<tt>TrialSieve</tt>: A Comprehensive Biomedical Information Extraction Framework for PICO, Meta-Analysis, and Drug Repurposing

<tt>TrialSieve</tt>: A Comprehensive Biomedical Information Extraction Framework for PICO, Meta-Analysis, and Drug Repurposing

This work introduces TrialSieve, a novel framework for biomedical information extraction that enhances clinical meta-analysis and drug repurposing. By extending traditional PICO (Patient, Intervention, Comparison, Outcome) methodologies, TrialSieve incorporates hierarchical, treatment group-based gr...

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Main Authors: David Kartchner, Haydn Turner, Christophe Ye, Irfan Al-Hussaini, Batuhan Nursal, Albert J. B. Lee, Jennifer Deng, Courtney Curtis, Hannah Cho, Eva L. Duvaris, Coral Jackson, Catherine E. Shanks, Sarah Y. Tan, Selvi Ramalingam, Cassie S. Mitchell
Format: Article
Language:English
Published: MDPI AG 2025-05-01
Series:Bioengineering
Subjects:
text mining
biomedical information extraction
biomedical literature annotation
biocuration
biomedical literature schema
named entity recognition
Online Access:https://www.mdpi.com/2306-5354/12/5/486
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Summary:This work introduces TrialSieve, a novel framework for biomedical information extraction that enhances clinical meta-analysis and drug repurposing. By extending traditional PICO (Patient, Intervention, Comparison, Outcome) methodologies, TrialSieve incorporates hierarchical, treatment group-based graphs, enabling more comprehensive and quantitative comparisons of clinical outcomes. TrialSieve was used to annotate 1609 PubMed abstracts, 170,557 annotations, and 52,638 final spans, incorporating 20 unique annotation categories that capture a diverse range of biomedical entities relevant to systematic reviews and meta-analyses. The performance (accuracy, precision, recall, F1-score) of four natural-language processing (NLP) models (BioLinkBERT, BioBERT, KRISSBERT, PubMedBERT) and the large language model (LLM), GPT-4o, was evaluated using the human-annotated TrialSieve dataset. BioLinkBERT had the best accuracy (0.875) and recall (0.679) for biomedical entity labeling, whereas PubMedBERT had the best precision (0.614) and F1-score (0.639). Error analysis showed that NLP models trained on noisy, human-annotated data can match or, in most cases, surpass human performance. This finding highlights the feasibility of fully automating biomedical information extraction, even when relying on imperfectly annotated datasets. An annotator user study (n = 39) revealed significant (<i>p</i> < 0.05) gains in efficiency and human annotation accuracy with the unique TrialSieve tree-based annotation approach. In summary, TrialSieve provides a foundation to improve automated biomedical information extraction for frontend clinical research.
ISSN:2306-5354

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