arXiv subjects

Julia A. Schnabel

Publications and source records attributed to Julia A. Schnabel.

At least 37 records · Page 2Linked to original sources

arXiv2026

Measuring and Aligning Abstraction in Vision-Language Models with Medical Taxonomies

Vision-Language Models show strong zero-shot performance for chest X-ray classification, but standard flat metrics fail to distinguish between clinically minor and severe errors. This work investigates how to quantify and mitigate abstraction errors by leveraging medical taxonomies. We benchmark several state-of-the-art VLMs using hierarchical metrics and introduce Catastrophic Abstraction Errors to capture cross-branch mistakes. Our results reveal substantial misalignment of VLMs with clinical taxonomies despite high flat performance. To address this, we propose risk-constrained thresholding and taxonomy-aware fine-tuning with radial embeddings, which reduce severe abstraction errors to below 2 per cent while maintaining competitive performance. These findings highlight the importance of hierarchical evaluation and representation-level alignment for safer and more clinically meaningful deployment of VLMs.

cs.AI↗

arXiv2025

TomoGraphView: 3D Medical Image Classification with Omnidirectional Slice Representations and Graph Neural Networks

The sharp rise in medical tomography examinations has created a demand for automated systems that can reliably extract informative features for downstream tasks such as tumor characterization. Although 3D volumes contain richer information than individual slices, effective 3D classification remains difficult: volumetric data encode complex spatial dependencies, and the scarcity of large-scale 3D datasets has constrained progress toward 3D foundation models. As a result, many recent approaches rely on 2D vision foundation models trained on natural images, repurposing them as feature extractors for medical scans with surprisingly strong performance. Despite their practical success, current methods that apply 2D foundation models to 3D scans via slice-based decomposition remain fundamentally limited. Standard slicing along axial, sagittal, and coronal planes often fails to capture the true spatial extent of a structure when its orientation does not align with these canonical views. More critically, most approaches aggregate slice features independently, ignoring the underlying 3D geometry and losing spatial coherence across slices. To overcome these limitations, we propose TomoGraphView, a novel framework that integrates omnidirectional volume slicing with spherical graph-based feature aggregation. Instead of restricting the model to axial, sagittal, or coronal planes, our method samples both canonical and non-canonical cross-sections generated from uniformly distributed points on a sphere enclosing the volume. We publicly share our accessible code base at http://github.com/compai-lab/2025-MedIA-kiechle and provide a user-friendly library for omnidirectional volume slicing at https://pypi.org/project/OmniSlicer.

eess.IV↗

arXiv2025

Denoising Diffusion Models for Anomaly Localization in Medical Images

This review explores anomaly localization in medical images using denoising diffusion models. After providing a brief methodological background of these models, including their application to image reconstruction and their conditioning using guidance mechanisms, we provide an overview of available datasets and evaluation metrics suitable for their application to anomaly localization in medical images. In this context, we discuss supervision schemes ranging from fully supervised segmentation to semi-supervised, weakly supervised, self-supervised, and unsupervised methods, and provide insights into the effectiveness and limitations of these approaches. Furthermore, we highlight open challenges in anomaly localization, including detection bias, domain shift, computational cost, and model interpretability. Our goal is to provide an overview of the current state of the art in the field, outline research gaps, and highlight the potential of diffusion models for robust anomaly localization in medical images.

eess.IV↗

arXiv2025

Covariance Descriptors Meet General Vision Encoders: Riemannian Deep Learning for Medical Image Classification

Covariance descriptors capture second-order statistics of image features. They have shown strong performance in general computer vision tasks, but remain underexplored in medical imaging. We investigate their effectiveness for both conventional and learning-based medical image classification, with a particular focus on SPDNet, a classification network specifically designed for symmetric positive definite (SPD) matrices. We propose constructing covariance descriptors from features extracted by pre-trained general vision encoders (GVEs) and comparing them with handcrafted descriptors. Two GVEs - DINOv2 and MedSAM - are evaluated across eleven binary and multi-class datasets from the MedMNSIT benchmark. Our results show that covariance descriptors derived from GVE features consistently outperform those derived from handcrafted features. Moreover, SPDNet yields superior performance to state-of-the-art methods when combined with DINOv2 features. Our findings highlight the potential of combining covariance descriptors with powerful pretrained vision encoders for medical image analysis.

