A transformer-based deep learning approach for classifying brain metastases into primary organ sites using clinical whole brain MRI

Treatment decisions for brain metastatic disease rely on knowledge of the primary organ site, and currently made with biopsy and histology. Here we develop a novel deep learning approach for accurate non-invasive digital histology with whole-brain MRI data. Our IRB-approved single-site retrospective study was comprised of patients (n=1,399) referred for MRI treatment-planning and gamma knife radiosurgery over 19 years. Contrast-enhanced T1-weighted and T2-weighted Fluid-Attenuated Inversion Recovery brain MRI exams (n=1,582) were preprocessed and input to the proposed deep learning workflow for tumor segmentation, modality transfer, and primary site classification into one of five classes (lung, breast, melanoma, renal, and others). Ten-fold cross-validation generated overall AUC of 0.947 (95%CI:0.938,0.955), lung class AUC of 0.899 (95%CI:0.884,0.915), breast class AUC of 0.990 (95%CI:0.983,0.997), melanoma class AUC of 0.882 (95%CI:0.858,0.906), renal class AUC of 0.870 (95%CI:0.823,0.918), and other class AUC of 0.885 (95%CI:0.843,0.949). These data establish that whole-brain imaging features are discriminative to allow accurate diagnosis of the primary organ site of malignancy. Our end-to-end deep radiomic approach has great potential for classifying metastatic tumor types from whole-brain MRI images. Further refinement may offer an invaluable clinical tool to expedite primary cancer site identification for precision treatment and improved outcomes.