CACER: Clinical concept Annotations for Cancer Events and Relations

Abstract

Abstract Objective Clinical notes contain unstructured representations of patient histories, including the relationships between medical problems and prescription drugs. To investigate the relationship between cancer drugs and their associated symptom burden, we extract structured, semantic representations of medical problem and drug information from the clinical narratives of oncology notes. Materials and Methods We present Clinical concept Annotations for Cancer Events and Relations (CACER), a novel corpus with fine-grained annotations for over 48 000 medical problems and drug events and 10 000 drug-problem and problem-problem relations. Leveraging CACER, we develop and evaluate transformer-based information extraction models such as Bidirectional Encoder Representations from Transformers (BERT), Fine-tuned Language Net Text-To-Text Transfer Transformer (Flan-T5), Large Language Model Meta AI (Llama3), and Generative Pre-trained Transformers-4 (GPT-4) using fine-tuning and in-context learning (ICL). Results In event extraction, the fine-tuned BERT and Llama3 models achieved the highest performance at 88.2-88.0 F1, which is comparable to the inter-annotator agreement (IAA) of 88.4 F1. In relation extraction, the fine-tuned BERT, Flan-T5, and Llama3 achieved the highest performance at 61.8-65.3 F1. GPT-4 with ICL achieved the worst performance across both tasks. Discussion The fine-tuned models significantly outperformed GPT-4 in ICL, highlighting the importance of annotated training data and model optimization. Furthermore, the BERT models performed similarly to Llama3. For our task, large language models offer no performance advantage over the smaller BERT models. Conclusions We introduce CACER, a novel corpus with fine-grained annotations for medical problems, drugs, and their relationships in clinical narratives of oncology notes. State-of-the-art transformer models achieved performance comparable to IAA for several extraction tasks.