# MiM: Mask in Mask Self-Supervised Pre-Training for 3D Medical Image Analysis

arXiv: https://arxiv.org/abs/2404.15580 · HTML: https://mlsanity.com/paper/2404.15580/

## Key facts

- Cited by 19 papers in the map (data through 14 Oct 2026).
- Builds on 71 of its 113 references that are in the map.
- First posted on arXiv 24 Apr 2024.

## Builds on (most cited first, 30 of 71)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Improved Baselines with Momentum Contrastive Learning](https://mlsanity.com/paper/2003.04297/) (2020)
- [An Empirical Study of Training Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.02057/) (2021)
- [Context Encoders: Feature Learning by Inpainting](https://mlsanity.com/paper/1604.07379/) (2016)
- [Big Self-Supervised Models are Strong Semi-Supervised Learners](https://mlsanity.com/paper/2006.10029/) (2020)
- [VideoMAE: Masked Autoencoders are Data-Efficient Learners for Self-Supervised Video Pre-Training](https://mlsanity.com/paper/2203.12602/) (2022)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Multiscale Vision Transformers](https://mlsanity.com/paper/2104.11227/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [VideoMAE V2: Scaling Video Masked Autoencoders with Dual Masking](https://mlsanity.com/paper/2303.16727/) (2023)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [Hard Negative Mixing for Contrastive Learning](https://mlsanity.com/paper/2010.01028/) (2020)
- [Deep Learning for Medical Image Analysis](https://mlsanity.com/paper/1708.08987/) (2017)
- [A large annotated medical image dataset for the development and evaluation of segmentation algorithms](https://mlsanity.com/paper/1902.09063/) (2019)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)

## Built on by (most cited first, 19 of 19)

- [Large-Scale 3D Medical Image Pre-training with Geometric Context Priors](https://mlsanity.com/paper/2410.09890/) (2024)
- [Triad: Vision Foundation Model for 3D Magnetic Resonance Imaging](https://mlsanity.com/paper/2502.14064/) (2025)
- [UniBiomed: A Universal Foundation Model for Grounded Biomedical Image Interpretation](https://mlsanity.com/paper/2504.21336/) (2025)
- [Scaling Artificial Intelligence for Multi-Tumor Early Detection with More Reports, Fewer Masks](https://mlsanity.com/paper/2510.14803/) (2025)
- [MG-3D: Multi-Grained Knowledge-Enhanced 3D Medical Vision-Language Pre-training](https://mlsanity.com/paper/2412.05876/) (2024)
- [Beyond [cls]: Exploring the true potential of Masked Image Modeling representations](https://mlsanity.com/paper/2412.03215/) (2024)
- [Structure-aware Semantic Discrepancy and Consistency for 3D Medical Image Self-supervised Learning](https://mlsanity.com/paper/2507.02581/) (2025)
- [Adaptation of Foundation Models for Medical Image Analysis: Strategies, Challenges, and Future Directions](https://mlsanity.com/paper/2511.01284/) (2025)
- [Learning Robust Visual Features in Computed Tomography Enables Efficient Transfer Learning for Clinical Tasks](https://mlsanity.com/paper/2604.04133/) (2026)
- [GenMed: A Pairwise Generative Reformulation of Medical Diagnostic Tasks](https://mlsanity.com/paper/2605.10645/) (2026)
- [Glance and Focus Reinforcement for Pan-cancer Screening](https://mlsanity.com/paper/2601.19103/) (2026)
- [MeDUET: Disentangled Unified Pretraining for 3D Medical Image Synthesis and Analysis](https://mlsanity.com/paper/2602.17901/) (2026)
- [ASAP: Advancing Medical Volumetric Representation Learning with Anatomy-aware Semantically-adaptive Pre-training](https://mlsanity.com/paper/2606.00602/) (2026)
- [NEARL: Interacted Query Adaptation with Orthogonal Regularization for Medical Vision-Language Understanding](https://mlsanity.com/paper/2508.04101/) (2025)
- [ModAn-MulSupCon: Modality-and Anatomy-Aware Multi-Label Supervised Contrastive Pretraining for Medical Imaging](https://mlsanity.com/paper/2508.18613/) (2025)
- [Vascular anatomy-aware self-supervised pre-training for X-ray angiogram analysis](https://mlsanity.com/paper/2602.11536/) (2026)
- [Toward Clinically Ready Foundation Models in Medical Image Analysis: Adaptation Mechanisms and Deployment Trade-offs](https://mlsanity.com/paper/2603.14271/) (2026)
- [Where to Look Matters: Rethinking Sub-Volume Sampling in 3D Medical Self-supervised Learning](https://mlsanity.com/paper/2610.13915/) (2026)
- [LiFUSE: Frequency-Spatial Unified Self-Supervised Pretraining for Liver Disease Analysis on Non-contrast CT](https://mlsanity.com/paper/2610.18243/) (2026)

## Abstract (arXiv)

The Vision Transformer (ViT) has demonstrated remarkable performance in Self-Supervised Learning (SSL) for 3D medical image analysis. Masked AutoEncoder (MAE) for feature pre-training can further unleash the potential of ViT on various medical vision tasks. However, due to large spatial sizes with much higher dimensions of 3D medical images, the lack of hierarchical design for MAE may hinder the performance of downstream tasks. In this paper, we propose a novel textitMask in Mask (MiM) pre-training framework for 3D medical images, which aims to advance MAE by learning discriminative representation from hierarchical visual tokens across varying scales. We introduce multiple levels of granularity for masked inputs from the volume, which are then reconstructed simultaneously ranging at both fine and coarse levels. Additionally, a cross-level alignment mechanism is applied to adjacent level volumes to enforce anatomical similarity hierarchically. Furthermore, we adopt a hybrid backbone to enhance the hierarchical representation learning efficiently during the pre-training. MiM was pre-trained on a large scale of available 3D volumetric images, textiti.e., Computed Tomography (CT) images containing various body parts. Extensive experiments on thirteen public datasets demonstrate the superiority of MiM over other SSL methods in organ/lesion/tumor segmentation and disease classification. We further scale up the MiM to large pre-training datasets with more than 10k volumes, showing that large-scale pre-training can further enhance the performance of downstream tasks. The improvement also concluded that the research community should pay more attention to the scale of the pre-training dataset towards the healthcare foundation model for 3D medical images.