Related papers: From unicellular fatgraphs to trees
A tree T is invertible if and only if T has a perfect matching. Godsil considers an invertible tree T and finds that the inverse of the adjacency matrix of T has entries in {0, 1, -1} and is the signed adjacency matrix of a graph which…
In this work, we present a neural approach to reconstructing rooted tree graphs describing hierarchical interactions, using a novel representation we term the Lowest Common Ancestor Generations (LCAG) matrix. This compact formulation is…
A spanning tree $T$ of a connected graph $G$ is a subgraph of $G$ that is a tree covers all vertices of $G$. The leaf distance of $T$ is defined as the minimum of distances between any two leaves of $T$. A fractional matching of a graph $G$…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
We study a generating function for the sum over fatgraphs with specified valences of vertices and faces, inversely weighted by the order of their symmetry group. A compact expression is found for general (i.e. non necessarily connected)…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
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 introduce a decomposition method for the distributed calculation of exact Euclidean Minimum Spanning Trees in high dimensions (where sub-quadratic algorithms are not effective), or more generalized geometric-minimum spanning trees of…
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…
An edge-card of a graph G is a subgraph formed by deleting an edge. The edge-reconstruction number of a graph G, ern(G), is the minimum number of edge-cards required to determine G up to isomorphism. A da-ecard is an edge-card which also…
Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…
Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…
A unicellular map is a map which has only one face. We give a bijection between a dominant subset of rooted unicellular maps of fixed genus and a set of rooted plane trees with distinguished vertices. The bijection applies as well to the…
Untangling is a process in which some vertices of a planar graph are moved to obtain a straight-line plane drawing. The aim is to move as few vertices as possible. We present an algorithm that untangles the cycle graph C_n while keeping at…
A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…
The edge-reconstruction number ern$(G)$ of a graph $G$ is equal to the minimum number of edge-deleted subgraphs $G-e$ of $G$ which are sufficient to determine $G$ up to isomorphsim. Building upon the work of Molina and using results from…
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…
Much information about a graph can be obtained by studying its spanning trees. On the other hand, a graph can be regarded as a 1-dimensional cell complex, raising the question of developing a theory of trees in higher dimension. As observed…
A straight-line drawing $\delta$ of a planar graph $G$ need not be plane, but can be made so by \emph{untangling} it, that is, by moving some of the vertices of $G$. Let shift$(G,\delta)$ denote the minimum number of vertices that need to…