FPT). We show an almost complete dichotomy on which parameters lead to fixed-parameter tractability and which lead to hardness. To this end, we obtain FPT-time algorithms with respect to the vertex deletion distance to cluster graphs and with respect to the treewidth. By exploiting the close relationship to Hamiltonian Cycle, we show that FPT-time algorithms for many smaller parameters are unlikely under standard parameterized complexity assumptions. Regarding problem-specific parameters, we observe that Unweighted Flexible Graph Connectivity admits an FPT-time algorithm when parameterized by the number of unsafe edges. Furthermore, we investigate a below-upper-bound parameter for the number of edges of a solution. We show that this parameter also leads to an FPT-time algorithm.
Cite as

Matthias Bentert, Jannik Schestag, and Frank Sommer. On the Complexity of Finding a Sparse Connected Spanning Subgraph in a Non-Uniform Failure Model. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{bentert_et_al:LIPIcs.IPEC.2023.4,
  author =	{Bentert, Matthias and Schestag, Jannik and Sommer, Frank},
  title =	{{On the Complexity of Finding a Sparse Connected Spanning Subgraph in a Non-Uniform Failure Model}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{4:1--4:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-305-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{285},
  editor =	{Misra, Neeldhara and Wahlstr\"{o}m, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.4},
  URN =		{urn:nbn:de:0030-drops-194232},
  doi =		{10.4230/LIPIcs.IPEC.2023.4},
  annote =	{Keywords: Flexible graph connectivity, NP-hard problem, parameterized complexity, below-guarantee parameterization, treewidth}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2023.19
Finding Degree-Constrained Acyclic Orientations

Authors: Jaroslav Garvardt, Malte Renken, Jannik Schestag, and Mathias Weller

Published in: LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)

Abstract
We consider the problem of orienting a given, undirected graph into a (directed) acyclic graph such that the in-degree of each vertex v is in a prescribed list λ(v). Variants of this problem have been studied for a long time and with various applications, but mostly without the requirement for acyclicity. Without this requirement, the problem is closely related to the classical General Factor problem, which is known to be NP-hard in general, but polynomial-time solvable if no list λ(v) contains large "gaps" [Cornuéjols, J. Comb. Theory B, 1988]. In contrast, we show that deciding if an acyclic orientation exists is NP-hard even in the absence of such "gaps". On the positive side, we design parameterized algorithms for various, natural parameterizations of the acyclic orientation problem. A special case of the orientation problem with degree constraints recently came up in the context of reconstructing evolutionary histories (that is, phylogenetic networks). This phylogenetic setting imposes additional structure onto the problem that can be exploited algorithmically, allowing us to show fixed-parameter tractability when parameterized by either the treewidth of G (a smaller parameter than the frequently employed "level"), by the number of vertices v for which |λ(v)| ≥ 2, by the number of vertices v for which the highest value in λ(v) is at least 2. While the latter result can be extended to the general degree-constraint acyclic orientation problem, we show that the former cannot unless FPT=W[1].
Cite as

Jaroslav Garvardt, Malte Renken, Jannik Schestag, and Mathias Weller. Finding Degree-Constrained Acyclic Orientations. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 19:1-19:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{garvardt_et_al:LIPIcs.IPEC.2023.19,
  author =	{Garvardt, Jaroslav and Renken, Malte and Schestag, Jannik and Weller, Mathias},
  title =	{{Finding Degree-Constrained Acyclic Orientations}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{19:1--19:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-305-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{285},
  editor =	{Misra, Neeldhara and Wahlstr\"{o}m, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.19},
  URN =		{urn:nbn:de:0030-drops-194383},
  doi =		{10.4230/LIPIcs.IPEC.2023.19},
  annote =	{Keywords: Graph Orientation, Phylogenetic Networks, General Factor, NP-hardness, Parameterized Algorithms, Treewidth}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2023.30
How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks

Authors: Mark Jones and Jannik Schestag

Published in: LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)

