相关论文: Distorted metrics on trees and phylogenetic forest…

Decision trees are popular machine learning models that are simple to build and easy to interpret. Even though algorithms to learn decision trees date back to almost 50 years, key properties affecting their generalization error are still…

Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…

Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…

In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of…

A classical result in distance based tree-reconstruction characterizes when for a distance $D$ on some finite set $X$ there exist a uniquely determined dendrogram on $X$ (essentially a rooted tree $T=(V,E)$ with leaf set $X$ and no degree…

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

Evolutionary relationships between species are represented by phylogenetic trees, but these relationships are subject to uncertainty due to the random nature of evolution. A geometry for the space of phylogenetic trees is necessary in order…

Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…

An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…

Graham-Pollak showed that for $D = D_T$ the distance matrix of a tree $T$, det$(D)$ depends only on its number of edges. Several other variants of $D$, including directed/multiplicative/$q$- versions were studied, and always, det$(D)$…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…

In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…

Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number 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…

A Discriminative Deep Forest (DisDF) as a metric learning algorithm is proposed in the paper. It is based on the Deep Forest or gcForest proposed by Zhou and Feng and can be viewed as a gcForest modification. The case of the fully…

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…

In this paper we describe an algorithm that embeds a graph metric $(V,d_G)$ on an undirected weighted graph $G=(V,E)$ into a distribution of tree metrics $(T,D_T)$ such that for every pair $u,v\in V$, $d_G(u,v)\leq d_T(u,v)$ and…

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…