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For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
We describe an involution on Tamari intervals and m-Tamari intervals. This involution switches two sets of statistics known as the "rises" and the "contacts" and so proves an open conjecture from Pr\'eville-Ratelle on intervals of the…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
In weighted trees, all edges are endowed with positive integral weight. We enumerate weighted bicolored plane trees according to their weight and number of edges.
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
A variant of Turing machines is introduced where the tape is replaced by a single tree which can be manipulated in a style akin to purely functional programming. This yields two benefits: first, the extra structure on the tape can be…
Higher dimensional permutations are tuples of d-1 permutations that can be identified with a point set in a d-dimensional grid. In N. Bonichon and P.-J. Morel, {\it J. Integer Sequences} 25 (2022), several conjectures regarding the…
Bertini classified the birational involutions of the complex projective plane, but his geometric approach does not allow to explicit these maps easily. In this article, we present an effective approach to this problem by associating to each…
Any permutation has a disjoint cycle decomposition and concept generates an equivalence class on the symmetry group called the cycle-type. The main focus of this work is on permutations of restricted cycle-types, with particular emphasis on…
We find presentations for subalgebras of invariants of the coordinate algebras of binary symmetric models of phylogenetic trees studied by Buczynska and Wisniewski in \cite{BW}. These algebras arise as toric degenerations of rings of global…
We show that there is a bijection between real-linear automorphisms of the multicomplex numbers of order $n$ and signed permutations of length $2^{n-1}$. This allows us to deduce a number of results on the multicomplex numbers, including a…
Contour trees describe the topology of level sets in scalar fields and are widely used in topological data analysis and visualization. A main challenge of utilizing contour trees for large-scale scientific data is their computation at scale…
We introduce some classes of increasing labeled and multilabeled trees, and we show that these trees provide combinatorial interpretations for certain Thron-type continued fractions with coefficients that are quasi-affine of period 2. Our…
Using the Lagrange inversion formula, $t$-ary trees are enumerated with respect to edge type (left, middle, right for ternary trees).
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
In a reconfiguration problem, given a problem and two feasible solutions of the problem, the task is to find a sequence of transformations to reach from one solution to the other such that every intermediate state is also a feasible…
In this paper, a 1d convolutional neural network is designed for classification tasks of plant leaves. This network based classifier is analyzed in two directions. In the forward direction, the proposed network can be used in two ways: a…
We present an extension of the duality theorem, previously defined by S. Catani et al. on the one-loop level, to higher loop orders. The duality theorem provides a relation between loop integrals and tree-level phase-space integrals. Here,…
A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…