Related papers: Uncertainty in phylogenetic tree estimates

As animals interact with their environments, they must infer properties of their surroundings. Some animals, including humans, can represent uncertainty about those properties. But when, if ever, do they use probability distributions to…

Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…

A new family of tree models is proposed, which we call "differential trees." A differential tree model is constructed from multiple data sets and aims to detect distributional differences between them. The new methodology differs from the…

We propose and study a multi-scale approach to vector quantization. We develop an algorithm, dubbed reconstruction trees, inspired by decision trees. Here the objective is parsimonious reconstruction of unsupervised data, rather than…

The issue of estimating residual variance in regression models has experienced relatively little attention in the machine learning community. However, the estimate is of primary interest in many practical applications, e.g. as a primary…

Data analysis and machine learning have become an integrative part of the modern scientific methodology, offering automated procedures for the prediction of a phenomenon based on past observations, unraveling underlying patterns in data and…

The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…

Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…

Tree search is a fundamental tool for planning, as many sequential decision-making problems can be framed as searching over tree-structured spaces. We propose an uncertainty-guided tree search algorithm for settings where the reward…

Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…

In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of…

Tree perception is an essential building block toward autonomous forestry operations. Current developments generally consider input data from lidar sensors to solve forest navigation, tree detection and diameter estimation problems. Whereas…

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

Random forests are decision tree ensembles that can be used to solve a variety of machine learning problems. However, as the number of trees and their individual size can be large, their decision making process is often incomprehensible. In…

Experts advising decision-makers are likely to display expertise which varies as a function of the problem instance. In practice, this may lead to sub-optimal or discriminatory decisions against minority cases. In this work we model such…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

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…

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…

A random forest prediction can be computed by the scalar product of the labels of the training examples and a set of weights that are determined by the leafs of the forest into which the test object falls; each prediction can hence be…