Related papers: Reticulation-visible networks
In our previous work, we introduced the random $k$-cut number for rooted graphs. In this paper, we show that the distribution of the $k$-cut number in complete binary trees of size $n$, after rescaling, is asymptotically a periodic function…
We give algorithms with provable guarantees that learn a class of deep nets in the generative model view popularized by Hinton and others. Our generative model is an $n$ node multilayer neural net that has degree at most $n^{\gamma}$ for…
Consider the following fundamental learning problem: given input examples $x \in \mathbb{R}^d$ and their vector-valued labels, as defined by an underlying generative neural network, recover the weight matrices of this network. We consider…
Given a set $S$ of points in the plane, a geometric network for $S$ is a graph $G$ with vertex set $S$ and straight edges. We consider a broadcasting situation, where one point $r \in S$ is a designated source. Given a dilation factor…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…
Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…
A graph is rectilinear planar if it admits a planar orthogonal drawing without bends. While testing rectilinear planarity is NP-hard in general (Garg and Tamassia, 2001), it is a long-standing open problem to establish a tight upper bound…
Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…
For a given graph G and integers b,f >= 0, let S be a subset of vertices of G of size b+1 such that the subgraph of G induced by S is connected and S can be separated from other vertices of G by removing f vertices. We prove that every…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
For successful estimation, the usual network tomography algorithms crucially require i) end-to-end data generated using multicast probe packets, real or emulated, and ii) the network to be a tree rooted at a single sender with destinations…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
If $x\in V(G)$, then $S\subseteq V(G)\setminus\{x\}$ is an $x$-visibility set if for any $y\in S$ there exists a shortest $x,y$-path avoiding $S$. The $x$-visibility number $v_x(G)$ is the maximum cardinality of an $x$-visibility set, and…
We present a deterministic algorithm that given a tree T with n vertices, a starting vertex v and a slackness parameter epsilon > 0, estimates within an additive error of epsilon the cover and return time, namely, the expected time it takes…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
An out-tree $T$ of a directed graph $D$ is a rooted tree subgraph with all arcs directed outwards from the root. An out-branching is a spanning out-tree. By $l(D)$ and $l_s(D)$ we denote the maximum number of leaves over all out-trees and…
A phylogenetic network is a simplex (or 1-component tree-child) network if the child of every reticulation node is a network leaf. Simplex networks are a superclass of phylogenetic trees and a subclass of tree-child networks. Generalizing…