arXiv subjects

Georg Langs

Publications and source records attributed to Georg Langs.

At least 19 recordsLinked to original sources

arXiv2026

GRC-ProbNet: Uncertainty-aware Feature Extraction for Cardiovascular Disease Classification

The automatic detection and classification of cardiovascular disease (CVD) from computed tomography (CT) images plays an important role in clinical practice. Recently, a hybrid pipeline (GRC-Net) for CVD classification was proposed, which leverages a deep-learning-based segmentation and registration method to extract radiomic and geometric features. However, GRC-Net relies on a deterministic segmentation mask, without considering the inherent ambiguity associated with cardiac anatomy. In this paper, we propose GRC-ProbNet, which takes advantage of a deep ensemble to produce multiple segmentation masks for a given input. From these masks, we extract multiple uncertainty features. We analyze these uncertainty features for both their correlation with segmentation error and their propagation effects on downstream CVD classification performance. Our experiments on the publicly available MM-WHS and ASOCA datasets show that the uncertainty measure that best reflects segmentation quality is not necessarily the one that provides the strongest signal for downstream CVD classification. Overall, our results demonstrate that GRC-ProbNet utilizing uncertainty features substantially improves CVD classification AUROC (92.92\) compared to the baseline GRC-Net model (91.25%). Our code is publicly available: https://github.com/biomedia-mira/GRC-ProbNet.

cs.CV↗

arXiv2026

MApLe: Multi-instance Alignment of Diagnostic Reports and Large Medical Images

In diagnostic reports, experts encode complex imaging data into clinically actionable information. They describe subtle pathological findings that are meaningful in their anatomical context. Reports follow relatively consistent structures, expressing diagnostic information with few words that are often associated with tiny but consequential image observations. Standard vision language models struggle to identify the associations between these informative text components and small locations in the images. Here, we propose "MApLe", a multi-task, multi-instance vision language alignment approach that overcomes these limitations. It disentangles the concepts of anatomical region and diagnostic finding, and links local image information to sentences in a patch-wise approach. Our method consists of a text embedding trained to capture anatomical and diagnostic concepts in sentences, a patch-wise image encoder conditioned on anatomical structures, and a multi-instance alignment of these representations. We demonstrate that MApLe can successfully align different image regions and multiple diagnostic findings in free-text reports. We show that our model improves the alignment performance compared to state-of-the-art baseline models when evaluated on several downstream tasks. The code is available at https://github.com/cirmuw/MApLe.

cs.CV↗

arXiv2026

HyperFitS -- Hypernetwork Fitting Spectra for metabolic quantification of ${}^1$H MR spectroscopic imaging

Purpose: Proton magnetic resonance spectroscopic imaging ($^1$H MRSI) enables the mapping of whole-brain metabolites concentrations in-vivo. However, a long-standing problem for its clinical applicability is the metabolic quantification, which can require extensive time for spectral fitting. Recently, deep learning methods have been able to provide whole-brain metabolic quantification in only a few seconds. However, neural network implementations often lack configurability and require retraining to change predefined parameter settings. Methods: We introduce HyperFitS, a hypernetwork for spectral fitting for metabolite quantification in whole-brain $^1$H MRSI that flexibly adapts to a broad range of baseline corrections and water suppression factors. Metabolite maps of human subjects acquired at 3T and 7T with isotropic resolutions of 10 mm, 3.4 mm and 2 mm by water-suppressed and water-unsuppressed MRSI were quantified with HyperFitS and compared to conventional LCModel fitting. Results: Metabolic maps show a substantial agreement between the new and gold-standard methods, with significantly faster fitting times by HyperFitS. Quantitative results further highlight the impact of baseline parametrization on metabolic quantification, which can alter results by up to 30%. Conclusion: HyperFitS shows strong agreement with state-of-the-art conventional methods, while reducing processing times from hours to a few seconds. Compared to prior deep learning based spectral fitting methods, HyperFitS enables a wide range of configurability and can adapt to data quality acquired with multiple protocols and field strengths without retraining.

cs.LG↗

arXiv2026

Chronological Contrastive Learning: Few-Shot Progression Assessment in Irreversible Diseases

