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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).…
In recent work (Forum Math.~Sigma, 2024), we established a correspondence between MAT-labeled graphs arising from hyperplane arrangements and regular vines from probability theory. In this paper, we extend this connection to Arrow's…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Thin spanning trees lie at the intersection of graph theory, approximation algorithms, and combinatorial optimization. They are central to the long-standing \emph{thin tree conjecture}, which asks whether every $k$-edge-connected graph…
The architecture of a neural network constrains the potential dynamics that can emerge. Some architectures may only allow for a single dynamic regime, while others display a great deal of flexibility with qualitatively different dynamics…
Given a gene-tree labeled topology $G$ and a species tree $S$, the "ancestral configurations" at an internal node $k$ of $S$ represent the combinatorially different sets of gene lineages that can be present at $k$ when all possible…
Certain families of combinatorial objects admit recursive descriptions in terms of generating trees: each node of the tree corresponds to an object, and the branch leading to the node encodes the choices made in the construction of the…
The $k$-Young lattice $Y^k$ is a partial order on partitions with no part larger than $k$. This weak subposet of the Young lattice originated from the study of the $k$-Schur functions(atoms) $s_\lambda^{(k)}$, symmetric functions that form…
Tree-like tableaux are objects in bijection with alternative or permutation tableaux. They have been the subject of a fruitful combinatorial study for the past few years. In the present work, we define and study a new subclass of tree-like…
Let $\mathcal{T}$ be an unrooted binary tree with $n$ distinctly labelled leaves. Deriving its name from the field of phylogenetics, a convex character on $\mathcal{T}$ is simply a partition of the leaves such that the minimal spanning…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…
Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…
The study of representations of affine Hecke algebras has led to a new notion of shapes and standard Young tableaux which works for the root system of any finite Coxeter group. This paper is completely independent of affine Hecke algebra…
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,…
We propose the class of galled tree-child networks which is obtained as intersection of the classes of galled networks and tree-child networks. For the latter two classes, (asymptotic) counting results and stochastic results have been…
We show that an algorithmic construction of sequences of recursive trees leads to a direct proof of the convergence of random recursive trees in an associated Doob-Martin compactification; it also gives a representation of the limit in…
We analyze dynamic random network models where younger vertices connect to older ones with probabilities proportional to their degrees as well as a propensity kernel governed by their attribute types. Using stochastic approximation…
Life and language are discrete combinatorial systems (DCSs) in which the basic building blocks are finite sets of elementary units: nucleotides or codons in a DNA sequence and letters or words in a language. Different combinations of these…
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks. To find bigger networks, one can attempt to combine small…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…