Papers › AnatoMask: Enhancing Medical Image Segmentation with Reconstruction-guided Self-masking

AnatoMask: Enhancing Medical Image Segmentation with Reconstruction-guided Self-masking

9 Jul 2024arXiv:2407.06468archive 2025-07-28

Yuheng Li, Tianyu Luan, Yizhou Wu, Shaoyan Pan, Yenho Chen, Xiaofeng Yang

Due to the scarcity of labeled data, self-supervised learning (SSL) has gained much attention in 3D medical image segmentation, by extracting semantic representations from unlabeled data. Among SSL strategies, Masked image modeling (MIM) has shown effectiveness by reconstructing randomly masked images to learn detailed representations. However, conventional MIM methods require extensive training data to achieve good performance, which still poses a challenge for medical imaging. Since random masking uniformly samples all regions within medical images, it may overlook crucial anatomical regions and thus degrade the pretraining efficiency. We propose AnatoMask, a novel MIM method that leverages reconstruction loss to dynamically identify and mask out anatomically significant regions to improve pretraining efficacy. AnatoMask takes a self-distillation approach, where the model learns both how to find more significant regions to mask and how to reconstruct these masked regions. To avoid suboptimal learning, Anatomask adjusts the pretraining difficulty progressively using a masking dynamics function. We have evaluated our method on 4 public datasets with multiple imaging modalities (CT, MRI, and PET). AnatoMask demonstrates superior performance and scalability compared to existing SSL methods. The code is available at https://github.com/ricklisz/AnatoMask.

Code

Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.

Code Syntology ran Syntology

6 samples harvested; 1 ran; 0 honoured the contract we drafted; 5 have no recorded run. Read from Syntology's graph 2026-09-24; that is when this build read the record, not when the samples ran.

Licence: 0 of the 6 samples are pointer only, meaning Syntology does not serve that copy's text. This page shows no code text for any sample; each one links to its file in the repository.

Harvested from ricklisz/anatomask. “Ran” means the sample executed on a synthesized input. It does not mean the output is correct, and nothing here reproduces the paper's results. “Honoured” and “violated” refer to a contract Syntology drafted from the code itself; “our draft was wrong” and “fixture could not drive it” are failures of Syntology's instrument, not of the code.

Each sample ends with its code_sha256, Syntology's identity for that exact code. An agent fetches the stored sample with Syntology's MCP tool get_code(code_sha256="…") (how to connect); click an identity to copy that call.

Repository labels, per sample. official repository: The archive marks this repository official for the paper. named in the paper: The archive records that the paper mentions this repository; it is not marked official. community (archive-listed): In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper. found in paper text by Syntology: Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted. community: Not in the archive's code links for this paper; a community repository Syntology harvested. Samples from a repository marked official are listed first. Licence labels name the repository's licence as recorded at harvest. “Pointer only” means Syntology does not serve that copy's text, for one of four reasons: no licence file was found; the licence was not identified; the licence is recorded as permissive but that copy's record is not marked cleared; or the licence is outside the permissive list Syntology serves text under (MIT, Apache-2.0, BSD and similar). Some licences outside that list permit redistribution, such as WTFPL, and GPL-3.0 under its conditions; they are simply not on the list. Hover a licence label for the reason. File links open the file on GitHub at the default branch, which may have changed since the harvest.

Tasks

Results from the paper archive 2025-07-28

No leaderboard rows for this paper in the archive.

Methods

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections