arXiv subjects

Kim-Celine Kahl

Publications and source records attributed to Kim-Celine Kahl.

7 recordsLinked to original sources

arXiv2026

Resolution Meets Reduction: Efficient Visual Context for 3D Radiology Report Generation

Vision-language models offer a promising path toward automating radiology report generation, but applying them to full 3D CT volumes poses substantial computational challenges. Modern foundation vision encoders (VEs) can produce tens of thousands of vision tokens per scan, making the visual sequence passed to the large language model (LLM) a primary computational bottleneck. Vision-to-language projectors can compress this sequence to reduce computation, but may discard clinically relevant detail; conversely, effective compression can accommodate higher-resolution inputs while keeping the downstream token count fixed. How this vision-token budget should be allocated across input field of view, spatial resolution, and vision-to-language projection therefore remains an open design question. We systematically evaluate four heterogeneous VEs (CNN- and ViT-based), five token-reducing projectors at up to 64x compression alongside a non-reducing MLP projector baseline, and five instruction-tuned LLMs (1.7B--4B) on two large-scale CT report datasets (CT-RATE and Merlin). At matched LLM token budgets, anatomy-guided region of interest cropping is the most consistent strategy, improving clinical macro F1 in 19 of 20 settings by +3.7 points on average for the 3D ViT Primus encoder and +1.1 for the slice-based 2D ViT Curia encoder. Increasing input resolution further is strongly projector-dependent: the PerceiverResampler, paired with higher-resolution Curia features, yields the strongest configuration in the resolution study on both datasets. Our best configurations achieve state-of-the-art clinical macro F1 on the test sets, reaching 49.5 on CT-RATE and 49.0 on Merlin. Code and models will be published upon publication.

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arXiv2026

Rethinking Post-Hoc Calibration in Semantic Segmentation

Reliable confidence estimates are essential in semantic segmentation, especially in safety-critical settings where overconfident errors can mislead downstream decisions. Yet modern segmentation models often remain miscalibrated. Post-hoc calibration offers a practical way to correct confidence estimates without retraining the segmentation model, but its use in dense prediction raises structural issues that are often overlooked. We study two such issues. First, adding a constant to all logits leaves the softmax probabilities unchanged, but several standard calibrators can still depend on this arbitrary offset. As a result, two logit representations encoding the same predictive distribution may yield different calibrated probabilities. We define translation-invariant (TI) calibrators as those whose outputs are unchanged under such shifts, characterize which common calibrators satisfy this property, and construct TI counterparts of shift-sensitive calibrators to isolate the effect of removing representation dependence. Second, post-hoc calibration is typically fitted by minimizing a likelihood-based objective, whereas segmentation models are trained with task-specific metrics such as Dice. This mismatch can cause calibration to alter class orderings and degrade the deployed segmentation map. We study decision-preserving calibration under argmax- and order-preservation constraints. Since enforcing these constraints collapses affine softmax calibrators to temperature scaling, we introduce class-conditional affine calibrators that can be made argmax- or order-preserving while retaining greater expressivity, allowing us to quantify the calibration-segmentation trade-off induced by decision preservation. Across natural-image and medical segmentation benchmarks, and under corruption-based covariate shift, matched comparisons show that TI variants generally improve calibration metrics, while decision-preserving variants prevent segmentation degradation and retain strong calibration performance. These results provide practical design principles for well-defined post-hoc calibration pipelines in semantic segmentation.

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arXiv2026

Lost in the Folds: When Cross-Validation Is Not a Deep Ensemble for Uncertainty Estimation

Ensemble disagreement is widely used as a proxy for epistemic uncertainty in medical image segmentation. In practice, many studies form ensembles via K-fold cross-validation (CV), yet refer to them as ``deep ensembles'' (DE). Because CV members are trained on different data subsets, their disagreement mixes seed-driven variability with data-exposure effects, which can change how uncertainty should be interpreted. We audit recent segmentation uncertainty studies and find that terminology--implementation mismatches are common. We then compare a standard 5-fold CV ensemble to a 5-member DE (fixed training set, different random seeds) under otherwise identical configurations on three multi-rater segmentation datasets spanning three modalities. We evaluate uncertainty for calibration, failure detection, ambiguity modeling, and robustness under distribution shift. DE match segmentation accuracy while improving calibration and failure detection, whereas CV ensembles sometimes correlate more strongly with inter-rater variability on the studied datasets. Thus, ensemble construction should be chosen to match the research question: DE for reliability-oriented use (e.g., selective referral/failure detection) and CV ensembles as a proxy for ambiguity. We provide a lightweight nnU-Net modification enabling DE training within the default pipeline.

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arXiv2026

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.

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arXiv2025

nnActive: A Framework for Evaluation of Active Learning in 3D Biomedical Segmentation

Semantic segmentation is crucial for various biomedical applications, yet its reliance on large annotated datasets presents a bottleneck due to the high cost and specialized expertise required for manual labeling. Active Learning (AL) aims to mitigate this challenge by querying only the most informative samples, thereby reducing annotation effort. However, in the domain of 3D biomedical imaging, there is no consensus on whether AL consistently outperforms Random sampling. Four evaluation pitfalls hinder the current methodological assessment. These are (1) restriction to too few datasets and annotation budgets, (2) using 2D models on 3D images without partial annotations, (3) Random baseline not being adapted to the task, and (4) measuring annotation cost only in voxels. In this work, we introduce nnActive, an open-source AL framework that overcomes these pitfalls by (1) means of a large scale study spanning four biomedical imaging datasets and three label regimes, (2) extending nnU-Net by using partial annotations for training with 3D patch-based query selection, (3) proposing Foreground Aware Random sampling strategies tackling the foreground-background class imbalance of medical images and (4) propose the foreground efficiency metric, which captures the low annotation cost of background-regions. We reveal the following findings: (A) while all AL methods outperform standard Random sampling, none reliably surpasses an improved Foreground Aware Random sampling; (B) benefits of AL depend on task specific parameters; (C) Predictive Entropy is overall the best performing AL method, but likely requires the most annotation effort; (D) AL performance can be improved with more compute intensive design choices. As a holistic, open-source framework, nnActive can serve as a catalyst for research and application of AL in 3D biomedical imaging. Code is at: https://github.com/MIC-DKFZ/nnActive

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arXiv2025

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 key 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. To address this gap, we introduce a novel framework, called SURE-VQA, centered around three key requirements to overcome current pitfalls and systematically analyze VLM robustness: 1) Since robustness on synthetic shifts does not necessarily translate to real-world shifts, it 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 (FT) methods across three medical datasets with four types of distribution shifts. Our study highlights key insights into robustness: 1) No FT method consistently outperforms others in robustness, and 2) robustness trends are more stable across FT methods than across distribution shifts. Additionally, we find that simple sanity baselines that do not use the image data can perform surprisingly well and confirm LoRA as the best-performing FT method on in-distribution data. Code is provided at https://github.com/IML-DKFZ/sure-vqa.

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arXiv2024

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

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