A deep learning approach for medication disposition and corresponding attributes extraction

This article summarizes our approach to extracting medication and corresponding attributes from clinical notes, which is the focus of track 1 of the 2022 National Natural Language Processing (NLP) Clinical Challenges(n2c2) shared task.

The dataset was prepared using Contextualized Medication Event Dataset (CMED), including 500 notes from 296 patients. Our system consisted of three components: medication named entity recognition (NER), event classification (EC), and context classification (CC). These three components were built using transformer models with slightly different architecture and input text engineering. A zero-shot learning solution for CC was also explored.

Our best performance systems achieved micro-average F1 scores of 0.973, 0.911, and 0.909 for the NER, EC, and CC, respectively.

In this study, we implemented a deep learning-based NLP system and demonstrated that our approach of (1) utilizing special tokens helps our model to distinguish multiple medications mentions in the same context; (2) aggregating multiple events of a single medication into multiple labels improves our model's performance.