cs.CV↗

arXiv2025

Learning to reason about rare diseases through retrieval-augmented agents

Rare diseases represent the long tail of medical imaging, where AI models often fail due to the scarcity of representative training data. In clinical workflows, radiologists frequently consult case reports and literature when confronted with unfamiliar findings. Following this line of reasoning, we introduce RADAR, Retrieval Augmented Diagnostic Reasoning Agents, an agentic system for rare disease detection in brain MRI. Our approach uses AI agents with access to external medical knowledge by embedding both case reports and literature using sentence transformers and indexing them with FAISS to enable efficient similarity search. The agent retrieves clinically relevant evidence to guide diagnostic decision making on unseen diseases, without the need of additional training. Designed as a model-agnostic reasoning module, RADAR can be seamlessly integrated with diverse large language models, consistently improving their rare pathology recognition and interpretability. On the NOVA dataset comprising 280 distinct rare diseases, RADAR achieves up to a 10.2% performance gain, with the strongest improvements observed for open source models such as DeepSeek. Beyond accuracy, the retrieved examples provide interpretable, literature grounded explanations, highlighting retrieval-augmented reasoning as a powerful paradigm for low-prevalence conditions in medical imaging.

cs.CL↗

arXiv2025

Progressive Growing of Patch Size: Curriculum Learning for Accelerated and Improved Medical Image Segmentation

In this work, we introduce Progressive Growing of Patch Size, an automatic curriculum learning approach for 3D medical image segmentation. Our approach progressively increases the patch size during model training, resulting in an improved class balance for smaller patch sizes and accelerated convergence of the training process. We evaluate our curriculum approach in two settings: a resource-efficient mode and a performance mode, both regarding Dice score performance and computational costs across 15 diverse and popular 3D medical image segmentation tasks. The resource-efficient mode matches the Dice score performance of the conventional constant patch size sampling baseline with a notable reduction in training time to only 44%. The performance mode improves upon constant patch size segmentation results, achieving a statistically significant relative mean performance gain of 1.28% in Dice Score. Remarkably, across all 15 tasks, our proposed performance mode manages to surpass the constant patch size baseline in Dice Score performance, while simultaneously reducing training time to only 89%. The benefits are particularly pronounced for highly imbalanced tasks such as lesion segmentation tasks. Rigorous experiments demonstrate that our performance mode not only improves mean segmentation performance but also reduces performance variance, yielding more trustworthy model comparison. Furthermore, our findings reveal that the proposed curriculum sampling is not tied to a specific architecture but represents a broadly applicable strategy that consistently boosts performance across diverse segmentation models, including UNet, UNETR, and SwinUNETR. In summary, we show that this simple yet elegant transformation on input data substantially improves both Dice Score performance and training runtime, while being compatible across diverse segmentation backbones.

cs.CV↗

arXiv2025

Lightweight Data-Free Denoising for Detail-Preserving Biomedical Image Restoration

Current self-supervised denoising techniques achieve impressive results, yet their real-world application is frequently constrained by substantial computational and memory demands, necessitating a compromise between inference speed and reconstruction quality. In this paper, we present an ultra-lightweight model that addresses this challenge, achieving both fast denoising and high quality image restoration. Built upon the Noise2Noise training framework-which removes the reliance on clean reference images or explicit noise modeling-we introduce an innovative multistage denoising pipeline named Noise2Detail (N2D). During inference, this approach disrupts the spatial correlations of noise patterns to produce intermediate smooth structures, which are subsequently refined to recapture fine details directly from the noisy input. Extensive testing reveals that Noise2Detail surpasses existing dataset-free techniques in performance, while requiring only a fraction of the computational resources. This combination of efficiency, low computational cost, and data-free approach make it a valuable tool for biomedical imaging, overcoming the challenges of scarce clean training data-due to rare and complex imaging modalities-while enabling fast inference for practical use.

cs.CV↗

arXiv2025

From Mean to Extreme: Formal Differential Privacy Bounds on the Success of Real-World Data Reconstruction Attacks

