Related papers: The word problem and the metric for the Thompson-S…
The kTree problem is a special case of Subgraph Isomorphism where the pattern graph is a tree, that is, the input is an $n$-node graph $G$ and a $k$-node tree $T$, and the goal is to determine whether $G$ has a subgraph isomorphic to $T$.…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
We extend the theory of minimal absent words to (rooted and unrooted) trees, having edges labeled by letters from an alphabet $\Sigma$ of cardinality $\sigma$. We show that the set $\text{MAW}(T)$ of minimal absent words of a rooted (resp.…
This paper focuses on the well-known problem due to Stanley of whether two non-isomorphic trees can have the same $U$-polynomial (or, equivalently, the same chromatic symmetric function). We consider the $U_k$-polynomial, which is a…
We study a generalization of the Steiner tree problem, where we are given a weighted network $G$ together with a collection of $k$ subsets of its vertices and a root $r$. We wish to construct a minimum cost network such that the network…
In this paper, we focus on the prediction phase of a random forest and study the problem of representing a bag of decision trees using a smaller bag of decision trees, where we only consider binary decision problems on the binary domain and…
We give a unified solution to the conjugacy problem for Thompson's groups F, T, and V. The solution uses strand diagrams, which are similar in spirit to braids and generalize tree-pair diagrams for elements of Thompson's groups. Strand…
We introduce a new method for computing the word length of an element of Thompson's group F with respect to a "consecutive" generating set of the form X_n={x_0,x_1,...,x_n}, which is a subset of the standard infinite generating set for F.…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
For a $k$-tree $T$, we prove that the maximum local mean order is attained in a $k$-clique of degree $1$ and that it is not more than twice the global mean order. We also bound the global mean order if $T$ has no $k$-cliques of degree $2$…
The Steiner distance of a set of vertices in a graph is the fewest number of edges in any connected subgraph containing those vertices. The order-$k$ Steiner distance hypermatrix of an $n$-vertex graph is the $n \times \cdots \times n$ ($k$…
Higher-dimensional Thompson's groups nV are finitely presented groups described by Brin which generalize dyadic self-maps of the unit interval to dyadic self-maps of n-dimensional unit cubes. We describe some of the metric properties of…
We extend results regarding a combinatorial model introduced by Black, Drellich, and Tymoczko (2017+) which generalizes the folding of the RNA molecule in biology. Consider a word on alphabet $\{A_1, \overline{A}_1, \ldots, A_m,…
We derive lower and upper bounds on possible growth rates of certain sets of positive integers $A_k=\{1= a_1 < a_2 < ... < a_{k}\}$ such that all integers $n\in \{0, 1, 2, ..., ka_{k}\}$ can be represented as a sum of no more than $k$…
Let G be a group of automorphisms of a ranked poset Q and let N_{k} denote the number of orbits on the elements of rank k in Q. What can be said about the N_{k} for standard posets, such as finite projective spaces or the Boolean lattice?…
Given a finite word $w$ over a finite alphabet $V$, consider the graph with vertex set $V$ and with an edge between two elements of $V$ if and only if the two elements alternate in the word $w$. Such a graph is said to be word-representable…
The threshold-$k$ metric dimension ($\mathrm{Tmd}_k$) of a graph is the minimum number of sensors -- a subset of the vertex set -- needed to uniquely identify any vertex in the graph, solely based on its distances from the sensors, when the…
Recent years have witnessed a surge of biological interest in the minimum spanning tree (MST) problem for its relevance to automatic model construction using the distances between data points. Despite the increasing use of MST algorithms…