Leveraging Foundation Models for Clinical Text Analysis

Infectious diseases are a significant public health concern globally, and extracting relevant information from scientific literature can facilitate the development of effective prevention and treatment strategies. However, the large amount of clinical data available presents a challenge for information extraction. To address this challenge, this study proposes a natural language processing (NLP) framework that uses a pre-trained transformer model fine-tuned on task-specific data to extract key information related to infectious diseases from free-text clinical data. The proposed framework includes a data layer for preparing datasets from clinical texts, a foundation model layer for entity extraction, and an assessment layer for performance analysis. The results of the evaluation indicate that the proposed method outperforms standard methods, and leveraging prior knowledge through the pre-trained transformer model makes it useful for investigating other infectious diseases in the future.