Bootstrapping BI-RADS classification using large language models and transformers in breast magnetic resonance imaging reports

Abstract Breast cancer is one of the most common malignancies among women globally. Magnetic resonance imaging (MRI), as the final non-invasive diagnostic tool before biopsy, provides detailed free-text reports that support clinical decision-making. Therefore, the effective utilization of the information in MRI reports to make reliable decisions is crucial for patient care. This study proposes a novel method for BI-RADS classification using breast MRI reports. Large language models are employed to transform free-text reports into structured reports. Specifically, missing category information (MCI) that is absent in the free-text reports is supplemented by assigning default values to the missing categories in the structured reports. To ensure data privacy, a locally deployed Qwen-Chat model is employed. Furthermore, to enhance the domain-specific adaptability, a knowledge-driven prompt is designed. The Qwen-7B-Chat model is fine-tuned specifically for structuring breast MRI reports. To prevent information loss and enable comprehensive learning of all report details, a fusion strategy is introduced, combining free-text and structured reports to train the classification model. Experimental results show that the proposed BI-RADS classification method outperforms existing report classification methods across multiple evaluation metrics. Furthermore, an external test set from a different hospital is used to validate the robustness of the proposed approach. The proposed structured method surpasses GPT-4o in terms of performance. Ablation experiments confirm that the knowledge-driven prompt, MCI, and the fusion strategy are crucial to the model’s performance.