Related papers: The Existence and Structure of Universal Partial C…

Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…

We introduce the Insertion Chain Complex, a higher-dimensional extension of insertion graphs, as a new framework for analyzing finite sets of words. We study its topological and combinatorial properties, in particular its homology groups,…

The nodes of the de Bruijn graph B(d,3) consist of all strings of length 3, taken from an alphabet of size d, with edges between words which are distinct substrings of a word of length 4. We give an inductive characterization of the maximum…

It is known that there are no more Lyndon words of length n than there are periodic necklaces of same length. This paper considers a similar problem where, additionally, the necklaces must be without some forbidden factors. This problem…

An automaton is partially ordered if the only cycles in its transition diagram are self-loops. The expressivity of partially ordered NFAs (poNFAs) can be characterized by the Straubing-Th\'erien hierarchy. Level 3/2 is recognized by poNFAs,…

Let $0<k\in\mathbb{Z}$. The anchored Dyck words of length $n=2k+1$ (obtained by prefixing a 0-bit to each Dyck word of length $2k$ and used to reinterpret the Hamilton cycles in the odd graph $O_k$ and the middle-levels graph $M_k$ found by…

We show that for every $n \geq 1$ and over any finite alphabet, there is a word whose circular factors of length $n$ have a one-to-one correspondence with the set of primitive words. In particular, we prove that such a word can be obtained…

Ulam words are binary words defined recursively as follows: the length-$1$ Ulam words are $0$ and $1$, and a binary word of length $n$ is Ulam if and only if it is expressible uniquely as a concatenation of two shorter, distinct Ulam words.…

Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…

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…

The graph of overlapping permutations is defined in a way analogous to the De Bruijn graph on strings of symbols. That is, for every permutation $\pi = \pi_{1} \pi_{2} ... \pi_{n+1}$ there is a directed edge from the standardization of…

We extend results regarding a combinatorial model introduced by Black, Drellich, and Tymoczko (2017+) which generalizes the folding of the RNA molecule in biology. Consider a word on alphabet $\{A_1, \overline{A}_1, \ldots, A_m,…

In this paper we study cycles in random bipartite graph $G(n,n,p)$. We prove that if $p\gg n^{-2/3}$, then $G(n,n,p)$ a.a.s. satisfies the following. Every subgraph $G'\subset G(n,n,p)$ with more than $(1+o(1))n^2p/2$ edges contains a cycle…

The de Bruijn torus (or grid) problem looks to find an $n$-by-$m$ binary matrix in which every possible $j$-by-$k$ submatrix appears exactly once. The existence and construction of these binary matrices was determined in the 70's, with…

We consider the problem of computing the diameter of a unicycle graph (i.e., a graph with a unique cycle). We present an O(n) time algorithm for the problem, where n is the number of vertices of the graph. This improves the previous best…

Let the root of the word $w$ be the smallest prefix $v$ of $w$ such that $w$ is a prefix of $vvv...$. $per(w)$ is the length of the root of $w$. For any $n\ge5$, an $n$-ary threshold word is a word $w$ such that for any factor (subword) $v$…

The classical Ulam sequence is defined recursively as follows: $a_1=1$, $a_2=2$, and $a_n$, for $n > 2$, is the smallest integer not already in the sequence that can be written uniquely as the sum of two distinct earlier terms. This…

This study aims to determine the algebraic structures of $\alpha$-constacyclic codes of length $3p^s$ over the finite commutative non-chain ring $\mathcal{R}=\frac{\mathbb{F}_{p^m}[u, v]}{\langle u^2, v^2, uv-vu\rangle}$, for a prime $p…

Motivated by generalizations of de Bruijn cycles to various combinatorial structures (Chung, Diaconis, and Graham), we study various Euler tours in set systems. Let $\mathcal{G}$ be a hypergraph whose corank and rank are $c\geq 3$ and $k$,…

Overlap-free words are words over the binary alphabet $A=\{a, b\}$ that do not contain factors of the form $xvxvx$, where $x \in A$ and $v \in A^*$. We analyze the asymptotic growth of the number $u_n$ of overlap-free words of length $n$ as…