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Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
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…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
We consider the problem of minimising the number of states in a multiplicity tree automaton over the field of rational numbers. We give a minimisation algorithm that runs in polynomial time assuming unit-cost arithmetic. We also show that a…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Hash codes are efficient data representations for coping with the ever growing amounts of data. In this paper, we introduce a random forest semantic hashing scheme that embeds tiny convolutional neural networks (CNN) into shallow random…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
We present two effective tools for computing the positive tropicalization of algebraic varieties. First, we outline conditions under which the initial ideal can be used to compute the positive tropicalization, offering a real analogue to…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
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…
Most research on query optimization has centered on binary join algorithms like hash join and sort-merge join. However, recent years have seen growing interest in theoretically optimal algorithms, notably Yannakakis' algorithm. These…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
Identifying a subset of taxa that maximizes Phylogenetic Diversity (PD) is a cornerstone of quantitative conservation planning. Traditionally, PD is defined over a phylogenetic tree in which leaves resemble present-day taxa and the branch…
Polyploidization, whereby an organism inherits multiple copies of the genome of their parents, is an important evolutionary event that has been observed in plants and animals. One way to study such events is in terms of the ploidy number of…
We study the crossing-minimization problem in a layered graph drawing of planar-embedded rooted trees whose leaves have a given total order on the first layer, which adheres to the embedding of each individual tree. The task is then to…
Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…
The use of machine learning algorithms in finance, medicine, and criminal justice can deeply impact human lives. As a consequence, research into interpretable machine learning has rapidly grown in an attempt to better control and fix…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…