The Data-Adaptive Fellegi-Sunter Model for Probabilistic Record Linkage: Algorithm Development and Validation for Incorporating Missing Data and Field Selection

J Med Internet Res. 2022 Sep 29;24(9):e33775. doi: 10.2196/33775.


Background: Quality 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.

Objective: In 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.

Methods: We 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.

Results: Incorporating 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.

Conclusions: MAR 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.

Keywords: Fellegi-Sunter model; latent class model; matching field selection; missing at random; record linkage.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Health Information Exchange*
  • Humans
  • Infant, Newborn
  • Medical Record Linkage* / methods
  • Registries
  • Research Design