Abstract
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. We consider an extension of PD to phylogenetic networks. Given a phylogenetic network with weighted edges and a subset S of leaves, the all-paths phylogenetic diversity of S is the summed weight of all edges on a path from the root to some leaf in S. The problem of finding a bounded-size set S that maximizes this measure is polynomial-time solvable on trees, but NP-hard on networks. We study the latter from a parameterized perspective. While this problem is W[2]-hard with respect to the size of S (and W[1]-hard with respect to the size of the complement of S), we show that it is FPT with respect to several other parameters, including the phylogenetic diversity of S, the acceptable loss of phylogenetic diversity, the number of reticulations in the network, and the treewidth of the underlying graph.
Cite as

Mark Jones and Jannik Schestag. How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 30:1-30:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{jones_et_al:LIPIcs.IPEC.2023.30,
  author =	{Jones, Mark and Schestag, Jannik},
  title =	{{How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{30:1--30:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-305-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{285},
  editor =	{Misra, Neeldhara and Wahlstr\"{o}m, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.30},
  URN =		{urn:nbn:de:0030-drops-194496},
  doi =		{10.4230/LIPIcs.IPEC.2023.30},
  annote =	{Keywords: Phylogenetic Networks, Phylogenetic Diversity, Parameterized Complexity, W-hierarchy, FPT algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.18
On the Complexity of Parameterized Local Search for the Maximum Parsimony Problem

Authors: Christian Komusiewicz, Simone Linz, Nils Morawietz, and Jannik Schestag

Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)

Abstract
Maximum Parsimony is the problem of computing a most parsimonious phylogenetic tree for a taxa set X from character data for X. A common strategy to attack this notoriously hard problem is to perform a local search over the phylogenetic tree space. Here, one is given a phylogenetic tree T and wants to find a more parsimonious tree in the neighborhood of T. We study the complexity of this problem when the neighborhood contains all trees within distance k for several classic distance functions. For the nearest neighbor interchange (NNI), subtree prune and regraft (SPR), tree bisection and reconnection (TBR), and edge contraction and refinement (ECR) distances, we show that, under the exponential time hypothesis, there are no algorithms with running time |I|^o(k) where |I| is the total input size. Hence, brute-force algorithms with running time |X|^𝒪(k) ⋅ |I| are essentially optimal. In contrast to the above distances, we observe that for the sECR-distance, where the contracted edges are constrained to form a subtree, a better solution within distance k can be found in k^𝒪(k) ⋅ |I|^𝒪(1) time.
Cite as

Christian Komusiewicz, Simone Linz, Nils Morawietz, and Jannik Schestag. On the Complexity of Parameterized Local Search for the Maximum Parsimony Problem. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 18:1-18:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{komusiewicz_et_al:LIPIcs.CPM.2023.18,
  author =	{Komusiewicz, Christian and Linz, Simone and Morawietz, Nils and Schestag, Jannik},
  title =	{{On the Complexity of Parameterized Local Search for the Maximum Parsimony Problem}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{18:1--18:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-276-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{259},
  editor =	{Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.18},
  URN =		{urn:nbn:de:0030-drops-179729},
  doi =		{10.4230/LIPIcs.CPM.2023.18},
  annote =	{Keywords: phylogenetic trees, parameterized complexity, tree distances, NNI, TBR}
}
  • Refine by Type
  • 10 Document/PDF
  • 5 Document/HTML

  • Refine by Publication Year
  • 1 2026
  • 4 2025
  • 1 2024
  • 4 2023

  • Refine by Author
  • 7 Schestag, Jannik
  • 3 Jones, Mark
  • 2 Bentert, Matthias
  • 2 Komusiewicz, Christian
  • 2 Morawietz, Nils
  • Show More...

  • Refine by Series/Journal
  • 10 LIPIcs

  • Refine by Classification
  • 5 Theory of computation → Fixed parameter tractability
  • 5 Theory of computation → Parameterized complexity and exact algorithms
  • 3 Applied computing → Computational biology
  • 1 Applied computing → Bioinformatics
  • 1 Applied computing → Computational genomics
  • Show More...

  • Refine by Keyword
  • 3 Parameterized Complexity
  • 3 Phylogenetic Networks
  • 2 NP-hard problem
  • 2 Phylogenetic Diversity
  • 2 Treewidth
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact