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Documents authored by Schestag, Jannik

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)

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@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)

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@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)

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@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)

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@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)

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@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}
}
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