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We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
In this paper, we study three matching problems all of which came up quite recently in the field of machine teaching. The cost of a matching is defined in such a way that, for some formal model of teaching, it equals (or bounds) the number…
Covers are a kind of quasiperiodicity in strings. A string $C$ is a cover of another string $T$ if any position of $T$ is inside some occurrence of $C$ in $T$. The shortest and longest cover arrays of $T$ have the lengths of the shortest…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
We compute the expected number of commutations appearing in a reduced word for the longest element in the symmetric group. The asymptotic behavior of this value is analyzed and shown to approach the length of the permutation, meaning that…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
We consider the longest common subsequence problem in the context of subsequences with gap constraints. In particular, following Day et al. 2022, we consider the setting when the distance (i. e., the gap) between two consecutive symbols of…
We give the proof of a tight lower bound on the probability that a binomial random variable exceeds its expected value. The inequality plays an important role in a variety of contexts, including the analysis of relative deviation bounds in…
Let $G$ be a regular graph and $H$ a subgraph on the same vertex set. We give surprisingly compact formulas for the number of copies of $H$ one expects to find in a random subgraph of $G$.
In this note we put forward a conjecture on the average optimal length for bipartite matching with a finite number of elements where the different lengths are independent one from the others and have an exponential distribution.
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
In this paper we provide an overview of a series of recent results regarding algorithms for searching for subsequences in words or for the analysis of the sets of subsequences occurring in a word.
We say that a string of length $d$ occurs, in a Bernoulli sequence, if a success is followed by exactly $(d-1)$ failures before the next success. The counts of such $d$-strings are of interest, and in specific independent Bernoulli…
A binary string transmitted via a memoryless i.i.d. deletion channel is received as a subsequence of the original input. From this, one obtains a posterior distribution on the channel input, corresponding to a set of candidate…
Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…
This paper addresses an important problem in Example-Based Machine Translation (EBMT), namely how to measure similarity between a sentence fragment and a set of stored examples. A new method is proposed that measures similarity according to…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
Define a permutation to be any sequence of distinct positive integers. Given two permutations p and s on disjoint underlying sets, we denote by p sh s the set of shuffles of p and s (the set of all permutations obtained by interleaving the…
Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…