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Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
In a previous work, we gave a coalgebraic framework of directed graphs equipped with weights (or probability vectors) in terms of (Markov) L-coalgebras. They are K-vector spaces equipped with two co-operations, \Delta_M, \tilde{\Delta}_M…
Let $R$ be a finite commutative chain ring, $D_{2n}$ be the dihedral group of size $2n$ and $R[D_{2n}]$ be the dihedral group ring. In this paper, we completely characterize left ideals of $R[D_{2n}]$ (called left $D_{2n}$-codes) when ${\rm…
We will define an operad $\mathcal{B}^0$ on planar rooted trees. $\mathcal{B}^0$ is analgous to the $NAP$-operad in the non-planar tree setting. We will define a family of "current-preserving" operads $\mathcal{B}^\lambda$ depending on a…
We consider two decomposition problems in directed graphs. We say that a digraph is $k$-bounded for some $k \in \mathbb{Z}_{\geq 1}$ if each of its connected components contains at most $k$ arcs. For the first problem, a directed linear…
A family T of digraphs is a complete set of obstructions for a digraph H if for an arbitrary digraph G the existence of a homomorphism from G to H is equivalent to the non-existence of a homomorphism from any member of T to G. A digraph H…
An m-extracting procedure produces unbiased random bits from a loaded dice with m faces. A binarization takes inputs from an m-faced dice and produce bit sequences to be fed into a (binary) extracting procedure to obtain random bits. Thus,…
A distributive lattice structure ${\mathbf M}(G)$ has been established on the set of perfect matchings of a plane bipartite graph $G$. We call a lattice {\em matchable distributive lattice} (simply MDL) if it is isomorphic to such a…
We introduce the notion of doubly rooted plane trees and give a decomposition of these trees, called the butterfly decomposition which turns out to have many applications. From the butterfly decomposition we obtain a one-to-one…
The first-order theory of finite and infinite trees has been studied since the eighties, especially by the logic programming community. Following Djelloul, Dao and Fr\"uhwirth, we consider an extension of this theory with an additional…
We present a new definition of non-ambiguous trees (NATs) as labelled binary trees. We thus get a differential equation whose solution can be described combinatorially. This yields a new formula for the number of NATs. We also obtain…
Let $L$ be an algebra over a field $F$ with the binary operations $+$ and $[,]$. Then $L$ is called a left Leibniz algebra if it satisfies the left Leibniz identity: $[[a,b],c]=[a,[b,c]]-[b,[a,c]]$ for all elements $a,b,c\in L$. A linear…
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…
In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
We give closed form expressions for the numbers of multi-rooted plane trees with specified degrees of root vertices. This results in an infinite number of integer sequences some of which are known to have an alternative interpretation. We…
The aim of this paper is to further explore an idea from J.-L. Loday briefly exposed in [5]. We impose a natural and simple symmetry on a unit action over the most general quadratic relation which can be written. This leads us to two…
The binary products of right, left or double division in semigroups that are semilattices of groups give interesting groupoid structures that are in one to one correspondence with semigroups that are semilattices of groups. This work is…
We introduce a new geometric structure on differentiable manifolds. A \textit{Contact} \textit{Pair}on a manifold $M$ is a pair $(\alpha,\eta) $ of Pfaffian forms of constant classes $2k+1$ and $2h+1$ respectively such that $\alpha\wedge…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…