The gold standard for privacy in machine learning, Differential Privacy (DP), is often interpreted through its guarantees against membership inference. However, translating DP budgets into quantitative protection against the more damaging threat of data reconstruction remains a challenging open problem. Existing theoretical analyses of reconstruction risk are typically based on an "identification" threat model, where an adversary with a candidate set seeks a perfect match. When applied to the realistic threat of "from-scratch" attacks, these bounds can lead to an inefficient privacy-utility trade-off. This paper bridges this critical gap by deriving the first formal privacy bounds tailored to the mechanics of demonstrated Analytic Gradient Inversion Attacks (AGIAs). We first formalize the optimal from-scratch attack strategy for an adversary with no prior knowledge, showing it reduces to a mean estimation problem. We then derive closed-form, probabilistic bounds on this adversary's success, measured by Mean Squared Error (MSE) and Peak Signal-to-Noise Ratio (PSNR). Our empirical evaluation confirms these bounds remain tight even when the attack is concealed within large, complex network architectures. Our work provides a crucial second anchor for risk assessment. By establishing a tight, worst-case bound for the from-scratch threat model, we enable practitioners to assess a "risk corridor" bounded by the identification-based worst case on one side and our from-scratch worst case on the other. This allows for a more holistic, context-aware judgment of privacy risk, empowering practitioners to move beyond abstract budgets toward a principled reasoning framework for calibrating the privacy of their models.

cs.LG↗

arXiv2025

Influence of Classification Task and Distribution Shift Type on OOD Detection in Fetal Ultrasound

Reliable out-of-distribution (OOD) detection is important for safe deployment of deep learning models in fetal ultrasound amidst heterogeneous image characteristics and clinical settings. OOD detection relies on estimating a classification model's uncertainty, which should increase for OOD samples. While existing research has largely focused on uncertainty quantification methods, this work investigates the impact of the classification task itself. Through experiments with eight uncertainty quantification methods across four classification tasks, we demonstrate that OOD detection performance significantly varies with the task, and that the best task depends on the defined ID-OOD criteria; specifically, whether the OOD sample is due to: i) an image characteristic shift or ii) an anatomical feature shift. Furthermore, we reveal that superior OOD detection does not guarantee optimal abstained prediction, underscoring the necessity to align task selection and uncertainty strategies with the specific downstream application in medical image analysis.

cs.CV↗

arXiv2025

INR meets Multi-Contrast MRI Reconstruction

Multi-contrast MRI sequences allow for the acquisition of images with varying tissue contrast within a single scan. The resulting multi-contrast images can be used to extract quantitative information on tissue microstructure. To make such multi-contrast sequences feasible for clinical routine, the usually very long scan times need to be shortened e.g. through undersampling in k-space. However, this comes with challenges for the reconstruction. In general, advanced reconstruction techniques such as compressed sensing or deep learning-based approaches can enable the acquisition of high-quality images despite the acceleration. In this work, we leverage redundant anatomical information of multi-contrast sequences to achieve even higher acceleration rates. We use undersampling patterns that capture the contrast information located at the k-space center, while performing complementary undersampling across contrasts for high frequencies. To reconstruct this highly sparse k-space data, we propose an implicit neural representation (INR) network that is ideal for using the complementary information acquired across contrasts as it jointly reconstructs all contrast images. We demonstrate the benefits of our proposed INR method by applying it to multi-contrast MRI using the MPnRAGE sequence, where it outperforms the state-of-the-art parallel imaging compressed sensing (PICS) reconstruction method, even at higher acceleration factors.

eess.IV↗

arXiv2025

Knowledge to Sight: Reasoning over Visual Attributes via Knowledge Decomposition for Abnormality Grounding

In this work, we address the problem of grounding abnormalities in medical images, where the goal is to localize clinical findings based on textual descriptions. While generalist Vision-Language Models (VLMs) excel in natural grounding tasks, they often struggle in the medical domain due to rare, compositional, and domain-specific terms that are poorly aligned with visual patterns. Specialized medical VLMs address this challenge via large-scale domain pretraining, but at the cost of substantial annotation and computational resources. To overcome these limitations, we propose \textbf{Knowledge to Sight (K2Sight)}, a framework that introduces structured semantic supervision by decomposing clinical concepts into interpretable visual attributes, such as shape, density, and anatomical location. These attributes are distilled from domain ontologies and encoded into concise instruction-style prompts, which guide region-text alignment during training. Unlike conventional report-level supervision, our approach explicitly bridges domain knowledge and spatial structure, enabling data-efficient training of compact models. We train compact models with 0.23B and 2B parameters using only 1.5\% of the data required by state-of-the-art medical VLMs. Despite their small size and limited training data, these models achieve performance on par with or better than 7B+ medical VLMs, with up to 9.82\% improvement in $mAP_{50}$. Code and models: \href{https://lijunrio.github.io/K2Sight/}{\textcolor{SOTAPink}{https://lijunrio.github.io/K2Sight/}}.

cs.CV↗

arXiv2025

Temporal Neural Cellular Automata: Application to modeling of contrast enhancement in breast MRI

