# HySparK: Hybrid Sparse Masking for Large Scale Medical Image Pre-Training

arXiv: https://arxiv.org/abs/2408.05815 · HTML: https://mlsanity.com/paper/2408.05815/

## Key facts

- Cited by 12 papers in the map (data through 14 Oct 2026).
- Builds on 36 of its 39 references that are in the map.
- First posted on arXiv 11 Aug 2024.

## Builds on (most cited first, 30 of 36)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [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)
- [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)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Context Encoders: Feature Learning by Inpainting](https://mlsanity.com/paper/1604.07379/) (2016)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation](https://mlsanity.com/paper/2001.06535/) (2020)
- [Context Autoencoder for Self-Supervised Representation Learning](https://mlsanity.com/paper/2202.03026/) (2022)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [Submanifold Sparse Convolutional Networks](https://mlsanity.com/paper/1706.01307/) (2017)
- [UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer](https://mlsanity.com/paper/2109.04335/) (2021)

## Built on by (most cited first, 12 of 12)

- [Revisiting MAE pre-training for 3D medical image segmentation](https://mlsanity.com/paper/2410.23132/) (2024)
- [An OpenMind for 3D medical vision self-supervised learning](https://mlsanity.com/paper/2412.17041/) (2024)
- [MambaMIM: Pre-training Mamba with State Space Token Interpolation and its Application to Medical Image Segmentation](https://mlsanity.com/paper/2408.08070/) (2024)
- [Pre-Trained LLM is a Semantic-Aware and Generalizable Segmentation Booster](https://mlsanity.com/paper/2506.18034/) (2025)
- [Mobile U-ViT: Revisiting large kernel and U-shaped ViT for efficient medical image segmentation](https://mlsanity.com/paper/2508.01064/) (2025)
- [SimCroP: Radiograph Representation Learning with Similarity-driven Cross-granularity Pre-training](https://mlsanity.com/paper/2509.08311/) (2025)
- [U-RWKV: Lightweight medical image segmentation with direction-adaptive RWKV](https://mlsanity.com/paper/2507.11415/) (2025)
- [LGMSNet: Thinning a medical image segmentation model via dual-level multiscale fusion](https://mlsanity.com/paper/2508.15476/) (2025)
- [UCAD: Uncertainty-guided Contour-aware Displacement for semi-supervised medical image segmentation](https://mlsanity.com/paper/2601.17366/) (2026)
- [Concept-to-Pixel: Prompt-Free Universal Medical Image Segmentation](https://mlsanity.com/paper/2603.17746/) (2026)
- [nnFoundation: 3D Foundation Models for Radiology](https://mlsanity.com/paper/2609.26924/) (2026)
- [Where to Look Matters: Rethinking Sub-Volume Sampling in 3D Medical Self-supervised Learning](https://mlsanity.com/paper/2610.13915/) (2026)

## Abstract (arXiv)

The generative self-supervised learning strategy exhibits remarkable learning representational capabilities. However, there is limited attention to end-to-end pre-training methods based on a hybrid architecture of CNN and Transformer, which can learn strong local and global representations simultaneously. To address this issue, we propose a generative pre-training strategy called Hybrid Sparse masKing (HySparK) based on masked image modeling and apply it to large-scale pre-training on medical images. First, we perform a bottom-up 3D hybrid masking strategy on the encoder to keep consistency masking. Then we utilize sparse convolution for the top CNNs and encode unmasked patches for the bottom vision Transformers. Second, we employ a simple hierarchical decoder with skip-connections to achieve dense multi-scale feature reconstruction. Third, we implement our pre-training method on a collection of multiple large-scale 3D medical imaging datasets. Extensive experiments indicate that our proposed pre-training strategy demonstrates robust transfer-ability in supervised downstream tasks and sheds light on HySparK's promising prospects. The code is available at https://github.com/FengheTan9/HySparK