相关论文: A tree without leaves
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…
Let $\mathcal{B}$ be the set of rooted trees containing an infinite binary subtree starting at the root. This set satisfies the metaproperty that a tree belongs to it if and only if its root has children $u$ and $v$ such that the subtrees…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
Staged trees are probabilistic graphical models capable of representing any class of non-symmetric independence via a coloring of its vertices. Several structural learning routines have been defined and implemented to learn staged trees…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
The weighted ancestor problem is a well-known generalization of the predecessor problem to trees. It is known to require $\Omega(\log\log n)$ time for queries provided $O(n\mathop{\mathrm{polylog}} n)$ space is available and weights are…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
Jigsaw puzzle solving is an intriguing problem which has been explored in computer vision for decades. This paper focuses on a specific variant of the problem - solving puzzles with eroded boundaries. Such erosion makes the problem…
We investigate the statistics of trees grown from some initial tree by attaching links to preexisting vertices, with attachment probabilities depending only on the valence of these vertices. We consider the asymptotic mass distribution that…
Tree-like tableaux are certain fillings of Ferrers diagrams originally introduced by Aval et al., which are in simple bijections with permutation tableaux coming from Postnikov's study of totally nonnegative Grassmanian and alternative…
We find a duality between two well-known trees, the Calkin-Wilf tree and the Stern-Brocot tree, derived from cluster algebra theory. The vertex sets of these trees are the set of rational numbers, and they have cluster structures induced by…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…
It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict…
P\'olya trees are rooted, unlabeled trees on $n$ vertices. This paper gives an efficient, new way to generate P\'olya trees. This allows comparing typical unlabeled and labeled tree statistics and comparing asymptotic theorems with…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
A uniform attachment tree is a random tree that is generated dynamically. Starting from a fixed "seed" tree, vertices are added sequentially by attaching each vertex to an existing vertex chosen uniformly at random. Upon observing a large…
We consider a general metric Steiner problem which is of finding a set $\mathcal{S}$ with minimal length such that $\mathcal{S} \cup A$ is connected, where $A$ is a given compact subset of a given complete metric space $X$; a solution is…
A convincing physical picture for the Lyman-alpha forest has emerged from simulations and related semi-analytic studies of structure formation models. Observations can be be used in the context of this picture to study cosmology using the…
We give a simple graph-theoretic proof of a classical result due to C. St. J. A. Nash-Williams on covering graphs by forests. Moreover we derive a slight generalisation of this statement where some edges are preassigned to distinct forests.
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…