Recent studies on automatic note generation have shown that doctors can save significant amounts of time when using automatic clinical note generation (Knoll et al., 2022). Summarization models have been used for this task to generate clinical notes as summaries of doctor-patient conversations (Krishna et al., 2021; Cai et al., 2022). However, assessing which model would best serve clinicians in their daily practice is still a challenging task due to the large set of possible correct summaries, and the potential limitations of automatic evaluation metrics. In this paper, we study evaluation methods and metrics for the automatic generation of clinical notes from medical conversations. In particular, we propose new task-specific metrics and we compare them to SOTA evaluation metrics in text summarization and generation, including: (i) knowledge-graph embedding-based metrics, (ii) customized model-based metrics, (iii) domain-adapted/fine-tuned metrics, and (iv) ensemble metrics. To study the correlation between the automatic metrics and manual judgments, we evaluate automatic notes/summaries by comparing the system and reference facts and computing the factual correctness, and the hallucination and omission rates for critical medical facts. This study relied on seven datasets manually annotated by domain experts. Our experiments show that automatic evaluation metrics can have substantially different behaviors on different types of clinical notes datasets. However, the results highlight one stable subset of metrics as the most correlated with human judgments with a relevant aggregation of different evaluation criteria.

Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such models do not take into consideration expert domain knowledge. In this work, we introduced UmlsBERT, a contextual embedding model that integrates domain knowledge during the pre-training process via a novel knowledge augmentation strategy. More specifically, the augmentation on UmlsBERT with the Unified Medical Language System (UMLS) Metathesaurus was performed in two ways: i) connecting words that have the same underlying `concept' in UMLS, and ii) leveraging semantic group knowledge in UMLS to create clinically meaningful input embeddings. By applying these two strategies, UmlsBERT can encode clinical domain knowledge into word embeddings and outperform existing domain-specific models on common named-entity recognition (NER) and clinical natural language inference clinical NLP tasks.

Record fusion is the task of aggregating multiple records that correspond to the same real-world entity in a database. We can view record fusion as a machine learning problem where the goal is to predict the "correct" value for each attribute for each entity. Given a database, we use a combination of attribute-level, recordlevel, and database-level signals to construct a feature vector for each cell (or (row, col)) of that database. We use this feature vector alongwith the ground-truth information to learn a classifier for each of the attributes of the database. Our learning algorithm uses a novel stagewise additive model. At each stage, we construct a new feature vector by combining a part of the original feature vector with features computed by the predictions from the previous stage. We then learn a softmax classifier over the new feature space. This greedy stagewise approach can be viewed as a deep model where at each stage, we are adding more complicated non-linear transformations of the original feature vector. We show that our approach fuses records with an average precision of ~98% when source information of records is available, and ~94% without source information across a diverse array of real-world datasets. We compare our approach to a comprehensive collection of data fusion and entity consolidation methods considered in the literature. We show that our approach can achieve an average precision improvement of ~20%/~45% with/without source information respectively.