Related papers: Practical combinations of repetition-aware data st…
The problem of detecting and measuring the repetitiveness of one-dimensional strings has been extensively studied in data compression and text indexing. Our understanding of these issues has been significantly improved by the introduction…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
Flexible neural sequence models outperform grammar- and automaton-based counterparts on a variety of tasks. However, neural models perform poorly in settings requiring compositional generalization beyond the training data -- particularly to…
We investigate symbolic sequences and in particular information carriers as e.g. books and DNA--strings. First the higher order Shannon entropies are calculated, a characteristic root law is detected. Then the algorithmic entropy is…
Tries are among the most versatile and widely used data structures on words. They are pertinent to the (internal) structure of (stored) words and several splitting procedures used in diverse contexts ranging from document taxonomy to IP…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
In this paper, we propose a novel approach to combine \emph{compact directed acyclic word graphs} (CDAWGs) and grammar-based compression. This leads us to an efficient self-index, called Linear-size CDAWGs (L-CDAWGs), which can be…
The research on indexing repetitive string collections has focused on the same search problems used for regular string collections, though they can make little sense in this scenario. For example, the basic pattern matching query "list all…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
We raise the question of approximating the compressibility of a string with respect to a fixed compression scheme, in sublinear time. We study this question in detail for two popular lossless compression schemes: run-length encoding (RLE)…
Dominant sequence models like the Transformer represent structure implicitly through dense attention weights, incurring quadratic complexity. We propose RewriteNets, a novel neural architecture built on an alternative paradigm: explicit,…
Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s (SPIRE 2010) original implementation, a reference genome is…
Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…
We propose a new approach for calculating the Lempel-Ziv factorization of a string, based on run length encoding (RLE). We present a conceptually simple off-line algorithm based on a variant of suffix arrays, as well as an on-line algorithm…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
Given a string of characters, the Burrows-Wheeler Transform rearranges the characters in it so as to produce another string of the same length which is more amenable to compression techniques such as move to front, run-length encoding, and…
The Burrows-Wheeler Transform (BWT) moves characters with similar contexts in a text together, where a character's context consists of the characters immediately following it. We say that a property has contextual locality if characters…