Quantitative disease severity scoring in medical imaging is costly, time-consuming, and subject to inter-reader variability. At the same time, clinical archives contain far more longitudinal imaging data than expert-annotated severity scores. Existing self-supervised methods typically ignore this chronological structure. We introduce ChronoCon, a contrastive learning approach that replaces label-based ranking losses with rankings derived solely from the visitation order of a patient's longitudinal scans. Under the clinically plausible assumption of monotonic progression in irreversible diseases, the method learns disease-relevant representations without using any expert labels. This generalizes the idea of Rank-N-Contrast from label distances to temporal ordering. Evaluated on rheumatoid arthritis radiographs for severity assessment, the learned representations substantially improve label efficiency. In low-label settings, ChronoCon significantly outperforms a fully supervised baseline initialized from ImageNet weights. In a few-shot learning experiment, fine-tuning ChronoCon on expert scores from only five patients yields an intraclass correlation coefficient of 86% for severity score prediction. These results demonstrate the potential of chronological contrastive learning to exploit routinely available imaging metadata to reduce annotation requirements in the irreversible disease domain. Code is available at https://github.com/cirmuw/ChronoCon.

cs.CV↗

arXiv2025

MRI-derived quantification of hepatic vessel-to-volume ratios in chronic liver disease using a deep learning approach

Background: We aimed to quantify hepatic vessel volumes across chronic liver disease stages and healthy controls using deep learning-based magnetic resonance imaging (MRI) analysis, and assess correlations with biomarkers for liver (dys)function and fibrosis/portal hypertension. Methods: We assessed retrospectively healthy controls, non-advanced and advanced chronic liver disease (ACLD) patients using a 3D U-Net model for hepatic vessel segmentation on portal venous phase gadoxetic acid-enhanced 3-T MRI. Total (TVVR), hepatic (HVVR), and intrahepatic portal vein-to-volume ratios (PVVR) were compared between groups and correlated with: albumin-bilirubin (ALBI) and model for end-stage liver disease-sodium (MELD-Na) score, and fibrosis/portal hypertension (Fibrosis-4 [FIB-4] score, liver stiffness measurement [LSM], hepatic venous pressure gradient [HVPG], platelet count [PLT], and spleen volume). Results: We included 197 subjects, aged 54.9 $\pm$ 13.8 years (mean $\pm$ standard deviation), 111 males (56.3\%): 35 healthy controls, 44 non-ACLD, and 118 ACLD patients. TVVR and HVVR were highest in controls (3.9; 2.1), intermediate in non-ACLD (2.8; 1.7), and lowest in ACLD patients (2.3; 1.0) ($p \leq 0.001$). PVVR was reduced in both non-ACLD and ACLD patients (both 1.2) compared to controls (1.7) ($p \leq 0.001$), but showed no difference between CLD groups ($p = 0.999$). HVVR significantly correlated indirectly with FIB-4, ALBI, MELD-Na, LSM, and spleen volume ($\rho$ ranging from -0.27 to -0.40), and directly with PLT ($\rho = 0.36$). TVVR and PVVR showed similar but weaker correlations. Conclusions: Deep learning-based hepatic vessel volumetry demonstrated differences between healthy liver and chronic liver disease stages and shows correlations with established markers of disease severity.

physics.med-ph↗

arXiv2025

Temporal Representation Learning of Phenotype Trajectories for pCR Prediction in Breast Cancer

Effective therapy decisions require models that predict the individual response to treatment. This is challenging since the progression of disease and response to treatment vary substantially across patients. Here, we propose to learn a representation of the early dynamics of treatment response from imaging data to predict pathological complete response (pCR) in breast cancer patients undergoing neoadjuvant chemotherapy (NACT). The longitudinal change in magnetic resonance imaging (MRI) data of the breast forms trajectories in the latent space, serving as basis for prediction of successful response. The multi-task model represents appearance, fosters temporal continuity and accounts for the comparably high heterogeneity in the non-responder cohort.In experiments on the publicly available ISPY-2 dataset, a linear classifier in the latent trajectory space achieves a balanced accuracy of 0.761 using only pre-treatment data (T0), 0.811 using early response (T0 + T1), and 0.861 using four imaging time points (T0 -> T3). The code will be made available upon paper acceptance.

cs.CV↗

arXiv2025

AREPAS: Anomaly Detection in Fine-Grained Anatomy with Reconstruction-Based Semantic Patch-Scoring

