Related papers: Block Crossings in One-Sided Tanglegrams
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
We consider the problem of finding a 1-planar drawing for a general graph, where a 1-planar drawing is a drawing in which each edge participates in at most one crossing. Since this problem is known to be NP-hard we investigate the…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
We consider the task of drawing a graph on multiple horizontal layers, where each node is assigned a layer, and each edge connects nodes of different layers. Known algorithms determine the orders of nodes on each layer to minimize crossings…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
For a set $P$ of $n$ points in the plane in general position, a non-crossing spanning tree is a spanning tree of the points where every edge is a straight-line segment between a pair of points and no two edges intersect except at a common…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…
Let $R$ and $B$ be a set of red points and a set of blue points in the plane, respectively, such that $R\cup B$ is in general position, and let $f:R \to \{2,3,4, \ldots \}$ be a function. We show that if $2\le |B|\le \sum_{x\in R}(f(x)-2) +…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
In this paper, we introduce a new approach for drawing diagrams that have applications in software visualization. Our approach is to use a technique we call confluent drawing for visualizing non-planar diagrams in a planar way. This…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
Color-constrained subgraph problems are those where we are given an edge-colored (directed or undirected) graph and the task is to find a specific type of subgraph, like a spanning tree, an arborescence, a single-source shortest path tree,…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
The use of machine learning algorithms in finance, medicine, and criminal justice can deeply impact human lives. As a consequence, research into interpretable machine learning has rapidly grown in an attempt to better control and fix…
We define the crossing graph of a given embedded graph (such as a road network) to be a graph with a vertex for each edge of the embedding, with two crossing graph vertices adjacent when the corresponding two edges of the embedding cross…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
Biclustering, also called co-clustering, block clustering, or two-way clustering, involves the simultaneous clustering of both the rows and columns of a data matrix into distinct groups, such that the rows and columns within a group display…