EQ-5D Classification Using Biomedical Entity-Enriched Pre-trained Language Models and Multiple Instance Learning

TL;DR

This paper enhances EQ-5D publication detection by fine-tuning biomedical language models with entity enrichment and applying multiple instance learning, achieving high accuracy and recall for systematic review screening.

Contribution

It introduces a novel approach combining biomedical entity-enriched PLMs and MIL for improved detection of EQ-5D usage in abstracts.

Findings

F1-score improved to 0.82

Achieved nearly perfect recall at study level

Entity enrichment significantly boosts model performance

Abstract

The EQ-5D (EuroQol 5-Dimensions) is a standardized instrument for the evaluation of health-related quality of life. In health economics, systematic literature reviews (SLRs) depend on the correct identification of publications that use the EQ-5D, but manual screening of large volumes of scientific literature is time-consuming, error-prone, and inconsistent. In this study, we investigate fine-tuning of general-purpose (BERT) and domain-specific (SciBERT, BioBERT) pre-trained language models (PLMs), enriched with biomedical entity information extracted through scispaCy models for each statement, to improve EQ-5D detection from abstracts. We conduct nine experimental setups, including combining three scispaCy models with three PLMs, and evaluate their performance at both the sentence and study levels. Furthermore, we explore a Multiple Instance Learning (MIL) approach with attention pooling to aggregate sentence-level information into study-level predictions, where each abstract is represented as a bag of enriched sentences (by scispaCy). The findings indicate consistent improvements in F1-scores (reaching 0.82) and nearly perfect recall at the study-level, significantly exceeding classical bag-of-words baselines and recently reported PLM baselines. These results show that entity enrichment significantly improves domain adaptation and model generalization, enabling more accurate automated screening in systematic reviews.