Daily Papers

Text-driven controllable dance generation remains under-explored, primarily due to the severe scarcity of high-quality datasets and the inherent difficulty of articulating complex choreographies. Characterizing dance is particularly challenging owing to its intricate spatial dynamics, strong directionality, and the highly decoupled movements of distinct body parts. To overcome these bottlenecks, we bridge principles from dance studies, human anatomy, and biomechanics to propose Choreographic Syntax, a novel theoretical framework with a tailored annotation system. Grounded in this syntax, we combine professional dance archives with high-fidelity motion capture data to construct DanceFlow, the most fine-grained dance dataset to date. It encompasses 41 hours of high-quality motions paired with 6.34 million words of detailed descriptions. At the model level, we introduce DanceCrafter, a tailored motion transformer built upon the Momentum Human Rig. To circumvent optimization instabilities, we construct a continuous manifold motion representation paired with a hybrid normalization strategy. Furthermore, we design an anatomy-aware loss to explicitly regulate the decoupled nature of body parts. Together, these adaptations empower DanceCrafter to achieve the high-fidelity and stable generation of complex dance sequences. Extensive evaluations and user studies demonstrate our state-of-the-art performance in motion quality, fine-grained controllability, and generation naturalness.

X-ray angiography is the gold standard imaging modality for cardiovascular diseases. However, current deep learning approaches for X-ray angiogram analysis are severely constrained by the scarcity of annotated data. While large-scale self-supervised learning (SSL) has emerged as a promising solution, its potential in this domain remains largely unexplored, primarily due to the lack of effective SSL frameworks and large-scale datasets. To bridge this gap, we introduce a vascular anatomy-aware masked image modeling (VasoMIM) framework that explicitly integrates domain-specific anatomical knowledge. Specifically, VasoMIM comprises two key designs: an anatomy-guided masking strategy and an anatomical consistency loss. The former strategically masks vessel-containing patches to compel the model to learn robust vascular semantics, while the latter preserves structural consistency of vessels between original and reconstructed images, enhancing the discriminability of the learned representations. In conjunction with VasoMIM, we curate XA-170K, the largest X-ray angiogram pre-training dataset to date. We validate VasoMIM on four downstream tasks across six datasets, where it demonstrates superior transferability and achieves state-of-the-art performance compared to existing methods. These findings highlight the significant potential of VasoMIM as a foundation model for advancing a wide range of X-ray angiogram analysis tasks. VasoMIM and XA-170K will be available at https://github.com/Dxhuang-CASIA/XA-SSL.

Accurate vessel segmentation in X-ray angiograms is crucial for numerous clinical applications. However, the scarcity of annotated data presents a significant challenge, which has driven the adoption of self-supervised learning (SSL) methods such as masked image modeling (MIM) to leverage large-scale unlabeled data for learning transferable representations. Unfortunately, conventional MIM often fails to capture vascular anatomy because of the severe class imbalance between vessel and background pixels, leading to weak vascular representations. To address this, we introduce Vascular anatomy-aware Masked Image Modeling (VasoMIM), a novel MIM framework tailored for X-ray angiograms that explicitly integrates anatomical knowledge into the pre-training process. Specifically, it comprises two complementary components: anatomy-guided masking strategy and anatomical consistency loss. The former preferentially masks vessel-containing patches to focus the model on reconstructing vessel-relevant regions. The latter enforces consistency in vascular semantics between the original and reconstructed images, thereby improving the discriminability of vascular representations. Empirically, VasoMIM achieves state-of-the-art performance across three datasets. These findings highlight its potential to facilitate X-ray angiogram analysis.

Widely adopted evaluation metrics for sparse-view CT reconstruction--such as Structural Similarity Index Measure and Peak Signal-to-Noise Ratio--prioritize pixel-wise fidelity but often fail to capture the completeness of critical anatomical structures, particularly small or thin regions that are easily missed. To address this limitation, we propose a suite of novel anatomy-aware evaluation metrics designed to assess structural completeness across anatomical structures, including large organs, small organs, intestines, and vessels. Building on these metrics, we introduce CARE, a Completeness-Aware Reconstruction Enhancement framework that incorporates structural penalties during training to encourage anatomical preservation of significant structures. CARE is model-agnostic and can be seamlessly integrated into analytical, implicit, and generative methods. When applied to these methods, CARE substantially improves structural completeness in CT reconstructions, achieving up to +32% improvement for large organs, +22% for small organs, +40% for intestines, and +36% for vessels.

Rich and accurate medical image segmentation is poised to underpin the next generation of AI-defined clinical practice by delineating critical anatomy for pre-operative planning, guiding real-time intra-operative navigation, and supporting precise post-operative assessment. However, commonly used learning methods for medical and surgical imaging segmentation tasks penalise all errors equivalently and thus fail to exploit any inter-class semantics in the labels space. This becomes particularly problematic as the cardinality and richness of labels increases to include subtly different classes. In this work, we propose two tree-based semantic loss functions which take advantage of a hierarchical organisation of the labels. We further incorporate our losses in a recently proposed approach for training with sparse, background-free annotations to extend the applicability of our proposed losses. Extensive experiments are reported on two medical and surgical image segmentation tasks, namely head MRI for whole brain parcellation (WBP) with full supervision and neurosurgical hyperspectral imaging (HSI) for scene understanding with sparse annotations. Results demonstrate that our proposed method reaches state-of-the-art performance in both cases.

Self-supervised learning (SSL) has recently achieved promising performance for 3D medical image analysis tasks. Most current methods follow existing SSL paradigm originally designed for photographic or natural images, which cannot explicitly and thoroughly exploit the intrinsic similar anatomical structures across varying medical images. This may in fact degrade the quality of learned deep representations by maximizing the similarity among features containing spatial misalignment information and different anatomical semantics. In this work, we propose a new self-supervised learning framework, namely Alice, that explicitly fulfills Anatomical invariance modeling and semantic alignment via elaborately combining discriminative and generative objectives. Alice introduces a new contrastive learning strategy which encourages the similarity between views that are diversely mined but with consistent high-level semantics, in order to learn invariant anatomical features. Moreover, we design a conditional anatomical feature alignment module to complement corrupted embeddings with globally matched semantics and inter-patch topology information, conditioned by the distribution of local image content, which permits to create better contrastive pairs. Our extensive quantitative experiments on three 3D medical image analysis tasks demonstrate and validate the performance superiority of Alice, surpassing the previous best SSL counterpart methods and showing promising ability for united representation learning. Codes are available at https://github.com/alibaba-damo-academy/alice.

Image enhancement improves visual quality and helps reveal details that are hard to see in the original image. In medical imaging, it can support clinical decision-making, but current models often over-edit. This can distort organs, create false findings, and miss small tumors because these models do not understand anatomy or contrast dynamics. We propose SMILE, an anatomy-aware diffusion model that learns how organs are shaped and how they take up contrast. It enhances only clinically relevant regions while leaving all other areas unchanged. SMILE introduces three key ideas: (1) structure-aware supervision that follows true organ boundaries and contrast patterns; (2) registration-free learning that works directly with unaligned multi-phase CT scans; (3) unified inference that provides fast and consistent enhancement across all contrast phases. Across six external datasets, SMILE outperforms existing methods in image quality (14.2% higher SSIM, 20.6% higher PSNR, 50% better FID) and in clinical usefulness by producing anatomically accurate and diagnostically meaningful images. SMILE also improves cancer detection from non-contrast CT, raising the F1 score by up to 10 percent.

Biomedical image segmentation is critical for accurate identification and analysis of anatomical structures in medical imaging, particularly in cardiac MRI. Manual segmentation is labor-intensive, time-consuming, and prone to errors, highlighting the need for automated methods. However, current machine learning approaches face challenges like overfitting and data demands. To tackle these issues, we propose a new UU-Mamba model, integrating the U-Mamba model with the Sharpness-Aware Minimization (SAM) optimizer and an uncertainty-aware loss function. SAM enhances generalization by locating flat minima in the loss landscape, thus reducing overfitting. The uncertainty-aware loss combines region-based, distribution-based, and pixel-based loss designs to improve segmentation accuracy and robustness. Evaluation of our method is performed on the ACDC cardiac dataset, outperforming state-of-the-art models including TransUNet, Swin-Unet, nnUNet, and nnFormer. Our approach achieves Dice Similarity Coefficient (DSC) and Mean Squared Error (MSE) scores, demonstrating its effectiveness in cardiac MRI segmentation.

Accurately segmenting thin tubular structures, such as vessels, nerves, roads or concrete cracks, is a crucial task in computer vision. Standard deep learning-based segmentation loss functions, such as Dice or Cross-Entropy, focus on volumetric overlap, often at the expense of preserving structural connectivity or topology. This can lead to segmentation errors that adversely affect downstream tasks, including flow calculation, navigation, and structural inspection. Although current topology-focused losses mark an improvement, they introduce significant computational and memory overheads. This is particularly relevant for 3D data, rendering these losses infeasible for larger volumes as well as increasingly important multi-class segmentation problems. To mitigate this, we propose a novel Skeleton Recall Loss, which effectively addresses these challenges by circumventing intensive GPU-based calculations with inexpensive CPU operations. It demonstrates overall superior performance to current state-of-the-art approaches on five public datasets for topology-preserving segmentation, while substantially reducing computational overheads by more than 90%. In doing so, we introduce the first multi-class capable loss function for thin structure segmentation, excelling in both efficiency and efficacy for topology-preservation.

We participated in the SynthRAD2025 challenge (Tasks 1 and 2) with a unified pipeline for synthetic CT (sCT) generation from MRI and CBCT, implemented using the KonfAI framework. Our model is a 2.5D U-Net++ with a ResNet-34 encoder, trained jointly across anatomical regions and fine-tuned per region. The loss function combined pixel-wise L1 loss with IMPACT-Synth, a perceptual loss derived from SAM and TotalSegmentator to enhance structural fidelity. Training was performed using AdamW (initial learning rate = 0.001, halved every 25k steps) on patch-based, normalized, body-masked inputs (320x320 for MRI, 256x256 for CBCT), with random flipping as the only augmentation. No post-processing was applied. Final predictions leveraged test-time augmentation and five-fold ensembling. The best model was selected based on validation MAE. Two registration strategies were evaluated: (i) Elastix with mutual information, consistent with the challenge pipeline, and (ii) IMPACT, a feature-based similarity metric leveraging pretrained segmentation networks. On the local test sets, IMPACT-based registration achieved more accurate and anatomically consistent alignments than mutual-information-based registration, resulting in improved sCT synthesis with lower MAE and more realistic anatomical structures. On the public validation set, however, models trained with Elastix-aligned data achieved higher scores, reflecting a registration bias favoring alignment strategies consistent with the evaluation pipeline. This highlights how registration errors can propagate into supervised learning, influencing both training and evaluation, and potentially inflating performance metrics at the expense of anatomical fidelity. By promoting anatomically consistent alignment, IMPACT helps mitigate this bias and supports the development of more robust and generalizable sCT synthesis models.

