Rickmer Braren

Fryderyk Kögl, Anna Reithmeir, Vasiliki Sideri-Lampretsa et al.

General vision encoders like DINOv2 and SAM have recently transformed computer vision. Even though they are trained on natural images, such encoder models have excelled in medical imaging, e.g., in classification, segmentation, and registration. However, no in-depth comparison of different state-of-the-art general vision encoders for medical registration is available. In this work, we investigate how well general vision encoder features can be used in the dissimilarity metrics for medical image registration. We explore two encoders that were trained on natural images as well as one that was fine-tuned on medical data. We apply the features within the well-established B-spline FFD registration framework. In extensive experiments on cardiac cine MRI data, we find that using features as additional guidance for conventional metrics improves the registration quality. The code is available at github.com/compai-lab/2024-miccai-koegl.

Soroosh Tayebi Arasteh, Alexander Ziller, Christiane Kuhl et al.

Artificial intelligence (AI) models are increasingly used in the medical domain. However, as medical data is highly sensitive, special precautions to ensure its protection are required. The gold standard for privacy preservation is the introduction of differential privacy (DP) to model training. Prior work indicates that DP has negative implications on model accuracy and fairness, which are unacceptable in medicine and represent a main barrier to the widespread use of privacy-preserving techniques. In this work, we evaluated the effect of privacy-preserving training of AI models regarding accuracy and fairness compared to non-private training. For this, we used two datasets: (1) A large dataset (N=193,311) of high quality clinical chest radiographs, and (2) a dataset (N=1,625) of 3D abdominal computed tomography (CT) images, with the task of classifying the presence of pancreatic ductal adenocarcinoma (PDAC). Both were retrospectively collected and manually labeled by experienced radiologists. We then compared non-private deep convolutional neural networks (CNNs) and privacy-preserving (DP) models with respect to privacy-utility trade-offs measured as area under the receiver-operator-characteristic curve (AUROC), and privacy-fairness trade-offs, measured as Pearson's r or Statistical Parity Difference. We found that, while the privacy-preserving trainings yielded lower accuracy, they did largely not amplify discrimination against age, sex or co-morbidity. Our study shows that -- under the challenging realistic circumstances of a real-life clinical dataset -- the privacy-preserving training of diagnostic deep learning models is possible with excellent diagnostic accuracy and fairness.

Sophie Starck, Yadunandan Vivekanand Kini, Jessica Johanna Maria Ritter et al.

Age prediction is an important part of medical assessments and research. It can aid in detecting diseases as well as abnormal ageing by highlighting potential discrepancies between chronological and biological age. To improve understanding of age-related changes in various body parts, we investigate the ageing of the human body on a large scale by using whole-body 3D images. We utilise the Grad-CAM method to determine the body areas most predictive of a person's age. In order to expand our analysis beyond individual subjects, we employ registration techniques to generate population-wide importance maps that show the most predictive areas in the body for a whole cohort of subjects. We show that the investigation of the full 3D volume of the whole body and the population-wide analysis can give important insights into which body parts play the most important roles in predicting a person's age. Our findings reveal three primary areas of interest: the spine, the autochthonous back muscles, and the cardiac region, which exhibits the highest importance. Finally, we investigate differences between subjects that show accelerated and decelerated ageing.

Tamara T. Mueller, Siyu Zhou, Sophie Starck et al.

Body fat volume and distribution can be a strong indication for a person's overall health and the risk for developing diseases like type 2 diabetes and cardiovascular diseases. Frequently used measures for fat estimation are the body mass index (BMI), waist circumference, or the waist-hip-ratio. However, those are rather imprecise measures that do not allow for a discrimination between different types of fat or between fat and muscle tissue. The estimation of visceral (VAT) and abdominal subcutaneous (ASAT) adipose tissue volume has shown to be a more accurate measure for named risk factors. In this work, we show that triangulated body surface meshes can be used to accurately predict VAT and ASAT volumes using graph neural networks. Our methods achieve high performance while reducing training time and required resources compared to state-of-the-art convolutional neural networks in this area. We furthermore envision this method to be applicable to cheaper and easily accessible medical surface scans instead of expensive medical images.

