Related papers: On Injective Embeddings of Tree Patterns
We discovered that certain patterns called injective patterns remain stable during the revolution process, allowing us to create many reversible CA simply by using them to design the revolution rules. By examining injective patterns, we…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Trees are partial orders in which every element has a linearly ordered set of predecessors. Here we initiate the exploration of the structural theory of trees with the study of different notions of \emph{branching in trees} and of…
We study the influence of the seed in random trees grown according to the uniform attachment model, also known as uniform random recursive trees. We show that different seeds lead to different distributions of limiting trees from a total…
Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…
Recent theory work has found that a special type of spatial partition tree - called a random projection tree - is adaptive to the intrinsic dimension of the data from which it is built. Here we examine this same question, with a combination…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
We investigate the size of vertex confidence sets for including part of (or the entirety of) the seed in seeded uniform attachment trees, given knowledge of some of the seed's properties, and with a prescribed probability of failure. We…
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…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
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…
The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a…
We study effective randomness-preserving transformations of path-incompressible trees. Some path-incompressible trees with infinitely many paths do not compute perfect path-random trees with computable oracle-use. Sparse perfect…
The characteristics (or numerical patterns) of a feature vector in the transform domain of a perturbation model differ significantly from those of its corresponding feature vector in the input domain. These differences - caused by the…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
A learning algorithm is presented which given the structure of a causal tree, will estimate its link probabilities by sequential measurements on the leaves only. Internal nodes of the tree represent conceptual (hidden) variables…
We study the crossing-minimization problem in a layered graph drawing of planar-embedded rooted trees whose leaves have a given total order on the first layer, which adheres to the embedding of each individual tree. The task is then to…
We study inferring a tree-structured representation from a single image for object shading. Prior work typically uses the parametric or measured representation to model shading, which is neither interpretable nor easily editable. We propose…