Related papers: Reticulation-visible networks
Over some types of trees with a given number of vertices, which trees minimize or maximize the total number of subtrees or leaf containing subtrees are studied. Here are some of the main results:\ (1)\, Sharp upper bound on the total number…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
In this paper, we give a constructive proof of the fact that the treewidth of a graph is at most its divisorial gonality. The proof gives a polynomial time algorithm to construct a tree decomposition of width at most $k$, when an effective…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
We contribute towards resolving the open question of how many hidden layers are required in ReLU networks for exactly representing all continuous and piecewise linear functions on $\mathbb{R}^d$. While the question has been resolved in…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
We study the growth behaviour of rational linear recurrence sequences. We show that for low-order sequences, divergence is decidable in polynomial time. We also exhibit a polynomial-time algorithm which takes as input a divergent rational…
The robust and efficient recognition of visual relations in images is a hallmark of biological vision. We argue that, despite recent progress in visual recognition, modern machine vision algorithms are severely limited in their ability to…
It is proved that the rectilinear crossing number of every graph with bounded tree-width and bounded degree is linear in the number of vertices. **** This paper has been withdrawn by the author. **** The results have been superseeded by the…
Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we improve known parameterized algorithms and…
We study the expressivity of rational neural networks (RationalNets) through the lens of algebraic geometry. We consider rational functions that arise from a given RationalNet to be tuples of fractions of homogeneous polynomials of fixed…
Let X be a complex, Gorenstein, Q-factorial, toric Fano variety. We prove two conjectures on the maximal Picard number of X in terms of its dimension and its pseudo-index, and characterize the boundary cases. Equivalently, we determine the…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…
Neural networks with piecewise linear activation functions, such as rectified linear units (ReLU) or maxout, are among the most fundamental models in modern machine learning. We make a step towards proving lower bounds on the size of such…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
Tree-child networks are an important class of phylogenetic network used to model reticulate evolutionary processes. These networks have attracted increasing attention from researchers with interests in both combinatorics and algorithms. A…
We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In…