Related papers: Visualizing Geophylogenies -- Internal and Externa…
A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
Spatial dependency and spatial embedding are basic physical properties of many phenomena modeled by networks. The most indicated computational environment to deal with spatial information is to use Georeferenced Information System (GIS) and…
Image geolocalization is the task of identifying the location depicted in a photo based only on its visual information. This task is inherently challenging since many photos have only few, possibly ambiguous cues to their geolocation.…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
A graphical model is a statistical model that is associated to a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models admit…
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…
Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context.…
A rooted tree $T$ with vertex labels $t(v)$ and set-valued edge labels $\lambda(e)$ defines maps $\delta$ and $\varepsilon$ on the pairs of leaves of $T$ by setting $\delta(x,y)=q$ if the last common ancestor $\text{lca}(x,y)$ of $x$ and…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
Hierarchical graph clustering is a common technique to reveal the multi-scale structure of complex networks. We propose a novel metric for assessing the quality of a hierarchical clustering. This metric reflects the ability to reconstruct…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Most biological data are multidimensional, posing a major challenge to human comprehension and computational analysis. Principal component analysis is the most popular approach to rendering two- or three-dimensional representations of the…
The visibility graph of a simple polygon represents visibility relations between its vertices. Knowing the correct order of the vertices around the boundary of a polygon and its visibility graph, it is an open problem to locate the vertices…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…
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…
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…