Related papers: Fast computation of approximate weak common interv…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
In group testing, the goal is to identify a subset of defective items within a larger set of items based on tests whose outcomes indicate whether at least one defective item is present. This problem is relevant in areas such as medical…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
An original approach to solving rather difficult probabilistic problems arising in studying the readout of random discrete fields and having no exact analytical solutions at the moment is proposed. Several algorithms for direct, iterative,…
The determination of block-entropies is a well established method for the investigation of discrete data, also called symbols (7). There is a large variety of such symbolic sequences, ranging from texts written in natural languages,…
While almost all existing works which optimally solve just-in-time scheduling problems propose dedicated algorithmic approaches, we propose in this work mixed integer formulations. We consider a single machine scheduling problem that aims…
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…
Many consensus string problems are based on Hamming distance. We replace Hamming distance by the more flexible (e.g., easily coping with different input string lengths) dynamic time warping distance, best known from applications in time…
Covers being one of the most popular form of regularities in strings, have drawn much attention over time. In this paper, we focus on the problem of linear time inference of strings from cover arrays using the least sized alphabet possible.…
In this paper we describe two simple, fast, space-efficient algorithms for finding all matches of an indeterminate pattern $p = p[1..m]$ in an indeterminate string $x = x[1..n]$, where both $p$ and $x$ are defined on a "small" ordered…
Statistical analysis of large and sparse graphs is a challenging problem in data science due to the high dimensionality and nonlinearity of the problem. This paper presents a fast and scalable algorithm for partitioning such graphs into…
Given a pattern string $P$ of length $n$ consisting of $\delta$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $\Sigma$ of size $\Delta$, the {\em exact string…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
Semantic segmentation of medical images is an essential first step in computer-aided diagnosis systems for many applications. However, given many disparate imaging modalities and inherent variations in the patient data, it is difficult to…
Strings form a fundamental data type in computer systems. String searching has been extensively studied since the inception of computer science. Increasingly many applications have to deal with imprecise strings or strings with fuzzy…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
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…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…