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A graph is reconstructible if it is determined up to isomorphism by the multiset of its proper induced subgraphs. The reconstruction conjecture postulates that every graph of order at least 3 is reconstructible. We show that interval graphs…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
Treewidth is a well-studied decompositional parameter to measure the tree-likeness of a graph. While the propositional satisfiability problem (SAT) is known to be tractable when parameterized by the treewidth of the underlying primal graph,…
We study semigroups of labellings associated to a graph. These generalize the Jukes-Cantor model and phylogenetic toric varieties defined by Buczy\'nska. Our main theorem bounds the degree of the generators of the semigroup by g+1 when the…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
The Subgraph Isomorphism problem is of considerable importance in computer science. We examine the problem when the pattern graph H is of bounded treewidth, as occurs in a variety of applications. This problem has a well-known algorithm via…
A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…
The Graph Isomorphism problem restricted to graphs of bounded treewidth or bounded tree distance width are known to be solvable in polynomial time [Bod90],[YBFT99]. We give restricted space algorithms for these problems proving the…
Cut ideals, introduced by Sturmfels and Sullivant, are used in phylogenetics and algebraic statistics. We study the minimal free resolutions of cut ideals of tree graphs. By employing basic methods from topological combinatorics, we obtain…
We study the problem of enumerating all rooted directed spanning trees (arborescences) of a directed graph (digraph) $G=(V,E)$ of $n$ vertices. An arborescence $A$ consisting of edges $e_1,\ldots,e_{n-1}$ can be represented as a monomial…
In many real-world applications data come as discrete metric spaces sampled around 1-dimensional filamentary structures that can be seen as metric graphs. In this paper we address the metric reconstruction problem of such filamentary…
We construct tree-decompositions of graphs that distinguish all their k-blocks and tangles of order k, for any fixed integer k. We describe a family of algorithms to construct such decompositions, seeking to maximize their diversity subject…
The Reeb graph of a scalar function defined on a domain gives a topologically meaningful summary of that domain. Reeb graphs have been shown in the past decade to be of great importance in geometric processing, image processing, computer…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…
We investigate path-, ray- and branch spaces of trees, certain topological spaces naturally associated with order theoretic trees, and provide topological characterisations for these spaces in terms of the existence of certain kinds of…
It is known that there is a Hopf algebra structure on the vector space with basis all heap-ordered trees. We give a new bialgebra structure on the space with basis all permutations and show that there is a direct bialgebra isomorphism…
A linear forest is a collection of vertex-disjoint paths. The Linear Arboricity Conjecture states that every graph of maximum degree $\Delta$ can be decomposed into at most $\lceil(\Delta+1)/2\rceil$ linear forests. We prove that $\Delta/2…
A graph is Cartesian decomposable if it is isomorphic to a Cartesian product of (more than one) strictly smaller graphs, each of which has more than one vertex and admits no such decomposition. These smaller graphs are called the…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
Given a class of graphs $\mathcal{H}$, the problem $\oplus\mathsf{Sub}(\mathcal{H})$ is defined as follows. The input is a graph $H\in \mathcal{H}$ together with an arbitrary graph $G$. The problem is to compute, modulo $2$, the number of…