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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}
}

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)

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@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.MFCS.2025.75

Temporal Graph Realization with Bounded Stretch

Authors: George B. Mertzios, Hendrik Molter, Nils Morawietz, and Paul G. Spirakis

Published in: LIPIcs, Volume 345, 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)

Abstract

A periodic temporal graph, in its simplest form, is a graph in which every edge appears exactly once in the first Δ time steps, and then it reappears recurrently every Δ time steps, where Δ is a given period length. This model offers a natural abstraction of transportation networks where each transportation link connects two destinations periodically. From a network design perspective, a crucial task is to assign the time-labels on the edges in a way that optimizes some criterion. In this paper we introduce a very natural optimality criterion that captures how the temporal distances of all vertex pairs are "stretched", compared to their physical distances, i.e. their distances in the underlying static (non-temporal) graph. Given a static graph G, the task is to assign to each edge one time-label between 1 and Δ such that, in the resulting periodic temporal graph with period Δ, the duration of the fastest temporal path from any vertex u to any other vertex v is at most α times the distance between u and v in G. Here, the value of α measures how much the shortest paths are allowed to be stretched once we assign the periodic time-labels. Our results span three different directions: First, we provide a series of approximation and NP-hardness results. Second, we provide approximation and fixed-parameter algorithms. Among them, we provide a simple polynomial-time algorithm (the radius-algorithm) which always guarantees an approximation strictly smaller than Δ, and which also computes the optimum stretch in some cases. Third, we consider a parameterized local search extension of the problem where we are given the temporal labeling of the graph, but we are allowed to change the time-labels of at most k edges; for this problem we prove that it is W[2]-hard but admits an XP algorithm with respect to k.

Cite as

George B. Mertzios, Hendrik Molter, Nils Morawietz, and Paul G. Spirakis. Temporal Graph Realization with Bounded Stretch. In 50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 345, pp. 75:1-75:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mertzios_et_al:LIPIcs.MFCS.2025.75,
  author =	{Mertzios, George B. and Molter, Hendrik and Morawietz, Nils and Spirakis, Paul G.},
  title =	{{Temporal Graph Realization with Bounded Stretch}},
  booktitle =	{50th International Symposium on Mathematical Foundations of Computer Science (MFCS 2025)},
  pages =	{75:1--75:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-388-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{345},
  editor =	{Gawrychowski, Pawe{\l} and Mazowiecki, Filip and Skrzypczak, Micha{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2025.75},
  URN =		{urn:nbn:de:0030-drops-241829},
  doi =		{10.4230/LIPIcs.MFCS.2025.75},
  annote =	{Keywords: Temporal graph, periodic temporal labeling, fastest temporal path, graph realization, temporal connectivity, stretch}
}

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)

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@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.SAND.2025.11

Hardness of Traversing Gadget Systems with Small Bandwidth

Authors: MIT Gadgets Group, Erik D. Demaine, Jenny Diomidova, Timothy Gomez, Markus Hecher, and Jayson Lynch

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract

The motion-planning-through-gadgets framework has enabled proofs of PSPACE-completeness for many motion-planning problems, ranging from swarm and modular robotics to DNA computing to video games. In this paper, we strengthen this framework to show that, for several useful gadgets and gadget families, motion planning remains PSPACE-complete even when gadgets are connected together into a graph of constant bandwidth (which implies constant pathwidth, treewidth, and cliquewidth). We then show how this result applies to several geometric/grid-based motion-planning problems, establishing PSPACE-completeness even when restricted to a rectangle/box where only one dimension is large (superconstant). On the positive side, we find one family of gadgets (DAG gadgets) for which motion planning is fixed-parameter tractable with respect to bandwidth.

