Optimizing Patient Record Linkage in a Master Patient Index Using Machine Learning: Algorithm Development and Validation

Walter Nelson; Nityan Khanna; Mohamed Ibrahim; Justin Fyfe; Maxwell Geiger; Keith Edwards; Jeremy Petch

doi:10.2196/44331

Optimizing Patient Record Linkage in a Master Patient Index Using Machine Learning: Algorithm Development and Validation

JMIR Form Res. 2023 Jun 29:7:e44331. doi: 10.2196/44331.

Authors

Walter Nelson^{1

2}, Nityan Khanna¹, Mohamed Ibrahim¹, Justin Fyfe³, Maxwell Geiger⁴, Keith Edwards⁵, Jeremy Petch^{1

6

7

8}

Affiliations

¹ Centre for Data Science and Digital Health, Hamilton Health Sciences, Hamilton, ON, Canada.
² Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada.
³ Fyfe Software, Hamilton, ON, Canada.
⁴ Department of Biology, University of Hawaii, Hilo, HI, United States.
⁵ Department of Computer Science, University of Hawaii, Hilo, HI, United States.
⁶ Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
⁷ Division of Cardiology, Department of Medicine, McMaster University, Hamilton, ON, Canada.
⁸ Population Health Research Institute, McMaster University, Hamilton, ON, Canada.

PMID: 37384382
PMCID: PMC10365597
DOI: 10.2196/44331

Abstract

Background: To provide quality care, modern health care systems must match and link data about the same patient from multiple sources, a function often served by master patient index (MPI) software. Record linkage in the MPI is typically performed manually by health care providers, guided by automated matching algorithms. These matching algorithms must be configured in advance, such as by setting the weights of patient attributes, usually by someone with knowledge of both the matching algorithm and the patient population being served.

Objective: We aimed to develop and evaluate a machine learning-based software tool, which automatically configures a patient matching algorithm by learning from pairs of patient records previously linked by humans already present in the database.

Methods: We built a free and open-source software tool to optimize record linkage algorithm parameters based on historical record linkages. The tool uses Bayesian optimization to identify the set of configuration parameters that lead to optimal matching performance in a given patient population, by learning from prior record linkages by humans. The tool is written assuming only the existence of a minimal HTTP application programming interface (API), and so is agnostic to the choice of MPI software, record linkage algorithm, and patient population. As a proof of concept, we integrated our tool with SantéMPI, an open-source MPI. We validated the tool using several synthetic patient populations in SantéMPI by comparing the performance of the optimized configuration in held-out data to SantéMPI's default matching configuration using sensitivity and specificity.

Results: The machine learning-optimized configurations correctly detect over 90% of true record linkages as definite matches in all data sets, with 100% specificity and positive predictive value in all data sets, whereas the baseline detects none. In the largest data set examined, the baseline matching configuration detects possible record linkages with a sensitivity of 90.2% (95% CI 88.4%-92.0%) and specificity of 100%. By comparison, the machine learning-optimized matching configuration attains a sensitivity of 100%, with a decreased specificity of 95.9% (95% CI 95.9%-96.0%). We report significant gains in sensitivity in all data sets examined, at the cost of only marginally decreased specificity. The configuration optimization tool, data, and data set generator have been made freely available.

Conclusions: Our machine learning software tool can be used to significantly improve the performance of existing record linkage algorithms, without knowledge of the algorithm being used or specific details of the patient population being served.

Keywords: Bayesian optimization; FEBRL; computerized; data linkage; electronic health records; health care system; machine learning; master index; master patient index; matching algorithm; medical record linkage; medical record systems; open-source software; pilot; quality of care; record link.

©Walter Nelson, Nityan Khanna, Mohamed Ibrahim, Justin Fyfe, Maxwell Geiger, Keith Edwards, Jeremy Petch. Originally published in JMIR Formative Research (https://formative.jmir.org), 29.06.2023.