Parametric shape models for vessels learned from segmentations via differentiable voxelization

Vessels are complex structures in the body that have been studied extensively in multiple representations. While voxelization is the most common of them, meshes and parametric models are critical in various applications due to their desirable properties. However, these representations are typically extracted through segmentations and used disjointly from each other. We propose a framework that joins the three representations under differentiable transformations. By leveraging differentiable voxelization, we automatically extract a parametric shape model of the vessels through shape-to-segmentation fitting, where we learn shape parameters from segmentations without the explicit need for ground-truth shape parameters. The vessel is parametrized as centerlines and radii using cubic B-splines, ensuring smoothness and continuity by construction. Meshes are differentiably extracted from the learned shape parameters, resulting in high-fidelity meshes that can be manipulated post-fit. Our method can accurately capture the geometry of complex vessels, as demonstrated by the volumetric fits in experiments on aortas, aneurysms, and brain vessels.

CINeMA: Conditional Implicit Neural Multi-Modal Atlas for a Spatio-Temporal Representation of the Perinatal Brain

Magnetic resonance imaging of fetal and neonatal brains reveals rapid neurodevelopment marked by substantial anatomical changes unfolding within days. Studying this critical stage of the developing human brain, therefore, requires accurate brain models-referred to as atlases-of high spatial and temporal resolution. To meet these demands, established traditional atlases and recently proposed deep learning-based methods rely on large and comprehensive datasets. This poses a major challenge for studying brains in the presence of pathologies for which data remains scarce. We address this limitation with CINeMA (Conditional Implicit Neural Multi-Modal Atlas), a novel framework for creating high-resolution, spatio-temporal, multimodal brain atlases, suitable for low-data settings. Unlike established methods, CINeMA operates in latent space, avoiding compute-intensive image registration and reducing atlas construction times from days to minutes. Furthermore, it enables flexible conditioning on anatomical features including GA, birth age, and pathologies like ventriculomegaly (VM) and agenesis of the corpus callosum (ACC). CINeMA supports downstream tasks such as tissue segmentation and age prediction whereas its generative properties enable synthetic data creation and anatomically informed data augmentation. Surpassing state-of-the-art methods in accuracy, efficiency, and versatility, CINeMA represents a powerful tool for advancing brain research. We release the code and atlases at https://github.com/m-dannecker/CINeMA.

Self-supervised feature learning for cardiac Cine MR image reconstruction

We propose a self-supervised feature learning assisted reconstruction (SSFL-Recon) framework for MRI reconstruction to address the limitation of existing supervised learning methods. Although recent deep learning-based methods have shown promising performance in MRI reconstruction, most require fully-sampled images for supervised learning, which is challenging in practice considering long acquisition times under respiratory or organ motion. Moreover, nearly all fully-sampled datasets are obtained from conventional reconstruction of mildly accelerated datasets, thus potentially biasing the achievable performance. The numerous undersampled datasets with different accelerations in clinical practice, hence, remain underutilized. To address these issues, we first train a self-supervised feature extractor on undersampled images to learn sampling-insensitive features. The pre-learned features are subsequently embedded in the self-supervised reconstruction network to assist in removing artifacts. Experiments were conducted retrospectively on an in-house 2D cardiac Cine dataset, including 91 cardiovascular patients and 38 healthy subjects. The results demonstrate that the proposed SSFL-Recon framework outperforms existing self-supervised MRI reconstruction methods and even exhibits comparable or better performance to supervised learning up to $16\times$ retrospective undersampling. The feature learning strategy can effectively extract global representations, which have proven beneficial in removing artifacts and increasing generalization ability during reconstruction.

Beyond Distillation: Pushing the Limits of Medical LLM Reasoning with Minimalist Rule-Based RL

Improving performance on complex tasks and enabling interpretable decision making in large language models (LLMs), especially for clinical applications, requires effective reasoning. Yet this remains challenging without supervised fine-tuning (SFT) on costly chain-of-thought (CoT) data distilled from closed-source models (e.g., GPT-4o). In this work, we present AlphaMed, the first medical LLM to show that reasoning capability can emerge purely through reinforcement learning (RL), using minimalist rule-based rewards on public multiple-choice QA datasets, without relying on SFT or distilled CoT data. AlphaMed achieves state-of-the-art results on six medical QA benchmarks, outperforming models trained with conventional SFT+RL pipelines. On challenging benchmarks (e.g., MedXpert), AlphaMed even surpasses larger or closed-source models such as DeepSeek-V3-671B and Claude-3.5-Sonnet. To understand the factors behind this success, we conduct a comprehensive data-centric analysis guided by three questions: (i) Can minimalist rule-based RL incentivize reasoning without distilled CoT supervision? (ii) How do dataset quantity and diversity impact reasoning? (iii) How does question difficulty shape the emergence and generalization of reasoning? Our findings show that dataset informativeness is a key driver of reasoning performance, and that minimalist RL on informative, multiple-choice QA data is effective at inducing reasoning without CoT supervision. We also observe divergent trends across benchmarks, underscoring limitations in current evaluation and the need for more challenging, reasoning-oriented medical QA benchmarks.

