Related papers: ER-index: a referential index for encrypted genomi…
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…
Accurate and efficient entity resolution (ER) is a significant challenge in many data mining and analysis projects requiring integrating and processing massive data collections. It is becoming increasingly important in real-world…
In this paper, we attempt to provide a privacy-preserving and efficient solution for the "similar patient search" problem among several parties (e.g., hospitals) by addressing the shortcomings of previous attempts. We consider a scenario in…
Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for…
Electronic Health Records (EHR) are data generated during routine clinical care. EHR offer researchers unprecedented phenotypic breadth and depth and have the potential to accelerate the pace of precision medicine at scale. A main EHR…
Machine learning models for clinical prediction rely on structured data extracted from Electronic Medical Records (EMRs), yet this process remains dominated by hardcoded, database-specific pipelines for cohort definition, feature selection,…
Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
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…
Entity resolution (ER) is a key data integration problem. Despite the efforts in 70+ years in all aspects of ER, there is still a high demand for democratizing ER - humans are heavily involved in labeling data, performing feature…
Privacy concerns in healthcare have gained interest recently via GDPR, with a rising need for privacy-preserving data collection methods that keep personal information hidden in otherwise usable data. Sometimes data needs to be encrypted…
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…
Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function. Advances in synthetic biology and the…
Cloud storage has become the backbone of modern data infrastructure, yet privacy and efficient data retrieval remain significant challenges. Traditional privacy-preserving approaches primarily focus on enhancing database security but fail…
A self-index is a compressed data structure that supports locate queries -- reporting all positions where a given pattern occurs in a string while maintaining the string in compressed form. While many self-indexes have been proposed,…
Fully Homomorphic Encryption (FHE) allows for computation directly on encrypted data and enables privacy-preserving neural inference in the cloud. Prior work has focused on models with dense inputs (e.g., CNNs), with less attention given to…
We present a method to search for a probe (or query) image representation against a large gallery in the encrypted domain. We require that the probe and gallery images be represented in terms of a fixed-length representation, which is…
Electronic Health Records are electronic data generated during or as a byproduct of routine patient care. Structured, semi-structured and unstructured EHR offer researchers unprecedented phenotypic breadth and depth and have the potential…
DNA fingerprinting is a cornerstone for human identification in forensics, where the sequence of highly polymorphic short tandem repeats (STRs) from an individual is compared against a DNA database. This presents significant privacy risks…