Organizations: School of Information Technology, Monash University Malaysia, Selangor, Malaysia · Centre for Data Science and Artificial Intelligence, School of Engineering and Computer Science, Victoria University of Wellington, Wellington, New Zealand
Abstract
Stochastic segmentation seeks to represent multiple plausible masks for a single image, which is essential in safety- and quality-critical applications such as medical imaging or building defect inspection. Most existing methods introduce stochasticity by injecting continuous latent variables or by iterative denoising trajectories, whose stochastic sources are difficult to search or audit directly. We propose architecture distributions as a new stochastic source for segmentation: instead of sampling a latent variable or noise, we sample a discrete architecture from a learned distribution over operator choices at multiple searchable positions in a segmentation backbone. Each sampled architecture yields one mask through the selected active path, so inference depends on the executed subnet rather than the complete candidate bank. This approach also supports architectural provenance, since each output corresponds to a specific architecture configuration. To reduce collapse toward averaged masks, we train with set-level supervision by matching a set of architecture-sampled predictions to the annotation set using an IoU-based energy-distance surrogate. We further construct the candidate bank with evolutionary search, making the support of the stochastic source optimizable before distribution learning. The proposed method achieves state-of-the-art distribution matching and hypothesis coverage on LIDC-IDRI, and remains effective on two extension tasks. To the best of our knowledge, this is the first work to formulate stochastic segmentation as learning an architecture distribution and realizing output diversity through architecture sampling.
Uncertainty arising from inter-observer variability in medical image segmentation plays an important role in developing treatment plans. Research in this area is inhibited by the lack of multiple annotations for large-scale medical datasets, especially for volumetric data, which suffers from additional scaling and computational complexity challenges. Flow matching has emerged as a powerful framework for generative modelling and has also been demonstrated to maintain strong performance when working with latent representations of images. In this work, we introduce a latent-to-latent flow technique for stochastic segmentation of medical volumes via encoded representations of both the image and label space. We evaluate our method on two challenging applications covering delineation uncertainty for radiotherapy planning and multiple organ structure segmentation, improving efficiency up to 14x compared with full resolution models while maintaining clinically relevant performance.
Precise medical image segmentation is crucial for clinical diagnosis and treatment planning, yet relies heavily on expensive expert annotations. Semi-supervised medical image segmentation (SSMIS) offers a cost-effective solution but typically operates under the assumption of independent and identically distributed (i.i.d.) data, defaulting to random sampling. While statistically valid at scale, this strategy suffers from severe representation bias in low-data regimes, failing to capture the heterogeneous medical data manifold. To address this, we propose a highly data-efficient framework driven by distribution alignment. First, we introduce an offline Distribution-Aware Sample Selection strategy. By leveraging Vision Foundation Models (VFMs) and our designed Density-K-Center algorithm, we explicitly identify representative structural anchors, establishing a more representative labeled domain. Second, to bridge the remaining distribution gap, we propose the Memory-guided Copy-Paste (MCP) module. Tailored for the inherent class imbalance in medical scans, MCP leverages a semantic memory mechanism to retrieve historically consistent priors for cross-domain alignment, encouraging semantic consistency. Coupled with an easy-to-hard progressive schedule, this framework effectively mitigates early-stage pseudo-label noise. Extensive experiments on six diverse 2D and 3D datasets demonstrate strong segmentation performance, particularly in extremely low-labeled scenarios (\eg, 1/16 ratio).
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.