Focus on Texture: Rethinking Pre-training in Masked Autoencoders for Medical Image Classification

Masked Autoencoders (MAEs) have emerged as a dominant strategy for self-supervised representation learning in natural images, where models are pre-trained to reconstruct masked patches with a pixel-wise mean squared error (MSE) between original and reconstructed RGB values as the loss. We observe that MSE encourages blurred image re-construction, but still works for natural images as it preserves dominant edges. However, in medical imaging, when the texture cues are more important for classification of a visual abnormality, the strategy fails. Taking inspiration from Gray Level Co-occurrence Matrix (GLCM) feature in Radiomics studies, we propose a novel MAE based pre-training framework, GLCM-MAE, using reconstruction loss based on matching GLCM. GLCM captures intensity and spatial relationships in an image, hence proposed loss helps preserve morphological features. Further, we propose a novel formulation to convert matching GLCM matrices into a differentiable loss function. We demonstrate that unsupervised pre-training on medical images with the proposed GLCM loss improves representations for downstream tasks. GLCM-MAE outperforms the current state-of-the-art across four tasks - gallbladder cancer detection from ultrasound images by 2.1%, breast cancer detection from ultrasound by 3.1%, pneumonia detection from x-rays by 0.5%, and COVID detection from CT by 0.6%. Source code and pre-trained models are available at: https://github.com/ChetanMadan/GLCM-MAE.