Strategies to Address the Lack of Labeled Data for Supervised Machine Learning Training With Electronic Health Records: Case Study for the Extraction of Symptoms From Clinical Notes

Background Automated extraction of symptoms from clinical notes is a challenging task owing to the multidimensional nature of symptom description. The availability of labeled training data is extremely limited owing to the nature of the data containing protected health information. Natural language processing and machine learning to process clinical text for such a task have great potential. However, supervised machine learning requires a great amount of labeled data to train a model, which is at the origin of the main bottleneck in model development. Objective The aim of this study is to address the lack of labeled data by proposing 2 alternatives to manual labeling for the generation of training labels for supervised machine learning with English clinical text. We aim to demonstrate that using lower-quality labels for training leads to good classification results. Methods We addressed the lack of labels with 2 strategies. The first approach took advantage of the structured part of electronic health records and used diagnosis codes (International Classification of Disease–10th revision) to derive training labels. The second approach used weak supervision and data programming principles to derive training labels. We propose to apply the developed framework to the extraction of symptom information from outpatient visit progress notes of patients with cardiovascular diseases. Results We used >500,000 notes for training our classification model with International Classification of Disease–10th revision codes as labels and >800,000 notes for training using labels derived from weak supervision. We show that the dependence between prevalence and recall becomes flat provided a sufficiently large training set is used (>500,000 documents). We further demonstrate that using weak labels for training rather than the electronic health record codes derived from the patient encounter leads to an overall improved recall score (10% improvement, on average). Finally, the external validation of our models shows excellent predictive performance and transferability, with an overall increase of 20% in the recall score. Conclusions This work demonstrates the power of using a weak labeling pipeline to annotate and extract symptom mentions in clinical text, with the prospects to facilitate symptom information integration for a downstream clinical task such as clinical decision support.