相关论文: Sound Colless-like balance indices for multifurcat…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
We introduce canonical correlation forests (CCFs), a new decision tree ensemble method for classification and regression. Individual canonical correlation trees are binary decision trees with hyperplane splits based on local canonical…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…
To understand the sample-to-sample fluctuations in disorder-generated multifractal patterns we investigate analytically as well as numerically the statistics of high values of the simplest model - the ideal periodic $1/f$ Gaussian noise. By…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
Containment-based trees encompass various handy structures such as B+-trees, R-trees and M-trees. They are widely used to build data indexes, range-queryable overlays, publish/subscribe systems both in centralized and distributed contexts.…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
For a tree $T$ and a function $f \colon E(T)\to \mathbb{S}^d$, the imbalance of a subtree $T'\subseteq T$ is given by $|\sum_{e \in E(T')} f(e)|$. The $d$-dimensional discrepancy of the tree $T$ is the minimum, over all functions $f$ as…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
Deep-learning has proved in recent years to be a powerful tool for image analysis and is now widely used to segment both 2D and 3D medical images. Deep-learning segmentation frameworks rely not only on the choice of network architecture but…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
It is a long-standing question of Stanley whether or not the chromatic symmetric function (CSF) distinguishes unrooted trees. Previously, the best computational result, due to Russell, proved that it distinguishes all trees with at most…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
There are many metrics available to compare phylogenetic trees since this is a fundamental task in computational biology. In this paper, we focus on one such metric, the $\ell^\infty$-cophenetic metric introduced by Cardona et al. This…