Domain adaptation (DA) has drawn high interest for its capacity to adapt a model trained on labeled source data to perform well on unlabeled or weakly labeled target data from a different domain. Most common DA techniques require concurrent access to the input images of both the source and target domains. However, in practice, privacy concerns often impede the availability of source images in the adaptation phase. This is a very frequent DA scenario in medical imaging, where, for instance, the source and target images could come from different clinical sites. We introduce a source-free domain adaptation for image segmentation. Our formulation is based on minimizing a label-free entropy loss defined over target-domain data, which we further guide with a domain-invariant prior on the segmentation regions. Many priors can be derived from anatomical information. Here, a class ratio prior is estimated from anatomical knowledge and integrated in the form of a Kullback Leibler (KL) divergence in our overall loss function. Furthermore, we motivate our overall loss with an interesting link to maximizing the mutual information between the target images and their label predictions. We show the effectiveness of our prior aware entropy minimization in a variety of domain-adaptation scenarios, with different modalities and applications, including spine, prostate, and cardiac segmentation. Our method yields comparable results to several state of the art adaptation techniques, despite having access to much less information, as the source images are entirely absent in our adaptation phase. Our straightforward adaptation strategy uses only one network, contrary to popular adversarial techniques, which are not applicable to a source-free DA setting. Our framework can be readily used in a breadth of segmentation problems, and our code is publicly available: https://github.com/mathilde-b/SFDA

Semi-supervised learning relaxes the need of large pixel-wise labeled datasets for image segmentation by leveraging unlabeled data. A prominent way to exploit unlabeled data is to regularize model predictions. Since the predictions of unlabeled data can be unreliable, uncertainty-aware schemes are typically employed to gradually learn from meaningful and reliable predictions. Uncertainty estimation methods, however, rely on multiple inferences from the model predictions that must be computed for each training step, which is computationally expensive. Moreover, these uncertainty maps capture pixel-wise disparities and do not consider global information. This work proposes a novel method to estimate segmentation uncertainty by leveraging global information from the segmentation masks. More precisely, an anatomically-aware representation is first learnt to model the available segmentation masks. The learnt representation thereupon maps the prediction of a new segmentation into an anatomically-plausible segmentation. The deviation from the plausible segmentation aids in estimating the underlying pixel-level uncertainty in order to further guide the segmentation network. The proposed method consequently estimates the uncertainty using a single inference from our representation, thereby reducing the total computation. We evaluate our method on two publicly available segmentation datasets of left atria in cardiac MRIs and of multiple organs in abdominal CTs. Our anatomically-aware method improves the segmentation accuracy over the state-of-the-art semi-supervised methods in terms of two commonly used evaluation metrics.

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

Deep learning underpins a wide range of applications in MRI, including reconstruction, artifact removal, and segmentation. However, progress has been driven largely by public datasets focused on brain and knee imaging, shaping how models are trained and evaluated. As a result, careful studies of the reliability of these models across diverse anatomical settings remain limited. In this work, we introduce MosaicMRI, a large and diverse collection of fully sampled raw musculoskeletal (MSK) MR measurements designed for training and evaluating machine-learning-based methods. MosaicMRI is the largest open-source raw MSK MRI dataset to date, comprising 2,671 volumes and 80,156 slices. The dataset offers substantial diversity in volume orientation (e.g., axial, sagittal), imaging contrasts (e.g., PD, T1, T2), anatomies (e.g., spine, knee, hip, ankle, and others), and numbers of acquisition coils. Using VarNet as a baseline for accelerated reconstruction task, we perform a comprehensive set of experiments to study scaling behavior with respect to both model capacity and dataset size. Interestingly, models trained on the combined anatomies significantly outperform anatomy-specific models in low-sample regimes, highlighting the benefits of anatomical diversity and the presence of exploitable cross-anatomical correlations. We further evaluate robustness and cross-anatomy generalization by training models on one anatomy (e.g., spine) and testing them on another (e.g., knee). Notably, we identify groups of body parts (e.g., foot and elbow) that generalize well with each other, and highlight that performance under domain shifts depends on both training set size, anatomy, and protocol-specific factors.

The detailed images produced by Magnetic Resonance Imaging (MRI) provide life-critical information for the diagnosis and treatment of prostate cancer. To provide standardized acquisition, interpretation and usage of the complex MRI images, the PI-RADS v2 guideline was proposed. An automated segmentation following the guideline facilitates consistent and precise lesion detection, staging and treatment. The guideline recommends a division of the prostate into four zones, PZ (peripheral zone), TZ (transition zone), DPU (distal prostatic urethra) and AFS (anterior fibromuscular stroma). Not every zone shares a boundary with the others and is present in every slice. Further, the representations captured by a single model might not suffice for all zones. This motivated us to design a dual-branch convolutional neural network (CNN), where each branch captures the representations of the connected zones separately. Further, the representations from different branches act complementary to each other at the second stage of training, where they are fine-tuned through an unsupervised loss. The loss penalises the difference in predictions from the two branches for the same class. We also incorporate multi-task learning in our framework to further improve the segmentation accuracy. The proposed approach improves the segmentation accuracy of the baseline (mean absolute symmetric distance) by 7.56%, 11.00%, 58.43% and 19.67% for PZ, TZ, DPU and AFS zones respectively.

Deep generative models have emerged as a transformative tool in medical imaging, offering substantial potential for synthetic data generation. However, recent empirical studies highlight a critical vulnerability: these models can memorize sensitive training data, posing significant risks of unauthorized patient information disclosure. Detecting memorization in generative models remains particularly challenging, necessitating scalable methods capable of identifying training data leakage across large sets of generated samples. In this work, we propose DeepSSIM, a novel self-supervised metric for quantifying memorization in generative models. DeepSSIM is trained to: i) project images into a learned embedding space and ii) force the cosine similarity between embeddings to match the ground-truth SSIM (Structural Similarity Index) scores computed in the image space. To capture domain-specific anatomical features, training incorporates structure-preserving augmentations, allowing DeepSSIM to estimate similarity reliably without requiring precise spatial alignment. We evaluate DeepSSIM in a case study involving synthetic brain MRI data generated by a Latent Diffusion Model (LDM) trained under memorization-prone conditions, using 2,195 MRI scans from two publicly available datasets (IXI and CoRR). Compared to state-of-the-art memorization metrics, DeepSSIM achieves superior performance, improving F1 scores by an average of +52.03% over the best existing method. Code and data of our approach are publicly available at the following link: https://github.com/brAIn-science/DeepSSIM.

Although the preservation of shape continuity and physiological anatomy is a natural assumption in the segmentation of medical images, it is often neglected by deep learning methods that mostly aim for the statistical modeling of input data as pixels rather than interconnected structures. In biological structures, however, organs are not separate entities; for example, in reality, a severed vessel is an indication of an underlying problem, but traditional segmentation models are not designed to strictly enforce the continuity of anatomy, potentially leading to inaccurate medical diagnoses. To address this issue, we propose a graph-based approach that enforces the continuity and connectivity of anatomical topology in medical images. Our method encodes the continuity of shapes as a graph constraint, ensuring that the network's predictions maintain this continuity. We evaluate our method on two public benchmarks on retinal vessel segmentation, showing significant improvements in connectivity metrics compared to traditional methods while getting better or on-par performance on segmentation metrics.

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

Vision-grounded medical report generation aims to produce clinically accurate descriptions of medical images, anchored in explicit visual evidence to improve interpretability and facilitate integration into clinical workflows. However, existing methods often rely on separately trained detection modules that require extensive expert annotations, introducing high labeling costs and limiting generalizability due to pathology distribution bias across datasets. To address these challenges, we propose Self-Supervised Anatomical Consistency Learning (SS-ACL) -- a novel and annotation-free framework that aligns generated reports with corresponding anatomical regions using simple textual prompts. SS-ACL constructs a hierarchical anatomical graph inspired by the invariant top-down inclusion structure of human anatomy, organizing entities by spatial location. It recursively reconstructs fine-grained anatomical regions to enforce intra-sample spatial alignment, inherently guiding attention maps toward visually relevant areas prompted by text. To further enhance inter-sample semantic alignment for abnormality recognition, SS-ACL introduces a region-level contrastive learning based on anatomical consistency. These aligned embeddings serve as priors for report generation, enabling attention maps to provide interpretable visual evidence. Extensive experiments demonstrate that SS-ACL, without relying on expert annotations, (i) generates accurate and visually grounded reports -- outperforming state-of-the-art methods by 10\% in lexical accuracy and 25\% in clinical efficacy, and (ii) achieves competitive performance on various downstream visual tasks, surpassing current leading visual foundation models by 8\% in zero-shot visual grounding.

Reconstructing complex structures from planar cross-sections is a challenging problem, with wide-reaching applications in medical imaging, manufacturing, and topography. Out-of-the-box point cloud reconstruction methods can often fail due to the data sparsity between slicing planes, while current bespoke methods struggle to reconstruct thin geometric structures and preserve topological continuity. This is important for medical applications where thin vessel structures are present in CT and MRI scans. This paper introduces CrossSDF, a novel approach for extracting a 3D signed distance field from 2D signed distances generated from planar contours. Our approach makes the training of neural SDFs contour-aware by using losses designed for the case where geometry is known within 2D slices. Our results demonstrate a significant improvement over existing methods, effectively reconstructing thin structures and producing accurate 3D models without the interpolation artifacts or over-smoothing of prior approaches.

