Related papers: Faster Longest Common Extension Queries in Strings…
Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
Multiple algorithms are known for efficiently calculating the prefix probability of a string under a probabilistic context-free grammar (PCFG). Good algorithms for the problem have a runtime cubic in the length of the input string. However,…
It is well-known that, given a probability distribution over $n$ characters, in the worst case it takes (\Theta (n \log n)) bits to store a prefix code with minimum expected codeword length. However, in this paper we first show that, for…
The constrained LCS problem asks one to find a longest common subsequence of two input strings $A$ and $B$ with some constraints. The STR-IC-LCS problem is a variant of the constrained LCS problem, where the solution must include a given…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
We discuss classical and quantum algorithms for solvability testing and finding integer solutions x,y of equations of the form af^x + bg^y = c over finite fields GF(q). A quantum algorithm with time complexity q^(3/8) (log q)^O(1) is…
Consider a pair of plane straight-line graphs, whose edges are colored red and blue, respectively, and let n be the total complexity of both graphs. We present a O(n log n)-time O(n)-space technique to preprocess such pair of graphs, that…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
In the oracle identification problem we have oracle access to bits of an unknown string $x$ of length $n$, with the promise that it belongs to a known set $C\subseteq\{0,1\}^n$. The goal is to identify $x$ using as few queries to the oracle…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
Given a string $T$ of length $n$ over an alphabet $\Sigma\subset \{1,2,\ldots,n^{O(1)}\}$ of size $\sigma$, we are to preprocess $T$ so that given a range $[i,j]$, we can return a representation of a shortest string over $\Sigma$ that is…
The suffix array and the suffix tree are the two most fundamental data structures for string processing. For a length-$n$ text, however, they use $\Theta(n \log n)$ bits of space, which is often too costly. To address this, Grossi and…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
Given an integer array $A[1..n]$, the Range Minimum Query problem (RMQ) asks to preprocess $A$ into a data structure, supporting RMQ queries: given $a,b\in [1,n]$, return the index $i\in[a,b]$ that minimizes $A[i]$, i.e.,…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
The suffix trees are fundamental data structures for various kinds of string processing. The suffix tree of a text string $T$ of length $n$ has $O(n)$ nodes and edges, and the string label of each edge is encoded by a pair of positions in…