Related papers: Random Ancestor Trees
Neural Networks and Decision Trees: two popular techniques for supervised learning that are seemingly disconnected in their formulation and optimization method, have recently been combined in a single construct. The connection pivots on…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In this article, we construct a generalization of the Blum-Fran\c{c}ois Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric…
We investigate properties of node centrality in random growing tree models. We focus on a measure of centrality that computes the maximum subtree size of the tree rooted at each node, with the most central node being the tree centroid. For…
We study the spreading dynamics on graphs with a power law degree distribution p_k ~ k^-gamma with 2<gamma<3, as an example of a branching process with diverging reproductive number. We provide evidence that the divergence of the second…
In this paper we introduce a model of spatial network growth in which nodes are placed at randomly selected locations on a unit square in $\mathbb{R}^2$, forming new connections to old nodes subject to the constraint that edges do not…
We propose a simple preferential attachment model of growing network using the complementary probability of Barab\'asi-Albert (BA) model, i.e., $\Pi(k_i) \propto 1-\frac{k_i}{\sum_j k_j}$. In this network, new nodes are preferentially…
We propose a method for cutting down a random recursive tree that focuses on its higher degree vertices. Enumerate the vertices of a random recursive tree of size $n$ according to a decreasing order of their degrees; namely, let…
We propose a general class of co-evolving tree network models driven by local exploration where new vertices attach to the current network via randomly sampling a vertex and then exploring the graph for a random number of steps in the…
We study the organization and dynamics of growing directed networks. These networks are built by adding nodes successively in such a way that each new node has $K$ directed links to the existing ones. The organization of a growing directed…
Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
In a recent paper, McDiarmid, Semple, and Welsh (2015) showed that the number of tree-child networks with $n$ leaves has the factor $n^{2n}$ in its main asymptotic growth term. In this paper, we improve this by completely identifying the…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
We consider a model of random tree growth, where at each time unit a new vertex is added and attached to an already existing vertex chosen at random. The probability with which a vertex with degree $k$ is chosen is proportional to $w(k)$,…
We present a model for growing information networks where the ageing of a node depends on the time at which it entered the network and on the last time it was cited. The model is shown to undergo a transition from a small-world to…
This paper studies the enumeration of seven subclasses of level-$2$ phylogenetic networks under various planarity and structural constraints, including terminal planar, tree-child, and galled networks. We derive their exponential generating…
Inspired by biological dynamics, we consider a growth Markov process taking values on the space of rooted binary trees, similar to the Aldous-Shields model. Fix $n\ge 1$ and $\beta>0$. We start at time 0 with the tree composed of a root…
We consider local leaders in random uncorrelated networks, i.e. nodes whose degree is higher or equal than the degree of all of their neighbors. An analytical expression is found for the probability of a node of degree $k$ to be a local…
We generalize the poissonian evolving random graph model of Bauer and Bernard to deal with arbitrary degree distributions. The motivation comes from biological networks, which are well-known to exhibit non poissonian degree distribution. A…