Boosting Biomedical Concept Extraction by Rule-Based Data Augmentation (2407.02719v1)

Abstract: Document-level biomedical concept extraction is the task of identifying biomedical concepts mentioned in a given document. Recent advancements have adapted pre-trained LLMs for this task. However, the scarcity of domain-specific data and the deviation of concepts from their canonical names often hinder these models' effectiveness. To tackle this issue, we employ MetaMapLite, an existing rule-based concept mapping system, to generate additional pseudo-annotated data from PubMed and PMC. The annotated data are used to augment the limited training data. Through extensive experiments, this study demonstrates the utility of a manually crafted concept mapping tool for training a better concept extraction model.