Cite as

MIT Gadgets Group, Erik D. Demaine, Jenny Diomidova, Timothy Gomez, Markus Hecher, and Jayson Lynch. Hardness of Traversing Gadget Systems with Small Bandwidth. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 11:1-11:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{mitgadgetsgroup_et_al:LIPIcs.SAND.2025.11,
  author =	{MIT Gadgets Group and Demaine, Erik D. and Diomidova, Jenny and Gomez, Timothy and Hecher, Markus and Lynch, Jayson},
  title =	{{Hardness of Traversing Gadget Systems with Small Bandwidth}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{11:1--11:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.11},
  URN =		{urn:nbn:de:0030-drops-230648},
  doi =		{10.4230/LIPIcs.SAND.2025.11},
  annote =	{Keywords: Gadgets, Motion Planning, Parameterized Complexity, Hardness}
}

Document

PACE Solver Description

DOI: 10.4230/LIPIcs.IPEC.2024.33

PACE Solver Description: Arcee

Authors: Kimon Boehmer, Lukas Lee George, Fanny Hauser, and Jesse Palarus

Published in: LIPIcs, Volume 321, 19th International Symposium on Parameterized and Exact Computation (IPEC 2024)

Abstract

The 2024 PACE Challenge focused on the One-Sided Crossing Minimization (OCM) problem, which aims to minimize edge crossings in a bipartite graph with a fixed order in one partition and a free order in the other. We describe our OCM solver submission that utilizes various reduction rules for OCM and, for the heuristic track, employs local search approaches as well as techniques to escape local minima. The exact solver uses an ILP formulation and branch & bound to solve an equivalent Feedback Arc Set instance.

Cite as

Kimon Boehmer, Lukas Lee George, Fanny Hauser, and Jesse Palarus. PACE Solver Description: Arcee. In 19th International Symposium on Parameterized and Exact Computation (IPEC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 321, pp. 33:1-33:4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boehmer_et_al:LIPIcs.IPEC.2024.33,
  author =	{Boehmer, Kimon and George, Lukas Lee and Hauser, Fanny and Palarus, Jesse},
  title =	{{PACE Solver Description: Arcee}},
  booktitle =	{19th International Symposium on Parameterized and Exact Computation (IPEC 2024)},
  pages =	{33:1--33:4},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-353-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{321},
  editor =	{Bonnet, \'{E}douard and Rz\k{a}\.{z}ewski, Pawe{\l}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2024.33},
  URN =		{urn:nbn:de:0030-drops-222595},
  doi =		{10.4230/LIPIcs.IPEC.2024.33},
  annote =	{Keywords: PACE 2024, One-Sided Crossing Minimization, OCM}
}

Document

Survey

DOI: 10.4230/TGDK.1.1.4

Knowledge Graph Embeddings: Open Challenges and Opportunities

Authors: Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract

While Knowledge Graphs (KGs) have long been used as valuable sources of structured knowledge, in recent years, KG embeddings have become a popular way of deriving numeric vector representations from them, for instance, to support knowledge graph completion and similarity search. This study surveys advances as well as open challenges and opportunities in this area. For instance, the most prominent embedding models focus primarily on structural information. However, there has been notable progress in incorporating further aspects, such as semantics, multi-modal, temporal, and multilingual features. Most embedding techniques are assessed using human-curated benchmark datasets for the task of link prediction, neglecting other important real-world KG applications. Many approaches assume a static knowledge graph and are unable to account for dynamic changes. Additionally, KG embeddings may encode data biases and lack interpretability. Overall, this study provides an overview of promising research avenues to learn improved KG embeddings that can address a more diverse range of use cases.

