Related papers: Vector encoding of phylogenetic trees by ordered l…
We observe that a standard transformation between \emph{ordinal} trees (arbitrary rooted trees with ordered children) and binary trees leads to interesting succinct binary tree representations. There are four symmetric versions of these…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
A tanglegram consists of two rooted binary trees with the same number of leaves and a perfect matching between the leaves of the trees. Given a size-$n$ tanglegram, i.e., a tanglegram for two trees with $n$ leaves, a multiset of induced…
Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
For a labelled tree on the vertex set $[n]:=\{1,2,..., n\}$, define the direction of each edge $ij$ to be $i\to j$ if $i<j$. The indegree sequence of $T$ can be considered as a partition $\lambda \vdash n-1$. The enumeration of trees with a…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
We introduce online probabilistic label trees (OPLTs), an algorithm that trains a label tree classifier in a fully online manner without any prior knowledge about the number of training instances, their features and labels. OPLTs are…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
Separation Logic (SL) with inductive definitions is a natural formalism for specifying complex recursive data structures, used in compositional verification of programs manipulating such structures. The key ingredient of any automated…
We consider Beta$(2-\alpha, \alpha)$-coalescents with parameter range $1 <\alpha<2$ starting from $n$ leaves. The length $\ell^{(n)}_r$ of order $r$ in the $n$-Beta$(2-\alpha, \alpha)$-coalescent tree is defined as the sum of the lengths of…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
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…
This paper presents an approach to Prolog-style term encoding of typed feature structures. The type feature structures to be encoded are constrained by appropriateness conditions as in Carpenter's ALE system. But unlike ALE, we impose a…
In this note we analyze the performance of a simple root-finding algorithm in uniform attachment trees. The leaf-stripping algorithm recursively removes all leaves of the tree for a carefully chosen number of rounds. We show that, with…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…