相关论文: Universal rooted phylogenetic tree shapes and univ…

A partial order is called semilinear iff the upper bounds of each element are linearly ordered and any two elements have a common upper bound. There exists, up to isomorphism, a unique countable existentially closed semilinear order, which…

Motivated by questions in number theory, Myerson asked how small the sum of 5 complex nth roots of unity can be. We obtain a uniform bound of O(n^{-4/3}) by perturbing the vertices of a regular pentagon, improving to O(n^{-7/3}) infinitely…

We present a randomized algorithm for reconstructing directed rooted trees of $n$ nodes and node degree at most $d$, by asking at most $O(dn\log^2 n)$ path queries. Each path query takes as input an origin node and a target node, and…

We provide a logarithmic upper bound for the disentangling number on unordered lists of leaf labeled trees. This results is useful for analyzing phylogenetic mixture models. The proof depends on interpreting multisets of trees as high…

Chung and Graham considered the problem of minimizing the number of edges in an $n$-vertex graph containing all $n$-vertex trees as a subgraph. They showed that such a graph has at least $\frac{1}{2}n \log{n}$ edges. In this note, we…

Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…

Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…

In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…

The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…

It is known that any planar graph with diameter D has treewidth O(D), and this fact has been used as the basis for several planar graph algorithms. We investigate the extent to which similar relations hold in other graph families. We show…

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…

This paper addresses the following questions for a given tree $T$ and integer $d\geq2$: (1) What is the minimum number of degree-$d$ subtrees that partition $E(T)$? (2) What is the minimum number of degree-$d$ subtrees that cover $E(T)$? We…

Unranked trees can be represented using their minimal dag (directed acyclic graph). For XML this achieves high compression ratios due to their repetitive mark up. Unranked trees are often represented through first child/next sibling (fcns)…

We ask the question, which oriented trees $T$ must be contained as subgraphs in every finite directed graph of sufficiently large minimum out-degree. We formulate the following simple condition: all vertices in $T$ of in-degree at least $2$…

We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…

The quantity that captures the asymptotic value of the maximum number of appearances of a given topological tree (a rooted tree with no vertices of outdegree $1$) $S$ with $k$ leaves in an arbitrary tree with sufficiently large number of…

We consider two varieties of labeled rooted trees, and the probability that a vertex chosen from all vertices of all trees of a given size uniformly at random has a given rank. We prove that this probability converges to a limit as the tree…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

We give a series of new lower bounds on the minimum number of vertices required by a graph to contain every graph of a given family as induced subgraph. In particular, we show that this induced-universal graph for $n$-vertex planar graphs…

Codes over trees were introduced recently to bridge graph theory and coding theory with diverse applications in computer science and beyond. A central challenge lies in determining the maximum number of labelled trees over $n$ nodes with…