Preserving differential privacy for similarity measurement in smart environments.
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ABSTRACT:
SUBMITTER: Wong KS
PROVIDER: S-EPMC4123612 | biostudies-other | 2014
REPOSITORIES: biostudies-other
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Project description:BackgroundThere is an urgent need for the development of global analytic frameworks that can perform analyses in a privacy-preserving federated environment across multiple institutions without privacy leakage. A few studies on the topic of federated medical analysis have been conducted recently with the focus on several algorithms. However, none of them have solved similar patient matching, which is useful for applications such as cohort construction for cross-institution observational studies, disease surveillance, and clinical trials recruitment.ObjectiveThe aim of this study was to present a privacy-preserving platform in a federated setting for patient similarity learning across institutions. Without sharing patient-level information, our model can find similar patients from one hospital to another.MethodsWe proposed a federated patient hashing framework and developed a novel algorithm to learn context-specific hash codes to represent patients across institutions. The similarities between patients can be efficiently computed using the resulting hash codes of corresponding patients. To avoid security attack from reverse engineering on the model, we applied homomorphic encryption to patient similarity search in a federated setting.ResultsWe used sequential medical events extracted from the Multiparameter Intelligent Monitoring in Intensive Care-III database to evaluate the proposed algorithm in predicting the incidence of five diseases independently. Our algorithm achieved averaged area under the curves of 0.9154 and 0.8012 with balanced and imbalanced data, respectively, in ?-nearest neighbor with ?=3. We also confirmed privacy preservation in similarity search by using homomorphic encryption.ConclusionsThe proposed algorithm can help search similar patients across institutions effectively to support federated data analysis in a privacy-preserving manner.
| S-EPMC5924379 | biostudies-literature
Project description:Process mining has been successfully applied in the healthcare domain and has helped touncover various insights for improving healthcare processes. While the benefits of process miningare widely acknowledged, many people rightfully have concerns about irresponsible uses of personaldata. Healthcare information systems contain highly sensitive information and healthcare regulationsoften require protection of data privacy. The need to comply with strict privacy requirements mayresult in a decreased data utility for analysis. Until recently, data privacy issues did not get muchattention in the process mining community; however, several privacy-preserving data transformationtechniques have been proposed in the data mining community. Many similarities between datamining and process mining exist, but there are key differences that make privacy-preserving datamining techniques unsuitable to anonymise process data (without adaptations). In this article, weanalyse data privacy and utility requirements for healthcare process data and assess the suitabilityof privacy-preserving data transformation methods to anonymise healthcare data. We demonstratehow some of these anonymisation methods affect various process mining results using three publiclyavailable healthcare event logs. We describe a framework for privacy-preserving process mining thatcan support healthcare process mining analyses. We also advocate the recording of privacy metadatato capture information about privacy-preserving transformations performed on an event log.
| S-EPMC7084661 | biostudies-literature
Project description:ObjectiveRecord linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human-machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data.MethodsIn the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding.ResultsWe synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework.ConclusionsHuman-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human-machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility.
| S-EPMC3932473 | biostudies-literature
Project description:Introduction:Available and practical methods for privacy preserving linkage have shortcomings: methods utilising anonymous linkage codes provide limited accuracy while methods based on Bloom filters have proven vulnerable to frequency-based attacks. Objectives:In this paper, we present and evaluate a novel protocol that aims to meld both the accuracy of the Bloom filter method with the privacy achievable through the anonymous linkage code methodology. Methods:The protocol involves creating multiple match-keys for each record, with the composition of each match-key depending on attributes of the underlying datasets being compared. The protocol was evaluated through de-duplication of four administrative datasets and two synthetic datasets; the 'answers' outlining which records belonged to the same individual were known for each dataset. The results were compared against results achieved with un-encoded linkage and other privacy preserving techniques on the same datasets. Results:The multiple match-key protocol presented here achieved high quality across all datasets, performing better than record-level Bloom filters and the SLK, but worse than field-level Bloom filters. Conclusion:The presented method provides high linkage quality while avoiding the frequency based attacks that have been demonstrated against the Bloom filter approach. The method appears promising for real world use.