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Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo. Knowledge Graph Embeddings: Open Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 4:1-4:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{biswas_et_al:TGDK.1.1.4,
  author =	{Biswas, Russa and Kaffee, Lucie-Aim\'{e}e and Cochez, Michael and Dumbrava, Stefania and Jendal, Theis E. and Lissandrini, Matteo and Lopez, Vanessa and Menc{\'\i}a, Eneldo Loza and Paulheim, Heiko and Sack, Harald and Vakaj, Edlira Kalemi and de Melo, Gerard},
  title =	{{Knowledge Graph Embeddings: Open Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:32},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.4},
  URN =		{urn:nbn:de:0030-drops-194783},
  doi =		{10.4230/TGDK.1.1.4},
  annote =	{Keywords: Knowledge Graphs, KG embeddings, Link prediction, KG applications}
}

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.2023.20

Graph Clustering Problems Under the Lens of Parameterized Local Search

Authors: Jaroslav Garvardt, Nils Morawietz, André Nichterlein, and Mathias Weller

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

Abstract

Cluster Editing is the problem of finding the minimum number of edge-modifications that transform a given graph G into a cluster graph G', that is, each connected component of G' is a clique. Similarly, in the Cluster Deletion problem, we further restrict the sought cluster graph G' to contain only edges that are also present in G. In this work, we consider the parameterized complexity of a local search variant for both problems: LS Cluster Deletion and LS Cluster Editing. Herein, the input also comprises an integer k and a partition 𝒞 of the vertex set of G that describes an initial cluster graph G^*, and we are to decide whether the "k-move-neighborhood" of G^* contains a cluster graph G' that is "better" (uses less modifications) than G^*. Roughly speaking, two cluster graphs G₁ and G₂ are k-move-neighbors if G₁ can be obtained from G₂ by moving at most k vertices to different connected components. We consider parameterizations by k + 𝓁 for some natural parameters 𝓁, such as the number of clusters in 𝒞, the size of a largest cluster in 𝒞, or the cluster-vertex-deletion number (cvd) of G. Our main lower-bound results are that LS Cluster Editing is W[1]-hard when parameterized by k even if 𝒞 has size two and that both LS Cluster Deletion and LS Cluster Editing are W[1]-hard when parameterized by k + 𝓁, where 𝓁 is the size of the largest cluster of 𝒞. On the positive side, we show that both problems admit an algorithm that runs in k^{𝒪(k)}⋅ cvd^{3k} ⋅ n^{𝒪(1)} time and either finds a better cluster graph or correctly outputs that there is no better cluster graph in the k-move-neighborhood of the initial cluster graph. As an intermediate result, we also obtain an algorithm that solves Cluster Deletion in cvd^{cvd} ⋅ n^{𝒪(1)} time.

Cite as

Jaroslav Garvardt, Nils Morawietz, André Nichterlein, and Mathias Weller. Graph Clustering Problems Under the Lens of Parameterized Local Search. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{garvardt_et_al:LIPIcs.IPEC.2023.20,
  author =	{Garvardt, Jaroslav and Morawietz, Nils and Nichterlein, Andr\'{e} and Weller, Mathias},
  title =	{{Graph Clustering Problems Under the Lens of Parameterized Local Search}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{20:1--20:19},
  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.2023.20},
  URN =		{urn:nbn:de:0030-drops-194391},
  doi =		{10.4230/LIPIcs.IPEC.2023.20},
  annote =	{Keywords: parameterized local search, permissive local search, FPT, W\lbrack1\rbrack-hardness}
}

Document

DOI: 10.4230/LIPIcs.ESA.2022.69

Embedding Phylogenetic Trees in Networks of Low Treewidth

Authors: Leo van Iersel, Mark Jones, and Mathias Weller

Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)

Abstract

Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called Tree Containment, arises when validating networks constructed by phylogenetic inference methods. We present the first algorithm for (rooted) Tree Containment using the treewidth t of the input network N as parameter, showing that the problem can be solved in 2^O(t²)⋅|N| time and space.