Vision-language models are increasingly integrated into clinical workflows. However, existing benchmarks primarily assess performance on common anatomical presentations and fail to capture the challenges posed by rare variants. To address this gap, we introduce AdversarialAnatomyBench, the first benchmark comprising naturally occurring rare anatomical variants across diverse imaging modalities and anatomical regions. We call such variants that violate learned priors about "typical" human anatomy natural adversarial anatomy. Benchmarking 22 state-of-the-art VLMs with AdversarialAnatomyBench yielded three key insights. First, when queried with basic medical perception tasks, mean accuracy dropped from 74% on typical to 29% on atypical anatomy. Even the best-performing models, GPT-5, Gemini 2.5 Pro, and Llama 4 Maverick, showed performance drops of 41-51%. Second, model errors closely mirrored expected anatomical biases. Third, neither model scaling nor interventions, including bias-aware prompting and test-time reasoning, resolved these issues. These findings highlight a critical and previously unquantified limitation in current VLM: their poor generalization to rare anatomical presentations. AdversarialAnatomyBench provides a foundation for systematically measuring and mitigating anatomical bias in multimodal medical AI systems.

Accurate disease interpretation from radiology remains challenging due to imaging heterogeneity. Achieving expert-level diagnostic decisions requires integration of subtle image features with clinical knowledge. Yet major vision-language models (VLMs) treat images as holistic entities and overlook fine-grained image details that are vital for disease diagnosis. Clinicians analyze images by utilizing their prior medical knowledge and identify anatomical structures as important region of interests (ROIs). Inspired from this human-centric workflow, we introduce Anatomy-VLM, a fine-grained, vision-language model that incorporates multi-scale information. First, we design a model encoder to localize key anatomical features from entire medical images. Second, these regions are enriched with structured knowledge for contextually-aware interpretation. Finally, the model encoder aligns multi-scale medical information to generate clinically-interpretable disease prediction. Anatomy-VLM achieves outstanding performance on both in- and out-of-distribution datasets. We also validate the performance of Anatomy-VLM on downstream image segmentation tasks, suggesting that its fine-grained alignment captures anatomical and pathology-related knowledge. Furthermore, the Anatomy-VLM's encoder facilitates zero-shot anatomy-wise interpretation, providing its strong expert-level clinical interpretation capabilities.

Medical imaging is crucial for diagnosing a patient's health condition, and accurate segmentation of these images is essential for isolating regions of interest to ensure precise diagnosis and treatment planning. Existing methods primarily rely on bounding boxes or point-based prompts, while few have explored text-related prompts, despite clinicians often describing their observations and instructions in natural language. To address this gap, we first propose a RAG-based free-form text prompt generator, that leverages the domain corpus to generate diverse and realistic descriptions. Then, we introduce FLanS, a novel medical image segmentation model that handles various free-form text prompts, including professional anatomy-informed queries, anatomy-agnostic position-driven queries, and anatomy-agnostic size-driven queries. Additionally, our model also incorporates a symmetry-aware canonicalization module to ensure consistent, accurate segmentations across varying scan orientations and reduce confusion between the anatomical position of an organ and its appearance in the scan. FLanS is trained on a large-scale dataset of over 100k medical images from 7 public datasets. Comprehensive experiments demonstrate the model's superior language understanding and segmentation precision, along with a deep comprehension of the relationship between them, outperforming SOTA baselines on both in-domain and out-of-domain datasets.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

As lung cancer evolves, the presence of enlarged and potentially malignant lymph nodes must be assessed to properly estimate disease progression and select the best treatment strategy. Following the clinical guidelines, estimation of short-axis diameter and mediastinum station are paramount for correct diagnosis. A method for accurate and automatic segmentation is hence decisive for quantitatively describing lymph nodes. In this study, the use of 3D convolutional neural networks, either through slab-wise schemes or the leveraging of downsampled entire volumes, is investigated. Furthermore, the potential impact from simple ensemble strategies is considered. As lymph nodes have similar attenuation values to nearby anatomical structures, we suggest using the knowledge of other organs as prior information to guide the segmentation task. To assess the segmentation and instance detection performances, a 5-fold cross-validation strategy was followed over a dataset of 120 contrast-enhanced CT volumes. For the 1178 lymph nodes with a short-axis diameter geq10 mm, our best performing approach reached a patient-wise recall of 92%, a false positive per patient ratio of 5, and a segmentation overlap of 80.5%. The method performs similarly well across all stations. Fusing a slab-wise and a full volume approach within an ensemble scheme generated the best performances. The anatomical priors guiding strategy is promising, yet a larger set than four organs appears needed to generate an optimal benefit. A larger dataset is also mandatory, given the wide range of expressions a lymph node can exhibit (i.e., shape, location, and attenuation), and contrast uptake variations.

Image registration is fundamental in medical imaging, enabling precise alignment of anatomical structures for diagnosis, treatment planning, image-guided treatment or longitudinal monitoring. This work introduces IMPACT (Image Metric with Pretrained model-Agnostic Comparison for Transmodality registration), a generic semantic similarity metric designed for seamless integration into diverse image registration frameworks (such as Elastix and Voxelmorph). It compares deep learning-based features extracted from medical images without requiring task-specific training, ensuring broad applicability across various modalities. By leveraging the features of the large-scale pretrained TotalSegmentator models and the ability to integrate Segment Anything Model (SAM) and other large-scale segmentation networks, this approach offers significant advantages. It provides robust, scalable, and efficient solutions for multimodal image registration. The IMPACT loss was evaluated on five challenging registration tasks involving thoracic CT/CBCT, and pelvic MR/CT datasets. Quantitative metrics, such as Target Registration Error and Dice Similarity Coefficient, demonstrated significant improvements in anatomical alignment compared to baseline methods. Qualitative analyses further confirmed the increased robustness of the proposed metric in the face of noise, artifacts, and modality variations. IMPACT's versatility and efficiency make it a valuable tool for advancing registration performance in clinical and research applications, addressing critical challenges in multimodal medical imaging.

Medical image registration is a critical task that estimates the spatial correspondence between pairs of images. However, current traditional and deep-learning-based methods rely on similarity measures to generate a deforming field, which often results in disproportionate volume changes in dissimilar regions, especially in tumor regions. These changes can significantly alter the tumor size and underlying anatomy, which limits the practical use of image registration in clinical diagnosis. To address this issue, we have formulated image registration with tumors as a constraint problem that preserves tumor volumes while maximizing image similarity in other normal regions. Our proposed strategy involves a two-stage process. In the first stage, we use similarity-based registration to identify potential tumor regions by their volume change, generating a soft tumor mask accordingly. In the second stage, we propose a volume-preserving registration with a novel adaptive volume-preserving loss that penalizes the change in size adaptively based on the masks calculated from the previous stage. Our approach balances image similarity and volume preservation in different regions, i.e., normal and tumor regions, by using soft tumor masks to adjust the imposition of volume-preserving loss on each one. This ensures that the tumor volume is preserved during the registration process. We have evaluated our strategy on various datasets and network architectures, demonstrating that our method successfully preserves the tumor volume while achieving comparable registration results with state-of-the-art methods. Our codes is available at: https://dddraxxx.github.io/Volume-Preserving-Registration/.

Clinical decision-making relies heavily on understanding relative positions of anatomical structures and anomalies. Therefore, for Vision-Language Models (VLMs) to be applicable in clinical practice, the ability to accurately determine relative positions on medical images is a fundamental prerequisite. Despite its importance, this capability remains highly underexplored. To address this gap, we evaluate the ability of state-of-the-art VLMs, GPT-4o, Llama3.2, Pixtral, and JanusPro, and find that all models fail at this fundamental task. Inspired by successful approaches in computer vision, we investigate whether visual prompts, such as alphanumeric or colored markers placed on anatomical structures, can enhance performance. While these markers provide moderate improvements, results remain significantly lower on medical images compared to observations made on natural images. Our evaluations suggest that, in medical imaging, VLMs rely more on prior anatomical knowledge than on actual image content for answering relative position questions, often leading to incorrect conclusions. To facilitate further research in this area, we introduce the MIRP , Medical Imaging Relative Positioning, benchmark dataset, designed to systematically evaluate the capability to identify relative positions in medical images.

A large-scale image-text pair dataset has greatly contributed to the development of vision-language pre-training (VLP) models, which enable zero-shot or few-shot classification without costly annotation. However, in the medical domain, the scarcity of data remains a significant challenge for developing a powerful VLP model. In this paper, we tackle the lack of image-text data in chest X-ray by expanding image-label pair as image-text pair via general prompt and utilizing multiple images and multiple sections in a radiologic report. We also design two contrastive losses, named ICL and TCL, for learning study-level characteristics of medical images and reports, respectively. Our model outperforms the state-of-the-art models trained under the same conditions. Also, enlarged dataset improve the discriminative power of our pre-trained model for classification, while sacrificing marginal retrieval performance. Code is available at https://github.com/kakaobrain/cxr-clip.

Building on the success of deep learning models in cardiovascular structure segmentation, increasing attention has been focused on improving generalization and robustness, particularly in small, annotated datasets. Despite recent advancements, current approaches often face challenges such as overfitting and accuracy limitations, largely due to their reliance on large datasets and narrow optimization techniques. This paper introduces the UU-Mamba model, an extension of the U-Mamba architecture, designed to address these challenges in both cardiac and vascular segmentation. By incorporating Sharpness-Aware Minimization (SAM), the model enhances generalization by targeting flatter minima in the loss landscape. Additionally, we propose an uncertainty-aware loss function that combines region-based, distribution-based, and pixel-based components to improve segmentation accuracy by capturing both local and global features. While the UU-Mamba model has already demonstrated great performance, further testing is required to fully assess its generalization and robustness. We expand our evaluation by conducting new trials on the ImageCAS (coronary artery) and Aorta (aortic branches and zones) datasets, which present more complex segmentation challenges than the ACDC dataset (left and right ventricles) used in our previous work, showcasing the model's adaptability and resilience. We confirm UU-Mamba's superior performance over leading models such as TransUNet, Swin-Unet, nnUNet, and nnFormer. Moreover, we provide a more comprehensive evaluation of the model's robustness and segmentation accuracy, as demonstrated by extensive experiments.

