Related papers: Species tree estimation using Neighbor Joining

Regression trees and their ensemble methods are popular methods for nonparametric regression: they combine strong predictive performance with interpretable estimators. To improve their utility for locally smooth response surfaces, we study…

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…

We present a novel method of stacking decision trees by projection into an ordered time split out-of-fold (OOF) one nearest neighbor (1NN) space. The predictions of these one nearest neighbors are combined through a linear model. This…

Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…

We introduce random spatial forests, a method of bagging regression trees allowing for spatial correlation. Our main contribution is the development of a computationally efficient tree building algorithm which selects each split of the tree…

Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene…

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…

Recent studies have shown that Dense Retrieval (DR) techniques can significantly improve the performance of first-stage retrieval in IR systems. Despite its empirical effectiveness, the application of DR is still limited. In contrast to…

Approximate nearest neighbor algorithms are used to speed up nearest neighbor search in a wide array of applications. However, current indexing methods feature several hyperparameters that need to be tuned to reach an acceptable…

Recursive partitioning is the core of several statistical methods including CART, random forest, and boosted trees. Despite the popularity of tree based methods, to date, there did not exist methods for combining multiple trees into a…

Accurate and consistent methods for counting trees based on remote sensing data are needed to support sustainable forest management, assess climate change mitigation strategies, and build trust in tree carbon credits. Two-dimensional remote…

The k-d tree is a classic binary space-partitioning tree used to organize points in k-dimensional space. While used in computational geometry and graphics, the data structure has a long history of application in nearest neighbor search. The…

Label ranking aims to learn a mapping from instances to rankings over a finite number of predefined labels. Random forest is a powerful and one of the most successful general-purpose machine learning algorithms of modern times. In this…

Estimating a joint Highest Posterior Density credible set for a multivariate posterior density is challenging as dimension gets larger. Credible intervals for univariate marginals are usually presented for ease of computation and…

Convolution trees, loopy belief propagation, and fast numerical p-convolution are combined for the first time to efficiently solve networks with several additive constraints between random variables. An implementation of this "convolution…

Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…

The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…

Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…

Urban trees help regulate temperature, reduce energy consumption, improve urban air quality, reduce wind speeds, and mitigating the urban heat island effect. Urban trees also play a key role in climate change mitigation and global warming…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…