Temporal Relation Extraction in Clinical Texts: A Span-based Graph Transformer Approach

Abstract

Temporal information extraction from unstructured text is essential for contextualizing events and deriving actionable insights, particularly in the medical domain. We address the task of extracting clinical events and their temporal relations using the well-studied I2B2 2012 Temporal Relations Challenge corpus. This task is inherently challenging due to complex clinical language, long documents, and sparse annotations. We introduce GraphTREx, a novel method integrating span-based entity-relation extraction, clinical large pre-trained language models (LPLMs), and Heterogeneous Graph Transformers (HGT) to capture local and global dependencies. Our HGT component facilitates information propagation across the document through innovative global landmarks that bridge distant entities and improves the state-of-the-art with 5.5% improvement in the tempeval F1 score over the previous best and up to 8.9% improvement on long-range relations, which presents a formidable challenge. We further demonstrate generalizability by establishing a strong baseline on the E3C corpus. Not only does this work advance temporal information extraction, but also lays the groundwork for improved diagnostic and prognostic models through enhanced temporal reasoning.