Related papers: Visualizing Multispecies Coalescent Trees: Drawing…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…
In transmission networks, power flows and network topology are deeply intertwined due to power flow physics. Recent literature shows that a specific more hierarchical network structure can effectively inhibit the propagation of line…
Manifold learning techniques play a pivotal role in machine learning by revealing lower-dimensional embeddings within high-dimensional data, thus enhancing both the efficiency and interpretability of data analysis by transforming the data…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
Tanglegrams are formed by taking two rooted binary trees $T$ and $S$ with the same number of leaves and uniquely matching each leaf in $T$ with a leaf in $S$. They are usually represented using layouts, which embed the trees and the…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Feature level sets (FLS) have shown significant potential in the analysis of multi-field data by using traits defined in attribute space to specify features in the domain. In this work, we address key challenges in the practical use of FLS:…
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…
In this paper, we give polynomial-time algorithms that can take a graph G with a given combinatorial embedding on an orientable surface S of genus g and produce a planar drawing of G in R^2, with a bounding face defined by a polygonal…
In this paper, we investigate the $k$-path coloring problem, a variant of vertex coloring arising in the context of integrated circuit manufacturing. In this setting, typical industrial instances exhibit a `tree-like' structure. We exploit…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Biclustering techniques have been widely used to identify homogeneous subgroups within large data matrices, such as subsets of genes similarly expressed across subsets of patients. Mining a max-sum sub-matrix is a related but distinct…
Arboricity is a graph parameter akin to chromatic number, in that it seeks to partition the vertices into the smallest number of sparse subgraphs. Where for the chromatic number we are partitioning the vertices into independent sets, for…
Graph drawing addresses the problem of finding a layout of a graph that satisfies given aesthetic and understandability objectives. The most important objective in graph drawing is minimization of the number of crossings in the drawing, as…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
A method for creating a forest of model trees to fit samples of a function defined on images is described in several steps: down-sampling the images, determining a tree's hyperplanes, applying convolutions to the hyperplanes to handle small…
Storyline visualizations show the structure of a story, by depicting the interactions of the characters over time. Each character is represented by an x-monotone curve from left to right, and a meeting is represented by having the curves of…