Implementing privacy-preserving record linkage: welcome to the real world

Record linkage represents the process of identifying records that refer to the same real-world entity across multiple sources. In the recent past, the large explosion of data from organizations and individuals has created critical challenges in record linkage process, leading the scientific community to develop a rich series of techniques. Among these recent developments, the design of record linkage solutions for medical data is a cornerstone for health-care systems, as personal identifying information, such as name and date of birth, is often used for linkage. In this setting, record linkage solutions are expected to preserve individual patients’ privacy in addition to be effective and efficient. In this chapter, we provide a broad review of the recent works in privacy preserving record linkage (PPRL). From a privacy-centric perspective, we summarize a comprehensive framework of the PPRL process and describe the privacy assurance techniques adopted for each step in the framework. With the applications in biomedical domain in mind, we identify several challenges for PPRL and discuss future research directions.

BackgroundData on newborns is regularly linked for epidemiological research. However, hospital data often suffers from incomplete data. We report on a linkage of two population-covering administrative health databases containing neonatal and perinatal data without unique personal identifiers and with incomplete information in standard patient identifiers.
 GoalTo study the effects of a policy-induced change from linking a national database without standard patient identifiers to a privacy-preserving Record Linkage method, we compare the linkage system in use to clear-text and privacy-preserving Record Linkage techniques. We expected large proportions of missing identifiers since they are not needed for clinical practice. Therefore, we expected missing links caused by missing identifiers. To study the impact of these missing identifiers on these successful links, we compared several linkage methods. Furthermore, we study the variations of linkage success between hospitals.
 MethodsPerinatal and neonatal data from population-covering real-world administrative databases was linked using several variants of state of the art methods, including Privacy-preserving Record Linkage (PPRL) techniques such as multiple match keys and Bloom filter methods.
 Results We report on the variation of linkage results between the hospitals and give possible explanations for the differences.
 The resulting linkage success is reported for each method. The impact of incomplete data on linkage success for each method is documented.
 Finally, we report on the relative performance of the modified techniques compared to standard linkage procedures used in practice.
 ConclusionImplementing a record linkage system based on identifiers not required for clinical practice caused a large number of missing identifiers. Since this information is essential for successful clear-text and private linkage methods, emphasizing the need for documenting patient identifiers, especially in cases where auxiliary information (such as stable addresses, date of birth or health insurance numbers) are missing, is of central importance for implementing a privacy-preserving Record Linkage system.

The process of merging data of different data sources is referred to as record linkage. A medical environment with increased preconditions on privacy protection demands the transformation of clear-text attributes like first name or date of birth into one-way encrypted pseudonyms. When performing an automated or privacy preserving record linkage there might be the need of a binary classification deciding whether two records should be classified as the same entity. The classification is the final of the four main phases of the record linkage process: Preprocessing, indexing, matching and classification. The choice of binary classification techniques in dependence of project specifications in particular data quality has not extensively been studied yet. The aim of this work is the introduction and evaluation of an automatable semi-supervised binary classification system applied within the field of record linkage capable of competing or even surpassing advanced automated techniques of the domain of unsupervised classification. This work describes the rationale leading to the model and the final implementation of an automatable semi-supervised binary classification system and the comparison of its classification performance to an advanced active learning approach out of the domain of unsupervised learning. The performance of both systems has been measured on a broad variety of artificial test sets (n = 400), based on real patient data, with distinct and unique characteristics. While the classification performance for both methods measured as F-measure was relatively close on test sets with maximum defined data quality, 0.996 for semi-supervised classification, 0.993 for unsupervised classification, it incrementally diverged for test sets of worse data quality dropping to 0.964 for semi-supervised classification and 0.803 for unsupervised classification. Aside from supplying a viable model for semi-supervised classification for automated probabilistic record linkage, the tests conducted on a large amount of test sets suggest that semi-supervised techniques might generally be capable of outperforming unsupervised techniques especially on data with lower levels of data quality.

ABSTRACTObjectiveIn most European settings, record linkage across different institutions has to be based on personal identifiers such as names, birthday or place of birth. To protect the privacy of research subjects, the identifiers have to be encrypted. In practice, these identifiers show error rates up to 20% per identifier, therefore linking on encrypted identifiers usually implies the loss of large subsets of the databases. In many applications, this loss of cases is related to variables of interest for the subject matter of the study. Therefore, this kind of record-linkage will generate biased estimates.
 These problems gave rise to techniques of Privacy Preserving Record Linkage (PPRL). Many different PPRL techniques have been suggested within the last 10 years, very few of them are suitable for practical applications with large database containing millions of records as they are typical for administrative or medical databases. One proven technique for PPRL for large scale applications is PPRL based on Bloom filters.MethodUsing appropriate parameter settings, Bloom filter approaches show linkage results comparable to linkage based on unencrypted identifiers. Furthermore, this approach has been used in real-world settings with data sets containing up to 100 Million records. By the application of suitable blocking strategies, linking can be done in reasonable time.ResultHowever, Bloom filters have been subject of cryptographic attacks. Previous research has shown that the straight application of Bloom filters has a nonzero re-identification risk. We will present new results on recently developed techniques to defy all known attacks on PPRL Bloom filters. These computationally simple algorithms modify the identifiers by different cryptographic diffusion techniques. The presentation will demonstrate these new algorithms and show their performance concerning precision, recall and re-identification risk on large databases.

