Related papers: Reconstructing Strings from Substrings: Optimal Ra…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
We study a variation of the classical Shortest Common Superstring (SCS) problem in which a shortest superstring of a finite set of strings $S$ is sought containing as a factor every string of $S$ or its reversal. We call this problem…
Strings form a fundamental data type in computer systems. String searching has been extensively studied since the inception of computer science. Increasingly many applications have to deal with imprecise strings or strings with fuzzy…
Given a string $S$ of $n$ integers in $[0,\sigma)$, a range minimum query RMQ$(i, j)$ asks for the index of the smallest integer in $S[i \dots j]$. It is well known that the problem can be solved with a succinct data structure of size $2n +…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
The ''trace reconstruction'' problem asks, given an unknown binary string $x$ and a channel that repeatedly returns ''traces'' of $x$ with each bit randomly deleted with some probability $p$, how many traces are needed to recover $x$? There…
Merging $T$ sorted, non-redundant lists containing $M$ elements into a single sorted, non-redundant result of size $N \ge M/T$ is a classic problem typically solved practically in $O(M \log T)$ time with a priority-queue data structure the…
In the oracle identification problem, we are given oracle access to an unknown N-bit string x promised to belong to a known set C of size M and our task is to identify x. We present a quantum algorithm for the problem that is optimal in its…
An occurrence of a repeated substring $u$ in a string $S$ is called a net occurrence if extending the occurrence to the left or to the right decreases the number of occurrences to 1. The net frequency (NF) of a repeated substring $u$ in a…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
Longest common substring (LCS), longest palindrome substring (LPS), and Ulam distance (UL) are three fundamental string problems that can be classically solved in near linear time. In this work, we present sublinear time quantum algorithms…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is transmitted through a probabilistic \emph{deletion channel} which independently deletes each bit with some fixed probability $\delta$ and concatenates…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a scenario where the sender transmits a codeword from some codebook, and the receiver obtains $N$ noisy outputs of the codeword. We study the problem of…
Encoding data structures store enough information to answer the queries they are meant to support but not enough to recover their underlying datasets. In this paper we give the first encoding data structure for the challenging problem of…
Minimizers sampling is one of the most widely-used mechanisms for sampling strings. Let $S=S[0]\ldots S[n-1]$ be a string over an alphabet $\Sigma$. In addition, let $w\geq 2$ and $k\geq 1$ be two integers and $\rho=(\Sigma^k,\leq)$ be a…
Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…
Statistical query (SQ) algorithms are algorithms that have access to an {\em SQ oracle} for the input distribution $D$ instead of i.i.d.~ samples from $D$. Given a query function $\phi:X \rightarrow [-1,1]$, the oracle returns an estimate…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
In this paper, we present and study the \emph{Hamming distance oracle problem}. In this problem, the task is to preprocess two strings $S$ and $T$ of lengths $n$ and $m$, respectively, to obtain a data-structure that is able to answer…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…