Related papers: Algorithms for Parameterized String Matching with …
We propose a new (theoretical) computational model for the study of massive data processing with limited computational resources. Our model measures the complexity of reading the very large data sets in terms of the data size N and analyzes…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…
We consider the first problem that appears in any application of synchronizing automata, namely, the problem of deciding whether or not a given $n$-state $k$-letter automaton is synchronizing. First we generalize results from…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
We investigate the problem of deterministic pattern matching in multiple streams. In this model, one symbol arrives at a time and is associated with one of s streaming texts. The task at each time step is to report if there is a new match…
Important papers have appeared recently on the problem of indexing binary strings for jumbled pattern matching, and further lowering the time bounds in terms of the input size would now be a breakthrough with broad implications. We can…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
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…
Binary size reduction is an increasingly important optimization objective for compilers. One emerging technique is function merging, where multiple similar functions are merged into one, thereby eliminating redundancy. The SOTA approach to…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
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…
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…
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…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
In the Longest Common Factor with $k$ Mismatches (LCF$_k$) problem, we are given two strings $X$ and $Y$ of total length $n$, and we are asked to find a pair of maximal-length factors, one of $X$ and the other of $Y$, such that their…
As a fundamental problem in pattern recognition, graph matching has applications in a variety of fields, from computer vision to computational biology. In graph matching, patterns are modeled as graphs and pattern recognition amounts to…
We revisit the complexity of one of the most basic problems in pattern matching. In the k-mismatch problem we must compute the Hamming distance between a pattern of length m and every m-length substring of a text of length n, as long as…