Background: Machine learning methods for clinical named entity recognition and entity normalization systems can utilize both labeled corpora and Knowledge Graphs (KGs) for learning. However, infrequently occurring concepts may have few mentions in training corpora and lack detailed descriptions or synonyms, even in large KGs. For Disease Entity Recognition (DER) and Disease Entity Normalization (DEN), this can result in fewer high quality training examples relative to the number of known diseases. Large Language Model (LLM) generation of synthetic training examples could improve performance in these information extraction tasks. Methods: We fine-tuned a LLaMa-2 13B Chat LLM to generate a synthetic corpus containing normalized mentions of concepts from the Unified Medical Language System (UMLS) Disease Semantic Group. We measured overall and Out of Distribution (OOD) performance for DER and DEN, with and without synthetic data augmentation. We evaluated performance on 3 different disease corpora using 4 different data augmentation strategies, assessed using BioBERT for DER and SapBERT and KrissBERT for DEN. Results: Our synthetic data yielded a substantial improvement for DEN, in all 3 training corpora the top 1 accuracy of both SapBERT and KrissBERT improved by 3-9 points in overall performance and by 20-55 points in OOD data. A small improvement (1-2 points) was also seen for DER in overall performance, but only one dataset showed OOD improvement. Conclusion: LLM generation of normalized disease mentions can improve DEN relative to normalization approaches that do not utilize LLMs to augment data with synthetic mentions. Ablation studies indicate that performance gains for DEN were only partially attributable to improvements in OOD performance. The same approach has only a limited ability to improve DER. We make our software and dataset publicly available.

This study reports a comprehensive environmental scan of the generative AI (GenAI) infrastructure in the national network for clinical and translational science across 36 institutions supported by the Clinical and Translational Science Award (CTSA) Program led by the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH) at the United States. With the rapid advancement of GenAI technologies, including large language models (LLMs), healthcare institutions face unprecedented opportunities and challenges. This research explores the current status of GenAI integration, focusing on stakeholder roles, governance structures, and ethical considerations by administering a survey among leaders of health institutions (i.e., representing academic medical centers and health systems) to assess the institutional readiness and approach towards GenAI adoption. Key findings indicate a diverse range of institutional strategies, with most organizations in the experimental phase of GenAI deployment. The study highlights significant variations in governance models, with a strong preference for centralized decision-making but notable gaps in workforce training and ethical oversight. Moreover, the results underscore the need for a more coordinated approach to GenAI governance, emphasizing collaboration among senior leaders, clinicians, information technology staff, and researchers. Our analysis also reveals concerns regarding GenAI bias, data security, and stakeholder trust, which must be addressed to ensure the ethical and effective implementation of GenAI technologies. This study offers valuable insights into the challenges and opportunities of GenAI integration in healthcare, providing a roadmap for institutions aiming to leverage GenAI for improved quality of care and operational efficiency.

Background: The semantics of entities extracted from a clinical text can be dramatically altered by modifiers, including entity negation, uncertainty, conditionality, severity, and subject. Existing models for determining modifiers of clinical entities involve regular expression or features weights that are trained independently for each modifier. Methods: We develop and evaluate a multi-task transformer architecture design where modifiers are learned and predicted jointly using the publicly available SemEval 2015 Task 14 corpus and a new Opioid Use Disorder (OUD) data set that contains modifiers shared with SemEval as well as novel modifiers specific for OUD. We evaluate the effectiveness of our multi-task learning approach versus previously published systems and assess the feasibility of transfer learning for clinical entity modifiers when only a portion of clinical modifiers are shared. Results: Our approach achieved state-of-the-art results on the ShARe corpus from SemEval 2015 Task 14, showing an increase of 1.1% on weighted accuracy, 1.7% on unweighted accuracy, and 10% on micro F1 scores. Conclusions: We show that learned weights from our shared model can be effectively transferred to a new partially matched data set, validating the use of transfer learning for clinical text modifiers