Probabilistic record linkage.
Ontology highlight
ABSTRACT:
SUBMITTER: Sayers A
PROVIDER: S-EPMC5005943 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundMethods for linking real-world healthcare data often use a latent class model, where the latent, or unknown, class is the true match status of candidate record-pairs. This commonly used model assumes that agreement patterns among multiple fields within a latent class are independent. When this assumption is violated, various approaches, including the most commonly proposed loglinear models, have been suggested to account for conditional dependence.MethodsWe present a step-by-step guide to identify important dependencies between fields through a correlation residual plot and demonstrate how they can be incorporated into loglinear models for record linkage. This method is applied to healthcare data from the patient registry for a large county health department.ResultsOur method could be readily implemented using standard software (with code supplied) to produce an overall better model fit as measured by BIC and deviance. Finding the most parsimonious model is known to reduce bias in parameter estimates.ConclusionsThis novel approach identifies and accommodates conditional dependence in the context of record linkage. The conditional dependence model is recommended for routine use due to its flexibility for incorporating conditional dependence and easy implementation using existing software.
| S-EPMC3766252 | biostudies-literature
Project description:We develop an algorithm for probabilistic linkage of de-identified research datasets at the patient level, when only diagnosis codes with discrepancies and no personal health identifiers such as name or date of birth are available. It relies on Bayesian modelling of binarized diagnosis codes, and provides a posterior probability of matching for each patient pair, while considering all the data at once. Both in our simulation study (using an administrative claims dataset for data generation) and in two real use-cases linking patient electronic health records from a large tertiary care network, our method exhibits good performance and compares favourably to the standard baseline Fellegi-Sunter algorithm. We propose a scalable, fast and efficient open-source implementation in the ludic R package available on CRAN, which also includes the anonymized diagnosis code data from our real use-case. This work suggests it is possible to link de-identified research databases stripped of any personal health identifiers using only diagnosis codes, provided sufficient information is shared between the data sources.
| S-EPMC6326114 | biostudies-literature
Project description:ObjectiveThe disjointed healthcare system and the nonexistence of a universal patient identifier across systems necessitates accurate record linkage (RL). We aim to describe the implementation and evaluation of a hybrid record linkage method in a statewide surveillance system for congenital heart disease.Materials and methodsClear-text personally identifiable information on individuals in the Colorado Congenital Heart Disease surveillance system was obtained from 5 electronic health record and medical claims data sources. Two deterministic methods and 1 probabilistic RL method using first name, last name, social security number, date of birth, and house number were initially implemented independently and then sequentially in a hybrid approach to assess RL performance.Results16 480 nonunique individuals with congenital heart disease were ascertained. Deterministic linkage methods, when performed independently, yielded 4505 linked pairs (consisting of 2 records linked together within or across data sources). Probabilistic RL, using 3 initial characters of last name and gender for blocking, yielded 6294 linked pairs when executed independently. Using a hybrid linkage routine resulted in 6451 linkages and an additional 18%-24% correct linked pairs as compared to the independent methods. A hybrid linkage routine resulted in higher recall and F-measure scores compared to probabilistic and deterministic methods performed independently.DiscussionThe hybrid approach resulted in increased linkage accuracy and identified pairs of linked record that would have otherwise been missed when using any independent linkage technique.ConclusionWhen performing RL within and across disparate data sources, the hybrid RL routine outperformed independent deterministic and probabilistic methods.
| S-EPMC7647290 | biostudies-literature
Project description:In retrospective cohort studies of interventions disseminated to communities, it is challenging to find comparison groups with high-quality data for evaluation. We present one methodological approach as part of our study of birth outcomes of second-born children in a home visiting (HV) program targeting first-time mothers. We used probabilistic record linkage to link Connecticut's Nurturing Families Network (NFN) HV program and birth-certificate data for children born from 2005 to 2015. We identified two potential comparison groups: a propensity-score-matched group from the remaining birth certificate sample and eligible-but-unenrolled families. An analysis of interpregnancy interval (IPI) is presented to exemplify the approach. We identified the birth certificates of 4822 NFN families. The propensity-score-matched group had 14,219 families (3-to-1 matching) and we identified 1101 eligible-but-unenrolled families. Covariates were well balanced for the propensity-score-matched group, but poorly balanced for the eligible-but-unenrolled group. No program effect on IPI was found. By combining propensity-score matching and probabilistic record linkage, we were able to retrospectively identify relatively large comparison groups for quasi-experimental research. Using birth certificate data, we accessed outcomes for all of these individuals from a single data source. Multiple comparison groups allow us to confirm findings when each method has some limitations. Other researchers seeking community-based comparison groups could consider a similar approach.
| S-EPMC9064948 | biostudies-literature
Project description:For the past 80 years, social scientists have been linking historical censuses across time to study economic and geographic mobility. In recent decades, the quantity of historical census record linkage has exploded, owing largely to the advent of new machine-readable data created by genealogical organizations. Investigators are examining economic and geographic mobility across multiple generations, but also engaging many new topics. Several analysts are exploring the effects of early-life socioeconomic conditions, environmental exposures, or natural disasters on family, health and economic outcomes in later life. Other studies exploit natural experiments to gauge the impact of policy interventions such as social welfare programs and educational reforms. The new data sources have led to a proliferation of record linkage methodology, and some widespread approaches inadvertently introduce errors that can lead to false inferences. A new generation of large-scale shared data infrastructure now in preparation will ameliorate weaknesses of current linkage methods.