ObjectiveTo introduce Linkja, an open-source, certified, Privacy-Preserving Record Linkage (PPRL) tool with the primary objective of facilitating secure and efficient record linkage across diverse datasets, while preserving individual privacy, providing a comprehensive and privacy-centric approach to program assessments. ApproachLinkja has been used to evaluate Chicago’s Flexible Housing Pool program by securely linking various datasets, including Homeless Management Information Systems (HMIS), Electronic Health Records, Jail records, Medical Examiner reports, and Public Health data. Data contributors used separate honest brokers for record linkage, and generation of salt and cryptography keys. ResultsLinkja enabled this multi-sector linkage by facilitating legal and data sharing agreements, avoided licensing fees and procurement processes for all parties, and provided a de-identified for analysis. The insights gleaned from the analysis motivated the FHP program to plan a follow-up evaluation that will add emergency serviced records from a separate City of Chicago department. The successful linkage provided a nuanced understanding of the association between stable housing and reduced healthcare utilization. ConclusionsLinkja's cryptographic certification ensures the highest standards of security during data linkage, safeguarding sensitive information. The matching rules, validated on hard-to-match populations, prove essential in maintaining accuracy and reliability in the linkage process. ImplicationsThe open-source nature of Linkja promotes transparency and collaboration in the development and enhancement of privacy-preserving record linkage techniques. This tool has broad implications for sectors dealing with sensitive data, fostering responsible data-sharing practices, and enabling secure collaborative research initiatives without compromising individual privacy.

IntroductionBusinesses worldwide are increasingly adopting the storage, compute and analytical services provided by cloud computing. Yet, few operational linkage units are keeping pace with this world of technological change - most use legacy systems approaching their limits with the rapidly increasing size and range of datasets now required for linkage.
 Objectives and ApproachTo meet the demands of linkage for the near future, it is important that new solutions for linkage consider the services provided by public cloud infrastructure for compute, storage and analytics. We examined Platform as a Service (PaaS) offerings for use in the development of a cost-effective cloud model for scalable, privacy-preserving record linkage (PPRL). PPRL techniques were adapted to maximise the quality of linkage and to automate as much of the process as possible. Finally, a prototype was created to demonstrate the capabilities and potential of the model.
 ResultsWe present our cloud model for PPRL, a platform for record linkage that provides rapid scaling of resources to meet demand, and the results of how our prototype performed on massive datasets.
 Conclusion/ImplicationsThe application of record linkage using relatively inexpensive cloud infrastructure represents a significant step towards providing an efficient and scalable record linkage service to researchers and government. Larger datasets can be linked efficiently, including national or cross-jurisdictional datasets, with little investment in private infrastructure, and improved turnaround times for researchers.

Examine the accuracy of privacy preserving record linkage (PPRL) matches in real world data (RWD). We conducted a systematic literature review to identify articles evaluating PPRL methods from January 1, 2013 to June 15, 2023. Eligible studies included original research reporting quantitative metrics such as precision and recall in health-related data sources. Covidence software was used to manage the review process. Five studies met our inclusion criteria. Tokenization and hash functions were used to hash and encrypt personally identifiable information (PII) including first and last names, dates of birth (DOB), and Social Security Numbers (SSNs) in a variety of RWD. All identified studies utilized deterministic matching. Combinations of tokenized or hashed PII that included "quasi-identifiers" like names and DOBs had consistently high precision (>95%) but lower recall, likely due to misspelled or inconsistently spelled names and name changes. SSN-based combinations demonstrated high precision but variable recall due to incomplete SSN data in RWD. Studies that employed algorithms in which at least one match was identified from a specified set of PII combinations provided high precision and high recall. The systematic review indicates that PPRL methods generally provide highly accurate patient data linkage while maintaining privacy. Researchers should carefully consider the completeness and stability of each PII element selected for PPRL and may want to employ a strategy that allows for patient records to be matched if they meet at least one of several combinations of PII.