Synthetic contrast enhancement offers fast image acquisition and eliminates the need for intravenous injection of contrast agent. This is particularly beneficial for breast imaging, where long acquisition times and high cost are significantly limiting the applicability of magnetic resonance imaging (MRI) as a widespread screening modality. Recent studies have demonstrated the feasibility of synthetic contrast generation. However, current state-of-the-art (SOTA) methods lack sufficient measures for consistent temporal evolution. Neural cellular automata (NCA) offer a robust and lightweight architecture to model evolving patterns between neighboring cells or pixels. In this work we introduce TeNCA (Temporal Neural Cellular Automata), which extends and further refines NCAs to effectively model temporally sparse, non-uniformly sampled imaging data. To achieve this, we advance the training strategy by enabling adaptive loss computation and define the iterative nature of the method to resemble a physical progression in time. This conditions the model to learn a physiologically plausible evolution of contrast enhancement. We rigorously train and test TeNCA on a diverse breast MRI dataset and demonstrate its effectiveness, surpassing the performance of existing methods in generation of images that align with ground truth post-contrast sequences.

eess.IV↗

arXiv2025

Fréchet Radiomic Distance (FRD): A Versatile Metric for Comparing Medical Imaging Datasets

Determining whether two sets of images belong to the same or different distributions or domains is a crucial task in modern medical image analysis and deep learning; for example, to evaluate the output quality of image generative models. Currently, metrics used for this task either rely on the (potentially biased) choice of some downstream task, such as segmentation, or adopt task-independent perceptual metrics (e.g., Fréchet Inception Distance/FID) from natural imaging, which we show insufficiently capture anatomical features. To this end, we introduce a new perceptual metric tailored for medical images, FRD (Fréchet Radiomic Distance), which utilizes standardized, clinically meaningful, and interpretable image features. We show that FRD is superior to other image distribution metrics for a range of medical imaging applications, including out-of-domain (OOD) detection, the evaluation of image-to-image translation (by correlating more with downstream task performance as well as anatomical consistency and realism), and the evaluation of unconditional image generation. Moreover, FRD offers additional benefits such as stability and computational efficiency at low sample sizes, sensitivity to image corruptions and adversarial attacks, feature interpretability, and correlation with radiologist-perceived image quality. Additionally, we address key gaps in the literature by presenting an extensive framework for the multifaceted evaluation of image similarity metrics in medical imaging -- including the first large-scale comparative study of generative models for medical image translation -- and release an accessible codebase to facilitate future research. Our results are supported by thorough experiments spanning a variety of datasets, modalities, and downstream tasks, highlighting the broad potential of FRD for medical image analysis.

cs.CV↗

arXiv2025

Agreement of Image Quality Metrics with Radiological Evaluation in the Presence of Motion Artifacts

Purpose: Reliable image quality assessment is crucial for evaluating new motion correction methods for magnetic resonance imaging. In this work, we compare the performance of commonly used reference-based and reference-free image quality metrics on a unique dataset with real motion artifacts. We further analyze the image quality metrics' robustness to typical pre-processing techniques. Methods: We compared five reference-based and five reference-free image quality metrics on data acquired with and without intentional motion (2D and 3D sequences). The metrics were recalculated seven times with varying pre-processing steps. The anonymized images were rated by radiologists and radiographers on a 1-5 Likert scale. Spearman correlation coefficients were computed to assess the relationship between image quality metrics and observer scores. Results: All reference-based image quality metrics showed strong correlation with observer assessments, with minor performance variations across sequences. Among reference-free metrics, Average Edge Strength offers the most promising results, as it consistently displayed stronger correlations across all sequences compared to the other reference-free metrics. Overall, the strongest correlation was achieved with percentile normalization and restricting the metric values to the skull-stripped brain region. In contrast, correlations were weaker when not applying any brain mask and using min-max or no normalization. Conclusion: Reference-based metrics reliably correlate with radiological evaluation across different sequences and datasets. Pre-processing steps, particularly normalization and brain masking, significantly influence the correlation values. Future research should focus on refining pre-processing techniques and exploring machine learning approaches for automated image quality evaluation.