| S-EPMC7482515 | biostudies-literature
Project description:BackgroundSearching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources.ResultsIn order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation.ConclusionWe proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information.
| S-EPMC4704467 | biostudies-literature
Project description:BackgroundThe current and future applications of genomic data may raise ethical and privacy concerns. Processing and storing of this data introduce a risk of abuse by potential offenders since the human genome contains sensitive personal information. For this reason, we have developed a privacy-preserving method, named Varlock providing secure storage of sequenced genomic data. We used a public set of population allele frequencies to mask the personal alleles detected in genomic reads. Each personal allele described by the public set is masked by a randomly selected population allele with respect to its frequency. Masked alleles are preserved in an encrypted confidential file that can be shared in whole or in part using public-key cryptography.ResultsOur method masked the personal variants and introduced new variants detected in a personal masked genome. Alternative alleles with lower population frequency were masked and introduced more often. We performed a joint PCA analysis of personal and masked VCFs, showing that the VCFs between the two groups cannot be trivially mapped. Moreover, the method is reversible and personal alleles in specific genomic regions can be unmasked on demand.ConclusionOur method masks personal alleles within genomic reads while preserving valuable non-sensitive properties of sequenced DNA fragments for further research. Personal alleles in the desired genomic regions may be restored and shared with patients, clinics, and researchers. We suggest that the method can provide an additional security layer for storing and sharing of the raw aligned reads.
| S-EPMC8487550 | biostudies-literature
Project description:MotivationAs genomics moves into the clinic, there has been much interest in using this medical data for research. At the same time the use of such data raises many privacy concerns. These circumstances have led to the development of various methods to perform genome-wide association studies (GWAS) on patient records while ensuring privacy. In particular, there has been growing interest in applying differentially private techniques to this challenge. Unfortunately, up until now all methods for finding high scoring SNPs in a differentially private manner have had major drawbacks in terms of either accuracy or computational efficiency.ResultsHere we overcome these limitations with a substantially modified version of the neighbor distance method for performing differentially private GWAS, and thus are able to produce a more viable mechanism. Specifically, we use input perturbation and an adaptive boundary method to overcome accuracy issues. We also design and implement a convex analysis based algorithm to calculate the neighbor distance for each SNP in constant time, overcoming the major computational bottleneck in the neighbor distance method. It is our hope that methods such as ours will pave the way for more widespread use of patient data in biomedical research.Availability and implementationA python implementation is available at http://groups.csail.mit.edu/cb/DiffPriv/Contactbab@csail.mit.eduSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4848404 | biostudies-literature
Project description:Differential privacy allows quantifying privacy loss resulting from accession of sensitive personal data. Repeated accesses to underlying data incur increasing loss. Releasing data as privacy-preserving synthetic data would avoid this limitation but would leave open the problem of designing what kind of synthetic data. We propose formulating the problem of private data release through probabilistic modeling. This approach transforms the problem of designing the synthetic data into choosing a model for the data, allowing also the inclusion of prior knowledge, which improves the quality of the synthetic data. We demonstrate empirically, in an epidemiological study, that statistical discoveries can be reliably reproduced from the synthetic data. We expect the method to have broad use in creating high-quality anonymized data twins of key datasets for research.
| S-EPMC8276015 | biostudies-literature
Project description:MotivationDeveloping targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual's collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies.ResultsTo address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis.Availability and implementationThe software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.htmlSupplementary informationSupplementary data are available at Bioinformatics online.Contacthcorrada@umiacs.umd.edu.
| S-EPMC4908319 | biostudies-literature
Project description:Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regarding the collection, storage and analysis of such sensitive human data. Recent results show that given some background information, it is possible for an adversary to reidentify an individual from a specific genomic data set. This can reveal the current association or future susceptibility of some diseases for that individual (and sometimes the kinship between individuals) resulting in a privacy violation. Regardless of these risks, our genomic data hold much importance in analyzing the well-being of us and the future generation. Thus, in this article, we discuss the different privacy and security-related problems revolving around human genomic data. In addition, we will explore some of the cardinal cryptographic concepts, which can bring efficacy in secure and private genomic data computation. This article will relate the gaps between these two research areas-Cryptography and Genomics.
| S-EPMC6585383 | biostudies-literature