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It is known that the size of the largest common subtree (i.e., the maximum agreement subtree) of two independent random binary trees with $n$ given labeled leaves is of order between $n^{0.366}$ and $n^{1/2}$. We improve the lower bound to…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
A tanglegram is a pair of binary trees with the same set of leaves. Unlabeled tanglegrams were counted recently by Billey, Konvalinka, and Matsen, who also proposed the problem of counting several variations of unlabeled tanglegrams…
We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…
Hex-trees are identified as a particular instance of weighted unary-binary trees. The Horton-Strahler numbers of these objects are revisited, and, thanks to a substitution that is not immediately intuitive, explicit results are possible.…
Labeled unranked trees are used as a model of XML documents, and logical languages for them have been studied actively over the past several years. Such logics have different purposes: some are better suited for extracting data, some for…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
In 1998, B\"{o}cker and Dress gave a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree $T$ with leaf set $X$ and a…
The Horton-Strahler (HS) index $r=\max{(i,j)}+\delta_{i,j}$ has been shown to be relevant to a number of physical (such at diffusion limited aggregation) geological (river networks), biological (pulmonary arteries, blood vessels, various…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
When using machine learning for imbalanced binary classification problems, it is common to subsample the majority class to create a (more) balanced training dataset. This biases the model's predictions because the model learns from data…
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…
In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…
Weight-balanced trees are a popular form of self-balancing binary search trees. Their popularity is due to desirable guarantees, for example regarding the required work to balance annotated trees. While usual weight-balanced trees perform…
Existing ordinal trees and random forests typically use scores that are assigned to the ordered categories, which implies that a higher scale level is used. Versions of ordinal trees are proposed that take the scale level seriously and…
Working with generating functions, the combinatorics of a recurrence relation can be expressed in a way that allows for more efficient calculation of the quantity. This is true of the Catalan numbers for an ordered binary tree…
The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a division are not…
We provide a short combinatorial proof of Cayley's formula by means of a bijective map to an outcome space of an urn-drawing problem. Furthermore we introduce an algebraic structure on the set of labeled trees, which provides a more…
The Colless index is one of the most popular and natural balance indices for bifurcating phylogenetic trees, but it makes no sense for multifurcating trees. In this paper we propose a family of Colless-like balance indices…