Medical decision-making requires integrating diverse medical information, from imaging to clinical narratives. These medical modalities are often acquired in a many-to-many manner. However, current medical vision-language pretraining models (Med-VLPMs) fail to directly account for this many-to-many mapping in their model training and embeddings. To address this, we present Probabilistic Modality-Enhanced Diagnosis (ProbMED), a multimodal Med-VLPM that employs probabilistic contrastive learning to model distributions over embeddings rather than deterministic estimates. ProbMED aligns four distinct modalities -- chest X-rays, electrocardiograms, echocardiograms, and clinical text -- into a unified probabilistic embedding space. We use InfoNCE loss with Hellinger distance to integrate inter-modality distributions. We introduce a probabilistic synthetic sampling loss that captures modality-specific mean and variance to improve intra-modality binding. Extensive experiments across 13 medical datasets demonstrate that our model outperforms current Med-VLPMs in cross-modality retrieval, zero-shot, and few-shot classification. We also demonstrate the robust integration of multiple modalities for prognostication, showing improved intra- and inter-medical modality binding.

Identification of vessel structures of different sizes in biomedical images is crucial in the diagnosis of many neurodegenerative diseases. However, the sparsity of good-quality annotations of such images makes the task of vessel segmentation challenging. Deep learning offers an efficient way to segment vessels of different sizes by learning their high-level feature representations and the spatial continuity of such features across dimensions. Semi-supervised patch-based approaches have been effective in identifying small vessels of one to two voxels in diameter. This study focuses on improving the segmentation quality by considering the spatial correlation of the features using the Maximum Intensity Projection~(MIP) as an additional loss criterion. Two methods are proposed with the incorporation of MIPs of label segmentation on the single~(z-axis) and multiple perceivable axes of the 3D volume. The proposed MIP-based methods produce segmentations with improved vessel continuity, which is evident in visual examinations of ROIs. Patch-based training is improved by introducing an additional loss term, MIP loss, to penalise the predicted discontinuity of vessels. A training set of 14 volumes is selected from the StudyForrest dataset comprising of 18 7-Tesla 3D Time-of-Flight~(ToF) Magnetic Resonance Angiography (MRA) images. The generalisation performance of the method is evaluated using the other unseen volumes in the dataset. It is observed that the proposed method with multi-axes MIP loss produces better quality segmentations with a median Dice of 80.245 pm 0.129. Also, the method with single-axis MIP loss produces segmentations with a median Dice of 79.749 pm 0.109. Furthermore, a visual comparison of the ROIs in the predicted segmentation reveals a significant improvement in the continuity of the vessels when MIP loss is incorporated into training.

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We achieve this by training a neural network estimator that maps query locations to atlas coordinates via regression. Efficiency is improved by sparsely sampling the input, enabling response times of less than 1 ms without additional accelerator hardware. We demonstrate the utility of the algorithm in both CT and MRI modalities.

An increasing number of public datasets have shown a marked impact on automated organ segmentation and tumor detection. However, due to the small size and partially labeled problem of each dataset, as well as a limited investigation of diverse types of tumors, the resulting models are often limited to segmenting specific organs/tumors and ignore the semantics of anatomical structures, nor can they be extended to novel domains. To address these issues, we propose the CLIP-Driven Universal Model, which incorporates text embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models. This CLIP-based label encoding captures anatomical relationships, enabling the model to learn a structured feature embedding and segment 25 organs and 6 types of tumors. The proposed model is developed from an assembly of 14 datasets, using a total of 3,410 CT scans for training and then evaluated on 6,162 external CT scans from 3 additional datasets. We rank first on the Medical Segmentation Decathlon (MSD) public leaderboard and achieve state-of-the-art results on Beyond The Cranial Vault (BTCV). Additionally, the Universal Model is computationally more efficient (6x faster) compared with dataset-specific models, generalized better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks.

Statistical shape modeling (SSM) enables population-based quantitative analysis of anatomical shapes, informing clinical diagnosis. Deep learning approaches predict correspondence-based SSM directly from unsegmented 3D images but require calibrated uncertainty quantification, motivating Bayesian formulations. Variational information bottleneck DeepSSM (VIB-DeepSSM) is an effective, principled framework for predicting probabilistic shapes of anatomy from images with aleatoric uncertainty quantification. However, VIB is only half-Bayesian and lacks epistemic uncertainty inference. We derive a fully Bayesian VIB formulation and demonstrate the efficacy of two scalable implementation approaches: concrete dropout and batch ensemble. Additionally, we introduce a novel combination of the two that further enhances uncertainty calibration via multimodal marginalization. Experiments on synthetic shapes and left atrium data demonstrate that the fully Bayesian VIB network predicts SSM from images with improved uncertainty reasoning without sacrificing accuracy.

Self-supervised learning (SSL) approaches have recently shown substantial success in learning visual representations from unannotated images. Compared with photographic images, medical images acquired with the same imaging protocol exhibit high consistency in anatomy. To exploit this anatomical consistency, this paper introduces a novel SSL approach, called PEAC (patch embedding of anatomical consistency), for medical image analysis. Specifically, in this paper, we propose to learn global and local consistencies via stable grid-based matching, transfer pre-trained PEAC models to diverse downstream tasks, and extensively demonstrate that (1) PEAC achieves significantly better performance than the existing state-of-the-art fully/self-supervised methods, and (2) PEAC captures the anatomical structure consistency across views of the same patient and across patients of different genders, weights, and healthy statuses, which enhances the interpretability of our method for medical image analysis.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

Transfer learning has become a central paradigm in modern machine learning, yet it suffers from the long-standing problem of negative transfer, where leveraging source representations can harm rather than help performance on the target task. Although empirical remedies have been proposed, there remains little theoretical understanding of how to reliably avoid negative transfer. In this paper, we investigate a simple yet remarkably effective strategy: augmenting frozen, pretrained source-side features with a trainable target-side encoder that adapts target features to capture residual signals overlooked by models pretrained on the source data. We show this residual feature integration strategy is sufficient to provably prevent negative transfer, by establishing theoretical guarantees that it has no worse convergence rate than training from scratch under the informative class of target distributions up to logarithmic factors, and that the convergence rate can transition seamlessly from nonparametric to near-parametric when source representations are informative. To our knowledge, this is the first theoretical work that ensures protection against negative transfer. We carry out extensive numerical experiments across image, text and tabular benchmarks, and empirically verify that the method consistently safeguards performance under distribution shift, label noise, semantic perturbation, and class imbalance. We additionally demonstrate that this residual integration mechanism uniquely supports adapt-time multimodality extension, enabling a pretrained single-cell foundation model to incorporate spatial signals for lymph-node anatomical classification despite the source model being trained without them. Our study thus advances the theory of safe transfer learning, and provides a principled approach that is simple, robust, architecture-agnostic, and broadly applicable.

In this study, we present a method for generating automated anatomy segmentation datasets using a sequential process that involves nnU-Net-based pseudo-labeling and anatomy-guided pseudo-label refinement. By combining various fragmented knowledge bases, we generate a dataset of whole-body CT scans with 142 voxel-level labels for 533 volumes providing comprehensive anatomical coverage which experts have approved. Our proposed procedure does not rely on manual annotation during the label aggregation stage. We examine its plausibility and usefulness using three complementary checks: Human expert evaluation which approved the dataset, a Deep Learning usefulness benchmark on the BTCV dataset in which we achieve 85% dice score without using its training dataset, and medical validity checks. This evaluation procedure combines scalable automated checks with labor-intensive high-quality expert checks. Besides the dataset, we release our trained unified anatomical segmentation model capable of predicting 142 anatomical structures on CT data.

Semantic image segmentation, the process of classifying each pixel in an image into a particular class, plays an important role in many visual understanding systems. As the predominant criterion for evaluating the performance of statistical models, loss functions are crucial for shaping the development of deep learning-based segmentation algorithms and improving their overall performance. To aid researchers in identifying the optimal loss function for their particular application, this survey provides a comprehensive and unified review of 25 loss functions utilized in image segmentation. We provide a novel taxonomy and thorough review of how these loss functions are customized and leveraged in image segmentation, with a systematic categorization emphasizing their significant features and applications. Furthermore, to evaluate the efficacy of these methods in real-world scenarios, we propose unbiased evaluations of some distinct and renowned loss functions on established medical and natural image datasets. We conclude this review by identifying current challenges and unveiling future research opportunities. Finally, we have compiled the reviewed studies that have open-source implementations on our GitHub page.

Modeling medical vessel-like anatomy is challenging due to its intricate topology and sensitivity to dataset shifts. Consequently, task-specific models often suffer from topological inconsistencies, including artificial disconnections and spurious merges. Motivated by the promise of multimodal large language models (MLLMs) for zero-shot generalization, we propose TubeMLLM, a unified foundation model that couples structured understanding with controllable generation for medical vessel-like anatomy. By integrating topological priors through explicit natural language prompting and aligning them with visual representations in a shared-attention architecture, TubeMLLM significantly enhances topology-aware perception. Furthermore, we construct TubeMData, a pionner multimodal benchmark comprising comprehensive topology-centric tasks, and introduce an adaptive loss weighting strategy to emphasize topology-critical regions during training. Extensive experiments on fifteen diverse datasets demonstrate our superiority. Quantitatively, TubeMLLM achieves state-of-the-art out-of-distribution performance, substantially reducing global topological discrepancies on color fundus photography (decreasing the β_{0} number error from 37.42 to 8.58 compared to baselines). Notably, TubeMLLM exhibits exceptional zero-shot cross-modality transferring ability on unseen X-ray angiography, achieving a Dice score of 67.50% while significantly reducing the β_{0} error to 1.21. TubeMLLM also maintains robustness against degradations such as blur, noise, and low resolution. Furthermore, in topology-aware understanding tasks, the model achieves 97.38% accuracy in evaluating mask topological quality, significantly outperforming standard vision-language baselines.

