Predicting ki-67 expression in breast cancer via transformer and multiple instance learning on DCE-MRI

Accurate assessment of Ki-67 expression levels in breast cancer is crucial for determining prognosis and making informed treatment decisions. Current immunohistochemical methods relying on needle biopsy introduce sampling errors due to tumor spatial heterogeneity, making the development of non-invasive, precise preoperative prediction methods of significant clinical importance. This study aims to explore and compare advanced deep learning models based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) for noninvasive assessment of Ki-67 expression. This retrospective study analyzed preoperative DCE-MRI data from 308 patients with histologically confirmed breast cancer. Adjacent slices centered on the tumor’s most significant cross-section were obtained to create a 2.5-dimensional (2·5D) dataset. We innovatively developed two deep learning models using the same dataset (1): a Multi-Instance Learning (MIL) model that combines slice-level predictive features with Predictive Likelihood Histogram (PLH) and Bag-of-Words (BoW) techniques (2); a Transformer-based fusion model that directly captures global contextual relationships between slices via self-attention mechanisms. The predictive performance of both models was systematically compared with traditional radiomics and clinical models. On an independent test set, the Transformer fusion model demonstrated optimal predictive performance with an area under the curve (AUC) of 0.875, achieving accuracy, sensitivity, and specificity of 0.839, 0.848, and 0.833, respectively. The MIL model ranked second (AUC = 0.825), with both models significantly outperforming traditional radiomics models (AUC = 0.698) and clinical models (AUC = 0.648). Deep learning models based on 2·5D DCE-MRI, especially Transformer models that achieve global feature fusion through self-attention mechanisms, can effectively and non-invasively predict Ki-67 expression status in breast cancer, surpassing traditional methods. This model shows potential as a reliable tool to help clinicians accurately assess tumor proliferation activity before surgery.