Related papers: COBS: a Compact Bit-Sliced Signature Index
Bloom Filter is a probabilistic data structure for the membership query, and it has been intensely experimented in various fields to reduce memory consumption and enhance a system's performance. Bloom Filter is classified into two key…
The limited number of qubits per chip remains a critical bottleneck in quantum computing, motivating the use of distributed architectures that interconnect multiple quantum processing units (QPUs). However, executing quantum algorithms…
Risk for autism can be influenced by genetic mutations in hundreds of genes. Based on findings showing that genes with highly correlated gene expressions are functionally interrelated, "guilt by association" methods such as DAWN have been…
Cell instance segmentation (CIS) is crucial for identifying individual cell morphologies in histopathological images, providing valuable insights for biological and medical research. While unsupervised CIS (UCIS) models aim to reduce the…
Recent research shows that copying is prevalent for Deep-Web data and considering copying can significantly improve truth finding from conflicting values. However, existing copy detection techniques do not scale for large sizes and numbers…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
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…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Segmenting medical images is critical to facilitating both patient diagnoses and quantitative research. A major limiting factor is the lack of labeled data, as obtaining expert annotations for each new set of imaging data and task can be…
This paper addresses the construction of inverted index for large-scale image retrieval. The inverted index proposed by J. Sivic brings a significant acceleration by reducing distance computations with only a small fraction of the database.…
Existing path lookup routines in file systems need to construct an auxiliary index in memory or traverse the dentries of the directory file sequentially, which brings either heavy writes or large timing cost. This paper designs a novel path…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
Bit arrays, or bitmaps, are used to significantly speed up set operations in several areas, such as data warehousing, information retrieval, and data mining, to cite a few. However, bitmaps usually use a large storage space, thus requiring…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…
Noisy shuffling channels capture the main characteristics of DNA storage systems where distinct segments of data are received out of order, after being corrupted by substitution errors. For realistic schemes with short-length segments,…
Finding desired information from large data set is a difficult problem. Information retrieval is concerned with the structure, analysis, organization, storage, searching, and retrieval of information. Index is the main constituent of an IR…
Distributed computing seems to be a natural approach to overcome size limitations of quantum computers in terms of number of qubits. But one lacks an efficient distribution approach to deal systematically with potential algorithms. This…
Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no consistent framework to integrate and run these tools across projects. Currently,…