Related papers: Visualizing Multispecies Coalescent Trees: Drawing…
This paper is devoted to a study of single-peakedness on arbitrary graphs. Given a collection of preferences (rankings of a set of alternatives), we aim at determining a connected graph G on which the preferences are single-peaked, in the…
This paper focuses on unsupervised modeling of morphological families, collectively comprising a forest over the language vocabulary. This formulation enables us to capture edgewise properties reflecting single-step morphological…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
We study a question that lies at the intersection of classical research subjects in Topological Graph Theory and Graph Drawing: Computing a drawing of a graph with a prescribed number of crossings on a given set $S$ of points, while…
This study introduces a new method of visualizing complex tree structured objects. The usefulness of this method is illustrated in the context of detecting unexpected features in a data set of very large trees. The major contribution is a…
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…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
For a fixed set $X$ containing $n$ taxon labels, an ordered pair consisting of a gene tree topology $G$ and a species tree $S$ bijectively labeled with the labels of $X$ possesses a set of coalescent histories -- mappings from the set of…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
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…
We introduce the problem of finding a spanning tree along with a partition of the tree edges into fewest number of feasible sets, where constraints on the edges define feasibility. The motivation comes from wireless networking, where we…
This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents some large data. A task can only be executed if all input and output data fit into memory, and a data can only…
We consider drawings of trees in which all edges incident to leaves can be extended to infinite rays without crossing, partitioning the plane into infinite convex polygons. Among all such drawings we seek the one maximizing the angular…
Species tree reconstruction is complicated by effects of Incomplete Lineage Sorting (ILS), commonly modeled by the multi-species coalescent model. While there has been substantial progress in developing methods that estimate a species tree…
Geometric embedding of graphs in a point set in the plane is a well known problem. In this paper, the complexity of a variant of this problem, where the point set is bounded by a simple polygon, is considered. Given a point set in the plane…
This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents a large IO file. A task can only be executed if all input and output files fit into memory, and a file can only…
Convolution trees, loopy belief propagation, and fast numerical p-convolution are combined for the first time to efficiently solve networks with several additive constraints between random variables. An implementation of this "convolution…
Partial edge drawing (PED) is a drawing style for non-planar graphs, in which edges are drawn only partially as pairs of opposing stubs on the respective end-vertices. In a PED, by erasing the central parts of edges, all edge crossings and…