Related papers: Lassoing and corraling rooted phylogenetic trees
We generalize the uniform spanning tree to construct a family of determinantal measures on essential spanning forests on periodic planar graphs in which every component tree is bi-infinite. Like the uniform spanning tree, these measures…
We identify the complexity of the classification problem for automorphisms of a given countable regularly branching tree up to conjugacy. We consider both the rooted and unrooted cases. Additionally, we calculate the complexity of the…
Clustering is a well-known and studied problem, one of its variants, called contiguity-constrained clustering, accepts as a second input a graph used to encode prior information about cluster structure by means of contiguity constraints…
A complete representation of 3D objects requires characterizing the space of deformations in an interpretable manner, from articulations of a single instance to changes in shape across categories. In this work, we improve on a prior…
It is folklore that tree-width is monotone under taking subgraphs (i.e. injective graph homomorphisms) and contractions (certain kinds of surjective graph homomorphisms). However, although tree-width is obviously not monotone under any…
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We provide time- and sample-efficient algorithms for learning and testing latent-tree Ising models, i.e. Ising models that may only be observed at their leaf nodes. On the learning side, we obtain efficient algorithms for learning a…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
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…
A high degree of structural complexity arises in dynamic neuronal dendrites due to extensive branching patterns and diverse spine morphologies, which enable the nervous system to adjust function, construct complex input pathways and thereby…
Motivated by the work of Lov\'asz and Szegedy on the convergence and limits of dense graph sequences, we investigate the convergence and limits of finite trees with respect to sampling in normalized distance. Based on separable real trees,…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
A tanglegram consists of two rooted binary trees with the same number of leaves and a perfect matching between the leaves of the trees. Given a size-$n$ tanglegram, i.e., a tanglegram for two trees with $n$ leaves, a multiset of induced…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…