RF-HiT: Rectified Flow Hierarchical Transformer for General Medical Image Segmentation

Flow matching has recently emerged as a principled framework for learning continuous-time transport maps, enabling efficient ODE-based sampling without relying on stochastic diffusion processes. While generative modeling has shown promise for medical image segmentation, particularly in capturing uncertainty and complex anatomical variability, existing approaches are predominantly based on diffusion models, which require iterative sampling and incur substantial computational overhead. In this work, we propose MedFlowSeg, a conditional flow matching framework that formulates medical image segmentation as learning a time-dependent vector field that transports a simple prior distribution to the target segmentation distribution. Compared to diffusion-based methods, our formulation enables more efficient inference through solving an ordinary differential equation, while preserving the flexibility of generative modeling. To effectively incorporate conditional information, we introduce a dual-conditioning mechanism. Specifically, we propose a Dual-Branch Spatial Attention (DB-SA) module to inject multi-frequency structural priors, and a Frequency-Aware Attention (FA-Attention) module to model interactions between spatial and spectral representations via discrepancy-aware fusion and time-dependent modulation. These components improve the alignment between noisy intermediate states and clean semantic features, leading to better structural consistency and boundary delineation. We conduct extensive experiments across multiple medical imaging modalities, where MedFlowSeg consistently outperforms prior state-of-the-art (SOTA) baselines, including diffusion-based and flow-based methods.

Vision Transformers (ViTs) achieve state-of-the-art segmentation accuracy but require large training datasets because each layer has unique parameters that must be learned independently. We present RD-ViT, a Recurrent-Depth Vision Transformer that adapts the Recurrent-Depth Transformer (RDT) architecture to dense prediction tasks, supporting both 2D and 3D inputs. RD-ViT replaces the deep stack of unique transformer blocks with a single shared block looped T times, augmented with LTI-stable state injection for guaranteed convergence, Adaptive Computation Time (ACT) for spatial compute allocation, depth-wise LoRA adaptation, and optional Mixture-of-Experts (MoE) feed-forward networks for category-specific specialization. We evaluate on the ACDC cardiac MRI segmentation benchmark in both 2D slice-level and 3D volumetric settings with exclusively real experiments executed in Google Colab. In 2D, RD-ViT outperforms standard ViT at 10% training data (Dice 0.774 vs 0.762) and at full data (0.882 vs 0.872). In 3D, RD-ViT with MoE achieves Dice 0.812 with 3.0M parameters, reaching 99.4% of standard ViT performance (0.817) at 53% of the parameter count. MoE expert utilization analysis reveals that different experts spontaneously specialize for different cardiac structures (RV, MYO, LV) without explicit routing supervision. ACT halting maps show higher compute allocation at cardiac boundaries, and the mean ponder time decreases from 2.6 to 1.4 iterations during training, demonstrating learned computational efficiency. Depth extrapolation enables inference with more loops than training without degradation. All code, notebooks, and results are publicly released.

Medical image segmentation relies on the ability of encoder-decoder architectures to translate rich feature representations into accurate pixel-level predictions under challenging conditions such as low contrast, structural ambiguity, and scale variability. While recent advances in large-scale pretraining and transformer-based encoders have substantially improved feature extraction, segmentation accuracy remains constrained by decoder design, particularly in terms of cross-scale alignment, contextual integration, and boundary preservation. In this work, we revisit medical image segmentation from a decoder-centric perspective and propose a context-aware gated decoder that systematically regulates feature fusion and contextual aggregation throughout the decoding process. The proposed decoder integrates lightweight multi-scale channel recalibration, gated skip fusion with spatial competition and a global context aggregation mechanism that injects encoder-wide information into intermediate decoding stages. This design enables effective translation of strong pretrained encoder representations into spatially consistent predictions. Extensive experiments across 11 medical image segmentation benchmarks validate the effectiveness and demonstrate that the proposed approach consistently outperforms strong baselines while remaining computationally practical. Code: https://github.com/saadwazir/MedCAGD