Generalised Focal Loss: Unifying Dice and Cross Entropy-based Losses to Handle Class Imbalanced Medical Image Segmentation

Automatic segmentation methods are an important advancement in medical imaging analysis. Machine learning techniques, and deep neural networks in particular, are the state-of-the-art for most medical image segmentation tasks. Issues with class imbalance pose a significant challenge in medical datasets, with lesions often occupying a considerably smaller volume relative to the background. Loss functions used in the training of deep learning algorithms differ in their robustness to class imbalance, with direct consequences for model convergence. The most commonly used loss functions for segmentation are based on either the cross entropy loss, Dice loss or a combination of the two. We propose a Generalised Focal loss, a new framework that unifies Dice and cross entropy-based losses for handling class imbalance. We evaluate our proposed loss function on three highly class imbalanced, publicly available medical imaging datasets: Breast Ultrasound 2017 (BUS2017), Brain Tumour Segmentation 2020 (BraTS20) and Kidney Tumour Segmentation 2019 (KiTS19). We compare our loss function performance to six Dice or cross entropy-based loss functions, and demonstrate that our proposed loss function is robust to class imbalance, outperforming the other loss functions across datasets. Finally, we use the Generalised Focal loss together with deep supervision to achieve state-of-the-art results without modification of the original U-Net architecture.