Biomedical text embeddings have primarily been developed using research literature from PubMed, yet clinical cardiology practice relies heavily on procedural knowledge and specialized terminology found in comprehensive textbooks rather than research abstracts. This research practice gap limits the effectiveness of existing embedding models for clinical applications incardiology. This study trained CardioEmbed, a domain-specialized embedding model based on Qwen3-Embedding-8B, using contrastive learning on a curated corpus of seven comprehensive cardiology textbooks totaling approximately 150,000 sentences after deduplication. The model employs InfoNCE loss with in-batch negatives and achieves 99.60% retrieval accuracy on cardiac-specific semantic retrieval tasks, a +15.94 percentage point improvement over MedTE, the current state-of-the-art medical embedding model. On MTEB medical benchmarks, the model obtained BIOSSES 0.77 Spearman and SciFact 0.61 NDCG@10, indicating competitive performance on related biomedical domains. Domain-specialized training on comprehensive clinical textbooks yields near-perfect cardiology retrieval (99.60% Acc@1), improving over MedTE by +15.94 percentage points.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

Learning to regress 3D human body shape and pose (e.g.~SMPL parameters) from monocular images typically exploits losses on 2D keypoints, silhouettes, and/or part-segmentation when 3D training data is not available. Such losses, however, are limited because 2D keypoints do not supervise body shape and segmentations of people in clothing do not match projected minimally-clothed SMPL shapes. To exploit richer image information about clothed people, we introduce higher-level semantic information about clothing to penalize clothed and non-clothed regions of the image differently. To do so, we train a body regressor using a novel Differentiable Semantic Rendering - DSR loss. For Minimally-Clothed regions, we define the DSR-MC loss, which encourages a tight match between a rendered SMPL body and the minimally-clothed regions of the image. For clothed regions, we define the DSR-C loss to encourage the rendered SMPL body to be inside the clothing mask. To ensure end-to-end differentiable training, we learn a semantic clothing prior for SMPL vertices from thousands of clothed human scans. We perform extensive qualitative and quantitative experiments to evaluate the role of clothing semantics on the accuracy of 3D human pose and shape estimation. We outperform all previous state-of-the-art methods on 3DPW and Human3.6M and obtain on par results on MPI-INF-3DHP. Code and trained models are available for research at https://dsr.is.tue.mpg.de/.

Virtual immunohistochemistry (IHC) staining from hematoxylin and eosin (H&E) images can accelerate diagnostics by providing preliminary molecular insight directly from routine sections, reducing the need for repeat sectioning when tissue is limited. Existing methods improve realism through contrastive objectives, prototype matching, or domain alignment, yet the generator itself receives no direct guidance from pathology foundation models. We present UNIStainNet, a SPADE-UNet conditioned on dense spatial tokens from a frozen pathology foundation model (UNI), providing tissue-level semantic guidance for stain translation. A misalignment-aware loss suite preserves stain quantification accuracy, and learned stain embeddings enable a single model to serve multiple IHC markers simultaneously. On MIST, UNIStainNet achieves state-of-the-art distributional metrics on all four stains (HER2, Ki67, ER, PR) from a single unified model, where prior methods typically train separate per-stain models. On BCI, it also achieves the best distributional metrics. A tissue-type stratified failure analysis reveals that remaining errors are systematic, concentrating in non-tumor tissue. Code is available at https://github.com/facevoid/UNIStainNet.

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

Within the domain of medical analysis, extensive research has explored the potential of mutual learning between Masked Autoencoders(MAEs) and multimodal data. However, the impact of MAEs on intermodality remains a key challenge. We introduce MedFLIP, a Fast Language-Image Pre-training method for Medical analysis. We explore MAEs for zero-shot learning with crossed domains, which enhances the model's ability to learn from limited data, a common scenario in medical diagnostics. We verify that masking an image does not affect inter-modal learning. Furthermore, we propose the SVD loss to enhance the representation learning for characteristics of medical images, aiming to improve classification accuracy by leveraging the structural intricacies of such data. Our theory posits that masking encourages semantic preservation, robust feature extraction, regularization, domain adaptation, and invariance learning. Lastly, we validate using language will improve the zero-shot performance for the medical image analysis. MedFLIP's scaling of the masking process marks an advancement in the field, offering a pathway to rapid and precise medical image analysis without the traditional computational bottlenecks. Through experiments and validation, MedFLIP demonstrates efficient performance improvements, helps for future research and application in medical diagnostics.

Intraoperative registration of real-time ultrasound (iUS) to preoperative Magnetic Resonance Imaging (MRI) remains an unsolved problem due to severe modality-specific differences in appearance, resolution, and field-of-view. To address this, we propose a novel 3D cross-modal keypoint descriptor for MRI-iUS matching and registration. Our approach employs a patient-specific matching-by-synthesis approach, generating synthetic iUS volumes from preoperative MRI. This enables supervised contrastive training to learn a shared descriptor space. A probabilistic keypoint detection strategy is then employed to identify anatomically salient and modality-consistent locations. During training, a curriculum-based triplet loss with dynamic hard negative mining is used to learn descriptors that are i) robust to iUS artifacts such as speckle noise and limited coverage, and ii) rotation-invariant. At inference, the method detects keypoints in MR and real iUS images and identifies sparse matches, which are then used to perform rigid registration. Our approach is evaluated using 3D MRI-iUS pairs from the ReMIND dataset. Experiments show that our approach outperforms state-of-the-art keypoint matching methods across 11 patients, with an average precision of 69.8%. For image registration, our method achieves a competitive mean Target Registration Error of 2.39 mm on the ReMIND2Reg benchmark. Compared to existing iUS-MR registration approaches, our framework is interpretable, requires no manual initialization, and shows robustness to iUS field-of-view variation. Code, data and model weights are available at https://github.com/morozovdd/CrossKEY.

Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. While current AI-driven medical research predominantly focuses on knowledge graphs or natural text pretraining paradigms to incorporate medical knowledge, these approaches primarily rely on implicitly encoded knowledge within model parameters, neglecting task-specific knowledge required by diverse downstream tasks. To address this limitation, we propose Retrieval-Augmented Diagnosis (RAD), a novel framework that explicitly injects external knowledge into multimodal models directly on downstream tasks. Specifically, RAD operates through three key mechanisms: retrieval and refinement of disease-centered knowledge from multiple medical sources, a guideline-enhanced contrastive loss that constrains the latent distance between multi-modal features and guideline knowledge, and the dual transformer decoder that employs guidelines as queries to steer cross-modal fusion, aligning the models with clinical diagnostic workflows from guideline acquisition to feature extraction and decision-making. Moreover, recognizing the lack of quantitative evaluation of interpretability for multimodal diagnostic models, we introduce a set of criteria to assess the interpretability from both image and text perspectives. Extensive evaluations across four datasets with different anatomies demonstrate RAD's generalizability, achieving state-of-the-art performance. Furthermore, RAD enables the model to concentrate more precisely on abnormal regions and critical indicators, ensuring evidence-based, trustworthy diagnosis. Our code is available at https://github.com/tdlhl/RAD.

MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

Recent advancements in Large Language Models (LLMs) have drawn increasing attention since the learned embeddings pretrained on large-scale datasets have shown powerful ability in various downstream applications. However, whether the learned knowledge by LLMs can be transferred to clinical cardiology remains unknown. In this work, we aim to bridge this gap by transferring the knowledge of LLMs to clinical Electrocardiography (ECG). We propose an approach for cardiovascular disease diagnosis and automatic ECG diagnosis report generation. We also introduce an additional loss function by Optimal Transport (OT) to align the distribution between ECG and language embedding. The learned embeddings are evaluated on two downstream tasks: (1) automatic ECG diagnosis report generation, and (2) zero-shot cardiovascular disease detection. Our approach is able to generate high-quality cardiac diagnosis reports and also achieves competitive zero-shot classification performance even compared with supervised baselines, which proves the feasibility of transferring knowledge from LLMs to the cardiac domain.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

While 3D body reconstruction methods have made remarkable progress recently, it remains difficult to acquire the sufficiently accurate and numerous 3D supervisions required for training. In this paper, we propose KNOWN, a framework that effectively utilizes body KNOWledge and uNcertainty modeling to compensate for insufficient 3D supervisions. KNOWN exploits a comprehensive set of generic body constraints derived from well-established body knowledge. These generic constraints precisely and explicitly characterize the reconstruction plausibility and enable 3D reconstruction models to be trained without any 3D data. Moreover, existing methods typically use images from multiple datasets during training, which can result in data noise (e.g., inconsistent joint annotation) and data imbalance (e.g., minority images representing unusual poses or captured from challenging camera views). KNOWN solves these problems through a novel probabilistic framework that models both aleatoric and epistemic uncertainty. Aleatoric uncertainty is encoded in a robust Negative Log-Likelihood (NLL) training loss, while epistemic uncertainty is used to guide model refinement. Experiments demonstrate that KNOWN's body reconstruction outperforms prior weakly-supervised approaches, particularly on the challenging minority images.

Pediatric medical imaging presents unique challenges due to significant anatomical and developmental differences compared to adults. Direct application of segmentation models trained on adult data often yields suboptimal performance, particularly for small or rapidly evolving structures. To address these challenges, several strategies leveraging the nnU-Net framework have been proposed, differing along four key axes: (i) the fingerprint dataset (adult, pediatric, or a combination thereof) from which the Training Plan -including the network architecture-is derived; (ii) the Learning Set (adult, pediatric, or mixed), (iii) Data Augmentation parameters, and (iv) the Transfer learning method (finetuning versus continual learning). In this work, we introduce PSAT (Pediatric Segmentation Approaches via Adult Augmentations and Transfer learning), a systematic study that investigates the impact of these axes on segmentation performance. We benchmark the derived strategies on two pediatric CT datasets and compare them with state-of-theart methods, including a commercial radiotherapy solution. PSAT highlights key pitfalls and provides actionable insights for improving pediatric segmentation. Our experiments reveal that a training plan based on an adult fingerprint dataset is misaligned with pediatric anatomy-resulting in significant performance degradation, especially when segmenting fine structures-and that continual learning strategies mitigate institutional shifts, thus enhancing generalization across diverse pediatric datasets. The code is available at https://github.com/ICANS-Strasbourg/PSAT.

Humans can develop internal world models that encode common sense knowledge, telling them how the world works and predicting the consequences of their actions. This concept has emerged as a promising direction for establishing general-purpose machine-learning models in recent preliminary works, e.g., for visual representation learning. In this paper, we present CheXWorld, the first effort towards a self-supervised world model for radiographic images. Specifically, our work develops a unified framework that simultaneously models three aspects of medical knowledge essential for qualified radiologists, including 1) local anatomical structures describing the fine-grained characteristics of local tissues (e.g., architectures, shapes, and textures); 2) global anatomical layouts describing the global organization of the human body (e.g., layouts of organs and skeletons); and 3) domain variations that encourage CheXWorld to model the transitions across different appearance domains of radiographs (e.g., varying clarity, contrast, and exposure caused by collecting radiographs from different hospitals, devices, or patients). Empirically, we design tailored qualitative and quantitative analyses, revealing that CheXWorld successfully captures these three dimensions of medical knowledge. Furthermore, transfer learning experiments across eight medical image classification and segmentation benchmarks showcase that CheXWorld significantly outperforms existing SSL methods and large-scale medical foundation models. Code & pre-trained models are available at https://github.com/LeapLabTHU/CheXWorld.

