Related papers: An Extension of Linear-size Suffix Tries for Param…
Two strings $x$ and $y$ over $\Sigma \cup \Pi$ of equal length are said to \emph{parameterized match} (\emph{p-match}) if there is a renaming bijection $f:\Sigma \cup \Pi \rightarrow \Sigma \cup \Pi$ that is identity on $\Sigma$ and…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…
In this paper we present a new problem, the fast set intersection problem, which is to preprocess a collection of sets in order to efficiently report the intersection of any two sets in the collection. In addition we suggest new solutions…
Document listing on string collections is the task of finding all documents where a pattern appears. It is regarded as the most fundamental document retrieval problem, and is useful in various applications. Many of the fastest-growing…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…
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 binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
In the problem of $\texttt{Generalised Pattern Matching}\ (\texttt{GPM})$ [STOC'94, Muthukrishnan and Palem], we are given a text $T$ of length $n$ over an alphabet $\Sigma_T$, a pattern $P$ of length $m$ over an alphabet $\Sigma_P$, and a…
Suffix sort plays a critical role in various computational algorithms including genomics as well as in frequently used day to day software applications. The sorting algorithm becomes tricky when we have lot of repeated characters in the…
In the minimum common string partition (MCSP) problem two related input strings are given. "Related" refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings.…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
Combining the techniques of approximation algorithms and parameterized complexity has long been considered a promising research area, but relatively few results are currently known. In this paper we study the parameterized approximability…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
We describe, analyze, and evaluate experimentally a new probabilistic model for word-sequence prediction in natural language based on prediction suffix trees (PSTs). By using efficient data structures, we extend the notion of PST to…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…