IntroductionResearch data combined with administrative data provides a robust resource capable of answering unique research questions. However, in cases where personal health data are encrypted, due to ethics requirements or institutional restrictions, traditional methods of deterministic and probabilistic record linkages are not feasible. Instead, privacy-preserving record linkages must be used to protect patients’ personal data during data linkage.ObjectivesTo determine the feasibility and validity of a deterministic privacy preserving data linkage protocol using homomorphically encrypted data.MethodsFeasibility was measured by the number of records that successfully matched via direct identifiers. Validity was measured by the number of records that matched with multiple indirect identifiers. The threshold for feasibility and validity were both set at 95%. The datasets shared a single, direct identifier (health card number) and multiple indirect identifiers (sex and date of birth). Direct identifiers were encrypted in both datasets and then transferred to a third-party server capable of linking the encrypted identifiers without decrypting individual records. Once linked, the study team used indirect identifiers to verify the accuracy of the linkage in the final dataset.ResultsWith a combination of manual and automated data transfer in a sample of 8,128 individuals, the privacy-preserving data linkage took 36 days to match to a population sample of over 3.2 million records. 99.9% of the records were successfully matched with direct identifiers, and 99.8% successfully matched with multiple indirect identifiers. We deemed the linkage both feasible and valid.ConclusionsAs combining administrative and research data becomes increasingly common, it is imperative to understand options for linking data when direct linkage is not feasible. The current linkage process ensured the privacy and security of patient data and improved data quality. While the initial implementations required significant computational and human resources, increased automation keeps the requirements within feasible bounds.

Privacy-preserving record linkage on large real world datasets

Record linkage is an emerging research area which is required by various real-world applications to identify which records in different data sources refer to the same real-world entities. Often privacy concerns and restrictions prevent the use of traditional record linkage applications across different organizations. Linking records in situations where no private or confidential information can be revealed is known as privacy-preserving record linkage (PPRL). As with traditional record linkage applications, scalability is a main challenge in PPRL. This challenge is generally addressed by employing a blocking technique that aims to reduce the number of candidate record pairs by removing record pairs that likely refer to non-matches without comparing them in detail. This paper presents an efficient private blocking technique based on a sorted neighborhood approach that combines k-anonymous clustering and the use of public reference values. An empirical study conducted on real-world databases shows that this approach is scalable to large databases, and that it can provide effective blocking while preserving k-anonymous characteristics. The proposed approach can be up-to two orders of magnitude faster than two state-of-the-art private blocking techniques, k-nearest neighbor clustering and Hamming based locality sensitive hashing.

Record linkage from multiple, independent and heterogeneous databases is a major area of database research. However, little attention has been paid to the privacy concerns of colluding databases. Activities such as sharing data for scientific research, monitoring disease symptoms over a region or developing large e-commerce market place, all require large scale data integration among different organizations. Legitimate concerns over data security and privacy have caused organizations to be reluctant to collaborate in any data sharing protocol; thus a data integration protocol applicable for private databases is needed. Privacy-preserving Record Linkage (PRL) deals with the development of such a protocol. This paper presents the PRL key ideas and research challenges.

Nearly 90% of today’s data have been produced only in the last two years! These data come from a multitude of human activities, including social networking sites, mobile phone applications, electronic medical records systems, e-commerce sites, etc. Integrating and analyzing this wealth and volume of data offers remarkable opportunities in sectors that are of high interest to businesses, governments, and academia. Given that the majority of the data are proprietary and may contain personal or business sensitive information, Privacy-Preserving Record Linkage (PPRL) techniques are essential to perform data integration. In this paper, we review existing work in PPRL, focusing on the computational aspect of the proposed algorithms, which is crucial when dealing with Big data. We propose an analysis tool for the computational aspects of PPRL, and characterize existing PPRL techniques along five dimensions. Based on our analysis, we identify research gaps in current literature and promising directions for future work.

Privacy-preserving record linkage (PPRL) can improve the utility of clinical data for research and discovery by merging disparate data sources to provide a more complete record of a patient. We assess the performance of record linkage across two data sets consisting of cancer registry data and electronic health records (EHRs). Using two data sources-EHR extracts and records from the Missouri Cancer Registry (MCR)-we performed various validation exercises, including an audit by the MCR and a comparative evaluation using multiple matching algorithms. Results indicated substantial matching performance, with high recall and precision rates. We conclude that the refined data linkage process significantly supports enhanced research capabilities without compromising patient privacy, thereby enabling reliable data integration for clinical research in oncology.

MRD Assessment in Patients with Newly Diagnosed Multiple Myeloma Using Tokenized Real World Data Sources

In privacy-preserving record linkage, a number of data custodians encode their records and submit them to a trusted third-party who is responsible for identifying those records that refer to the same real-world entity. In this paper, we propose FEDERAL, a novel record linkage framework that implements methods for anonymizing both string and numerical data values, which are typically present in data records. These methods rely on a strong theoretical foundation for rigorously specifying the dimensionality of the anonymization space, into which the original values are embedded, to provide accuracy and privacy guarantees under various models of privacy attacks. A key component of the applied embedding process is the threshold that is required by the distance computations, which we prove can be formally specified to guarantee accurate results. We evaluate our framework using three real-world data sets with varying characteristics. Our experimental findings show that FEDERAL offers a complete and effective solution for accurately identifying matching anonymized record pairs (with recall rates constantly above 93 percent) in large-scale privacy-preserving record linkage tasks.