Related papers: Neighbor joining with phylogenetic diversity estim…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Manifold learning now plays a very important role in machine learning and many relevant applications. Although its superior performance in dealing with nonlinear data distribution, data sparsity is always a thorny knot. There are few…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
A distance-based method to reconstruct a phylogenetic tree with $n$ leaves takes a distance matrix, $n \times n$ symmetric matrix with $0$s in the diagonal, as its input and reconstructs a tree with $n$ leaves using tools in combinatorics.…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
Given an ensemble of randomized regression trees, it is possible to restructure them as a collection of multilayered neural networks with particular connection weights. Following this principle, we reformulate the random forest method of…
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…
The paper presents an iterative version of join-tree clustering that applies the message passing of join-tree clustering algorithm to join-graphs rather than to join-trees, iteratively. It is inspired by the success of Pearl's belief…
We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the currently best algorithms for the binary case. The size of an…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
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…
In this article, we propose a new fast nearest neighbor search algorithm, based on vector quantization. Like many other branch and bound search algorithms [1,10], a preprocessing recursively partitions the data set into disjointed subsets…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…
Suppose $V$ is an $n$-element set where for each $x \in V$, the elements of $V \setminus \{x\}$ are ranked by their similarity to $x$. The $K$-nearest neighbor graph is a directed graph including an arc from each $x$ to the $K$ points of $V…
Most phylogenetic analyses result in a sample of trees, but summarizing and visualizing these samples can be challenging. Consensus trees often provide limited information about a sample, and so methods such as consensus networks,…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
This paper proposes FREEtree, a tree-based method for high dimensional longitudinal data with correlated features. Popular machine learning approaches, like Random Forests, commonly used for variable selection do not perform well when there…
We address the problem of recovering multiple structures of different classes in a dataset contaminated by noise and outliers. In particular, we consider geometric structures defined by a mixture of underlying parametric models (e.g. planes…