# HARE: an entity and relation centric evaluation framework for histopathology reports

arXiv: https://arxiv.org/abs/2509.16326 · HTML: https://mlsanity.com/paper/2509.16326/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 15 of its 34 references that are in the map.
- First posted on arXiv 19 Sep 2025.

## Builds on (most cited first, 15 of 15)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [HuggingFace's Transformers: State-of-the-art Natural Language Processing](https://mlsanity.com/paper/1910.03771/) (2019)
- [DeBERTaV3: Improving DeBERTa using ELECTRA-Style Pre-Training with Gradient-Disentangled Embedding Sharing](https://mlsanity.com/paper/2111.09543/) (2021)
- [CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT](https://mlsanity.com/paper/2004.09167/) (2020)
- [RadGraph: Extracting Clinical Entities and Relations from Radiology Reports](https://mlsanity.com/paper/2106.14463/) (2021)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [MAIRA-2: Grounded Radiology Report Generation](https://mlsanity.com/paper/2406.04449/) (2024)
- [GREEN: Generative Radiology Report Evaluation and Error Notation](https://mlsanity.com/paper/2405.03595/) (2024)
- [Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/2112.07869/) (2021)
- [HistGen: Histopathology Report Generation via Local-Global Feature Encoding and Cross-modal Context Interaction](https://mlsanity.com/paper/2403.05396/) (2024)
- [Overview of the First Shared Task on Clinical Text Generation: RRG24 and "Discharge Me!"](https://mlsanity.com/paper/2409.16603/) (2024)
- [PathologyBERT -- Pre-trained Vs. A New Transformer Language Model for Pathology Domain](https://mlsanity.com/paper/2205.06885/) (2022)
- [SLaVA-CXR: Small Language and Vision Assistant for Chest X-ray Report Automation](https://mlsanity.com/paper/2409.13321/) (2024)
- [Clinical-grade Multi-Organ Pathology Report Generation for Multi-scale Whole Slide Images via a Semantically Guided Medical Text Foundation Model](https://mlsanity.com/paper/2409.15574/) (2024)

## Abstract (arXiv)

Medical domain automated text generation is an active area of research and development; however, evaluating the clinical quality of generated reports remains a challenge, especially in instances where domain-specific metrics are lacking, e.g. histopathology. We propose HARE (Histopathology Automated Report Evaluation), a novel entity and relation centric framework, composed of a benchmark dataset, a named entity recognition (NER) model, a relation extraction (RE) model, and a novel metric, which prioritizes clinically relevant content by aligning critical histopathology entities and relations between reference and generated reports. To develop the HARE benchmark, we annotated 813 de-identified clinical diagnostic histopathology reports and 652 histopathology reports from The Cancer Genome Atlas (TCGA) with domain-specific entities and relations. We fine-tuned GatorTronS, a domain-adapted language model to develop HARE-NER and HARE-RE which achieved the highest overall F1-score (0.915) among the tested models. The proposed HARE metric outperformed traditional metrics including ROUGE and Meteor, as well as radiology metrics such as RadGraph-XL, with the highest correlation and the best regression to expert evaluations (higher than the second best method, GREEN, a large language model based radiology report evaluator, by Pearson r = 0.168, Spearman ρ = 0.161, Kendall τ = 0.123, R2 = 0.176, RMSE = 0.018). We release HARE, datasets, and the models at https://github.com/knowlab/HARE to foster advancements in histopathology report generation, providing a robust framework for improving the quality of reports.