Related papers: Technology Beats Algorithms (in Exact String Match…
We present OnPair, a dictionary-based compression algorithm designed to meet the needs of in-memory database systems that require both high compression and fast random access. Existing methods either achieve strong compression ratios at…
String sorting is an important part of tasks such as building index data structures. Unfortunately, current string sorting algorithms do not scale to massively parallel distributed-memory machines since they either have latency (at least)…
We propose a fast, parallel maximum clique algorithm for large sparse graphs that is designed to exploit characteristics of social and information networks. The method exhibits a roughly linear runtime scaling over real-world networks…
The maximum clique problem is a well known NP-Hard problem with applications in data mining, network analysis, informatics, and many other areas. Although there exist several algorithms with acceptable runtimes for certain classes of…
We introduce the natural notion of a matching frame in a $2$-dimensional string. A matching frame in a $2$-dimensional $n\times m$ string $M$, is a rectangle such that the strings written on the horizontal sides of the rectangle are…
The Exact Set Similarity Join problem aims to find all similar sets between two collections of sets, with respect to a threshold and a similarity function such as overlap, Jaccard, dice or cosine. The naive approach verifies all pairs of…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
The currently fastest algorithm for regular expression pattern matching and membership improves the classical O(nm) time algorithm by a factor of about log^{3/2}n. Instead of focussing on general patterns we analyse homogeneous patterns of…
We have developed a novel prediction method based on string invariants. The method does not require learning but a small set of parameters must be set to achieve optimal performance. We have implemented an evolutionary algorithm for the…
Efficient pattern matching is fundamental for practical term rewrite engines. By preprocessing the given patterns into a finite deterministic automaton the matching patterns can be decided in a single traversal of the relevant parts of the…
We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
Machine-translated text plays an important role in modern life by smoothing communication from various communities using different languages. However, unnatural translation may lead to misunderstanding, a detector is thus needed to avoid…
Pairwise comparison labels are more informative and less variable than class labels, but generating them poses a challenge: their number grows quadratically in the dataset size. We study a natural experimental design objective, namely,…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
The Permutation Pattern Matching problem asks, given two permutations $\sigma$ on $n$ elements and $\pi$, whether $\sigma$ admits a subsequence with the same relative order as $\pi$ (or, in the counting version, how many such subsequences…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
The rapid increase in symbolic data has underscored the significance of pattern matching and regular expression processing. While nondeterministic finite automata (NFA) are commonly used for these tasks, they are limited to detecting…
We propose novel algorithms for sequence prediction based on ideas from stringology. These algorithms are time and space efficient and satisfy mistake bounds related to particular stringological complexity measures of the sequence. In this…
Chase-like decoding algorithms are a popular choice for soft-input decoding of algebraic codes. In this paper, we evaluate the performance of different test pattern sets using three methods. For test pattern sets with a certain structure…