Related papers: Summarizing Diverging String Sequences, with Appli…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
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…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
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…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
Massive sizes of real-world graphs, such as social networks and web graph, impose serious challenges to process and perform analytics on them. These issues can be resolved by working on a small summary of the graph instead . A summary is a…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…
Data summarization aims at utilizing a small-scale summary to represent massive datasets as a whole, which is useful for visualization and information sipped generation. However, most existing studies of hierarchical summarization only work…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
Sequence theories are an extension of theories of strings with an infinite alphabet of letters, together with a corresponding alphabet theory (e.g. linear integer arithmetic). Sequences are natural abstractions of extendable arrays, which…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
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…