# Consensus Measures for Unstructured Biomedical Text Annotations

arXiv: https://arxiv.org/abs/2608.03529 · HTML: https://mlsanity.com/paper/2608.03529/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 48 references that are in the map.
- First posted on arXiv 4 Aug 2026.

## Builds on (most cited first, 12 of 12)

- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [SimCSE: Simple Contrastive Learning of Sentence Embeddings](https://mlsanity.com/paper/2104.08821/) (2021)
- [Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation](https://mlsanity.com/paper/1609.08144/) (2016)
- [LLM-in-the-loop: Leveraging Large Language Model for Thematic Analysis](https://mlsanity.com/paper/2310.15100/) (2023)
- [Can large language models replace humans in the systematic review process? Evaluating GPT-4's efficacy in screening and extracting data from peer-reviewed and grey literature in multiple languages](https://mlsanity.com/paper/2310.17526/) (2023)
- [From Alignment to Assignment: Frustratingly Simple Unsupervised Entity Alignment](https://mlsanity.com/paper/2109.02363/) (2021)
- [Improving Paraphrase Detection with the Adversarial Paraphrasing Task](https://mlsanity.com/paper/2106.07691/) (2021)
- [Measuring Annotator Agreement Generally across Complex Structured, Multi-object, and Free-text Annotation Tasks](https://mlsanity.com/paper/2212.09503/) (2022)
- [Counting on Consensus: Selecting the Right Inter-annotator Agreement Metric for NLP Annotation and Evaluation](https://mlsanity.com/paper/2603.06865/) (2026)
- [A Global Atlas of Digital Dermatology to Map Innovation and Disparities](https://mlsanity.com/paper/2601.00840/) (2025)

## Abstract (arXiv)

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.