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The Subgraph Isomorphism problem is of considerable importance in computer science. We examine the problem when the pattern graph H is of bounded treewidth, as occurs in a variety of applications. This problem has a well-known algorithm via…
A stable or locally-optimal cut of a graph is a cut whose weight cannot be increased by changing the side of a single vertex. In this paper we study Minimum Stable Cut, the problem of finding a stable cut of minimum weight. Since this…
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…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
In this paper, we consider tree decompositions, branch decompositions, and clique decompositions. We improve the running time of dynamic programming algorithms on these graph decompositions for a large number of problems as a function of…
We investigate the complexity of several fundamental polynomial-time solvable problems on graphs and on matrices, when the given instance has low treewidth; in the case of matrices, we consider the treewidth of the graph formed by non-zero…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…
We show that if k-SUM is hard, in the sense that the standard algorithm is essentially optimal, then a variant of the SETH called the Primal Treewidth SETH is true. Formally: if there is an $\varepsilon>0$ and an algorithm which solves SAT…
In the NP-hard Optimizing PD 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…
We prove the following theorem. Given a planar graph $G$ and an integer $k$, it is possible in polynomial time to randomly sample a subset $A$ of vertices of $G$ with the following properties: (i) $A$ induces a subgraph of $G$ of treewidth…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
At IPEC 2020, Bergougnoux, Bonnet, Brettell, and Kwon showed that a number of problems related to the classic Feedback Vertex Set (FVS) problem do not admit a $2^{o(k \log k)} \cdot n^{\mathcal{O}(1)}$-time algorithm on graphs of treewidth…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
It is well known that many local graph problems, like Vertex Cover and Dominating Set, can be solved in 2^{O(tw)}|V|^{O(1)} time for graphs G=(V,E) with a given tree decomposition of width tw. However, for nonlocal problems, like the…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
In the Steiner Tree problem we are given an undirected edge-weighted graph as input, along with a set $K$ of vertices called terminals. The task is to output a minimum-weight connected subgraph that spans all the terminals. The famous…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
Treewidth is a useful tool in designing graph algorithms. Although many NP-hard graph problems can be solved in linear time when the input graphs have small treewidth, there are problems which remain hard on graphs of bounded treewidth. In…