Related papers: Visualizing Co-Phylogenetic Reconciliations
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
NodeTrix representations are a popular way to visualize clustered graphs; they represent clusters as adjacency matrices and inter-cluster edges as curves connecting the matrix boundaries. We study the complexity of constructing NodeTrix…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
We introduce in this paper a runtime-efficient tree hashing algorithm for the identification of isomorphic subtrees, with two important applications in genetic programming for symbolic regression: fast, online calculation of population…
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…
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…
Supervised classification and representation learning are two widely used classes of methods to analyze multivariate images. Although complementary, these methods have been scarcely considered jointly in a hierarchical modeling. In this…
Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…
In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set $X$ of species from a multiset $\Pi$ of partitions corresponding to various attributes of these species. One approach that is used to…
Evolutionary algorithms usually explore a search space of solutions by means of crossover and mutation. While a mutation consists of a small, local modification of a solution, crossover mixes the genetic information of two solutions to…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We explore a generalization of set reconciliation, where the goal is to reconcile sets of sets. Alice and Bob each have a parent set consisting of $s$ child sets, each containing at most $h$ elements from a universe of size $u$. They want…
An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In…
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…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
Finding inherent or processed links within a dataset allows to discover potential knowledge. The main contribution of this article is to define a global framework that enables optimal knowledge discovery by visually rendering co-occurences…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
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…