Laplace Sample Information: Data Informativeness Through a Bayesian Lens

Accurately estimating the informativeness of individual samples in a dataset is an important objective in deep learning, as it can guide sample selection, which can improve model efficiency and accuracy by removing redundant or potentially harmful samples. We propose Laplace Sample Information (LSI) measure of sample informativeness grounded in information theory widely applicable across model architectures and learning settings. LSI leverages a Bayesian approximation to the weight posterior and the KL divergence to measure the change in the parameter distribution induced by a sample of interest from the dataset. We experimentally show that LSI is effective in ordering the data with respect to typicality, detecting mislabeled samples, measuring class-wise informativeness, and assessing dataset difficulty. We demonstrate these capabilities of LSI on image and text data in supervised and unsupervised settings. Moreover, we show that LSI can be computed efficiently through probes and transfers well to the training of large models.

Meta-learning Slice-to-Volume Reconstruction in Fetal Brain MRI using Implicit Neural Representations

High-resolution slice-to-volume reconstruction (SVR) from multiple motion-corrupted low-resolution 2D slices constitutes a critical step in image-based diagnostics of moving subjects, such as fetal brain Magnetic Resonance Imaging (MRI). Existing solutions struggle with image artifacts and severe subject motion or require slice pre-alignment to achieve satisfying reconstruction performance. We propose a novel SVR method to enable fast and accurate MRI reconstruction even in cases of severe image and motion corruption. Our approach performs motion correction, outlier handling, and super-resolution reconstruction with all operations being entirely based on implicit neural representations. The model can be initialized with task-specific priors through fully self-supervised meta-learning on either simulated or real-world data. In extensive experiments including over 480 reconstructions of simulated and clinical MRI brain data from different centers, we prove the utility of our method in cases of severe subject motion and image artifacts. Our results demonstrate improvements in reconstruction quality, especially in the presence of severe motion, compared to state-of-the-art methods, and up to 50% reduction in reconstruction time.

Automated Thoracolumbar Stump Rib Detection and Analysis in a Large CT Cohort

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.

Towards Cardiac MRI Foundation Models: Comprehensive Visual-Tabular Representations for Whole-Heart Assessment and Beyond

Cardiac magnetic resonance imaging is the gold standard for non-invasive cardiac assessment, offering rich spatio-temporal views of the cardiac anatomy and physiology. Patient-level health factors, such as demographics, metabolic, and lifestyle, are known to substantially influence cardiovascular health and disease risk, yet remain uncaptured by CMR alone. To holistically understand cardiac health and to enable the best possible interpretation of an individual's disease risk, CMR and patient-level factors must be jointly exploited within an integrated framework. Recent multi-modal approaches have begun to bridge this gap, yet they often rely on limited spatio-temporal data and focus on isolated clinical tasks, thereby hindering the development of a comprehensive representation for cardiac health evaluation. To overcome these limitations, we introduce ViTa, a step toward foundation models that delivers a comprehensive representation of the heart and a precise interpretation of individual disease risk. Leveraging data from 42,000 UK Biobank participants, ViTa integrates 3D+T cine stacks from short-axis and long-axis views, enabling a complete capture of the cardiac cycle. These imaging data are then fused with detailed tabular patient-level factors, enabling context-aware insights. This multi-modal paradigm supports a wide spectrum of downstream tasks, including cardiac phenotype and physiological feature prediction, segmentation, and classification of cardiac and metabolic diseases within a single unified framework. By learning a shared latent representation that bridges rich imaging features and patient context, ViTa moves beyond traditional, task-specific models toward a universal, patient-specific understanding of cardiac health, highlighting its potential to advance clinical utility and scalability in cardiac analysis.

From Pixels to Histopathology: A Graph-Based Framework for Interpretable Whole Slide Image Analysis

The histopathological classification of whole-slide images (WSIs) is a fundamental task in digital pathology; yet it requires extensive time and expertise from specialists. While deep learning methods show promising results, they typically process WSIs by dividing them into artificial patches, which inherently prevents a network from learning from the entire image context, disregards natural tissue structures and compromises interpretability. Our method overcomes this limitation through a novel graph-based framework that constructs WSI graph representations. The WSI-graph efficiently captures essential histopathological information in a compact form. We build tissue representations (nodes) that follow biological boundaries rather than arbitrary patches all while providing interpretable features for explainability. Through adaptive graph coarsening guided by learned embeddings, we progressively merge regions while maintaining discriminative local features and enabling efficient global information exchange. In our method's final step, we solve the diagnostic task through a graph attention network. We empirically demonstrate strong performance on multiple challenging tasks such as cancer stage classification and survival prediction, while also identifying predictive factors using Integrated Gradients. Our implementation is publicly available at https://github.com/HistoGraph31/pix2pathology

Evaluation of Alignment-Regularity Characteristics in Deformable Image Registration

Evaluating deformable image registration (DIR) is challenging due to the inherent trade-off between achieving high alignment accuracy and maintaining deformation regularity. In this work, we introduce a novel evaluation scheme based on the alignment-regularity characteristic (ARC) to systematically capture and analyze this trade-off. We first introduce the ARC curves, which describe the performance of a given registration algorithm as a spectrum measured by alignment and regularity metrics. We further adopt a HyperNetwork-based approach that learns to continuously interpolate across the full regularization range, accelerating the construction and improving the sample density of ARC curves. We empirically demonstrate our evaluation scheme using representative learning-based deformable image registration methods with various network architectures and transformation models on two public datasets. We present a range of findings not evident from existing evaluation practices and provide general recommendations for model evaluation and selection using our evaluation scheme. All code relevant is made publicly available.