| S-EPMC6200350 | biostudies-literature
Project description:BackgroundQuality patient care requires comprehensive health care data from a broad set of sources. However, missing data in medical records and matching field selection are 2 real-world challenges in patient-record linkage.ObjectiveIn this study, we aimed to evaluate the extent to which incorporating the missing at random (MAR)-assumption in the Fellegi-Sunter model and using data-driven selected fields improve patient-matching accuracy using real-world use cases.MethodsWe adapted the Fellegi-Sunter model to accommodate missing data using the MAR assumption and compared the adaptation to the common strategy of treating missing values as disagreement with matching fields specified by experts or selected by data-driven methods. We used 4 use cases, each containing a random sample of record pairs with match statuses ascertained by manual reviews. Use cases included health information exchange (HIE) record deduplication, linkage of public health registry records to HIE, linkage of Social Security Death Master File records to HIE, and deduplication of newborn screening records, which represent real-world clinical and public health scenarios. Matching performance was evaluated using the sensitivity, specificity, positive predictive value, negative predictive value, and F1-score.ResultsIncorporating the MAR assumption in the Fellegi-Sunter model maintained or improved F1-scores, regardless of whether matching fields were expert-specified or selected by data-driven methods. Combining the MAR assumption and data-driven fields optimized the F1-scores in the 4 use cases.ConclusionsMAR is a reasonable assumption in real-world record linkage applications: it maintains or improves F1-scores regardless of whether matching fields are expert-specified or data-driven. Data-driven selection of fields coupled with MAR achieves the best overall performance, which can be especially useful in privacy-preserving record linkage.
| S-EPMC9562057 | biostudies-literature
Project description:Key messageIn polyploids, linkage mapping is carried out using genotyping with discrete dosage scores. Here, we use probabilistic genotypes and we validate it for the construction of polyploid linkage maps. Marker genotypes are generally called as discrete values: homozygous versus heterozygous in the case of diploids, or an integer allele dosage in the case of polyploids. Software for linkage map construction and/or QTL analysis usually relies on such discrete genotypes. However, it may not always be possible, or desirable, to assign definite values to genotype observations in the presence of uncertainty in the genotype calling. Here, we present an approach that uses probabilistic marker dosages for linkage map construction in polyploids. We compare our method to an approach based on discrete dosages, using simulated SNP array and sequence reads data with varying levels of data quality. We validate our approach using experimental data from a potato (Solanum tuberosum L.) SNP array applied to an F1 mapping population. In comparison to the approach based on discrete dosages, we mapped an additional 562 markers. All but three of these were mapped to the expected chromosome and marker position. For the remaining three markers, no physical position was known. The use of dosage probabilities is of particular relevance for map construction in polyploids using sequencing data, as these often result in a higher level of uncertainty regarding allele dosage.
| S-EPMC8277618 | 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:BackgroundThe linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects - a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors.MethodsA method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage.ResultsThe system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol.ConclusionAlthough the protocols described in this paper are not unconditionally secure, they do suggest the feasibility, with the aid of modern cryptographic techniques and high speed communication networks, of a general purpose probabilistic record linkage system which permits record linkage studies to be carried out with negligible risk of invasion of personal privacy.
| S-EPMC471556 | biostudies-literature
Project description:IntroductionThe robustness of record linkage evaluation measures is of high importance since linkage techniques are assessed based on these. However, minimal research has been conducted to evaluate the suitability of existing evaluation measures in the context of linking groups of records. Linkage quality is generally evaluated based on traditional measures such as precision and recall. As we show, these traditional evaluation measures are not suitable for evaluating groups of linked records because they evaluate the quality of individual record pairs rather than the quality of records grouped into clusters.ObjectivesWe set out to highlight the shortcomings of traditional evaluation measures and then propose a novel method to evaluate clustering quality in the context of group-based record linkage.MethodsThe proposed linkage evaluation method assesses how well individual records have been allocated into predicted groups/clusters with respect to ground-truth data. We first identify the best representative predicted cluster for each ground-truth cluster and, based on the resulting mapping, each record in a ground-truth cluster is assigned to one of seven categories. These categories reflect how well the linkage technique assigned records into groups.ResultsWe empirically evaluated our proposed method using real-world data and showed that it better reflects the quality of clusters generated by three group-based record linkage techniques. We also showed that traditional measures such as precision and recall can produce ambiguous results whereas our method does not.ConclusionsThe proposed evaluation method provides unambiguous results regarding the assessed group-based record linkage approaches. The method comprises of seven categories which reflect how each record was predicted, providing more detailed information about the quality of the linkage result. This will help to make better-informed decisions about which linkage technique is best suited for a given linkage application.
| S-EPMC8142966 | biostudies-literature