# Recover Semantics First, Generate Better: Improved Latent Modeling for 3D MRI Reconstruction and Cross-Contrast Synthesis

arXiv: https://arxiv.org/abs/2606.17989 · HTML: https://mlsanity.com/paper/2606.17989/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 29 of its 37 references that are in the map.
- First posted on arXiv 16 Jun 2026.

## Builds on (most cited first, 29 of 29)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
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- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Neural Discrete Representation Learning](https://mlsanity.com/paper/1711.00937/) (2017)
- [Image-to-Image Translation with Conditional Adversarial Networks](https://mlsanity.com/paper/1611.07004/) (2016)
- [Taming Transformers for High-Resolution Image Synthesis](https://mlsanity.com/paper/2012.09841/) (2020)
- [Photo-Realistic Single Image Super-Resolution Using a Generative Adversarial Network](https://mlsanity.com/paper/1609.04802/) (2016)
- [Cosmos World Foundation Model Platform for Physical AI](https://mlsanity.com/paper/2501.03575/) (2025)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Representation Alignment for Generation: Training Diffusion Transformers Is Easier Than You Think](https://mlsanity.com/paper/2410.06940/) (2024)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [Finite Scalar Quantization: VQ-VAE Made Simple](https://mlsanity.com/paper/2309.15505/) (2023)
- [CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation](https://mlsanity.com/paper/2001.06535/) (2020)
- [Focal Frequency Loss for Image Reconstruction and Synthesis](https://mlsanity.com/paper/2012.12821/) (2020)
- [ResViT: Residual vision transformers for multi-modal medical image synthesis](https://mlsanity.com/paper/2106.16031/) (2021)
- [3D Self-Supervised Methods for Medical Imaging](https://mlsanity.com/paper/2006.03829/) (2020)
- [Representation Entanglement for Generation: Training Diffusion Transformers Is Much Easier Than You Think](https://mlsanity.com/paper/2507.01467/) (2025)
- [SwinMM: Masked Multi-view with Swin Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2307.12591/) (2023)
- [Evaluating General Purpose Vision Foundation Models for Medical Image Analysis: An Experimental Study of DINOv2 on Radiology Benchmarks](https://mlsanity.com/paper/2312.02366/) (2023)
- [Self-Consistent Recursive Diffusion Bridge for Medical Image Translation](https://mlsanity.com/paper/2405.06789/) (2024)
- [SegDINO: An Efficient Design for Medical and Natural Image Segmentation with DINO-V3](https://mlsanity.com/paper/2509.00833/) (2025)
- [HACA3: A Unified Approach for Multi-site MR Image Harmonization](https://mlsanity.com/paper/2212.06065/) (2022)
- [Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge](https://mlsanity.com/paper/2405.09787/) (2024)
- [VAEVQ: Enhancing Discrete Visual Tokenization through Variational Modeling](https://mlsanity.com/paper/2511.06863/) (2025)
- [VQ-Seg: Vector-Quantized Token Perturbation for Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2601.10124/) (2026)
- [A Comprehensive Survey on Magnetic Resonance Image Reconstruction](https://mlsanity.com/paper/2503.07097/) (2025)

## Abstract (arXiv)

Multi-contrast magnetic resonance imaging (MRI) provides complementary information for clinical diagnosis. However, acquiring all MRI sequences is often time-consuming and costly. Recent generative models perform cross-contrast synthesis to address this issue by inferring absent contrasts from the available ones. Nevertheless, synthesizing 3D MRI presents significant challenges. Due to the massive volume sizes, operating directly in the pixel space is computationally prohibitive; therefore, a common approach is to first compress the 3D volumes into a latent space and subsequently train generative models in that space. We observe that existing compression architectures face several critical issues: they under-preserve long-range anatomical coherence, discard clinically meaningful semantics, and rely on optimization objectives that lead to over-smoothed reconstructions. Ultimately, these shortcomings compromise the performance of subsequent generative models. In this work, we propose a semantics-first latent modeling framework for 3D MRI reconstruction and cross-contrast synthesis. Specifically, we introduce a Latent Harmonization Encoder (LHE) to capture global anatomical dependencies, ensuring coherent volumetric representations. To mitigate semantic degradation during latent compression, we further design a Semantic Recovery Block (SRB) that injects high-level priors from a self-supervised semantic teacher, enhancing contrast-aware separability in the latent space. Additionally, we propose an Anatomy-aware Frequency Loss (AFL) to adaptively preserve diagnostically relevant high-frequency structures. Extensive experiments on two public multi-contrast MRI datasets demonstrate consistent improvements in reconstruction fidelity and cross-contrast synthesis quality. Our code is available at https://github.com/script-Yang/RSF.