# Fake It Right: Injecting Anatomical Logic into Synthetic Supervised Pre-training for Medical Segmentation

arXiv: https://arxiv.org/abs/2603.00979 · HTML: https://mlsanity.com/paper/2603.00979/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 18 references that are in the map.
- First posted on arXiv 1 Mar 2026.

## Builds on (most cited first, 14 of 14)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [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)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [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)
- [Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis](https://mlsanity.com/paper/1908.06912/) (2019)
- [VoCo: A Simple-yet-Effective Volume Contrastive Learning Framework for 3D Medical Image Analysis](https://mlsanity.com/paper/2402.17300/) (2024)
- [SwinMM: Masked Multi-view with Swin Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2307.12591/) (2023)
- [Visual Atoms: Pre-training Vision Transformers with Sinusoidal Waves](https://mlsanity.com/paper/2303.01112/) (2023)
- [Pre-training Vision Transformers with Very Limited Synthesized Images](https://mlsanity.com/paper/2307.14710/) (2023)
- [SegRCDB: Semantic Segmentation via Formula-Driven Supervised Learning](https://mlsanity.com/paper/2309.17083/) (2023)

## Abstract (arXiv)

Vision Transformers (ViTs) excel in 3D medical segmentation but require massive annotated datasets. While Self-Supervised Learning (SSL) mitigates this using unlabeled data, it still faces strict privacy and logistical barriers. Formula-Driven Supervised Learning (FDSL) offers a privacy-preserving alternative by pre-training on synthetic mathematical primitives. However, a critical semantic gap limits its efficacy: generic shapes lack the morphological fidelity, fixed spatial layouts, and inter-organ relationships of real anatomy, preventing models from learning essential global structural priors. To bridge this gap, we propose an Anatomy-Informed Synthetic Supervised Pre-training framework unifying FDSL's infinite scalability with anatomical realism. We replace basic primitives with a lightweight shape bank with de-identified, label-only segmentation masks from 5 subjects. Furthermore, we introduce a structure-aware sequential placement strategy to govern the patch synthesis process. Instead of random placement, we enforce physiological plausibility using spatial anchors for correct localization and a topological graph to manage inter-organ interactions (e.g., preventing impossible overlaps). Extensive experiments on BTCV and MSD datasets demonstrate that our method significantly outperforms state-of-the-art FDSL baselines and SSL methods by 1.74% and up to 1.66%, while exhibiting a robust scaling effect where performance improves with increased synthetic data volume. This provides a data-efficient, privacy-compliant solution for medical segmentation. The code will be made publicly available upon acceptance.