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A key technique of machine learning and computer vision is to embed discrete weighted graphs into continuous spaces for further downstream processing. Embedding discrete hierarchical structures in hyperbolic geometry has proven very…
We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for…
We show NP-completeness for various problems about the existence of arithmetic expression trees. When given a set of operations, inputs, and a target value does there exist an expression tree with those inputs and operations that evaluates…
Many discrete optimization problems amount to selecting a feasible set of edges of least weight. We consider in this paper the context of spatial graphs where the positions of the vertices are uncertain and belong to known uncertainty sets.…
Ordered matchings, defined as graphs with linearly ordered vertices, where each vertex is connected to exactly one edge, play a crucial role in the area of ordered graphs and their homomorphisms. Therefore, we consider related problems from…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
A point visibility graph is a graph induced by a set of points in the plane, where every vertex corresponds to a point, and two vertices are adjacent whenever the two corresponding points are visible from each other, that is, the open…
A graph is geometric 1-planar if it admits a straight-line drawing where each edge is crossed at most once. We provide the first systematic study of the parameterized complexity of recognizing geometric 1-planar graphs. By substantially…
The Metric Embedding problem takes as input two metric spaces $(X,D_X)$ and $(Y,D_Y)$, and a positive integer $d$. The objective is to determine whether there is an embedding $F:X \rightarrow Y$ such that $d_{F} \leq d$, where $d_{F}$…
Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing $D(G)$ of a graph $G$ by inserting a…
We revisit the minimum-link path problem: Given a polyhedral domain and two points in it, connect the points by a polygonal path with minimum number of edges. We consider settings where the vertices and/or the edges of the path are…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
We study Clustered Planarity with Linear Saturators, which is the problem of augmenting an $n$-vertex planar graph whose vertices are partitioned into independent sets (called clusters) with paths - one for each cluster - that connect all…
The tree-depth problem can be seen as finding an elimination tree of minimum height for a given input graph $G$. We introduce a bicriteria generalization in which additionally the width of the elimination tree needs to be bounded by some…
The weak variant of Hanani-Tutte theorem says that a graph is planar, if it can be drawn in the plane so that every pair of edges cross an even number of times. Moreover, we can turn such a drawing into an embedding without changing the…
A rectangle visibility representation (RVR) of a graph consists of an assignment of axis-aligned rectangles to vertices such that for every edge there exists a horizontal or vertical line of sight between the rectangles assigned to its…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
A treedepth decomposition of an undirected graph $G$ is a rooted forest $F$ on the vertex set of $G$ such that every edge $uv\in E(G)$ is in ancestor-descendant relationship in $F$. Given a weight function $w\colon V(G)\rightarrow…
Given a planar graph $G$, we consider drawings of $G$ in the plane where edges are represented by straight line segments (which possibly intersect). Such a drawing is specified by an injective embedding $\pi$ of the vertex set of $G$ into…