Related papers: Testing the Agreement of Trees with Internal Label…

The independence number of a tree decomposition is the size of a largest independent set contained in a single bag. The tree-independence number of a graph $G$ is the minimum independence number of a tree decomposition of $G$. As shown…

Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…

We study the complexity and expressive power of conjunctive queries over unranked labeled trees represented using a variety of structure relations such as ``child'', ``descendant'', and ``following'' as well as unary relations for node…

Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…

We focus on counting the number of labeled graphs on $n$ vertices and treewidth at most $k$ (or equivalently, the number of labeled partial $k$-trees), which we denote by $T_{n,k}$. So far, only the particular cases $T_{n,1}$ and $T_{n,2}$…

A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…

A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…

The well-studied Tai mapping between two rooted labeled trees $T_1(V_1, E_1)$ and $T_2(V_2, E_2)$ defines a one-to-one mapping between nodes in $T_1$ and $T_2$ that preserves ancestor relationship. For unordered trees the problem of finding…

A $k$-decision tree $t$ (or $k$-tree) is a recursive partition of a matrix (2D-signal) into $k\geq 1$ block matrices (axis-parallel rectangles, leaves) where each rectangle is assigned a real label. Its regression or classification loss to…

Let ${\cal T}=(T,w)$ be a weighted finite tree with leaves $1,..., n$. For any $I :=\{i_1,..., i_k \} \subset \{1,...,n\}$, let $D_I ({\cal T})$ be the weight of the minimal subtree of $T$ connecting $i_1,..., i_k$; the $D_{I} ({\cal T})$…

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…

Given a connected undirected graph $G$, a spanning tree is a subgraph $T$ of $G$ such that $V(T) = V(G)$ and $T$ is a tree. A collection of $\ell$ spanning trees $T_1,\ldots,T_\ell$ is pairwise $k$-diverse if for every $i \neq j$, $|E(T_i)…

We consider the problem of testing if two input forests are isomorphic or are far from being so. An algorithm is called an $\varepsilon$-tester for forest-isomorphism if given an oracle access to two forests $G$ and $H$ in the adjacency…

Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…

We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…

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…

A new 2-parameter family of central structures in trees, called central forests, is introduced. Minieka's $m$-center problem and McMorris's and Reid's central-$k$-tree can be seen as special cases of central forests in trees. A central…

A binary tanglegram is a pair <S,T> of 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 or software engineering, it is required…

Whereas for strings, higher-order empirical entropy is the standard entropy measure, several different notions of empirical entropy for trees have been proposed in the past, notably label entropy, degree entropy, conditional versions of the…

We study the problem of learning a hierarchical tree representation of data from labeled samples, taken from an arbitrary (and possibly adversarial) distribution. Consider a collection of data tuples labeled according to their hierarchical…