Related papers: Resampling Residuals on Phylogenetic Trees: Extend…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…
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…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
We devise a generalization of tree approximation that generates conforming meshes, i.e., meshes with a particular structure like edge-to-edge triangulations. A key feature of this generalization is that the choices of the cells to be…
We present a new finite-time analysis of the estimation error of the Ordinary Least Squares (OLS) estimator for stable linear time-invariant systems. We characterize the number of observed samples (the length of the observed trajectory)…
The usual Euclidean distance may be generalized to extended objects such as polymers or membranes. Here, this distance is used for the first time as a cost function to align structures. We examined the alignment of extended strands to…
Partial least squares (PLS) is a dimensionality reduction technique used as an alternative to ordinary least squares (OLS) in situations where the data is colinear or high dimensional. Both PLS and OLS provide mean based estimates, which…
We consider random forests and LASSO methods for model-based small area estimation when the number of areas with sampled data is a small fraction of the total areas for which estimates are required. Abundant auxiliary information is…
Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by…
It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
Concerning bivariate least squares linear regression, the classical approach pursued for functional models in earlier attempts is reviewed using a new formalism in terms of deviation (matrix) traces. Within the framework of classical error…
Single-cell omics enable the profiles of cells, which contain large numbers of biological features, to be quantified. Cluster analysis, a dimensionality reduction process, is used to reduce the dimensions of the data to make it…
Balanced minimum evolution (BME) is a statistically consistent distance-based method to reconstruct a phylogenetic tree from an alignment of molecular data. In 2000, Pauplin showed that the BME method is equivalent to optimizing a linear…
Logistic regression is a standard method in multivariate analysis for binary outcome data in epidemiological and clinical studies; however, the resultant odds-ratio estimates fail to provide directly interpretable effect measures. The…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
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…