Related papers: RAMBO: Repeated And Merged BloOm Filter for Ultra-…

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…

A Bloom filter is a memory-efficient data structure for approximate membership queries used in numerous fields of computer science. Recently, learned Bloom filters that achieve better memory efficiency using machine learning models have…

Long maximal exact matches (MEMs) are used in many genomics applications such as read classification and sequence alignment. Li's ropebwt3 finds long MEMs quickly because it can often ignore much of its input. In this paper we show that a…

K-mer counting is a requisite process for DNA assembly because it speeds up its overall process. The frequency of K-mers is used for estimating the parameters of DNA assembly, error correction, etc. The process also provides a list of…

We suggest a method for holding a dictionary data structure, which maps keys to values, in the spirit of Bloom Filters. The space requirements of the dictionary we suggest are much smaller than those of a hashtable. We allow storing n keys,…

Bloom filter is a space-efficient probabilistic data structure for checking elements' membership in a set. Given multiple sets, however, a standard Bloom filter is not sufficient when looking for the items to which an element or a set of…

A retrieval data structure stores a static function f : S -> {0,1}^r . For all x in S, it returns the r-bit value f(x), while for other inputs it may return an arbitrary result. The structure cannot answer membership queries, so it does not…

A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…

Bloom Filter is an important probabilistic data structure to reduce memory consumption for membership filters. It is applied in diverse domains such as Computer Networking, Network Security and Privacy, IoT, Edge Computing, Cloud Computing,…

The retrieval problem is the problem of associating data with keys in a set. Formally, the data structure must store a function f: U ->{0,1}^r that has specified values on the elements of a given set S, a subset of U, |S|=n, but may have…

This paper presents new alternatives to the well-known Bloom filter data structure. The Bloom filter, a compact data structure supporting set insertion and membership queries, has found wide application in databases, storage systems, and…

Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…

Membership (membership query / membership testing) is a fundamental problem across databases, networks and security. However, previous research has primarily focused on either approximate solutions, such as Bloom Filters, or exact methods,…

A retrieval data structure for a static function $f:S\rightarrow \{0,1\}^r$ supports queries that return $f(x)$ for any $x \in S$. Retrieval data structures can be used to implement a static approximate membership query data structure…

With the growing scale of big data, probabilistic structures receive increasing popularity for efficient approximate storage and query processing. For example, Bloom filters (BF) can achieve satisfactory performance for approximate…

Gene sequence search is a fundamental operation in computational genomics. Due to the petabyte scale of genome archives, most gene search systems now use hashing-based data structures such as Bloom Filters (BF). The state-of-the-art systems…

Bloom filters are widely used data structures that compactly represent sets of elements. Querying a Bloom filter reveals if an element is not included in the underlying set or is included with a certain error rate. This membership testing…

Bloom filter is a widely used classic data structure for approximate membership queries. Learned Bloom filters improve memory efficiency by leveraging machine learning, with the partitioned learned Bloom filter (PLBF) being among the most…

This paper investigates approaches to parallelizing Bounded Model Checking (BMC) for shared memory environments as well as for clusters of workstations. We present a generic framework for parallelized BMC named Tarmo. Our framework can be…

Code completion is essential in software development, helping developers by predicting code snippets based on context. Among completion tasks, Method Body Completion (MBC) is particularly challenging as it involves generating complete…