Mucopolysaccharidosis type II detection by Naïve Bayes Classifier: An example of patient classification for a rare disease using electronic medical records from the Canadian Primary Care Sentinel Surveillance Network

• Published in: PloS one Vol. 13; no. 12; p. e0209018
• Main Authors: Ehsani-Moghaddam, Behrouz, Queenan, John A, MacKenzie, Jennifer, Birtwhistle, Richard V
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 19.12.2018; Public Library of Science (PLoS)
• Subjects: Algorithms; Artificial intelligence; Bayes Theorem; Bayesian analysis; Canada; Classification; Classifiers; Computer and Information Sciences; Data Mining; Dependent variables; Diagnosis; Diagnosis, Computer-Assisted - methods; Electronic Health Records; Electronic medical records; Females; Genetic disorders; Health care; Humans; Knowledge discovery; Male; Males; Medical diagnosis; Medical personnel; Medical records; Medicine; Medicine and Health Sciences; Metabolic disorders; Model accuracy; Mucopolysaccharidosis; Mucopolysaccharidosis II - classification; Mucopolysaccharidosis II - diagnosis; Patients; Pattern Recognition, Automated; Physical Sciences; Physicians; Primary care; Primary Health Care; R&D; Rare diseases; Rare Diseases - classification; Rare Diseases - diagnosis; Resampling; Research & development; Research and Analysis Methods; Sentinel Surveillance; Studies; Surveillance; Training; Young Adult; Canada; Ontario Canada
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0209018

Identifying patients with rare diseases associated with common symptoms is challenging. Hunter syndrome, or Mucopolysaccharidosis type II is a progressive rare disease caused by a deficiency in the activity of the lysosomal enzyme, iduronate 2-sulphatase. It is inherited in an X-linked manner resulting in males being significantly affected. Expression in females varies with the majority being unaffected although symptoms may emerge over time. We developed a Naïve Bayes classification (NBC) algorithm utilizing the clinical diagnosis and symptoms of patients contained within their de-identified and unstructured electronic medical records (EMR) extracted by the Canadian Primary Care Sentinel Surveillance Network (CPCSSN). To do so, we created a training dataset using published results in the scientific literature and from all MPS II symptoms and applied the training dataset and its independent features to compute the conditional posterior probabilities of having MPS II disease as a categorical dependent variable for 506497 male patients. The classifier identified 125 patients with the highest likelihood for having the disease and 18 features were selected to be necessary for forecasting. Next, a Recursive Backward Feature Elimination algorithm was employed, for optimal input features of the NBC model, using a k-fold Cross-Validation with 3 replicates. The accuracy of the final model was estimated by the Validation Set Approach technique and the bootstrap resampling. We also investigated that whether the NBC is as accurate as three other Bayesian networks. The Naïve Bayes Classifier appears to be an efficient algorithm in assisting physicians with the diagnosis of Hunter syndrome allowing optimal patient management.