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

Kyeonghun Kim, Hyeonseok Jung, Youngung Han, Junsu Lim, YeonJu Jean, Seongbin Park, Eunseob Choi, Hyunsu Go, SeoYoung Ju, Seohyoung Park, Gyeongmin Kim, MinJu Kwon, KyungSeok Yuh, Soo Yong Kim, Ken Ying-Kai Liao, Nam-Joon Kim, Hyuk-Jae Lee

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.

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

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.

Paper Structure

This paper contains 11 sections, 3 figures, 3 tables.

Table of Contents

  1. Introduction
  2. Related Work
  3. Methods
  4. Superpatching and Masking
  5. Encoder-Decoder Architecture
  6. Experiments and Results
  7. Dataset
  8. Comparison Results
  9. Discussion
  10. Conclusion
  11. Acknowledgment

Figures (3)

  • Figure 1: Overview of the proposed MAESIL framework, which masks a high ratio of an input 3D superpatch, feeds only the visible portions to an encoder, and uses a decoder to reconstruct the original superpatch from the encoded information and learnable mask tokens.
  • Figure 2: The 3D input processing pipeline. A full 3D CT scans is first partitioned into 'superpatches'. Each superpatch is then densely tokenized into smaller 'standardized patches', which serve as the input tokens for the Transformer.
  • Figure 3: Qualitative reconstruction results of MAESIL across different anatomical views. The original input and reconstruction output are compared. From left to right: Axial, Coronal and Sagittal views.