# Large Language Model-Assisted Cleaning of Report-Derived Labels in a Large-Scale Chest CT Dataset

arXiv: https://arxiv.org/abs/2606.22382 · HTML: https://mlsanity.com/paper/2606.22382/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 15 references that are in the map.
- First posted on arXiv 21 Jun 2026.

## Builds on (most cited first, 4 of 4)

- [DeepSeek-V3.2: Pushing the Frontier of Open Large Language Models](https://mlsanity.com/paper/2512.02556/) (2025)
- [CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT](https://mlsanity.com/paper/2004.09167/) (2020)
- [A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises](https://mlsanity.com/paper/2008.09104/) (2020)
- [Generalist Foundation Models from a Multimodal Dataset for 3D Computed Tomography](https://mlsanity.com/paper/2403.17834/) (2024)

## Abstract (arXiv)

Purpose: To evaluate whether large language model (LLM)-assisted label cleaning can identify label-report discordance in CT-RATE, a large-scale public chest CT dataset. Materials and Methods: After report-level deduplication, 24,446 unique radiology reports were identified. Twelve reports were excluded from the primary GPT-5.4 analysis because of Microsoft Azure AI Foundry content-safety filtering, leaving 24,434 reports and 439,812 label instances across 18 abnormality categories. GPT-5.4-derived binary labels were generated from report text using structured JSON output and compared with existing CT-RATE labels. Discordant instances were adjudicated by radiologists. In addition, 100 randomly sampled reports were manually annotated to compare CT-RATE labels, individual LLM-derived labels, and multi-LLM majority-vote labels against radiologist-annotated reference labels. Results: Overall agreement between GPT-5.4-derived and CT-RATE labels was 96.4%, with Cohen's kappa of 0.884. Lymphadenopathy showed the lowest agreement and kappa. In discordance review, radiologist adjudication supported GPT-5.4-derived labels in 72 of 97 (74.2%) general discordant instances and 91 of 99 (91.9%) targeted lymphadenopathy discordant instances. Against radiologist-annotated reference labels, multi-LLM majority-vote labels achieved the highest label-macro-averaged F1 score and Cohen's kappa. Conclusion: LLM-assisted label cleaning identified clinically meaningful label-report discordance in CT-RATE and may support scalable quality improvement of public imaging datasets. The cleaned dataset will be made publicly available to support future research.