Related papers: Counting common substrings effectively
This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
We study the problem of cutting a length-$n$ string of positive real numbers into $k$ pieces so that every piece has sum at least $b$. The problem can also be phrased as transforming such a string into a new one by merging adjacent numbers.…
The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…
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 a supervised learning algorithm for text categorization which has brought the team of authors the 2nd place in the text categorization division of the 2012 Cybersecurity Data Mining Competition (CDMC'2012) and a 3rd prize…
Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
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…
We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
Regularities in strings are often related to periods and covers, which have extensively been studied, and algorithms for their efficient computation have broad application. In this paper we concentrate on computing cyclic regularities of…
The Shortest Common Superstring problem (SCS) consists, for a set of strings S = {s_1,...,s_n}, in finding a minimum length string that contains all s_i, 1<= i <= n, as substrings. While a 2+11/30 approximation ratio algorithm has recently…
Adaptations of features commonly applied in the field of visual computing, co-occurrence matrix (COM) and run-length matrix (RLM), are proposed for the similarity computation of strings in general (words, phrases, codes and texts). The…
We introduce string2string, an open-source library that offers a comprehensive suite of efficient algorithms for a broad range of string-to-string problems. It includes traditional algorithmic solutions as well as recent advanced neural…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
Subword units are an effective way to alleviate the open vocabulary problems in neural machine translation (NMT). While sentences are usually converted into unique subword sequences, subword segmentation is potentially ambiguous and…
Under categorial grammars that have powerful rules like composition, a simple n-word sentence can have exponentially many parses. Generating all parses is inefficient and obscures whatever true semantic ambiguities are in the input. This…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Community identification is a long-standing challenge in the modern network science, especially for very large scale networks containing millions of nodes. In this paper, we propose a new metric to quantify the structural similarity between…