Early detection of newly emerging diseases, lesion severity assessment, differentiation of medical conditions and automated screening are examples for the wide applicability and importance of anomaly detection (AD) and unsupervised segmentation in medicine. Normal fine-grained tissue variability such as present in pulmonary anatomy is a major challenge for existing generative AD methods. Here, we propose a novel generative AD approach addressing this issue. It consists of an image-to-image translation for anomaly-free reconstruction and a subsequent patch similarity scoring between observed and generated image-pairs for precise anomaly localization. We validate the new method on chest computed tomography (CT) scans for the detection and segmentation of infectious disease lesions. To assess generalizability, we evaluate the method on an ischemic stroke lesion segmentation task in T1-weighted brain MRI. Results show improved pixel-level anomaly segmentation in both chest CTs and brain MRIs, with relative DICE score improvements of +1.9% and +4.4%, respectively, compared to other state-of-the-art reconstruction-based methods.

cs.CV↗

arXiv2025

No Modality Left Behind: Dynamic Model Generation for Incomplete Medical Data

In real world clinical environments, training and applying deep learning models on multi-modal medical imaging data often struggles with partially incomplete data. Standard approaches either discard missing samples, require imputation or repurpose dropout learning schemes, limiting robustness and generalizability. To address this, we propose a hypernetwork-based method that dynamically generates task-specific classification models conditioned on the set of available modalities. Instead of training a fixed model, a hypernetwork learns to predict the parameters of a task model adapted to available modalities, enabling training and inference on all samples, regardless of completeness. We compare this approach with (1) models trained only on complete data, (2) state of the art channel dropout methods, and (3) an imputation-based method, using artificially incomplete datasets to systematically analyze robustness to missing modalities. Results demonstrate superior adaptability of our method, outperforming state of the art approaches with an absolute increase in accuracy of up to 8% when trained on a dataset with 25% completeness (75% of training data with missing modalities). By enabling a single model to generalize across all modality configurations, our approach provides an efficient solution for real-world multi-modal medical data analysis.

cs.CV↗

arXiv2025

Disentanglement of Biological and Technical Factors via Latent Space Rotation in Clinical Imaging Improves Disease Pattern Discovery

Identifying new disease-related patterns in medical imaging data with the help of machine learning enlarges the vocabulary of recognizable findings. This supports diagnostic and prognostic assessment. However, image appearance varies not only due to biological differences, but also due to imaging technology linked to vendors, scanning- or re- construction parameters. The resulting domain shifts impedes data representation learning strategies and the discovery of biologically meaningful cluster appearances. To address these challenges, we introduce an approach to actively learn the domain shift via post-hoc rotation of the data latent space, enabling disentanglement of biological and technical factors. Results on real-world heterogeneous clinical data showcase that the learned disentangled representation leads to stable clusters representing tissue-types across different acquisition settings. Cluster consistency is improved by +19.01% (ARI), +16.85% (NMI), and +12.39% (Dice) compared to the entangled representation, outperforming four state-of-the-art harmonization methods. When using the clusters to quantify tissue composition on idiopathic pulmonary fibrosis patients, the learned profiles enhance Cox survival prediction. This indicates that the proposed label-free framework facilitates biomarker discovery in multi-center routine imaging data. Code is available on GitHub https://github.com/cirmuw/latent-space-rotation-disentanglement.

cs.CV↗

arXiv2025

Improving Vessel Segmentation with Multi-Task Learning and Auxiliary Data Available Only During Model Training

Liver vessel segmentation in magnetic resonance imaging data is important for the computational analysis of vascular remodelling, associated with a wide spectrum of diffuse liver diseases. Existing approaches rely on contrast enhanced imaging data, but the necessary dedicated imaging sequences are not uniformly acquired. Images without contrast enhancement are acquired more frequently, but vessel segmentation is challenging, and requires large-scale annotated data. We propose a multi-task learning framework to segment vessels in liver MRI without contrast. It exploits auxiliary contrast enhanced MRI data available only during training to reduce the need for annotated training examples. Our approach draws on paired native and contrast enhanced data with and without vessel annotations for model training. Results show that auxiliary data improves the accuracy of vessel segmentation, even if they are not available during inference. The advantage is most pronounced if only few annotations are available for training, since the feature representation benefits from the shared task structure. A validation of this approach to augment a model for brain tumor segmentation confirms its benefits across different domains. An auxiliary informative imaging modality can augment expert annotations even if it is only available during training.

