Enhancing chest X-ray datasets with privacy-preserving large language models and multi-type annotations: a data-driven approach for improved classification
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arXiv
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| author | Lanfredi, Ricardo Bigolin Mukherjee, Pritam Summers, Ronald |
| author_facet | Lanfredi, Ricardo Bigolin Mukherjee, Pritam Summers, Ronald |
| contents | In chest X-ray (CXR) image analysis, rule-based systems are usually employed to extract labels from reports for dataset releases. However, there is still room for improvement in label quality. These labelers typically output only presence labels, sometimes with binary uncertainty indicators, which limits their usefulness. Supervised deep learning models have also been developed for report labeling but lack adaptability, similar to rule-based systems. In this work, we present MAPLEZ (Medical report Annotations with Privacy-preserving Large language model using Expeditious Zero shot answers), a novel approach leveraging a locally executable Large Language Model (LLM) to extract and enhance findings labels on CXR reports. MAPLEZ extracts not only binary labels indicating the presence or absence of a finding but also the location, severity, and radiologists' uncertainty about the finding. Over eight abnormalities from five test sets, we show that our method can extract these annotations with an increase of 3.6 percentage points (pp) in macro F1 score for categorical presence annotations and more than 20 pp increase in F1 score for the location annotations over competing labelers. Additionally, using the combination of improved annotations and multi-type annotations in classification supervision, we demonstrate substantial advancements in model quality, with an increase of 1.1 pp in AUROC over models trained with annotations from the best alternative approach. We share code and annotations. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_04024 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Enhancing chest X-ray datasets with privacy-preserving large language models and multi-type annotations: a data-driven approach for improved classification Lanfredi, Ricardo Bigolin Mukherjee, Pritam Summers, Ronald Image and Video Processing Computer Vision and Pattern Recognition In chest X-ray (CXR) image analysis, rule-based systems are usually employed to extract labels from reports for dataset releases. However, there is still room for improvement in label quality. These labelers typically output only presence labels, sometimes with binary uncertainty indicators, which limits their usefulness. Supervised deep learning models have also been developed for report labeling but lack adaptability, similar to rule-based systems. In this work, we present MAPLEZ (Medical report Annotations with Privacy-preserving Large language model using Expeditious Zero shot answers), a novel approach leveraging a locally executable Large Language Model (LLM) to extract and enhance findings labels on CXR reports. MAPLEZ extracts not only binary labels indicating the presence or absence of a finding but also the location, severity, and radiologists' uncertainty about the finding. Over eight abnormalities from five test sets, we show that our method can extract these annotations with an increase of 3.6 percentage points (pp) in macro F1 score for categorical presence annotations and more than 20 pp increase in F1 score for the location annotations over competing labelers. Additionally, using the combination of improved annotations and multi-type annotations in classification supervision, we demonstrate substantial advancements in model quality, with an increase of 1.1 pp in AUROC over models trained with annotations from the best alternative approach. We share code and annotations. |
| title | Enhancing chest X-ray datasets with privacy-preserving large language models and multi-type annotations: a data-driven approach for improved classification |
| topic | Image and Video Processing Computer Vision and Pattern Recognition |
| url | https://arxiv.org/abs/2403.04024 |