Related papers: Technology Beats Algorithms (in Exact String Match…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
Two new algorithms are described for matching two dimensional coordinate lists of point sources that are signifcantly faster than previous methods. By matching rarely occurring triangles (or more complex shapes) in the two lists, and by…
Associative memories are data structures addressed using part of the content rather than an index. They offer good fault reliability and biological plausibility. Among different families of associative memories, sparse ones are known to…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
The maximal clique enumeration (MCE) problem has numerous applications in biology, chemistry, sociology, and graph modeling. Though this problem is well studied, most current research focuses on finding solutions in large sparse graphs or…
Fast exact algorithms are known for Hamiltonian paths in undirected and directed bipartite graphs through elegant though involved algorithms that are quite different from each other. We devise algorithms that are simple and similar to each…
Matching pursuits are a class of greedy algorithms commonly used in signal processing, for solving the sparse approximation problem. They rely on an atom selection step that requires the calculation of numerous projections, which can be…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…
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…
In many important applications -- such as search engines and relational database systems -- data is stored in the form of arrays of integers. Encoding and, most importantly, decoding of these arrays consumes considerable CPU time.…
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…
The parameterized matching problem is a variant of string matching, which is to search for all parameterized occurrences of a pattern $P$ in a text $T$. In considering matching algorithms, the combinatorial natures of strings, especially…
Exact String Matching is an essential issue in many computer science applications. Unfortunately, the performance of Exact String Matching algorithms, namely, executing time, does not address the needs of these applications. This paper…
Mixed-integer optimisation problems can be computationally challenging. Here, we introduce and analyse two efficient algorithms with a specific sequential design that are aimed at dealing with sampled problems within this class. At each…
In runtime verification, pattern matching, which searches for occurrences of a specific pattern within a word, provides more information than a simple violation detection of the monitored property, by locating concrete evidence of the…
Code semantics similarity can be used for many tasks such as code recommendation, automated software defect correction, and clone detection. Yet, the accuracy of such systems has not yet reached a level of general purpose reliability. To…
The abelian pattern matching problem consists in finding all substrings of a text which are permutations of a given pattern. This problem finds application in many areas and can be solved in linear time by a naive sliding window approach.…