cs.CV↗

arXiv2025

Conditional Fetal Brain Atlas Learning for Automatic Tissue Segmentation

Magnetic Resonance Imaging (MRI) of the fetal brain has become a key tool for studying brain development in vivo. Yet, its assessment remains challenging due to variability in brain maturation, imaging protocols, and uncertain estimates of Gestational Age (GA). To overcome these, brain atlases provide a standardized reference framework that facilitates objective evaluation and comparison across subjects by aligning the atlas and subjects in a common coordinate system. In this work, we introduce a novel deep-learning framework for generating continuous, age-specific fetal brain atlases for real-time fetal brain tissue segmentation. The framework combines a direct registration model with a conditional discriminator. Trained on a curated dataset of 219 neurotypical fetal MRIs spanning from 21 to 37 weeks of gestation. The method achieves high registration accuracy, captures dynamic anatomical changes with sharp structural detail, and robust segmentation performance with an average Dice Similarity Coefficient (DSC) of 86.3% across six brain tissues. Furthermore, volumetric analysis of the generated atlases reveals detailed neurotypical growth trajectories, providing valuable insights into the maturation of the fetal brain. This approach enables individualized developmental assessment with minimal pre-processing and real-time performance, supporting both research and clinical applications. The model code is available at https://github.com/cirmuw/fetal-brain-atlas

eess.IV↗

arXiv2025

Semantic Mosaicing of Histo-Pathology Image Fragments using Visual Foundation Models

In histopathology, tissue samples are often larger than a standard microscope slide, making stitching of multiple fragments necessary to process entire structures such as tumors. Automated stitching is a prerequisite for scaling analysis, but is challenging due to possible tissue loss during preparation, inhomogeneous morphological distortion, staining inconsistencies, missing regions due to misalignment on the slide, or frayed tissue edges. This limits state-of-the-art stitching methods using boundary shape matching algorithms to reconstruct artificial whole mount slides (WMS). Here, we introduce SemanticStitcher using latent feature representations derived from a visual histopathology foundation model to identify neighboring areas in different fragments. Robust pose estimation based on a large number of semantic matching candidates derives a mosaic of multiple fragments to form the WMS. Experiments on three different histopathology datasets demonstrate that SemanticStitcher yields robust WMS mosaicing and consistently outperforms the state of the art in correct boundary matches.

cs.CV↗

arXiv2025

LesiOnTime -- Joint Temporal and Clinical Modeling for Small Breast Lesion Segmentation in Longitudinal DCE-MRI

Accurate segmentation of small lesions in Breast Dynamic Contrast-Enhanced MRI (DCE-MRI) is critical for early cancer detection, especially in high-risk patients. While recent deep learning methods have advanced lesion segmentation, they primarily target large lesions and neglect valuable longitudinal and clinical information routinely used by radiologists. In real-world screening, detecting subtle or emerging lesions requires radiologists to compare across timepoints and consider previous radiology assessments, such as the BI-RADS score. We propose LesiOnTime, a novel 3D segmentation approach that mimics clinical diagnostic workflows by jointly leveraging longitudinal imaging and BIRADS scores. The key components are: (1) a Temporal Prior Attention (TPA) block that dynamically integrates information from previous and current scans; and (2) a BI-RADS Consistency Regularization (BCR) loss that enforces latent space alignment for scans with similar radiological assessments, thus embedding domain knowledge into the training process. Evaluated on a curated in-house longitudinal dataset of high-risk patients with DCE-MRI, our approach outperforms state-of-the-art single-timepoint and longitudinal baselines by 5% in terms of Dice. Ablation studies demonstrate that both TPA and BCR contribute complementary performance gains. These results highlight the importance of incorporating temporal and clinical context for reliable early lesion segmentation in real-world breast cancer screening. Our code is publicly available at https://github.com/cirmuw/LesiOnTime

cs.CV↗

arXiv2025

CADS: A Comprehensive Anatomical Dataset and Segmentation for Whole-Body Anatomy in Computed Tomography

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.

eess.IV↗

arXiv2025

Identifying Signatures of Image Phenotypes to Track Treatment Response in Liver Disease

Quantifiable image patterns associated with disease progression and treatment response are critical tools for guiding individual treatment, and for developing novel therapies. Here, we show that unsupervised machine learning can identify a pattern vocabulary of liver tissue in magnetic resonance images that quantifies treatment response in diffuse liver disease. Deep clustering networks simultaneously encode and cluster patches of medical images into a low-dimensional latent space to establish a tissue vocabulary. The resulting tissue types capture differential tissue change and its location in the liver associated with treatment response. We demonstrate the utility of the vocabulary on a randomized controlled trial cohort of non-alcoholic steatohepatitis patients. First, we use the vocabulary to compare longitudinal liver change in a placebo and a treatment cohort. Results show that the method identifies specific liver tissue change pathways associated with treatment, and enables a better separation between treatment groups than established non-imaging measures. Moreover, we show that the vocabulary can predict biopsy derived features from non-invasive imaging data. We validate the method on a separate replication cohort to demonstrate the applicability of the proposed method.