Veronika Spieker, Hannah Eichhorn, Wenqi Huang et al.

Neural implicit k-space representations (NIK) have shown promising results for dynamic magnetic resonance imaging (MRI) at high temporal resolutions. Yet, reducing acquisition time, and thereby available training data, results in severe performance drops due to overfitting. To address this, we introduce a novel self-supervised k-space loss function $\mathcal{L}_\mathrm{PISCO}$, applicable for regularization of NIK-based reconstructions. The proposed loss function is based on the concept of parallel imaging-inspired self-consistency (PISCO), enforcing a consistent global k-space neighborhood relationship without requiring additional data. Quantitative and qualitative evaluations on static and dynamic MR reconstructions show that integrating PISCO significantly improves NIK representations. Particularly for high acceleration factors (R$\geq$54), NIK with PISCO achieves superior spatio-temporal reconstruction quality compared to state-of-the-art methods. Furthermore, an extensive analysis of the loss assumptions and stability shows PISCO's potential as versatile self-supervised k-space loss function for further applications and architectures. Code is available at: https://github.com/compai-lab/2025-pisco-spieker

Johannes Brandt, Maulik Chevli, Rickmer Braren et al.

Lung cancer risk estimation is gaining increasing importance as more countries introduce population-wide screening programs using low-dose CT (LDCT). As imaging volumes grow, scalable methods that can process entire lung volumes efficiently are essential to tap into the full potential of these large screening datasets. Existing approaches either over-rely on pixel-level annotations, limiting scalability, or analyze the lung in fragments, weakening performance. We present LungEvaty, a fully transformer-based framework for predicting 1-6 year lung cancer risk from a single LDCT scan. The model operates on whole-lung inputs, learning directly from large-scale screening data to capture comprehensive anatomical and pathological cues relevant for malignancy risk. Using only imaging data and no region supervision, LungEvaty matches state-of-the-art performance, refinable by an optional Anatomically Informed Attention Guidance (AIAG) loss that encourages anatomically focused attention. In total, LungEvaty was trained on more than 90,000 CT scans, including over 28,000 for fine-tuning and 6,000 for evaluation. The framework offers a simple, data-efficient, and fully open-source solution that provides an extensible foundation for future research in longitudinal and multimodal lung cancer risk prediction.

Markus R. Bujotzek, Ünal Akünal, Stefan Denner et al.

Objective: Federated Learning (FL) enables collaborative model training while keeping data locally. Currently, most FL studies in radiology are conducted in simulated environments due to numerous hurdles impeding its translation into practice. The few existing real-world FL initiatives rarely communicate specific measures taken to overcome these hurdles, leaving behind a significant knowledge gap. Minding efforts to implement real-world FL, there is a notable lack of comprehensive assessment comparing FL to less complex alternatives. Materials & Methods: We extensively reviewed FL literature, categorizing insights along with our findings according to their nature and phase while establishing a FL initiative, summarized to a comprehensive guide. We developed our own FL infrastructure within the German Radiological Cooperative Network (RACOON) and demonstrated its functionality by training FL models on lung pathology segmentation tasks across six university hospitals. We extensively evaluated FL against less complex alternatives in three distinct evaluation scenarios. Results: The proposed guide outlines essential steps, identified hurdles, and proposed solutions for establishing successful FL initiatives conducting real-world experiments. Our experimental results show that FL outperforms less complex alternatives in all evaluation scenarios, justifying the effort required to translate FL into real-world applications. Discussion & Conclusion: Our proposed guide aims to aid future FL researchers in circumventing pitfalls and accelerating translation of FL into radiological applications. Our results underscore the value of efforts needed to translate FL into real-world applications by demonstrating advantageous performance over alternatives, and emphasize the importance of strategic organization, robust management of distributed data and infrastructure in real-world settings.

