Consensus Measures for Unstructured Biomedical Text Annotations

arXiv:2608.03529 · cs.CL · Submitted 2026-08-04 · Read on arXiv

Pascal Wullschleger, Christian Kreis, Martin A. Walter, Jennifer Foster, Marc Pouly

cs.CL

Submitted: 2026-08-04

Code: https://github.com/neuml/papers

License: http://creativecommons.org/licenses/by/4.0/

The gist: Biomedical literature is increasingly mined for knowledge beyond the questions it was written to answer.

Terminology

Abstract

Biomedical literature is increasingly mined for knowledge beyond the questions it was written to answer. Because the target concepts are not known in advance, annotators prefer open-ended labels, whose agreement is hard to quantify. We study soft inter-rater reliability for annotators providing unstructured texts for biomedical annotation tasks. Synthetic experiments show that soft reliability can be quantified using a variety of semantic equivalence measures, and that the choice of measure affects failure modes of the estimation. Embeddings are scalable, but limited when differentiating similar but distinct concepts. Large language models are promising, but limited by scalability for estimating agreement by chance. Finally, we suggest measures based on natural language inference as a sensible compromise.

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