# Multimodal Masked Autoencoder Pre-training for 3D MRI-Based Brain Tumor Analysis with Missing Modalities

arXiv: https://arxiv.org/abs/2505.00568 · HTML: https://mlsanity.com/paper/2505.00568/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 33 references that are in the map.
- First posted on arXiv 1 May 2025.

## Builds on (most cited first, 23 of 23)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [MultiMAE: Multi-modal Multi-task Masked Autoencoders](https://mlsanity.com/paper/2204.01678/) (2022)
- [4M: Massively Multimodal Masked Modeling](https://mlsanity.com/paper/2312.06647/) (2023)
- [HeMIS: Hetero-Modal Image Segmentation](https://mlsanity.com/paper/1607.05194/) (2016)
- [mmFormer: Multimodal Medical Transformer for Incomplete Multimodal Learning of Brain Tumor Segmentation](https://mlsanity.com/paper/2206.02425/) (2022)
- [A Scalable Discrete-Time Survival Model for Neural Networks](https://mlsanity.com/paper/1805.00917/) (2018)
- [Continuous and Discrete-Time Survival Prediction with Neural Networks](https://mlsanity.com/paper/1910.06724/) (2019)
- [Self Pre-training with Masked Autoencoders for Medical Image Classification and Segmentation](https://mlsanity.com/paper/2203.05573/) (2022)
- [Hetero-Modal Variational Encoder-Decoder for Joint Modality Completion and Segmentation](https://mlsanity.com/paper/1907.11150/) (2019)
- [Knowledge distillation from multi-modal to mono-modal segmentation networks](https://mlsanity.com/paper/2106.09564/) (2021)
- [M3AE: Multimodal Representation Learning for Brain Tumor Segmentation with Missing Modalities](https://mlsanity.com/paper/2303.05302/) (2023)
- [ACN: Adversarial Co-training Network for Brain Tumor Segmentation with Missing Modalities](https://mlsanity.com/paper/2106.14591/) (2021)
- [Brain Tumor Segmentation on MRI with Missing Modalities](https://mlsanity.com/paper/1904.07290/) (2019)
- [SMU-Net: Style matching U-Net for brain tumor segmentation with missing modalities](https://mlsanity.com/paper/2204.02961/) (2022)
- [Representation Disentanglement for Multi-modal brain MR Analysis](https://mlsanity.com/paper/2102.11456/) (2021)
- [DeepSeg: Deep Neural Network Framework for Automatic Brain Tumor Segmentation using Magnetic Resonance FLAIR Images](https://mlsanity.com/paper/2004.12333/) (2020)
- [Can We Break Free from Strong Data Augmentations in Self-Supervised Learning?](https://mlsanity.com/paper/2404.09752/) (2024)

## Built on by (most cited first, 3 of 3)

- [BrainDINO: A Brain MRI Foundation Model for Generalizable Clinical Representation Learning](https://mlsanity.com/paper/2604.27277/) (2026)
- [PRIME: Prototype-Driven Multimodal Pretraining for Cancer Prognosis with Missing Modalities](https://mlsanity.com/paper/2604.04999/) (2026)
- [Contrastive Joint-Embedding Prediction for Representation Learning in Structural MRI](https://mlsanity.com/paper/2607.11962/) (2026)

## Abstract (arXiv)

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE