Finally Outshining the Random Baseline: A Simple and Effective Solution for Active Learning in 3D Biomedical Imaging

Active learning (AL) has the potential to drastically reduce annotation costs in 3D biomedical image segmentation, where expert labeling of volumetric data is both time-consuming and expensive. Yet, existing AL methods are unable to consistently outperform improved random sampling baselines adapted to 3D data, leaving the field without a reliable solution. We introduce Class-stratified Scheduled Power Predictive Entropy (ClaSP PE), a simple and effective query strategy that addresses two key limitations of standard uncertainty-based AL methods: class imbalance and redundancy in early selections. ClaSP PE combines class-stratified querying to ensure coverage of underrepresented structures and log-scale power noising with a decaying schedule to enforce query diversity in early-stage AL and encourage exploitation later. In our evaluation on 24 experimental settings using four 3D biomedical datasets within the comprehensive nnActive benchmark, ClaSP PE is the only method that generally outperforms improved random baselines in terms of both segmentation quality with statistically significant gains, whilst remaining annotation efficient. Furthermore, we explicitly simulate the real-world application by testing our method on four previously unseen datasets without manual adaptation, where all experiment parameters are set according to predefined guidelines. The results confirm that ClaSP PE robustly generalizes to novel tasks without requiring dataset-specific tuning. Within the nnActive framework, we present compelling evidence that an AL method can consistently outperform random baselines adapted to 3D segmentation, in terms of both performance and annotation efficiency in a realistic, close-to-production scenario. Our open-source implementation and clear deployment guidelines make it readily applicable in practice. Code is at https://github.com/MIC-DKFZ/nnActive.

SURE-VQA: Systematic Understanding of Robustness Evaluation in Medical VQA Tasks

Vision-Language Models (VLMs) have great potential in medical tasks, like Visual Question Answering (VQA), where they could act as interactive assistants for both patients and clinicians. Yet their robustness to distribution shifts on unseen data remains a critical concern for safe deployment. Evaluating such robustness requires a controlled experimental setup that allows for systematic insights into the model's behavior. However, we demonstrate that current setups fail to offer sufficiently thorough evaluations, limiting their ability to accurately assess model robustness. To address this gap, our work introduces a novel framework, called SURE-VQA, centered around three key requirements to overcome the current pitfalls and systematically analyze the robustness of VLMs: 1) Since robustness on synthetic shifts does not necessarily translate to real-world shifts, robustness should be measured on real-world shifts that are inherent to the VQA data; 2) Traditional token-matching metrics often fail to capture underlying semantics, necessitating the use of large language models (LLMs) for more accurate semantic evaluation; 3) Model performance often lacks interpretability due to missing sanity baselines, thus meaningful baselines should be reported that allow assessing the multimodal impact on the VLM. To demonstrate the relevance of this framework, we conduct a study on the robustness of various fine-tuning methods across three medical datasets with four different types of distribution shifts. Our study reveals several important findings: 1) Sanity baselines that do not utilize image data can perform surprisingly well; 2) We confirm LoRA as the best-performing PEFT method; 3) No PEFT method consistently outperforms others in terms of robustness to shifts. Code is provided at https://github.com/IML-DKFZ/sure-vqa.

ValUES: A Framework for Systematic Validation of Uncertainty Estimation in Semantic Segmentation

Uncertainty estimation is an essential and heavily-studied component for the reliable application of semantic segmentation methods. While various studies exist claiming methodological advances on the one hand, and successful application on the other hand, the field is currently hampered by a gap between theory and practice leaving fundamental questions unanswered: Can data-related and model-related uncertainty really be separated in practice? Which components of an uncertainty method are essential for real-world performance? Which uncertainty method works well for which application? In this work, we link this research gap to a lack of systematic and comprehensive evaluation of uncertainty methods. Specifically, we identify three key pitfalls in current literature and present an evaluation framework that bridges the research gap by providing 1) a controlled environment for studying data ambiguities as well as distribution shifts, 2) systematic ablations of relevant method components, and 3) test-beds for the five predominant uncertainty applications: OoD-detection, active learning, failure detection, calibration, and ambiguity modeling. Empirical results on simulated as well as real-world data demonstrate how the proposed framework is able to answer the predominant questions in the field revealing for instance that 1) separation of uncertainty types works on simulated data but does not necessarily translate to real-world data, 2) aggregation of scores is a crucial but currently neglected component of uncertainty methods, 3) While ensembles are performing most robustly across the different downstream tasks and settings, test-time augmentation often constitutes a light-weight alternative. Code is at: https://github.com/IML-DKFZ/values