Related papers: Deterministic Sparse Suffix Sorting in the Restore…
This paper reformulates the problem of finding a longest common increasing subsequence of the two given input sequences in a very succinct way. An extremely simple linear space algorithm based on the new formula can find a longest common…
We consider computing a longest palindrome in the streaming model, where the symbols arrive one-by-one and we do not have random access to the input. While computing the answer exactly using sublinear space is not possible in such a…
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…
Re-Pair is a grammar compression scheme with favorably good compression rates. The computation of Re-Pair comes with the cost of maintaining large frequency tables, which makes it hard to compute Re-Pair on large scale data sets. As a…
We propose a new approach for calculating the Lempel-Ziv factorization of a string, based on run length encoding (RLE). We present a conceptually simple off-line algorithm based on a variant of suffix arrays, as well as an on-line algorithm…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…
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 problem of finding repetitive structures and inherent patterns in a given string $\s{s}$ of length $n$ over a finite totally ordered alphabet. A border $\s{u}$ of a string $\s{s}$ is both a prefix and a suffix of $\s{s}$…
We revisit the classic border tree data structure [Gu, Farach, Beigel, SODA 1994] that answers the following prefix-suffix queries on a string $T$ of length $n$ over an integer alphabet $\Sigma=[0,\sigma)$: for any $i,j \in [0,n)$ return…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Reordering poses a major challenge in machine translation (MT) between two languages with significant differences in word order. In this paper, we present a novel reordering approach utilizing sparse features based on dependency word pairs.…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
We present an algorithm computing the determinant of an integer matrix A. The algorithm is introspective in the sense that it uses several distinct algorithms that run in a concurrent manner. During the course of the algorithm partial…
We present a sorting algorithm for the case of recurrent random comparison errors. The algorithm essentially achieves simultaneously good properties of previous algorithms for sorting $n$ distinct elements in this model. In particular, it…
The Lyndon array stores, at each position of a word, the length of the longest maximal Lyndon subword starting at that position, and plays an important role in combinatorics on words, for example in the construction of fundamental data…
Given a dynamic set $K$ of $k$ strings of total length $n$ whose characters are drawn from an alphabet of size $\sigma$, a keyword dictionary is a data structure built on $K$ that provides locate, prefix search, and update operations on…