A hybrid system to understand the relations between assessments and plans in progress notes

The paper presents a novel solution to the 2022 National NLP Clinical Challenges (n2c2) Track 3, which aims to predict the relations between assessment and plan subsections in progress notes. Our approach goes beyond standard transformer models and incorporates external information such as medical ontology and order information to comprehend the semantics of progress notes. We fine-tuned transformers to understand the textual data and incorporated medical ontology concepts and their relationships to enhance the model’s accuracy. We also captured order information that regular transformers cannot by taking into account the position of the assessment and plan subsections in progress notes. Our submission earned third place in the challenge phase with a macro-F1 score of 0.811. After refining our pipeline further, we achieved a macro-F1 of 0.826, outperforming the top-performing system during the challenge phase. Our approach, which combines fine-tuned transformers, medical ontology, and order information, outperformed other systems in predicting the relationships between assessment and plan subsections in progress notes. This highlights the importance of incorporating external information beyond textual data in natural language processing (NLP) tasks related to medical documentation. Our work could potentially improve the efficiency and accuracy of progress note analysis. [Display omitted] •An NLP pipeline that achieved a top-3 performance in 2022 n2c2 Track 3.•Fine-tuned transformer-based models to understand the semantics of progress notes.•Integrated medical ontology and order information to imporve the transformer models.•Designed an ensemble strategy to further boost our system performance.