Cite as

Leo van Iersel, Mark Jones, and Mathias Weller. Embedding Phylogenetic Trees in Networks of Low Treewidth. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 69:1-69:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{vaniersel_et_al:LIPIcs.ESA.2022.69,
  author =	{van Iersel, Leo and Jones, Mark and Weller, Mathias},
  title =	{{Embedding Phylogenetic Trees in Networks of Low Treewidth}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{69:1--69:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva 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.2022.69},
  URN =		{urn:nbn:de:0030-drops-170070},
  doi =		{10.4230/LIPIcs.ESA.2022.69},
  annote =	{Keywords: fixed-parameter tractability, treewidth, phylogenetic tree, phylogenetic network, display graph, tree containment, embedding}
}

Document

DOI: 10.4230/LIPIcs.WABI.2021.6

Treewidth-Based Algorithms for the Small Parsimony Problem on Networks

Authors: Celine Scornavacca and Mathias Weller

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

Abstract

Phylogenetic reconstruction is one of the paramount challenges of contemporary bioinformatics. A subtask of existing tree reconstruction algorithms is modeled by the Small Parsimony problem: given a tree T and an assignment of character-states to its leaves, assign states to the internal nodes of T such as to minimize the parsimony score, that is, the number of edges of T connecting nodes with different states. While this problem is polynomial-time solvable on trees, the matter is more complicated if T contains reticulate events such as hybridizations or recombinations, i.e. when T is a network. Indeed, three different versions of the parsimony score on networks have been proposed and each of them is NP-hard to decide. Existing parameterized algorithms focus on combining the number of possible character-states with the number of reticulate events (per biconnected component). Here, we consider the treewidth of the undirected graph underlying the input network as parameter, presenting dynamic programming algorithms for (slight generalizations of) all three versions of the parsimony problem on networks. Our algorithms use a formulation of the treewidth that may facilitate formalizing treewidth-based dynamic programming algorithms on phylogenetic networks for other problems.

Cite as

Celine Scornavacca and Mathias Weller. Treewidth-Based Algorithms for the Small Parsimony Problem on Networks. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{scornavacca_et_al:LIPIcs.WABI.2021.6,
  author =	{Scornavacca, Celine and Weller, Mathias},
  title =	{{Treewidth-Based Algorithms for the Small Parsimony Problem on Networks}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{6:1--6:21},
  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.2021.6},
  URN =		{urn:nbn:de:0030-drops-143591},
  doi =		{10.4230/LIPIcs.WABI.2021.6},
  annote =	{Keywords: Phylogenetics, parsimony, phylogenetic networks, parameterized complexity, dynamic programming, treewidth}
}

Document

DOI: 10.4230/LIPIcs.MFCS.2020.71

A Timecop’s Work Is Harder Than You Think

Authors: Nils Morawietz, Carolin Rehs, and Mathias Weller

Published in: LIPIcs, Volume 170, 45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020)

Abstract

We consider the (parameterized) complexity of a cop and robber game on periodic, temporal graphs and a problem on periodic sequences to which these games relate intimately. In particular, we show that it is NP-hard to decide (a) whether there is some common index at which all given periodic, binary sequences are 0, and (b) whether a single cop can catch a single robber on an edge-periodic temporal graph. We further present results for various parameterizations of both problems and show that hardness not only applies in general, but also for highly limited instances. As one main result we show that even if the graph has a size-2 vertex cover and is acyclic in each time step, the cop and robber game on periodic, temporal graphs is NP-hard and W[1]-hard when parameterized by the size of the underlying input graph.

Cite as

Nils Morawietz, Carolin Rehs, and Mathias Weller. A Timecop’s Work Is Harder Than You Think. In 45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 170, pp. 71:1-71:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{morawietz_et_al:LIPIcs.MFCS.2020.71,
  author =	{Morawietz, Nils and Rehs, Carolin and Weller, Mathias},
  title =	{{A Timecop’s Work Is Harder Than You Think}},
  booktitle =	{45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020)},
  pages =	{71:1--71:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-159-7},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{170},
  editor =	{Esparza, Javier and Kr\'{a}l', Daniel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2020.71},
  URN =		{urn:nbn:de:0030-drops-127404},
  doi =		{10.4230/LIPIcs.MFCS.2020.71},
  annote =	{Keywords: edge-periodic temporal graphs, cops and robbers, tally-intersection, congruence satisfyability}
}

