A clustering approach for detecting implausible observation values in electronic health records data

BACKGROUND: Identifying implausible clinical observations (e.g., laboratory test and vital sign values) in Electronic Health Record (EHR) data using rule-based procedures is challenging. Anomaly/outlier detection methods can be applied as an alternative algorithmic approach to flagging such implausible values in EHRs. METHODS: The primary objectives of this research were to develop and test an unsupervised clustering-based anomaly/outlier detection approach for detecting implausible observations in EHR data as an alternative algorithmic solution to the existing procedures. Our approach is built upon two underlying hypotheses that, (i) when there are large number of observations, implausible records should be sparse, and therefore (ii) if these data are clustered properly, clusters with sparse populations should represent implausible observations. To test these hypotheses, we applied an unsupervised clustering algorithm to EHR observation data on 50 laboratory tests from Partners HealthCare. We tested different specifications of the clustering approach and computed confusion matrix indices against a set of silver-standard plausibility thresholds. We compared the results from the proposed approach with conventional anomaly detection (CAD) approaches, including standard deviation and Mahalanobis distance. RESULTS: We found that the clustering approach produced results with exceptional specificity and high sensitivity. Compared with the conventional anomaly detection approaches, our proposed clustering approach resulted in significantly smaller number of false positive cases. CONCLUSION: Our contributions include (i) a clustering approach for identifying implausible EHR observations, (ii) evidence that implausible observations are sparse in EHR laboratory test results, (iii) a parallel implementation of the clustering approach on i2b2 star schema, and (3) a set of silver-standard plausibility thresholds for 50 laboratory tests that can be used in other studies for validation. The proposed algorithmic solution can augment human decisions to improve data quality. Therefore, a workflow is needed to complement the algorithm’s job and initiate necessary actions that need to be taken in order to improve the quality of data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12911-019-0852-6) contains supplementary material, which is available to authorized users.