3D medical image generation is essential for data augmentation and patient privacy, calling for reliable and efficient models suited for clinical practice. However, current methods suffer from limited anatomical fidelity, restricted axial length, and substantial computational cost, placing them beyond reach for regions with limited resources and infrastructure. We introduce TRACE, a framework that generates 3D medical images with spatiotemporal alignment using a 2D multimodal-conditioned diffusion approach. TRACE models sequential 2D slices as video frame pairs, combining segmentation priors and radiology reports for anatomical alignment, incorporating optical flow to sustain temporal coherence. During inference, an overlapping-frame strategy links frame pairs into a flexible length sequence, reconstructed into a spatiotemporally and anatomically aligned 3D volume. Experimental results demonstrate that TRACE effectively balances computational efficiency with preserving anatomical fidelity and spatiotemporal consistency. Code is available at: https://github.com/VinyehShaw/TRACE.

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

Humans effortlessly interpret images by parsing them into part-whole hierarchies; deep learning excels in learning multi-level feature spaces, but they often lack explicit coding of part-whole relations, a prominent property of medical imaging. To overcome this limitation, we introduce Adam-v2, a new self-supervised learning framework extending Adam [79] by explicitly incorporating part-whole hierarchies into its learning objectives through three key branches: (1) Localizability, acquiring discriminative representations to distinguish different anatomical patterns; (2) Composability, learning each anatomical structure in a parts-to-whole manner; and (3) Decomposability, comprehending each anatomical structure in a whole-to-parts manner. Experimental results across 10 tasks, compared to 11 baselines in zero-shot, few-shot transfer, and full fine-tuning settings, showcase Adam-v2's superior performance over large-scale medical models and existing SSL methods across diverse downstream tasks. The higher generality and robustness of Adam-v2's representations originate from its explicit construction of hierarchies for distinct anatomical structures from unlabeled medical images. Adam-v2 preserves a semantic balance of anatomical diversity and harmony in its embedding, yielding representations that are both generic and semantically meaningful, yet overlooked in existing SSL methods. All code and pretrained models are available at https://github.com/JLiangLab/Eden.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark. The code is made public at https://github.com/krishnabits001/domain_specific_cl.

In contrastive learning, two views of an original image, generated by different augmentations, are considered a positive pair, and their similarity is required to be high. Similarly, two views of distinct images form a negative pair, with encouraged low similarity. Typically, a single similarity measure, provided by a lone projection head, evaluates positive and negative sample pairs. However, due to diverse augmentation strategies and varying intra-sample similarity, views from the same image may not always be similar. Additionally, owing to inter-sample similarity, views from different images may be more akin than those from the same image. Consequently, enforcing high similarity for positive pairs and low similarity for negative pairs may be unattainable, and in some cases, such enforcement could detrimentally impact performance. To address this challenge, we propose using multiple projection heads, each producing a distinct set of features. Our pre-training loss function emerges from a solution to the maximum likelihood estimation over head-wise posterior distributions of positive samples given observations. This loss incorporates the similarity measure over positive and negative pairs, each re-weighted by an individual adaptive temperature, regulated to prevent ill solutions. Our approach, Adaptive Multi-Head Contrastive Learning (AMCL), can be applied to and experimentally enhances several popular contrastive learning methods such as SimCLR, MoCo, and Barlow Twins. The improvement remains consistent across various backbones and linear probing epochs, and becomes more significant when employing multiple augmentation methods.

Computed Tomography (CT) is one of the most widely used and diagnostically information-dense imaging modalities, covering critical organs such as the heart, lungs, liver, and colon. Clinical interpretation relies on both slice-driven local features (e.g., sub-centimeter nodules, lesion boundaries) and volume-driven spatial representations (e.g., tumor infiltration, inter-organ anatomical relations). However, existing Large Vision-Language Models (LVLMs) remain fragmented in CT slice versus volumetric understanding: slice-driven LVLMs show strong generalization but lack cross-slice spatial consistency, while volume-driven LVLMs explicitly capture volumetric semantics but suffer from coarse granularity and poor compatibility with slice inputs. The absence of a unified modeling paradigm constitutes a major bottleneck for the clinical translation of medical LVLMs. We present OmniCT, a powerful unified slice-volume LVLM for CT scenarios, which makes three contributions: (i) Spatial Consistency Enhancement (SCE): volumetric slice composition combined with tri-axial positional embedding that introduces volumetric consistency, and an MoE hybrid projection enables efficient slice-volume adaptation; (ii) Organ-level Semantic Enhancement (OSE): segmentation and ROI localization explicitly align anatomical regions, emphasizing lesion- and organ-level semantics; (iii) MedEval-CT: the largest slice-volume CT dataset and hybrid benchmark integrates comprehensive metrics for unified evaluation. OmniCT consistently outperforms existing methods with a substantial margin across diverse clinical tasks and satisfies both micro-level detail sensitivity and macro-level spatial reasoning. More importantly, it establishes a new paradigm for cross-modal medical imaging understanding. Our project is available at https://github.com/ZJU4HealthCare/OmniCT.

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

Self-supervised learning (SSL) has achieved major advances in natural images and video understanding, but challenges remain in domains like echocardiography (heart ultrasound) due to subtle anatomical structures, complex temporal dynamics, and the current lack of domain-specific pre-trained models. Existing SSL approaches such as contrastive, masked modeling, and clustering-based methods struggle with high intersample similarity, sensitivity to low PSNR inputs common in ultrasound, or aggressive augmentations that distort clinically relevant features. We present DISCOVR (Distilled Image Supervision for Cross Modal Video Representation), a self-supervised dual branch framework for cardiac ultrasound video representation learning. DISCOVR combines a clustering-based video encoder that models temporal dynamics with an online image encoder that extracts fine-grained spatial semantics. These branches are connected through a semantic cluster distillation loss that transfers anatomical knowledge from the evolving image encoder to the video encoder, enabling temporally coherent representations enriched with fine-grained semantic understanding. Evaluated on six echocardiography datasets spanning fetal, pediatric, and adult populations, DISCOVR outperforms both specialized video anomaly detection methods and state-of-the-art video-SSL baselines in zero-shot and linear probing setups, and achieves superior segmentation transfer.

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.

Vision--language models (VLMs) often process visual inputs through a pretrained vision encoder, followed by a projection into the language model's embedding space via a connector component. While crucial for modality fusion, the potential information loss induced by this projection step and its direct impact on model capabilities remain understudied. We introduce two complementary approaches to examine and quantify this loss by analyzing the latent representation space. First, we evaluate semantic information preservation by analyzing changes in k-nearest neighbor relationships between image representations, before and after projection. Second, we directly measure information loss by reconstructing visual embeddings from the projected representation, localizing loss at an image patch level. Experiments reveal that connectors substantially distort the local geometry of visual representations, with k-nearest neighbors diverging by 40--60\% post-projection, correlating with degradation in retrieval performance. The patch-level embedding reconstruction provides interpretable insights for model behavior on visually grounded question-answering tasks, finding that areas of high information loss reliably predict instances where models struggle.

Osteoporotic vertebral compression fractures (VCFs) are prevalent in the elderly population, typically assessed on computed tomography (CT) scans by evaluating vertebral height loss. This assessment helps determine the fracture's impact on spinal stability and the need for surgical intervention. However, clinical data indicate that many VCFs exhibit irregular compression, complicating accurate diagnosis. While deep learning methods have shown promise in aiding VCFs screening, they often lack interpretability and sufficient sensitivity, limiting their clinical applicability. To address these challenges, we introduce a novel vertebra synthesis-height loss quantification-VCFs grading framework. Our proposed model, HealthiVert-GAN, utilizes a coarse-to-fine synthesis network designed to generate pseudo-healthy vertebral images that simulate the pre-fracture state of fractured vertebrae. This model integrates three auxiliary modules that leverage the morphology and height information of adjacent healthy vertebrae to ensure anatomical consistency. Additionally, we introduce the Relative Height Loss of Vertebrae (RHLV) as a quantification metric, which divides each vertebra into three sections to measure height loss between pre-fracture and post-fracture states, followed by fracture severity classification using a Support Vector Machine (SVM). Our approach achieves state-of-the-art classification performance on both the Verse2019 dataset and our private dataset, and it provides cross-sectional distribution maps of vertebral height loss. This practical tool enhances diagnostic sensitivity in clinical settings and assisting in surgical decision-making. Our code is available: https://github.com/zhibaishouheilab/HealthiVert-GAN.

Vision-and-language models (VLMs) have been increasingly explored in the medical domain, particularly following the success of CLIP in general domain. However, unlike the relatively straightforward pairing of 2D images and text, curating large-scale paired data in the medical field for volumetric modalities such as CT scans remains a challenging and time-intensive process. This difficulty often limits the performance on downstream tasks. To address these challenges, we propose a novel vision-language pre-training (VLP) framework, termed as VELVET-Med, specifically designed for limited volumetric data such as 3D CT and associated radiology reports. Instead of relying on large-scale data collection, our method focuses on the development of effective pre-training objectives and model architectures. The key contributions are: 1) We incorporate uni-modal self-supervised learning into VLP framework, which are often underexplored in the existing literature. 2) We propose a novel language encoder, termed as TriBERT, for learning multi-level textual semantics. 3) We devise the hierarchical contrastive learning to capture multi-level vision-language correspondence. Using only 38,875 scan-report pairs, our approach seeks to uncover rich spatial and semantic relationships embedded in volumetric medical images and corresponding clinical narratives, thereby enhancing the generalization ability of the learned encoders. The resulting encoders exhibit strong transferability, achieving state-of-the-art performance across a wide range of downstream tasks, including 3D segmentation, cross-modal retrieval, visual question answering, and report generation.

