Related papers: Combinatorial generation via permutation languages…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
The associahedron $\mathcal{A}(G)$ of a graph $G$ has the property that its vertices can be thought of as the search trees on $G$ and its edges as the rotations between two search trees. If $G$ is a simple path, then $\mathcal{A}(G)$ is the…
We propose several constructions of commutative or cocommutative Hopf algebras based on various combinatorial structures, and investigate the relations between them. A commutative Hopf algebra of permutations is obtained by a general…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
Many fixed-parameter tractable algorithms using a bounded search tree have been repeatedly improved, often by describing a larger number of branching rules involving an increasingly complex case analysis. We introduce a novel and general…
We construct the ordinary irreducible representations of the group of automorphisms of a finite rooted tree and we get a natural parametrization of them. To achieve this goals, we introduce and study the combinatorics of tree compositions,…
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 studies algorithms for computing a Gomory-Hu tree, which is a classical data structure that compactly stores all minimum $s$-$t$ cuts of an undirected weighted graph. We consider two classes of algorithms: the original method by…
An invariant for cospectral graphs is a property shared by all cospectral graphs. In this paper, we establish three novel arithmetic invariants for cospectral graphs, revealing deep connections between spectral properties and combinatorial…
For a graph class $\mathcal{C}$, the $\mathcal{C}$-Edge-Deletion problem asks for a given graph $G$ to delete the minimum number of edges from $G$ in order to obtain a graph in $\mathcal{C}$. We study the $\mathcal{C}$-Edge-Deletion problem…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
We provide a new geometric representation of a family of fragmentation processes by nested laminations, which are compact subsets of the unit disk made of noncrossing chords. We specifically consider a fragmentation obtained by cutting a…
Representing a proof tree by a combinator term that reduces to the tree lets subtle forms of duplication within the tree materialize as duplicated subterms of the combinator term. In a DAG representation of the combinator term these…
Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…
We consider the problem of finding edges of a hidden weighted graph using a certain type of queries. Let $G$ be a weighted graph with $n$ vertices. In the most general setting, the $n$ vertices are known and no other information about $G$…
A graph $G$ contains a graph $H$ as an induced minor if $H$ can be obtained from $G$ by vertex deletions and edge contractions. The class of $H$-induced-minor-free graphs generalizes the class of $H$-minor-free graphs, but unlike…
We initiate the study of combinatorial algorithms for Triangle Detection in $H$-free graphs. The goal is to decide if a graph that forbids a fixed pattern $H$ as a subgraph contains a triangle, using only "combinatorial" methods that…
We revisit the generation of balanced octrees for adaptive mesh refinement (AMR) of Cartesian domains with immersed complex geometries. In a recent short note [Hasbestan and Senocak, J. Comput. Phys. vol. 351:473-477 (2017)], we showed that…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…
The Gomory-Hu tree, or a cut tree, is a classic data structure that stores minimum $s$-$t$ cuts of an undirected weighted graph for all pairs of nodes $(s,t)$. We propose a new approach for computing the cut tree based on a reduction to the…