Hendrik Möller, Hanna Schön, Alina Dima et al.

Thoracolumbar stump ribs are one of the essential indicators of thoracolumbar transitional vertebrae or enumeration anomalies. While some studies manually assess these anomalies and describe the ribs qualitatively, this study aims to automate thoracolumbar stump rib detection and analyze their morphology quantitatively. To this end, we train a high-resolution deep-learning model for rib segmentation and show significant improvements compared to existing models (Dice score 0.997 vs. 0.779, p-value < 0.01). In addition, we use an iterative algorithm and piece-wise linear interpolation to assess the length of the ribs, showing a success rate of 98.2%. When analyzing morphological features, we show that stump ribs articulate more posteriorly at the vertebrae (-19.2 +- 3.8 vs -13.8 +- 2.5, p-value < 0.01), are thinner (260.6 +- 103.4 vs. 563.6 +- 127.1, p-value < 0.01), and are oriented more downwards and sideways within the first centimeters in contrast to full-length ribs. We show that with partially visible ribs, these features can achieve an F1-score of 0.84 in differentiating stump ribs from regular ones. We publish the model weights and masks for public use.

Moritz Knolle, Alexander Ziller, Dmitrii Usynin et al.

We show that differentially private stochastic gradient descent (DP-SGD) can yield poorly calibrated, overconfident deep learning models. This represents a serious issue for safety-critical applications, e.g. in medical diagnosis. We highlight and exploit parallels between stochastic gradient Langevin dynamics, a scalable Bayesian inference technique for training deep neural networks, and DP-SGD, in order to train differentially private, Bayesian neural networks with minor adjustments to the original (DP-SGD) algorithm. Our approach provides considerably more reliable uncertainty estimates than DP-SGD, as demonstrated empirically by a reduction in expected calibration error (MNIST $\sim{5}$-fold, Pediatric Pneumonia Dataset $\sim{2}$-fold).

Alexander Ziller, Dmitrii Usynin, Moritz Knolle et al.

In recent years, formal methods of privacy protection such as differential privacy (DP), capable of deployment to data-driven tasks such as machine learning (ML), have emerged. Reconciling large-scale ML with the closed-form reasoning required for the principled analysis of individual privacy loss requires the introduction of new tools for automatic sensitivity analysis and for tracking an individual's data and their features through the flow of computation. For this purpose, we introduce a novel \textit{hybrid} automatic differentiation (AD) system which combines the efficiency of reverse-mode AD with an ability to obtain a closed-form expression for any given quantity in the computational graph. This enables modelling the sensitivity of arbitrary differentiable function compositions, such as the training of neural networks on private data. We demonstrate our approach by analysing the individual DP guarantees of statistical database queries. Moreover, we investigate the application of our technique to the training of DP neural networks. Our approach can enable the principled reasoning about privacy loss in the setting of data processing, and further the development of automatic sensitivity analysis and privacy budgeting systems.

Patrick Bilic, Patrick Christ, Hongwei Bran Li et al.

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

Patrick Ferdinand Christ, Florian Ettlinger, Felix Grün et al.

Automatic segmentation of the liver and hepatic lesions is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT and MRI abdomen images using cascaded fully convolutional neural networks (CFCNs) enabling the segmentation of a large-scale medical trial or quantitative image analysis. We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input for a second FCN. The second FCN solely segments lesions within the predicted liver ROIs of step 1. CFCN models were trained on an abdominal CT dataset comprising 100 hepatic tumor volumes. Validations on further datasets show that CFCN-based semantic liver and lesion segmentation achieves Dice scores over 94% for liver with computation times below 100s per volume. We further experimentally demonstrate the robustness of the proposed method on an 38 MRI liver tumor volumes and the public 3DIRCAD dataset.