Related papers: Extremal Distances for Subtree Transfer Operations…
The register function (or Horton-Strahler number) of a binary tree is a well-known combinatorial parameter. We study a reduction procedure for binary trees which offers a new interpretation for the register function as the maximal number of…
Binary neural networks (BNNs) have been widely adopted to reduce the computational cost and memory storage on edge-computing devices by using one-bit representation for activations and weights. However, as neural networks become…
The space of phylogenetic trees arises naturally in tropical geometry as the tropical Grassmannian. Tropical geometry therefore suggests a natural notion of a tropical path between two trees, given by a tropical line segment in the tropical…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
A fringe subtree of a rooted tree is a subtree induced by one of the vertices and all its descendants. We consider the problem of estimating the number of distinct fringe subtrees in two types of random trees: simply generated trees and…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Consider a binary tree, to the vertices of which are assigned independent Bernoulli random variables with mean $p\leq1/2$. How many of these Bernoullis one must look at in order to find a path of length $n$ from the root which maximizes, up…
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
Data augmentation methods for neural machine translation are particularly useful when limited amount of training data is available, which is often the case when dealing with low-resource languages. We introduce a novel augmentation method,…
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…
We consider additive functionals $X_n(\phi)$ with small toll functions on split trees and a generalization of split trees, which we call fractional split trees, where the split vector does not need to sum up to 1. These additive functionals…
The semi-streaming model is a variant of the streaming model frequently used for the computation of graph problems. It allows the edges of an $n$-node input graph to be read sequentially in $p$ passes using $\tilde{O}(n)$ space. In this…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Flips in triangulations of convex polygons arise in many different settings. They are isomorphic to rotations in binary trees, define edges in the 1-skeleton of the Associahedron and cover relations in the Tamari Lattice. The complexity of…
Rooted plane trees are reduced by four different operations on the fringe. The number of surviving nodes after reducing the tree repeatedly for a fixed number of times is asymptotically analyzed. The four different operations include…
For an undirected tree with $n$ edges labelled by single letters, we consider its substrings, which are labels of the simple paths between pairs of nodes. We prove that there are $O(n^{1.5})$ different palindromic substrings. This solves an…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Tree transducers are formal automata that transform trees into other trees. Many varieties of tree transducers have been explored in the automata theory literature, and more recently, in the machine translation literature. In this paper I…