Latent-to-Latent Flow for Volumetric Stochastic Segmentation

Generative models have achieved remarkable progress with the emergence of flow matching (FM). It has demonstrated strong generative capabilities and attracted significant attention as a simulation-free flow-based framework capable of learning exact data densities. Motivated by these advances, we propose LatentFM, a flow-based model operating in the latent space for medical image segmentation. To model the data distribution, we first design two variational autoencoders (VAEs) to encode both medical images and their corresponding masks into a lower-dimensional latent space. We then estimate a conditional velocity field that guides the flow based on the input image. By sampling multiple latent representations, our method synthesizes diverse segmentation outputs whose pixel-wise variance reliably captures the underlying data distribution, enabling both highly accurate and uncertainty-aware predictions. Furthermore, we generate confidence maps that quantify the model certainty, providing clinicians with richer information for deeper analysis. We conduct experiments on two datasets, ISIC-2018 and CVC-Clinic, and compare our method with several prior baselines, including both deterministic and generative approach models. Through comprehensive evaluations, both qualitative and quantitative results show that our approach achieves superior segmentation accuracy while remaining highly efficient in the latent space.

Ambiguous 3D medical image segmentation often involves boundaries where different expert delineations are non-identical yet clinically plausible. Modeling such inter-observer variability requires a careful balance between diversity and anatomical fidelity: deterministic models preserve coherent volumetric structures but collapse expert disagreement into a single mask, while stochastic generative models can produce diverse samples but may introduce disconnected components or slice-to-slice inconsistency when generating full 3D masks from unstructured noise. We propose Volumetric Directional Diffusion (VDD), a prior-anchored diffusion framework that shifts stochastic generation from full-mask synthesis to residual boundary exploration. VDD uses a coarse consensus prediction as an anatomical anchor and learns a directional diffusion process to generate plausible boundary variations around ambiguous regions while preserving stable volumetric topology. Experiments on three multi-rater datasets, including LIDC-IDRI, KiTS21, and ISBI 2015, show that VDD improves uncertainty distribution alignment while maintaining competitive segmentation accuracy and 3D structural consistency. These results suggest that prior-anchored residual diffusion can model clinically plausible expert disagreement without sacrificing anatomical fidelity.

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.