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A De Bruijn cycle is a cyclic sequence in which every word of length $n$ over an alphabet $\mathcal{A}$ appears exactly once. De Bruijn tori are a two-dimensional analogue. Motivated by recent progress on universal partial cycles and words,…
Orientable sequences of order n are infinite periodic sequences with symbols drawn from a finite alphabet of size k with the property that any particular subsequence of length n occurs at most once in a period in either direction. They were…
An elimination tree for a connected graph $G$ is a rooted tree on the vertices of $G$ obtained by choosing a root $x$ and recursing on the connected components of $G-x$ to produce the subtrees of $x$. Elimination trees appear in many guises…
This paper presents a method to find new De Bruijn cycles based on ones of lesser order. This is done by mapping a De Bruijn cycle to several vertex disjoint cycles in a De Bruijn digraph of higher order and connecting these cycles into one…
We construct combinatorial Hubbard trees for all unicritical polynomials, and for all exponential maps, for which the critical (singular) value does not escape. More precisely, out of an external angle, or more generally a kneading…
A connected digraph in which the in-degree of any vertex equals its out-degree is Eulerian, this baseline result is used as the basis of existence proofs for universal cycles (also known as generalized deBruijn cycles or U-cycles) of…
We propose a novel construction for the well-known prefer-max De Bruijn sequence, based on the cycle joining technique. We further show that the construction implies known results from the literature in a straightforward manner. First, it…
Various combinatorial classes such as outerplanar graphs and maps, series-parallel graphs, substitution-closed classes of permutations and many more allow bijective encodings by so-called enriched trees, which are rooted trees with…
We introduce the notion of unavoidable (complete) sets of word patterns, which is a refinement for that of words, and study certain numerical characteristics for unavoidable sets of patterns. In some cases we employ the graph of pattern…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
We build on recent work of Yeats, Courtiel, and others involving connected chord diagrams. We first derive from a Hopf-algebraic foundation a class of tree-like functional equations and prove that they are solved by weighted generating…
Work introduces a hierarchical binary tree-based reduction that replaces standard self-attention. The core idea is to use a recursive Gated Linear Unit merge operation, achieving O(n) total merge operations O(log n) parallel depth O(n d^2)…
Constrained coding is a fundamental field in coding theory that tackles efficient communication through constrained channels. While channels with fixed constraints have a general optimal solution, there is increasing demand for parametric…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
Consider the collection of all t-multisets of {1,...,n}. A universal cycle on multisets is a string of numbers, each of which is between 1 and n, such that if these numbers are considered in t-sized windows, every multiset in the collection…
This paper describes new, simple, recursive methods of construction for orientable sequences, i.e. periodic binary sequences in which any n-tuple occurs at most once in a period in either direction. As has been previously described, such…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
A superpermutation is a sequence that contains every permutation of $n$ distinct symbols as a contiguous substring. For instance, a valid example for three symbols is a sequence that contains all six permutations. This paper introduces a…
A universal cycle is a compact listing of a class of combinatorial objects. In this paper, we prove the existence of universal cycles of classes of labeled graphs, including simple graphs, trees, graphs with m edges, graphs with loops,…
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…