Related papers: ER-index: a referential index for encrypted genomi…

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…

Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and…

We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in $O(1)$ time per step while using $O(\log \sigma * n) + o(\log \sigma * \sigma * n)$ bits of space. This is done by replacing the…

The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…

Cryogenic electron microscopy (Cryo-EM) has become an essential tool for capturing high-resolution biological structures. Despite its advantage in visualizations, the large storage size of Cryo-EM data file poses significant challenges for…

Recent feature matching methods have achieved remarkable performance but lack efficiency consideration. In this paper, we revisit the mainstream detector-free matching pipeline and improve all its stages considering both accuracy and…

FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…

Electronic health records (EHRs) are invaluable for clinical research, yet privacy concerns severely restrict data sharing. Synthetic data generation offers a promising solution, but EHRs present unique challenges: they contain both…

In this paper, we introduce ACE, a consent-embedded searchable encryption scheme. ACE enables dynamic consent management by supporting the physical deletion of associated data at the time of consent revocation. This ensures instant real…

The rapid accumulation of Electronic Health Records (EHRs) has transformed healthcare by providing valuable data that enhance clinical predictions and diagnoses. While conventional machine learning models have proven effective, they often…

This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…

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…

At CCS 2015 Naveed et al. presented first attacks on efficiently searchable encryption, such as deterministic and order-preserving encryption. These plaintext guessing attacks have been further improved in subsequent work, e.g. by Grubbs et…

Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…

A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…

Efficiently querying data on embedded sensor and IoT devices is challenging given the very limited memory and CPU resources. With the increasing volumes of collected data, it is critical to process, filter, and manipulate data on the edge…

As a key ingredient of the DBMS, index plays an important role in the query optimization and processing. However, it is a non-trivial task to apply existing indexes or design new indexes for new applications, where both data distribution…

Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…

Trusted execution environments (TEE) such as Intel's Software Guard Extension (SGX) have been widely studied to boost security and privacy protection for the computation of sensitive data such as human genomics. However, a performance…

Quantized Indexing is a fast and space-efficient form of enumerative (combinatorial) coding, the strongest among asymptotically optimal universal entropy coding algorithms. The present advance in enumerative coding is similar to that made…