Related papers: Lassoing and corraling rooted phylogenetic trees
A tanglegram consists of two binary rooted trees with the same number of leaves and a perfect matching between the leaves of the trees. We show that the two halves of a random tanglegram essentially look like two independently chosen random…
We revisit the model of the ballistic deposition studied in \cite{bdeposition} and prove several combinatorial properties of the random tree structure formed by the underlying stochastic process. Our results include limit theorems for the…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
In an upward planar 2-slope drawing of a digraph, edges are drawn as straight-line segments in the upward direction without crossings using only two different slopes. We investigate whether a given upward planar digraph admits such a…
Decision trees are a fundamental tool in machine learning for representing, classifying, and generalizing data. It is desirable to construct ``small'' decision trees, by minimizing either the \textit{size} ($s$) or the \textit{depth} $(d)$…
Phylogenomic approaches developed thus far are either too time-consuming or lack a solid evolutionary basis. Moreover, no phylogenomic approach is capable of constructing a tree directly from unassembled raw sequencing data. A new…
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,…
Tanglegrams are drawings of two rooted binary phylogenetic trees and a matching between their leaf sets. The trees are drawn crossing-free on opposite sides with their leaf sets facing each other on two vertical lines. Instead of minimizing…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
In this survey on local additive invariants of real and complex definable singular germs we systematically present classical or more recent invariants of different nature as emerging from a tame degeneracy principle. For this goal, we…
A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…
In agglomerative hierarchical clustering, pair-group methods suffer from a problem of non-uniqueness when two or more distances between different clusters coincide during the amalgamation process. The traditional approach for solving this…
We present a new overlay, called the {\em Deterministic Decentralized tree} ($D^2$-tree). The $D^2$-tree compares favourably to other overlays for the following reasons: (a) it provides matching and better complexities, which are…
We introduce the concept of a class of graphs, or more generally, relational structures, being locally tree-decomposable. There are numerous examples of locally tree-decomposable classes, among them the class of planar graphs and all…
We derive a statistical model for estimation of a dendrogram from single linkage hierarchical clustering (SLHC) that takes account of uncertainty through noise or corruption in the measurements of separation of data. Our focus is on just…
Scientific investigations that incorporate next generation sequencing involve analyses of high-dimensional data where the need to organize, collate and interpret the outcomes are pressingly important. Currently, data can be collected at the…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
In this paper we study the minimum number of reversals needed to transform a unicellular fatgraph into a tree. We consider reversals acting on boundary components, having the natural interpretation as gluing, slicing or half-flipping of…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…