相关论文: R-enum: Enumeration of Characteristic Substrings i…

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…

The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…

The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the…

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…

The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present…

Classification of sequence data is the topic of interest for dynamic Bayesian models and Recurrent Neural Networks (RNNs). While the former can explicitly model the temporal dependencies between class variables, the latter have a capability…

Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…

Unconstrained text recognition is an important computer vision task, featuring a wide variety of different sub-tasks, each with its own set of challenges. One of the biggest promises of deep neural networks has been the convergence and…

Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Transform (BWT) with suffix array sampling to achieve space…

When comparing human with artificial intelligence, one major difference is apparent: Humans can generalize very broadly from sparse data sets because they are able to recombine and reintegrate data components in compositional manners. To…

We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…

Bille and G{\o}rtz (2011) recently introduced the problem of substring range counting, for which we are asked to store compactly a string $S$ of $n$ characters with integer labels in ([0, u]), such that later, given an interval ([a, b]) and…

In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…

We give recurrences, generating functions and explicit exact expressions for the enumeration of fundamental quantities involving runs in binary strings. We first focus on enumerations concerning runs of ones, and we then analyse the same…

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

Compression is beneficial because it helps detract resource usage. It reduces data storage space as well as transmission traffic and improves web pages loading. Run-length coding (RLC) is a lossless data compression algorithm. Data are…

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…

The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…