eess.IV↗

arXiv2025

Cardiovascular disease classification using radiomics and geometric features from cardiac CT

Automatic detection and classification of Cardiovascular disease (CVD) from Computed Tomography (CT) images play an important part in facilitating better-informed clinical decisions. However, most of the recent deep learning based methods either directly work on raw CT data or utilize it in pair with anatomical cardiac structure segmentation by training an end-to-end classifier. As such, these approaches become much more difficult to interpret from a clinical perspective. To address this challenge, in this work, we break down the CVD classification pipeline into three components: (i) image segmentation, (ii) image registration, and (iii) downstream CVD classification. Specifically, we utilize the Atlas-ISTN framework and recent segmentation foundational models to generate anatomical structure segmentation and a normative healthy atlas. These are further utilized to extract clinically interpretable radiomic features as well as deformation field based geometric features (through atlas registration) for CVD classification. Our experiments on the publicly available ASOCA dataset show that utilizing these features leads to better CVD classification accuracy (87.50\%) when compared against classification model trained directly on raw CT images (67.50\%). Our code is publicly available: https://github.com/biomedia-mira/grc-net

eess.IV↗

arXiv2025

Towards contrast- and pathology-agnostic clinical fetal brain MRI segmentation using SynthSeg

Magnetic resonance imaging (MRI) has played a crucial role in fetal neurodevelopmental research. Structural annotations of MR images are an important step for quantitative analysis of the developing human brain, with Deep Learning providing an automated alternative for this otherwise tedious manual process. However, segmentation performances of Convolutional Neural Networks often suffer from domain shift, where the network fails when applied to subjects that deviate from the distribution with which it is trained on. In this work, we aim to train networks capable of automatically segmenting fetal brain MRIs with a wide range of domain shifts pertaining to differences in subject physiology and acquisition environments, in particular shape-based differences commonly observed in pathological cases. We introduce a novel data-driven train-time sampling strategy that seeks to fully exploit the diversity of a given training dataset to enhance the domain generalizability of the trained networks. We adapted our sampler, together with other existing data augmentation techniques, to the SynthSeg framework, a generator that utilizes domain randomization to generate diverse training data. We ran thorough experimentations and ablation studies on a wide range of training/testing data to test the validity of the approaches. Our networks achieved notable improvements in the segmentation quality on testing subjects with intense anatomical abnormalities (p < 1e-4), though at the cost of a slighter decrease in performance in cases with fewer abnormalities. Our work also lays the foundation for future works on creating and adapting data-driven sampling strategies for other training pipelines.

eess.IV↗

arXiv2024

Evaluating Synthetic Data Generation for Domain Generalization in Fetal Brain MRI Segmentation

Fetal brain tissue segmentation from magnetic resonance imaging (MRI) is crucial for studying neurodevelopment, but remains challenging due to data heterogeneity and limited annotations. Domain randomization (DR) has recently emerged as a promising strategy for single-source domain generalization by synthesizing training images with randomized artifacts, contrast, and resolution. In this work, we investigate how to maximize the out-of-domain (OOD) generalization of DR-based methods. We evaluate several synthetic data generation strategies for DR, with a particular focus on our recently proposed framework, FetalSynthSeg. We show that simple Gaussian mixture-based intensity modeling outperforms more complex physics-based simulations, and that intensity clustering (subdividing tissue classes based on intensity) improves OOD robustness. Evaluated on 348 fetal subjects from four sites spanning 0.55-3T and both T1w and T2w contrasts, FetalSynthSeg reaches state-of-the-art performance on several FeTA 2024 testing datasets (80-85 Dice score) and, for the first time, offers robust segmentation on modalities other than T2w for fetal brain segmentation (80 Dice on dHCP-T1w dataset). Compared with state-of-the-art methods such as BOUNTI, nnU-Net ensemble, and the FeTA 2024 winner, FetalSynthSeg delivers comparable or superior accuracy while maintaining strong robustness across domain shifts. Our code, model weights, and Docker image ready for easy inference are available at https://hub.docker.com/r/vzalevskyi/fetalsynthseg.

eess.IV↗