MID: Mask-Image Distributional Divergence for Evaluating Medical Image Segmentation

Despite rapid advances in MIS, fair and reproducible comparisons of segmentation models remain challenging due to heterogeneous datasets, inconsistent evaluation protocols, and rapidly evolving architectures. In particular, comparisons often implicitly assume that model rankings are invariant to data partitioning, preprocessing, metric aggregation, uncertainty estimation, and computational constraints. The lack of extensible and unified evaluation frameworks further limits systematic investigation of new models, datasets, and training paradigms. We present MEDSEGBENCHMARKER (MSB), a configuration-driven framework for controlled benchmarking of 2D MIS. It integrates duplicate and near-duplicate image detection, group-aware data splitting, YAML study specifications, resumable training, hyperparameter optimization, cross-validation, and checkpoint-based evaluation. Rather than retaining only aggregate performance measures, MSB exports sample- and class-level pixel counts and predictions together with the evaluation context. These elementary artifacts enable post-hoc analyses without repeated inference. We demonstrate MSB in a case study involving three heterogeneous 2D datasets and multiple MIS and general-purpose vision models evaluated at 256- and 512-pixel input resolutions. Reaggregation of identical predictions changes the top-ranked architecture in three of six dataset-resolution settings, despite high rank correlations between aggregation strategies. Increasing input resolution produces model- and dataset-dependent performance gains and losses that must be considered alongside empirically measured inference complexity. These results show that seemingly minor choices in evaluation and experimental setup can affect benchmark conclusions. MSB, available at GitHub, provides a practical and extensible basis for making benchmark conditions and evaluation choices explicit and reproducible.

Data heterogeneity hinders clinical deployment of medical image analysis models, and generative data augmentation helps mitigate this issue. However, recent diffusion-based methods that synthesize image-mask pairs often ignore distribution shifts between generated and real images across scenarios, and such mismatches can markedly degrade downstream performance. To address this issue, we propose AlignFlow, a flow matching model that aligns with the target reference image distribution via differentiable reward fine-tuning, and remains effective even when only a small number of reference images are provided. Specifically, we divide the training of the flow matching model into two stages: in the first stage, the model fits the training data to generate plausible images; Then, we introduce a distribution alignment mechanism and employ differentiable reward to steer the generated images toward the distribution of the given samples from the target domain. In addition, to enhance the diversity of generated masks, we also design a flow matching based mask generation to complement the diversity in regions of interest. Extensive experiments demonstrate the effectiveness of our approach, i.e., performance improvement by 3.5-4.0% in mDice and 3.5-5.6% in mIoU across a variety of datasets and scenarios.

Medical segmentation uncertainty is often evaluated with calibration error or pixel-level error-detection scores, but these metrics do not show whether uncertainty improves downstream review decisions. We propose a decision-aware evaluation protocol that separates uncertainty estimation from deferral policy and evaluates their combination under fixed review budgets: which pixels, regions, or images should be accepted, and which should be reviewed. The protocol reports fixed-budget error reduction, risk-coverage behaviour, region-level review proxies, structural failure modes, probability-derived baselines, and sensitivity to review assumptions. We instantiate it across retinal vessel, skin lesion, and polyp segmentation with multiple backbones and uncertainty estimators. Under matched inference budgets and canonical multi-layer MC Dropout, test-time augmentation (TTA) gives a stronger error-detection signal across matched MC--TTA comparisons, including architecture and dropout-placement checks. However, estimator rankings are not universal. For example, probability-derived scores remain competitive, deep ensembles can outperform TTA, learned deferral helps mainly when the base estimator is weak, and rankings can change with review unit, uncertainty target, correction assumptions, and cost model. Structural and second-observer analyses further show that boundary and thin-structure failures are partly tied to annotation ambiguity. These findings support evaluating uncertainty as an estimator-policy-review configuration, not as a standalone score map. Code: https://anonymous.4open.science/r/Uncertainity-in-Medical-Image-Segmentation/README.md