Purpose: This study aims to explore training strategies to improve convolutional neural network-based image-to-image deformable registration for abdominal imaging. Methods: Different training strategies, loss functions, and transfer learning schemes were considered. Furthermore, an augmentation layer which generates artificial training image pairs on-the-fly was proposed, in addition to a loss layer that enables dynamic loss weighting. Results: Guiding registration using segmentations in the training step proved beneficial for deep-learning-based image registration. Finetuning the pretrained model from the brain MRI dataset to the abdominal CT dataset further improved performance on the latter application, removing the need for a large dataset to yield satisfactory performance. Dynamic loss weighting also marginally improved performance, all without impacting inference runtime. Conclusion: Using simple concepts, we improved the performance of a commonly used deep image registration architecture, VoxelMorph. In future work, our framework, DDMR, should be validated on different datasets to further assess its value.

Deep learning (DL) has become the dominant approach for medical image segmentation, yet ensuring the reliability and clinical applicability of these models requires addressing key challenges such as annotation variability, calibration, and uncertainty estimation. This is why we created the Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS), which highlights the critical role of multiple annotators in establishing a more comprehensive ground truth, emphasizing that segmentation is inherently subjective and that leveraging inter-annotator variability is essential for robust model evaluation. Seven teams participated in the challenge, submitting a variety of DL models evaluated using metrics such as Dice Similarity Coefficient (DSC), Expected Calibration Error (ECE), and Continuous Ranked Probability Score (CRPS). By incorporating consensus and dissensus ground truth, we assess how DL models handle uncertainty and whether their confidence estimates align with true segmentation performance. Our findings reinforce the importance of well-calibrated models, as better calibration is strongly correlated with the quality of the results. Furthermore, we demonstrate that segmentation models trained on diverse datasets and enriched with pre-trained knowledge exhibit greater robustness, particularly in cases deviating from standard anatomical structures. Notably, the best-performing models achieved high DSC and well-calibrated uncertainty estimates. This work underscores the need for multi-annotator ground truth, thorough calibration assessments, and uncertainty-aware evaluations to develop trustworthy and clinically reliable DL-based medical image segmentation models.

Respiratory sound classification is hindered by the limited size, high noise levels, and severe class imbalance of benchmark datasets like ICBHI 2017. While Transformer-based models offer powerful feature extraction capabilities, they are prone to overfitting and often converge to sharp minima in the loss landscape when trained on such constrained medical data. To address this, we introduce a framework that enhances the Audio Spectrogram Transformer (AST) using Sharpness-Aware Minimization (SAM). Instead of merely minimizing the training loss, our approach optimizes the geometry of the loss surface, guiding the model toward flatter minima that generalize better to unseen patients. We also implement a weighted sampling strategy to handle class imbalance effectively. Our method achieves a state-of-the-art score of 68.10% on the ICBHI 2017 dataset, outperforming existing CNN and hybrid baselines. More importantly, it reaches a sensitivity of 68.31%, a crucial improvement for reliable clinical screening. Further analysis using t-SNE and attention maps confirms that the model learns robust, discriminative features rather than memorizing background noise.

Mitotic figure (MF) detection in histopathology images is challenging due to large variations in slide scanners, staining protocols, tissue types, and the presence of artifacts. This paper presents a collection of training techniques - a bag of tricks - that enable robust, real-time MF detection across diverse domains. We build on the efficient RTMDet single stage object detector to achieve high inference speed suitable for clinical deployment. Our method addresses scanner variability and tumor heterogeneity via extensive multi-domain training data, balanced sampling, and careful augmentation. Additionally, we employ targeted, hard negative mining on necrotic and debris tissue to reduce false positives. In a grouped 5-fold cross-validation across multiple MF datasets, our model achieves an F1 score between 0.78 and 0.84. On the preliminary test set of the MItosis DOmain Generalization (MIDOG) 2025 challenge, our single-stage RTMDet-S based approach reaches an F1 of 0.81, outperforming larger models and demonstrating adaptability to new, unfamiliar domains. The proposed solution offers a practical trade-off between accuracy and speed, making it attractive for real-world clinical adoption.

We address the problem of regressing 3D human pose and shape from a single image, with a focus on 3D accuracy. The current best methods leverage large datasets of 3D pseudo-ground-truth (p-GT) and 2D keypoints, leading to robust performance. With such methods, we observe a paradoxical decline in 3D pose accuracy with increasing 2D accuracy. This is caused by biases in the p-GT and the use of an approximate camera projection model. We quantify the error induced by current camera models and show that fitting 2D keypoints and p-GT accurately causes incorrect 3D poses. Our analysis defines the invalid distances within which minimizing 2D and p-GT losses is detrimental. We use this to formulate a new loss Threshold-Adaptive Loss Scaling (TALS) that penalizes gross 2D and p-GT losses but not smaller ones. With such a loss, there are many 3D poses that could equally explain the 2D evidence. To reduce this ambiguity we need a prior over valid human poses but such priors can introduce unwanted bias. To address this, we exploit a tokenized representation of human pose and reformulate the problem as token prediction. This restricts the estimated poses to the space of valid poses, effectively providing a uniform prior. Extensive experiments on the EMDB and 3DPW datasets show that our reformulated keypoint loss and tokenization allows us to train on in-the-wild data while improving 3D accuracy over the state-of-the-art. Our models and code are available for research at https://tokenhmr.is.tue.mpg.de.

Foundation models for echocardiography often struggle to disentangle anatomical signal from the stochastic speckle and acquisition artifacts inherent to ultrasound. We present EchoJEPA, a foundation model trained on 18 million echocardiograms across 300K patients, representing the largest pretraining corpus for this modality to date. By leveraging a latent predictive objective, EchoJEPA learns robust anatomical representations that ignore speckle noise. We validate this using a novel multi-view probing framework with frozen backbones, where EchoJEPA outperforms leading baselines by approximately 20% in left ventricular ejection fraction (LVEF) estimation and 17% in right ventricular systolic pressure (RVSP) estimation. The model also exhibits remarkable sample efficiency, reaching 79% view classification accuracy with only 1% of labeled data versus 42% for the best baseline trained on 100%. Crucially, EchoJEPA demonstrates superior generalization, degrading by only 2% under physics-informed acoustic perturbations compared to 17% for competitors. Most remarkably, its zero-shot performance on pediatric patients surpasses fully fine-tuned baselines, establishing latent prediction as a superior paradigm for robust, generalizable medical AI.

Whole-body biometric recognition is a challenging multimodal task that integrates various biometric modalities, including face, gait, and body. This integration is essential for overcoming the limitations of unimodal systems. Traditionally, whole-body recognition involves deploying different models to process multiple modalities, achieving the final outcome by score-fusion (e.g., weighted averaging of similarity matrices from each model). However, these conventional methods may overlook the variations in score distributions of individual modalities, making it challenging to improve final performance. In this work, we present Quality-guided Mixture of score-fusion Experts (QME), a novel framework designed for improving whole-body biometric recognition performance through a learnable score-fusion strategy using a Mixture of Experts (MoE). We introduce a novel pseudo-quality loss for quality estimation with a modality-specific Quality Estimator (QE), and a score triplet loss to improve the metric performance. Extensive experiments on multiple whole-body biometric datasets demonstrate the effectiveness of our proposed approach, achieving state-of-the-art results across various metrics compared to baseline methods. Our method is effective for multimodal and multi-model, addressing key challenges such as model misalignment in the similarity score domain and variability in data quality.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

General image completion and extrapolation methods often fail on portrait images where parts of the human body need to be recovered - a task that requires accurate human body structure and appearance synthesis. We present a two-stage deep learning framework for tacking this problem. In the first stage, given a portrait image with an incomplete human body, we extract a complete, coherent human body structure through a human parsing network, which focuses on structure recovery inside the unknown region with the help of pose estimation. In the second stage, we use an image completion network to fill the unknown region, guided by the structure map recovered in the first stage. For realistic synthesis the completion network is trained with both perceptual loss and conditional adversarial loss. We evaluate our method on public portrait image datasets, and show that it outperforms other state-of-art general image completion methods. Our method enables new portrait image editing applications such as occlusion removal and portrait extrapolation. We further show that the proposed general learning framework can be applied to other types of images, e.g. animal images.

Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.

Medical vision-language pretraining increasingly relies on medical reports as large-scale supervisory signals; however, raw reports often exhibit substantial stylistic heterogeneity, variable length, and a considerable amount of image-irrelevant content. Although text normalization is frequently adopted as a preprocessing step in prior work, its design principles and empirical impact on vision-language pretraining remain insufficiently and systematically examined. In this study, we present MedTri, a deployable normalization framework for medical vision-language pretraining that converts free-text reports into a unified [Anatomical Entity: Radiologic Description + Diagnosis Category] triplet. This structured, anatomy-grounded normalization preserves essential morphological and spatial information while removing stylistic noise and image-irrelevant content, providing consistent and image-grounded textual supervision at scale. Across multiple datasets spanning both X-ray and computed tomography (CT) modalities, we demonstrate that structured, anatomy-grounded text normalization is an important factor in medical vision-language pretraining quality, yielding consistent improvements over raw reports and existing normalization baselines. In addition, we illustrate how this normalization can easily support modular text-level augmentation strategies, including knowledge enrichment and anatomy-grounded counterfactual supervision, which provide complementary gains in robustness and generalization without altering the core normalization process. Together, our results position structured text normalization as a critical and generalizable preprocessing component for medical vision-language learning, while MedTri provides this normalization platform. Code and data will be released at https://github.com/Arturia-Pendragon-Iris/MedTri.

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

In the domain of medical imaging, many supervised learning based methods for segmentation face several challenges such as high variability in annotations from multiple experts, paucity of labelled data and class imbalanced datasets. These issues may result in segmentations that lack the requisite precision for clinical analysis and can be misleadingly overconfident without associated uncertainty quantification. We propose the PULASki for biomedical image segmentation that accurately captures variability in expert annotations, even in small datasets. Our approach makes use of an improved loss function based on statistical distances in a conditional variational autoencoder structure (Probabilistic UNet), which improves learning of the conditional decoder compared to the standard cross-entropy particularly in class imbalanced problems. We analyse our method for two structurally different segmentation tasks (intracranial vessel and multiple sclerosis (MS) lesion) and compare our results to four well-established baselines in terms of quantitative metrics and qualitative output. Empirical results demonstrate the PULASKi method outperforms all baselines at the 5\% significance level. The generated segmentations are shown to be much more anatomically plausible than in the 2D case, particularly for the vessel task. Our method can also be applied to a wide range of multi-label segmentation tasks and and is useful for downstream tasks such as hemodynamic modelling (computational fluid dynamics and data assimilation), clinical decision making, and treatment planning.