physics.med-ph↗

arXiv2025

NOVA: A Benchmark for Anomaly Localization and Clinical Reasoning in Brain MRI

In many real-world applications, deployed models encounter inputs that differ from the data seen during training. Out-of-distribution detection identifies whether an input stems from an unseen distribution, while open-world recognition flags such inputs to ensure the system remains robust as ever-emerging, previously $unknown$ categories appear and must be addressed without retraining. Foundation and vision-language models are pre-trained on large and diverse datasets with the expectation of broad generalization across domains, including medical imaging. However, benchmarking these models on test sets with only a few common outlier types silently collapses the evaluation back to a closed-set problem, masking failures on rare or truly novel conditions encountered in clinical use. We therefore present $NOVA$, a challenging, real-life $evaluation-only$ benchmark of $\sim$900 brain MRI scans that span 281 rare pathologies and heterogeneous acquisition protocols. Each case includes rich clinical narratives and double-blinded expert bounding-box annotations. Together, these enable joint assessment of anomaly localisation, visual captioning, and diagnostic reasoning. Because NOVA is never used for training, it serves as an $extreme$ stress-test of out-of-distribution generalisation: models must bridge a distribution gap both in sample appearance and in semantic space. Baseline results with leading vision-language models (GPT-4o, Gemini 2.0 Flash, and Qwen2.5-VL-72B) reveal substantial performance drops across all tasks, establishing NOVA as a rigorous testbed for advancing models that can detect, localize, and reason about truly unknown anomalies.

eess.IV↗

arXiv2025

Simulating Dynamic Tumor Contrast Enhancement in Breast MRI using Conditional Generative Adversarial Networks

This paper presents a method for virtual contrast enhancement in breast MRI, offering a promising non-invasive alternative to traditional contrast agent-based DCE-MRI acquisition. Using a conditional generative adversarial network, we predict DCE-MRI images, including jointly-generated sequences of multiple corresponding DCE-MRI timepoints, from non-contrast-enhanced MRIs, enabling tumor localization and characterization without the associated health risks. Furthermore, we qualitatively and quantitatively evaluate the synthetic DCE-MRI images, proposing a multi-metric Scaled Aggregate Measure (SAMe), assessing their utility in a tumor segmentation downstream task, and conclude with an analysis of the temporal patterns in multi-sequence DCE-MRI generation. Our approach demonstrates promising results in generating realistic and useful DCE-MRI sequences, highlighting the potential of virtual contrast enhancement for improving breast cancer diagnosis and treatment, particularly for patients where contrast agent administration is contraindicated.

eess.IV↗

arXiv2025

Semantic Alignment of Unimodal Medical Text and Vision Representations

General-purpose AI models, particularly those designed for text and vision, demonstrate impressive versatility across a wide range of deep-learning tasks. However, they often underperform in specialised domains like medical imaging, where domain-specific solutions or alternative knowledge transfer approaches are typically required. Recent studies have noted that general-purpose models can exhibit similar latent spaces when processing semantically related data, although this alignment does not occur naturally. Building on this insight, it has been shown that applying a simple transformation - at most affine - estimated from a subset of semantically corresponding samples, known as anchors, enables model stitching across diverse training paradigms, architectures, and modalities. In this paper, we explore how semantic alignment - estimating transformations between anchors - can bridge general-purpose AI with specialised medical knowledge. Using multiple public chest X-ray datasets, we demonstrate that model stitching across model architectures allows general models to integrate domain-specific knowledge without additional training, leading to improved performance on medical tasks. Furthermore, we introduce a novel zero-shot classification approach for unimodal vision encoders that leverages semantic alignment across modalities. Our results show that our method not only outperforms general multimodal models but also approaches the performance levels of fully trained, medical-specific multimodal solutions

cs.CV↗

arXiv2025

Enhancing Abnormality Grounding for Vision Language Models with Knowledge Descriptions

Visual Language Models (VLMs) have demonstrated impressive capabilities in visual grounding tasks. However, their effectiveness in the medical domain, particularly for abnormality detection and localization within medical images, remains underexplored. A major challenge is the complex and abstract nature of medical terminology, which makes it difficult to directly associate pathological anomaly terms with their corresponding visual features. In this work, we introduce a novel approach to enhance VLM performance in medical abnormality detection and localization by leveraging decomposed medical knowledge. Instead of directly prompting models to recognize specific abnormalities, we focus on breaking down medical concepts into fundamental attributes and common visual patterns. This strategy promotes a stronger alignment between textual descriptions and visual features, improving both the recognition and localization of abnormalities in medical images.We evaluate our method on the 0.23B Florence-2 base model and demonstrate that it achieves comparable performance in abnormality grounding to significantly larger 7B LLaVA-based medical VLMs, despite being trained on only 1.5% of the data used for such models. Experimental results also demonstrate the effectiveness of our approach in both known and previously unseen abnormalities, suggesting its strong generalization capabilities.

cs.CV↗