相关论文: Reconstructing Trees from Subtree Weights

A {\em tree cover} of a metric space $(X,d)$ is a collection of trees, so that every pair $x,y\in X$ has a low distortion path in one of the trees. If it has the stronger property that every point $x\in X$ has a single tree with low…

We destroy a finite tree of size $n$ by cutting its edges one after the other and in uniform random order. Informally, the associated cut-tree describes the genealogy of the connected components created by this destruction process. We…

Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…

The constant rate birth--death process is a popular null model for speciation and extinction. If one removes extinct and non-sampled lineages, this process induces `reconstructed trees' which describe the relationship between extant…

Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…

In this note we analyze the performance of a simple root-finding algorithm in uniform attachment trees. The leaf-stripping algorithm recursively removes all leaves of the tree for a carefully chosen number of rounds. We show that, with…

We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…

We present a method for recovering the structure of a plant directly from a small set of widely-spaced images. Structure recovery is more complex than shape estimation, but the resulting structure estimate is more closely related to…

Humans recognize object structure from both their appearance and motion; often, motion helps to resolve ambiguities in object structure that arise when we observe object appearance only. There are particular scenarios, however, where…

Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…

In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…

Let ${\cal T}=(T,w)$ be a positive-weighted tree with at least $n$ vertices. For any $i,j \in \{1,...,n\}$, let $D_{i,j} ({\cal T})$ be the weight of the unique path in $T$ connecting $i$ and $j$. The $D_{i,j} ({\cal T})$ are called…

A common approach to implementing similarity search applications is the usage of distance functions, where small distances indicate high similarity. In the case of metric distance functions, metric index structures can be used to accelerate…

We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…

In this paper we investigate the use of the concept of tree dimension in Horn clause analysis and verification. The dimension of a tree is a measure of its non-linearity - for example a list of any length has dimension zero while a complete…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…

In the $L_0$ Fitting Tree Metrics problem, we are given all pairwise distances among the elements of a set $V$ and our output is a tree metric on $V$. The goal is to minimize the number of pairwise distance disagreements between the input…

A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…