Document

DOI: 10.4230/LIPIcs.SWAT.2018.9

Tree Containment With Soft Polytomies

Authors: Matthias Bentert, Josef Malík, and Mathias Weller

Published in: LIPIcs, Volume 101, 16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018)

Abstract

The Tree Containment problem has many important applications in the study of evolutionary history. Given a phylogenetic network N and a phylogenetic tree T whose leaves are labeled by a set of taxa, it asks if N and T are consistent. While the case of binary N and T has received considerable attention, the more practically relevant variant dealing with biological uncertainty has not. Such uncertainty manifests itself as high-degree vertices ("polytomies") that are "jokers" in the sense that they are compatible with any binary resolution of their children. Contrasting the binary case, we show that this problem, called Soft Tree Containment, is NP-hard, even if N is a binary, multi-labeled tree in which each taxon occurs at most thrice. On the other hand, we reduce the case that each label occurs at most twice to solving a 2-SAT instance of size O(|T|^3). This implies NP-hardness and polynomial-time solvability on reticulation-visible networks in which the maximum in-degree is bounded by three and two, respectively.

Cite as

Matthias Bentert, Josef Malík, and Mathias Weller. Tree Containment With Soft Polytomies. In 16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 101, pp. 9:1-9:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{bentert_et_al:LIPIcs.SWAT.2018.9,
  author =	{Bentert, Matthias and Mal{\'\i}k, Josef and Weller, Mathias},
  title =	{{Tree Containment With Soft Polytomies}},
  booktitle =	{16th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2018)},
  pages =	{9:1--9:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-068-2},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{101},
  editor =	{Eppstein, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2018.9},
  URN =		{urn:nbn:de:0030-drops-88353},
  doi =		{10.4230/LIPIcs.SWAT.2018.9},
  annote =	{Keywords: Phylogenetics, Reticulation-Visible Networks, Multifurcating Trees}
}

Document

DOI: 10.4230/LIPIcs.IPEC.2017.30

The PACE 2017 Parameterized Algorithms and Computational Experiments Challenge: The Second Iteration

Authors: Holger Dell, Christian Komusiewicz, Nimrod Talmon, and Mathias Weller

Published in: LIPIcs, Volume 89, 12th International Symposium on Parameterized and Exact Computation (IPEC 2017)

Abstract

In this article, the Program Committee of the Second Parameterized Algorithms and Computational Experiments challenge (PACE 2017) reports on the second iteration of the PACE challenge. Track A featured the Treewidth problem and Track B the Minimum Fill-In problem. Over 44 participants on 17 teams from 11 countries submitted their implementations to the competition.

Cite as

Holger Dell, Christian Komusiewicz, Nimrod Talmon, and Mathias Weller. The PACE 2017 Parameterized Algorithms and Computational Experiments Challenge: The Second Iteration. In 12th International Symposium on Parameterized and Exact Computation (IPEC 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 89, pp. 30:1-30:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{dell_et_al:LIPIcs.IPEC.2017.30,
  author =	{Dell, Holger and Komusiewicz, Christian and Talmon, Nimrod and Weller, Mathias},
  title =	{{The PACE 2017 Parameterized Algorithms and Computational Experiments Challenge: The Second Iteration}},
  booktitle =	{12th International Symposium on Parameterized and Exact Computation (IPEC 2017)},
  pages =	{30:1--30:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-051-4},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{89},
  editor =	{Lokshtanov, Daniel and Nishimura, Naomi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2017.30},
  URN =		{urn:nbn:de:0030-drops-85582},
  doi =		{10.4230/LIPIcs.IPEC.2017.30},
  annote =	{Keywords: treewidth, minimum fill-in, contest, implementation challenge, FPT}
}

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