Related papers: Uncertainty in phylogenetic tree estimates
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…
When solving ill-posed inverse problems, one often desires to explore the space of potential solutions rather than be presented with a single plausible reconstruction. Valuable insights into these feasible solutions and their associated…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
Earth's forests play an important role in the fight against climate change, and are in turn negatively affected by it. Effective monitoring of different tree species is essential to understanding and improving the health and biodiversity of…
Many data management applications must deal with data which is uncertain, incomplete, or noisy. However, on existing uncertain data representations, we cannot tractably perform the important query evaluation tasks of determining query…
We introduce a novel interpretable tree based algorithm for prediction in a regression setting. Our motivation is to estimate the unknown regression function from a functional decomposition perspective in which the functional components…
Bayesian averaging over classification models allows the uncertainty of classification outcomes to be evaluated, which is of crucial importance for making reliable decisions in applications such as financial in which risks have to be…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…
A new nonparametric approach, based on a decision tree algorithm, is proposed to calculate the overlap between two probability distributions. The devised framework is described analytically and numerically. The convergence of the estimated…
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…
Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
This work develops formal statistical inference procedures for machine learning ensemble methods. Ensemble methods based on bootstrapping, such as bagging and random forests, have improved the predictive accuracy of individual trees, but…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
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…
Imagine being able to ask questions to a black box model such as "Which adversarial examples exist?", "Does a specific attribute have a disproportionate effect on the model's prediction?" or "What kind of predictions could possibly be made…