Transformer-based Automatic Mapping of Clinical Notes to Specific Clinical Concepts

A significant proportion of medical errors exist in crucial medical information, and most stem from misinterpreting non-standardized clinical notes. Clinical Skills exam offered by the United States Medical Licensing Examination (USMLE) was put in place to certify patient note-taking skills before medical students joined professional practices, offering the first line of defense in protecting patients from medical errors. Nonetheless, the exams were discontinued in 2021 following high costs and resource usage in scoring the exams. This thesis compares four transformer-based models, namely BERT (Bidirectional Encoder Representations from Transformers) Base Uncased, Emilyalsentzer Bio_ClinicalBERT, RoBERTa (Robustly Optimized BERT Pre-Training Approach), and DeBERTa (Decoding-enhanced BERT with disentangled attention), with the goal to map free text in patient notes to clinical concepts present in the exam rubric. The impact of context-specific embeddings on BERT was also studied to determine the need for a clinical BERT in Clinical Skills exam. This thesis proposes the use of DeBERTa as a backbone model in patient note scoring for the USMLE Clinical Skills exam after comparing it with three other transformer models. Disentangled attention and enhanced mask decoder integrated into DeBERTa were credited for the high performance of DeBERTa as compared to the other models. Besides, the effect of meta pseudo labeling was also investigated in this thesis, which in turn, further enhanced DeBERTa’s performance.