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Background Improving the identification of people who inject drugs (PWID) in electronic medical records can improve clinical decision making, risk assessment and mitigation, and health service research. Identification of PWID currently consists of heterogeneous, nonspecific International Classification of Diseases (ICD) codes as proxies. Natural language processing (NLP) and machine learning (ML) methods may have better diagnostic metrics than nonspecific ICD codes for identifying PWID. Methods We manually reviewed 1000 records of patients diagnosed with Staphylococcus aureus bacteremia admitted to Veterans Health Administration hospitals from 2003 through 2014. The manual review was the reference standard. We developed and trained NLP/ML algorithms with and without regular expression filters for negation (NegEx) and compared these with 11 proxy combinations of ICD codes to identify PWID. Data were split 70% for training and 30% for testing. We calculated diagnostic metrics and estimated 95% confidence intervals (CIs) by bootstrapping the hold-out test set. Best models were determined by best F-score, a summary of sensitivity and positive predictive value. Results Random forest with and without NegEx were the best-performing NLP/ML algorithms in the training set. Random forest with NegEx outperformed all ICD -based algorithms. F-score for the best NLP/ML algorithm was 0.905 (95% CI,.786–.967) and 0.592 (95% CI,.550–.632) for the best ICD -based algorithm. The NLP/ML algorithm had a sensitivity of 92.6% and specificity of 95.4%. Conclusions NLP/ML outperformed ICD -based coding algorithms at identifying PWID in electronic health records. NLP/ML models should be considered in identifying cohorts of PWID to improve clinical decision making, health services research, and administrative surveillance. [ABSTRACT FROM AUTHOR]