Related papers: COBS: a Compact Bit-Sliced Signature Index
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Indexing is an effective way to support efficient query processing in large databases. Recently the concept of learned index, which replaces or complements traditional index structures with machine learning models, has been actively…
This paper presents a novel method for efficient image retrieval, based on a simple and effective hashing of CNN features and the use of an indexing structure based on Bloom filters. These filters are used as gatekeepers for the database of…
Natural language text corpora are often available as sets of syntactically parsed trees. A wide range of expressive tree queries are possible over such parsed trees that open a new avenue in searching over natural language text. They not…
In this paper, a new and novel data structure is proposed to dynamically insert and delete segments. Unlike the standard segment trees[3], the proposed data structure permits insertion of a segment with interval range beyond the interval…
Compressed inverted indices in use today are based on the idea of gap compression: documents pointers are stored in increasing order, and the gaps between successive document pointers are stored using suitable codes which represent smaller…
Compressed bitmap indexes are used to speed up simple aggregate queries in databases. Indeed, set operations like intersections, unions and complements can be represented as logical operations (AND,OR,NOT) that are ideally suited for…
The information-based optimal subdata selection (IBOSS) is a computationally efficient method to select informative data points from large data sets through processing full data by columns. However, when the volume of a data set is too…
Modern, large scale monitoring systems have to process and store vast amounts of log data in near real-time. At query time the systems have to find relevant logs based on the content of the log message using support structures that can…
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…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
One of the important factors that make a search engine fast and accurate is a concise and duplicate free index. In order to remove duplicate and near-duplicate documents from the index, a search engine needs a swift and reliable duplicate…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
Segmentation of brain magnetic resonance images (MRI) is crucial for the analysis of the human brain and diagnosis of various brain disorders. The drawbacks of time-consuming and error-prone manual delineation procedures are aimed to be…
This thesis develops computational methods in similarity-preserving hashing, classification, and cancer genomics. Standard space partitioning-based hashing relies on Binary Search Trees (BSTs), but their exponential growth and sparsity…
In large-scale image retrieval, many indexing methods have been proposed to narrow down the searching scope of retrieval. The features extracted from images usually are of high dimensions or unfixed sizes due to the existence of key points.…
Recent advances in text representation have shown that training on large amounts of text is crucial for natural language understanding. However, models trained without predefined notions of topical interest typically require careful…
In a dynamic retrieval system, documents must be ingested as they arrive, and be immediately findable by queries. Our purpose in this paper is to describe an index structure and processing regime that accommodates that requirement for…
The data structure at the core of large-scale search engines is the inverted index, which is essentially a collection of sorted integer sequences called inverted lists. Because of the many documents indexed by such engines and stringent…