Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT

Akshay Smit, Saahil Jain, Pranav Rajpurkar, Anuj Pareek, Andrew Ng, Matthew Lungren
2020 Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)   unpublished
The extraction of labels from radiology text reports enables large-scale training of medical imaging models. Existing approaches to report labeling typically rely either on sophisticated feature engineering based on medical domain knowledge or manual annotations by experts. In this work, we introduce a BERTbased approach to medical image report labeling that exploits both the scale of available rule-based systems and the quality of expert annotations. We demonstrate superior performance of a
more » ... medically pretrained BERT model first trained on annotations of a rulebased labeler and then fine-tuned on a small set of expert annotations augmented with automated backtranslation. We find that our final model, CheXbert, is able to outperform the previous best rule-based labeler with statistical significance, setting a new SOTA for report labeling on one of the largest datasets of chest x-rays.
doi:10.18653/v1/2020.emnlp-main.117 fatcat:kbdqwqwelfbyzldxb6xybh57jq