Clinical Text Deduplication Practices for Efficient Pretraining and Improved Clinical Tasks

Abstract: Despite being a unique source of information on patients' status and disease progression, clinical notes are characterized by high levels of duplication and information redundancy. In general domain text, it has been shown that deduplication does not harm LLM (LM) pretraining, thus helping reduce the training cost. Although large LMs have proven to learn medical knowledge, they still require specialized domain adaptation for improved downstream clinical tasks. By leveraging large real-world clinical corpora, we first provided a fine-grained characterization of duplicates stemming from common writing practices and clinical relevancy. Second, we demonstrated that deduplicating clinical text can help clinical LMs encode less redundant information in a more efficient manner and do not harm classification tasks via prompt-based learning.