Related papers: On the quartet distance given partial information
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
Given two phylogenetic trees on the same set of taxa X, the maximum parsimony distance d_MP is defined as the maximum, ranging over all characters c on X, of the absolute difference in parsimony score induced by c on the two trees. In this…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
We consider a neutral haploid population whose generations are not overlapping and whose size is large and constantly of $N$ individuals. Any generation is replaced by a new one and any individual has a single parent. We do not choose the…
We give a quasipolynomial-time algorithm for learning stochastic decision trees that is optimally resilient to adversarial noise. Given an $\eta$-corrupted set of uniform random samples labeled by a size-$s$ stochastic decision tree, our…
We focus on the average-case analysis: A function w : V -> Z+ is given which defines the likelihood for a node to be the one marked, and we want the strategy that minimizes the expected number of queries. Prior to this paper, very little…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
We generalize the results from [X.-D. Zhang, X.-P. Lv, Y.-H. Chen, \textit{Ordering trees by the Laplacian coefficients}, Linear Algebra Appl. (2009), doi:10.1016/j.laa.2009.04.018] on the partial ordering of trees with given diameter. For…
We determine the maximum distance between any two of the center, centroid, and subtree core among trees with a given order. Corresponding results are obtained for trees with given maximum degree and also for trees with given diameter. The…
We consider spanning trees of $n$ points in convex position whose edges are pairwise non-crossing. Applying a flip to such a tree consists in adding an edge and removing another so that the result is still a non-crossing spanning tree.…
The notion of task similarity is at the core of various machine learning paradigms, such as domain adaptation and meta-learning. Current methods to quantify it are often heuristic, make strong assumptions on the label sets across the tasks,…
Recently it was shown that, if the subtree and chain reduction rules have been applied exhaustively to two unrooted phylogenetic trees, the reduced trees will have at most 15k-9 taxa where k is the TBR (Tree Bisection and Reconnection)…
We bound the mean distance in a connected graph which is not a tree in function of its order $n$ and its girth $g$. On one hand, we show that mean distance is at most $\frac{n+1}{3}-\frac{g(g^2-4)}{12n(n-1)}$ if $g$ is even and at most…
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…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…