David Kartchner

TrialSieve: An Information Extraction Dataset for Automating Clinical Meta Analysis

Christophe Ye
Irfan Al-Hussaini
Zihan Wei
Courtney Curtis
Eva Duvaris
Coral Jackson
Sarah Tan
Hannah Cho
Preprint, 2024

Abstract

This work presents Trialsieve, a unique biomedical entity extractiondataset designed to streamline clinical meta-analysis of studies pertinent to drug repurposing. TrialSieve focuses on linking quantitative clinical outcomes to interventions, enabling automated monitoring and synthesis of clincal outcomes at scale.The dataset comprises 1,609 abstracts from PubMed, each carefully annotated by human evaluators. The abstracts are annotated with 20 categories that supersede and extend beyond the widely adopted patient-intervention-comparator-outcome (PICO) approach. These labels are complemented by a set of relation annotations that organize tagged spans by treatment group and enable outcomes to be compared between patient groups. Each abstract was scrutinized by three distinct annotators (trained biomedical students). Senior annotators review and cross-check a flagged subset to uphold quality standards. Essential dataset characteristics such as reviewer concordance, label co-occurrence, and confidence scores are provided to highlight the robustness and reliability of the annotations. In summary, TrialSieve offers a vital yet demanding biomedical entity tagging task to accelerate drug repurposing efforts. The comprehensively annotated dataset is open to the public to promote the development of enhanced entity tagging algorithms and facilitate drug repurposing and clinical meta-analysis. Additionally, a comprehensive evaluation of various state-of-the-art sequence tagging models is performed to compare their efficacy in biomedical entity recognition with TrialSieve.

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