MAESIL: Masked Autoencoder for Enhanced Self-supervised Medical Image Learning

TL;DR

MAESIL introduces a 3D masked autoencoder framework utilizing superpatches to improve self-supervised learning for medical imaging, effectively capturing spatial context and enhancing downstream task performance.

Contribution

It proposes a novel superpatch-based 3D autoencoder with dual-masking for better spatial representation in self-supervised medical image learning.

Findings

MAESIL outperforms AE, VAE, and VQ-VAE in reconstruction metrics.

The framework effectively captures 3D structural information.

Validated on three large-scale public CT datasets.

Abstract

Training deep learning models for three-dimensional (3D) medical imaging, such as Computed Tomography (CT), is fundamentally challenged by the scarcity of labeled data. While pre-training on natural images is common, it results in a significant domain shift, limiting performance. Self-Supervised Learning (SSL) on unlabeled medical data has emerged as a powerful solution, but prominent frameworks often fail to exploit the inherent 3D nature of CT scans. These methods typically process 3D scans as a collection of independent 2D slices, an approach that fundamentally discards critical axial coherence and the 3D structural context. To address this limitation, we propose the autoencoder for enhanced self-supervised medical image learning(MAESIL), a novel self-supervised learning framework designed to capture 3D structural information efficiently. The core innovation is the 'superpatch', a 3D chunk-based input unit that balances 3D context preservation with computational efficiency. Our framework partitions the volume into superpatches and employs a 3D masked autoencoder strategy with a dual-masking strategy to learn comprehensive spatial representations. We validated our approach on three diverse large-scale public CT datasets. Our experimental results show that MAESIL demonstrates significant improvements over existing methods such as AE, VAE and VQ-VAE in key reconstruction metrics such as PSNR and SSIM. This establishes MAESIL as a robust and practical pre-training solution for 3D medical imaging tasks.