Related papers: All-Pairs Suffix-Prefix on Fully Dynamic Set of St…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
We consider the problems of computing maximal palindromes and distinct palindromes in a trie. A trie is a natural generalization of a string, which can be seen as a single-path tree. There is a linear-time offline algorithm to compute…
We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a…
A palindrome is a string that reads the same forward and backward. A palindromic substring $P$ of a string $S$ is called a shortest unique palindromic substring ($\mathit{SUPS}$) for an interval $[x, y]$ in $S$, if $P$ occurs exactly once…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
The domains of data mining and knowledge discovery make use of large amounts of textual data, which need to be handled efficiently. Specific problems, like finding the maximum weight ordered common subset of a set of ordered sets or…
One of the most fundamental method for comparing two given strings $A$ and $B$ is the longest common subsequence (LCS), where the task is to find (the length) of an LCS of $A$ and $B$. In this paper, we deal with the STR-IC-LCS problem…
We present OnPair, a dictionary-based compression algorithm designed to meet the needs of in-memory database systems that require both high compression and fast random access. Existing methods either achieve strong compression ratios at…
Consider an input text string T[1,N] drawn from an unbounded alphabet. We study partial computation in suffix-based problems for Data Compression and Text Indexing such as (I) retrieve any segment of K<=N consecutive symbols from the…
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 =…
The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array…
Suffix trees and suffix arrays are two of the most widely used data structures for text indexing. Each uses linear space and can be constructed in linear time for polynomially sized alphabets. However, when it comes to answering queries…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
A fully-dynamic dictionary is a data structure for maintaining sets that supports insertions, deletions and membership queries. A filter approximates membership queries with a one-sided error. We present two designs: 1. The first…
At CPM 2017, Castelli et al. define and study a new variant of the Longest Common Subsequence Problem, termed the Longest Filled Common Subsequence Problem (LFCS). For the LFCS problem, the input consists of two strings $A$ and $B$ and a…
We consider the all pairs all shortest paths (APASP) problem, which maintains all of the multiple shortest paths for every vertex pair in a directed graph $G=(V,E)$ with a positive real weight on each edge. We present two fully dynamic…
We study the approximability of two related problems on graphs with $n$ nodes and $m$ edges: $n$-Pairs Shortest Paths ($n$-PSP), where the goal is to find a shortest path between $O(n)$ prespecified pairs, and All Node Shortest Cycles…
The problem of aligning two strings A,B in order to determine their similarity is fundamental in the field of pattern matching. An important concept in this domain is the "all scores matrix" that encodes the local alignment comparison of…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…