BioPIE: A Biomedical Protocol Information Extraction Dataset for Experiment Understanding

Abstract

Understanding biomedical experiments provides a foundation for downstream tasks, e.g., laboratory automation, and facilitates effective cross-disciplinary communication. Two challenges, High Information Density (HID) and Multi-Step Reasoning (MSR), pose unique difficulties for precise automatic experimental understanding. Extracting structured knowledge, e.g., Knowledge Graphs (KGs), is an effective approach to address the HID and MSR. However, existing biomedical datasets for structured knowledge Information Extraction (IE) are limited to a general or coarse-grained level, hindering fine-grained experimental understanding. To address this gap, we introduce Biomedical Protocol Information Extraction Dataset (BioPIE), a dataset providing procedure-centric KGs that captures entities, actions, and relations at a scale sufficient for reasoning across biomedical protocols. We evaluate both supervised and LLM-based IE methods on BioPIE to verify its effectiveness, and implement a biomedical question answering system to provide a quantitative illustration of BioPIE's effectiveness for downstream understanding tasks. The experimental results demonstrate improved understanding performance on both the HID and MSR question sets.