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Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
This paper considers the enumeration of ternary trees (i.e. rooted ordered trees in which each vertex has 0 or 3 children) avoiding a contiguous ternary tree pattern. We begin by finding recurrence relations for several simple tree…
This paper is a detailled study of the coding of real trees by real valued functions that is motivated by probabilistic problems related to continuum random trees. Indeed it is known since the works of Aldous (1993) and Le Gall (1991) that…
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…
Tree shape statistics quantify some aspect of the shape of a phylogenetic tree. They are commonly used to compare reconstructed trees to evolutionary models and to find evidence of tree reconstruction bias. Historically, to find a useful…
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…
We consider a probability distribution on the set of Boolean functions in n variables which is induced by random Boolean expressions. Such an expression is a random rooted plane tree where the internal vertices are labelled with connectives…
An alphabetic binary tree formulation applies to problems in which an outcome needs to be determined via alphabetically ordered search prior to the termination of some window of opportunity. Rather than finding a decision tree minimizing…
We study the polyregular string-to-string functions, which are certain functions of polynomial output size that can be described using automata and logic. We describe a system of combinators that generates exactly these functions. Unlike…
Measures of tree balance play an important role in different research areas such as mathematical phylogenetics or theoretical computer science. The balance of a tree is usually quantified in a single number, called a balance or imbalance…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
It is shown that the problem of computing the Strahler number of a binary tree given as a term is complete for the circuit complexity class uniform $\mathsf{NC}^1$. For several variants, where the binary tree is given by a pointer structure…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
A compacted binary tree is a graph created from a binary tree such that repeatedly occurring subtrees in the original tree are represented by pointers to existing ones, and hence every subtree is unique. Such representations form a special…
This paper provides answers to questions regarding the almost sure limiting behavior of rooted, binary tree-structured rules for regression. Examples show that questions raised by Gordon and Olshen in 1984 have negative answers. For these…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
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…
Monotone trees - trees with a function defined on their vertices that decreases the further away from a root node one travels, are a natural model for a process that weakens the further one gets from its source. Given an aggregation of…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…