Related papers: Properties of Consensus Methods for Inferring Spec…
We propose a method for the classification of objects that are structured as random trees. Our aim is to model a distribution over the node label assignments in settings where the tree data structure is associated with node attributes…
We investigate at decision trees that incorporate both traditional queries based on one attribute and queries based on hypotheses about the values of all attributes. Such decision trees are similar to ones studied in exact learning, where…
Eliciting preferences from human judgements is inherently imprecise, yet most decision analysis methods force a single priority vector from pairwise comparisons, discarding the information embedded in inconsistencies. We instead leverage…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
Random forests are a very effective and commonly used statistical method, but their full theoretical analysis is still an open problem. As a first step, simplified models such as purely random forests have been introduced, in order to shed…
Algorithms for community detection are usually stochastic, leading to different partitions for different choices of random seeds. Consensus clustering has proven to be an effective technique to derive more stable and accurate partitions…
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 study various types of consistency of honest decision trees and random forests in the regression setting. In contrast to related literature, our proofs are elementary and follow the classical arguments used for smoothing methods. Under…
A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called \textit{anomalous}. Species trees that can generate such anomalous gene trees are said to be in the \textit{anomaly…
Recently, there has been interest in extending long-known results about the multispecies coalescent tree to other models of gene trees. Results about the gene duplication and loss (GDL) tree have mathematical proofs, including species tree…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
A novel approach rooted on the notion of consensus clustering, a strategy developed for community detection in complex networks, is proposed to cope with the heterogeneity that characterizes connectivity matrices in health and disease. The…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
Tree-based ensemble methods such as random forests, gradient-boosted trees, and Bayesianadditive regression trees have been successfully used for regression problems in many applicationsand research studies. In this paper, we study ensemble…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
We study the influence of the seed in random trees grown according to the uniform attachment model, also known as uniform random recursive trees. We show that different seeds lead to different distributions of limiting trees from a total…
Summary: Both theory and empirical evidence indicate that phylogenies (trees) of different genes (loci) do not display precisely matched topologies. This phylogenetic incongruence is attributed to the reticulated evolutionary history of…
We present convincing empirical evidence for an effective and general strategy for building accurate small models. Such models are attractive for interpretability and also find use in resource-constrained environments. The strategy is to…