Related papers: Maximally probable tree topologies with $r$-furcat…

We study random labelings of graphs conditioned on a small number (typically one or two) peaks, i.e., local maxima. We show that the boundaries of level sets of a random labeling of a square with a single peak have dimension 2, in a…

We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…

We provide a short combinatorial proof of Cayley's formula by means of a bijective map to an outcome space of an urn-drawing problem. Furthermore we introduce an algebraic structure on the set of labeled trees, which provides a more…

Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum…

Given a graph and a root, the Maximum Bounded Rooted-Tree Packing (MBRTP) problem aims at finding K rooted-trees that span the largest subset of vertices, when each vertex has a limited outdegree. This problem is motivated by peer-to-peer…

We study a fragmentation of the $\mathbf p$-trees of Camarri and Pitman [Elect. J. Probab., vol. 5, pp. 1--18, 2000]. We give exact correspondences between the $\mathbf p$-trees and trees which encode the fragmentation. We then use these…

We study the asymptotic shape of random unlabelled graphs subject to certain subcriticality conditions. The graphs are sampled with probability proportional to a product of Boltzmann weights assigned to their $2$-connected components. As…

We prove local convergence results for the uniformly random, labelled or unlabelled, graphs from subcritical families. As an example special case, we prove Benjamini-Schramm convergence for the uniform random unlabelled tree. We introduce a…

The seminal work of Chow and Liu (1968) shows that approximation of a finite probabilistic system by Markov trees can achieve the minimum information loss with the topology of a maximum spanning tree. Our current paper generalizes the…

The goal of this paper is to provide a general purpose result for the coupling of exploration processes of random graphs, both undirected and directed, with their local weak limits when this limit is a marked Galton-Watson process. This…

We study a broad class of random labelled trees in which integer-valued labels evolve along the edges according to increments in $\{-1, 0, 1\}$. These models include e.g. branching random walks, embedded complete and incomplete binary…

Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…

We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…

Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…

For an $n$-vertex graph $G$, let $z(G;k)$ denote the number of zero forcing sets of size $k$. A conjecture of Boyer et al. asserts that the path $P_n$ maximizes these numbers coefficientwise among all $n$-vertex graphs; equivalently, the…

The need to learn from positive and unlabeled data, or PU learning, arises in many applications and has attracted increasing interest. While random forests are known to perform well on many tasks with positive and negative data, recent PU…

We propose an algorithm named best-scored random forest for binary classification problems. The terminology "best-scored" means to select the one with the best empirical performance out of a certain number of purely random tree candidates…

Given a gene-tree labeled topology $G$ and a species tree $S$, the "ancestral configurations" at an internal node $k$ of $S$ represent the combinatorially different sets of gene lineages that can be present at $k$ when all possible…

In this article we consider several probabilistic processes defining random grapha. One of these processes appeared recently in connection with a factorization problem in the symmetric group. For each of the probabilistic processes, we…

Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical representations of tree topologies, known as F-matrices, allow for…