Related papers: Forbidden substrings on weighted alphabets
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
An integer array y = y[1..n] is said to be feasible if and only if y[1] = n and, for every i \in 2..n, i \le i+y[i] \le n+1. A string is said to be indeterminate if and only if at least one of its elements is a subset of cardinality greater…
In the study of random access machines (RAMs) it has been shown that the availability of an extra input integer, having no special properties other than being sufficiently large, is enough to reduce the computational complexity of some…
In the course of proving the strong perfect graph theorem, Chudnovsky, Robertson, Seymour, and Thomas showed that every perfect graph either belongs to one of five basic classes or admits one of several decompositions. Four of the basic…
We address the problem of constructing a fast lossless code in the case when the source alphabet is large. The main idea of the new scheme may be described as follows. We group letters with small probabilities in subsets (acting as super…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
In combinatorics on words, a word w over an alphabet Sigma is said to avoid a pattern p over an alphabet Delta if there is no factor x of w and no non-erasing morphism h from Delta^* to Sigma^* such that h(p) = x. Bell and Goh have recently…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Given a combinatorial structure, a ``twin'' is a pair of disjoint substructures which are isomorphic (or look the same in some sense). In recent years, there have been many problems about finding large twins in various combinatorial…
Entringer, Jackson, and Schatz conjectured in 1974 that every infinite cubefree binary word contains arbitrarily long squares. In this paper we show this conjecture is false: there exist infinite cubefree binary words avoiding all squares…
Lattice-based string formation algorithms can, at least in principle, be reduced to the study of the statistics of the corresponding aperiodic random walk. Since in three or more dimensions such walks are transient this approach necessarily…
Polynomial algorithms are given for the following two problems: given a graph with $n$ vertices and $m$ edges, where $m \ge 3 n^{3/2}$, find a complete balanced bipartite subgraph with parts about $\ln n/(\ln (n^2/m))$, given a graph with…
A word $x$ that is absent from a word $y$ is called minimal if all its proper factors occur in $y$. Given a collection of $k$ words $y_1,y_2,\ldots,y_k$ over an alphabet $\Sigma$, we are asked to compute the set…
The notion of containment and avoidance provides a natural partial ordering on set partitions. Work of Sagan and of Goyt has led to enumerative results in avoidance classes of set partitions, which were refined by Dahlberg et al. through…
We consider the enumeration of ordered set partitions avoiding a permutation pattern, as introduced by Godbole, Goyt, Herdan and Pudwell. Let $\op_{n,k}(p)$ be the number of ordered set partitions of $\{1,2,\ldots,n\}$ into $k$ blocks that…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
In this paper, we study two examples of minimum weight random graphs with edge constraints. First we consider the complete graph on ${n}$ vertices equipped with uniformly heavy edge weights and use iteration methods to obtain deviation…
We establish a list of characterizations of bounded twin-width for hereditary, totally ordered binary structures. This has several consequences. First, it allows us to show that a (hereditary) class of matrices over a finite alphabet either…
In this paper we find closed form for the generating function of powers of any non-degenerate second-order recurrence sequence, completing a study begun by Carlitz and Riordan in 1962. Moreover, we generalize a theorem of Horadam on partial…
Recently, Andrews, Chan, Kim and Osburn introduced the even strings and the odd strings in the overpartitions. We show that their conjecture $A_k (n) \geq B_k (n)$ holds for large enough positive integers n, where A_k(n) (resp. B_k(n)) is…