Related papers: Highly Scalable Algorithms for Robust String Barco…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through…
This paper presents segmentation-free strategies for the recognition of handwritten numeral strings of unknown length. A synthetic dataset of touching numeral strings of sizes 2-, 3- and 4-digits was created to train end-to-end solutions…
A new method to identify all sufficiently long repeating substrings in one or several symbol sequences is proposed. The method is based on a specific gauge applied to symbol sequences that guarantees identification of the repeating…
The string-matching field has grown at a such complicated stage that various issues come into play when studying it: data structure and algorithmic design, database principles, compression techniques, architectural features, cache and…
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…
The sparse dictionary coding framework represents signals as a linear combination of a few predefined dictionary atoms. It has been employed for images, time series, graph signals and recently for 2-way (or 2D) spatio-temporal data…
Research on the localization of the genetic basis associated with diseases or traits has been widely conducted in the last a few decades. Scan methods have been developed for region-based analysis in whole-genome association studies,…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
In recent years, the distinctive advancement of handling huge data promotes the evolution of ubiquitous computing and analysis technologies. With the constantly upward system burden and computational complexity, adaptive coding has been a…
Accumulation of standardized data collections is opening up novel opportunities for holistic characterization of genome function. The limited scalability of current preprocessing techniques has, however, formed a bottleneck for full…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
In this paper, we propose a scalable and highly efficient index structure for the reachability problem over graphs. We build on the well-known node interval labeling scheme where the set of vertices reachable from a particular node is…
The modern cryptographic primitives are known to generate large volumes of sequential data like keystreams, ciphertext blocks, and hash outputs. Traditional cryptgraphic evaluation methods rely primarily on statistical randomness tests and…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant…
In big data analysis, a simple task such as linear regression can become very challenging as the variable dimension $p$ grows. As a result, variable screening is inevitable in many scientific studies. In recent years, randomized algorithms…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards…