Related papers: A note on convex characters, Fibonacci numbers and…
This paper investigates convex quadratic optimization problems involving $n$ indicator variables, each associated with a continuous variable, particularly focusing on scenarios where the matrix $Q$ defining the quadratic term is positive…
We study the dominion zeta(G), defined as the number of minimum dominating sets of a graph G, and analyze how local forcing and boundary effects control the flexibility of optimal domination in trees. For path-based pendant constructions,…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
The Steiner Tree problem is a classical problem in combinatorial optimization: the goal is to connect a set $T$ of terminals in a graph $G$ by a tree of minimum size. Karpinski and Zelikovsky (1996) studied the $\delta$-dense version of…
The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…
We give a fixed-parameter tractable algorithm that, given a parameter $k$ and two graphs $G_1,G_2$, either concludes that one of these graphs has treewidth at least $k$, or determines whether $G_1$ and $G_2$ are isomorphic. The running time…
We propose a new topological invariant of unlabeled trees of N nodes. The invariant is a set of Nx2 matrices of integers, with sum_j k^{d_{i,j}} and v_i as the matrix elements, where d_{i,j} are the elements of the distance matrix and v_i…
The set of all permutations with $n$ symbols is a symmetric group denoted by $S_n$. A transposition tree, $T$, is a spanning tree over its $n$ vertices $V_T=${$1, 2, 3, \ldots n$} where the vertices are the positions of a permutation $\pi$…
We present a deterministic algorithm that given a tree T with n vertices, a starting vertex v and a slackness parameter epsilon > 0, estimates within an additive error of epsilon the cover and return time, namely, the expected time it takes…
Data compression has been widely applied in many data processing areas. Compression methods use variable-size codes with the shorter codes assigned to symbols or groups of symbols that appear in the data frequently. Fibonacci coding, as a…
An independent set in a graph $G$ is a set of pairwise non-adjacent vertices. A tree decomposition of $G$ is a pair $(T, \chi)$ where $T$ is a tree and $\chi : V(T) \rightarrow 2^{V(G)}$ is a function satisfying the following two axioms:…
In the NP-hard Optimizing PD with Dependencies (PDD) problem, the input consists of a phylogenetic tree $T$ over a set of taxa $X$, a food-web that describes the prey-predator relationships in $X$, and integers $k$ and $D$. The task is to…
The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…
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…
Let $G$ be a graph on $n$ vertices and $1 \le k \le n$ a fixed integer. The \textit{$k$-token graph} of $G$ is the graph $F_k(G)$ whose vertex set consists of all $k$-subsets of the vertex set of $G$, where two vertices $A$ and $B$ are…
In this paper, we give a new representation of the Fibonacci numbers. This is achieved using Fibonacci trees. With the help of this representation, the nth Fibonacci number can be calculated without having any knowledge about the previous…
For a graph $G$, the parameter treedepth measures the minimum depth among all forests $F$, called elimination forests, such that $G$ is a subgraph of the ancestor-descendant closure of $F$. We introduce a logic, called neighborhood operator…
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
We improve the previously best known lower and upper bounds on the number n_g of numerical semigroups of genus g. Starting from a known recursive description of the tree T of numerical semigroups, we analyze some of its properties and use…