Extracranial tissues visible on brain magnetic resonance imaging (MRI) may hold significant value for characterizing health conditions and clinical decision-making, yet they are rarely quantified. Current tools have not been widely validated, particularly in settings of developing brains or underlying pathology. We present TissUnet, a deep learning model that segments skull bone, subcutaneous fat, and muscle from routine three-dimensional T1-weighted MRI, with or without contrast enhancement. The model was trained on 155 paired MRI-computed tomography (CT) scans and validated across nine datasets covering a wide age range and including individuals with brain tumors. In comparison to AI-CT-derived labels from 37 MRI-CT pairs, TissUnet achieved a median Dice coefficient of 0.79 [IQR: 0.77-0.81] in a healthy adult cohort. In a second validation using expert manual annotations, median Dice was 0.83 [IQR: 0.83-0.84] in healthy individuals and 0.81 [IQR: 0.78-0.83] in tumor cases, outperforming previous state-of-the-art method. Acceptability testing resulted in an 89% acceptance rate after adjudication by a tie-breaker(N=108 MRIs), and TissUnet demonstrated excellent performance in the blinded comparative review (N=45 MRIs), including both healthy and tumor cases in pediatric populations. TissUnet enables fast, accurate, and reproducible segmentation of extracranial tissues, supporting large-scale studies on craniofacial morphology, treatment effects, and cardiometabolic risk using standard brain T1w MRI.

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

In this paper, we present a practical approach to improve anatomical shape accuracy in whole-body medical segmentation. Our analysis shows that a shape-focused toolkit can enhance segmentation performance by over 8%, without the need for model re-training or fine-tuning. In comparison, modifications to model architecture typically lead to marginal gains of less than 3%. Motivated by this observation, we introduce ShapeKit, a flexible and easy-to-integrate toolkit designed to refine anatomical shapes. This work highlights the underappreciated value of shape-based tools and calls attention to their potential impact within the medical segmentation community.

Deep learning has driven significant advances in medical image analysis, yet its adoption in clinical practice remains constrained by the large size and lack of transparency in modern models. Advances in interpretability techniques such as DL-Backtrace, Layer-wise Relevance Propagation, and Integrated Gradients make it possible to assess the contribution of individual components within neural networks trained on medical imaging tasks. In this work, we introduce an interpretability-guided pruning framework that reduces model complexity while preserving both predictive performance and transparency. By selectively retaining only the most relevant parts of each layer, our method enables targeted compression that maintains clinically meaningful representations. Experiments across multiple medical image classification benchmarks demonstrate that this approach achieves high compression rates with minimal loss in accuracy, paving the way for lightweight, interpretable models suited for real-world deployment in healthcare settings.

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

Precision medicine, such as patient-adaptive treatments assisted by medical image analysis, poses new challenges for segmentation algorithms in adapting to new patients, due to the large variability across different patients and the limited availability of annotated data for each patient. In this work, we propose a data-efficient segmentation algorithm, namely Part-aware Prompted Segment Anything Model (P^2SAM). Without any model fine-tuning, P^2SAM enables seamless adaptation to any new patients relying only on one-shot patient-specific data. We introduce a novel part-aware prompt mechanism to select multiple-point prompts based on the part-level features of the one-shot data, which can be extensively integrated into different promptable segmentation models, such as SAM and SAM 2. Moreover, to determine the optimal number of parts for each specific case, we propose a distribution-guided retrieval approach that further enhances the robustness of the part-aware prompt mechanism. P^2SAM improves the performance by +8.0% and +2.0% mean Dice score for two different patient-adaptive segmentation applications, respectively. In addition, P^2SAM also exhibits impressive generalizability in other adaptive segmentation tasks in the natural image domain, e.g., +6.4% mIoU within personalized object segmentation task. The code is available at: https://github.com/Zch0414/p2sam

The field of computer vision is undergoing a paradigm shift toward large-scale foundation model pre-training via self-supervised learning (SSL). Leveraging large volumes of unlabeled brain MRI data, such models can learn anatomical priors that improve few-shot performance in diverse neuroimaging tasks. However, most SSL frameworks are tailored to natural images, and their adaptation to capture multi-modal MRI information remains underexplored. This work proposes a modality-invariant representation learning setup and evaluates its effectiveness in stroke and epilepsy lesion segmentation, following large-scale pre-training. Experimental results suggest that despite successful cross-modality alignment, lesion segmentation primarily benefits from preserving fine-grained modality-specific features. Model checkpoints and code are made publicly available.

Driven by advancements in deep learning, computer-aided diagnoses have made remarkable progress. However, outside controlled laboratory settings, algorithms may encounter several challenges. In the medical domain, these difficulties often stem from limited data availability due to ethical and legal restrictions, as well as the high cost and time required for expert annotations-especially in the face of emerging or rare diseases. In this context, open-set recognition plays a vital role by identifying whether a sample belongs to one of the known classes seen during training or should be rejected as an unknown. Recent studies have shown that features learned in the later stages of deep neural networks are observed to cluster around their class means, which themselves are arranged as individual vertices of a regular simplex [32]. The proposed method introduces a loss function designed to reject samples of unknown classes effectively by penalizing open space regions using auxiliary datasets. This approach achieves significant performance gain across four MedMNIST datasets-BloodMNIST, OCTMNIST, DermaMNIST, TissueMNIST and a publicly available skin dataset [29] outperforming state-of-the-art techniques.

Segmentation of biomedical images can assist radiologists to make a better diagnosis and take decisions faster by helping in the detection of abnormalities, such as tumors. Manual or semi-automated segmentation, however, can be a time-consuming task. Most deep learning based automated segmentation methods are supervised and rely on manually segmented ground-truth. A possible solution for the problem would be an unsupervised deep learning based approach for automated segmentation, which this research work tries to address. We use a W-Net architecture and modified it, such that it can be applied to 3D volumes. In addition, to suppress noise in the segmentation we added attention gates to the skip connections. The loss for the segmentation output was calculated using soft N-Cuts and for the reconstruction output using SSIM. Conditional Random Fields were used as a post-processing step to fine-tune the results. The proposed method has shown promising results, with a dice coefficient of 0.88 for the liver segmentation compared against manual segmentation.

Current Vision-Language Models (VLMs) struggle to ground anatomical regions in 3D medical images and reason about them in a step-by-step manner, a key requirement of real-world diagnostic assessment. This ability is essential for aligning model outputs with the diagnostic workflows clinicians use in practice, enabling trustworthy clinician-AI collaboration. Existing 3D datasets provide localization labels, but none support this "grounded reasoning" ability. To address this gap, we introduce 3DReasonKnee, the first 3D grounded reasoning dataset for medical images, which provides 494k high-quality quintuples derived from 7,970 3D knee MRI volumes. Each quintuple includes: (1) the 3D MRI volume, (2) a diagnostic question targeting a specific anatomical region (3) a 3D bounding box localizing the relevant anatomical structures, (4) clinician-generated diagnostic reasoning steps that explicitly detail the 3D reasoning process, and (5) structured severity assessments for the relevant anatomical region. The creation and validation of 3DReasonKnee, involving over 450 hours of expert clinician time for manually segmenting MRIs and generating reasoning chains, ensures its superior quality and clinical relevance. We establish ReasonKnee-Bench to evaluate localization and diagnostic accuracy, providing insight into VLM ability to perform grounding and severity assessment across anatomical regions and diagnostic inquiries. We benchmark five state-of-the-art VLMs, providing baseline performance for ReasonKnee-Bench. By providing this unique resource of expert-annotated 3D reasoning pathways, 3DReasonKnee serves as a repository of orthopedic surgeons' diagnostic expertise and offers a vital testbed for advancing multimodal medical AI systems towards 3D, clinically aligned, localized decision-making capabilities. The dataset can be found in: https://huggingface.co/datasets/rajpurkarlab/3DReasonKnee

We propose a generalized focal loss function based on the Tversky index to address the issue of data imbalance in medical image segmentation. Compared to the commonly used Dice loss, our loss function achieves a better trade off between precision and recall when training on small structures such as lesions. To evaluate our loss function, we improve the attention U-Net model by incorporating an image pyramid to preserve contextual features. We experiment on the BUS 2017 dataset and ISIC 2018 dataset where lesions occupy 4.84% and 21.4% of the images area and improve segmentation accuracy when compared to the standard U-Net by 25.7% and 3.6%, respectively.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Accurate anatomical labeling and analysis of the pulmonary structure and its surrounding anatomy from thoracic CT is getting increasingly important for understanding the etilogy of abnormalities or supporting targetted therapy and early interventions. Whilst lung and airway cell atlases have been attempted, there is a lack of fine-grained morphological atlases that are clinically deployable. In this work, we introduce AirMorph, a robust, end-to-end deep learning pipeline enabling fully automatic and comprehensive airway anatomical labeling at lobar, segmental, and subsegmental resolutions that can be used to create digital atlases of the lung. Evaluated across large-scale multi-center datasets comprising diverse pulmonary conditions, the AirMorph consistently outperformed existing segmentation and labeling methods in terms of accuracy, topological consistency, and completeness. To simplify clinical interpretation, we further introduce a compact anatomical signature quantifying critical morphological airway features, including stenosis, ectasia, tortuosity, divergence, length, and complexity. When applied to various pulmonary diseases such as pulmonary fibrosis, emphysema, atelectasis, consolidation, and reticular opacities, it demonstrates strong discriminative power, revealing disease-specific morphological patterns with high interpretability and explainability. Additionally, AirMorph supports efficient automated branching pattern analysis, potentially enhancing bronchoscopic navigation planning and procedural safety, offering a valuable clinical tool for improved diagnosis, targeted treatment, and personalized patient care.

Automated radiology report generation offers an effective solution to alleviate radiologists' workload. However, most existing methods focus primarily on single or fixed-view images to model current disease conditions, which limits diagnostic accuracy and overlooks disease progression. Although some approaches utilize longitudinal data to track disease progression, they still rely on single images to analyze current visits. To address these issues, we propose enhanced contrastive learning with Multi-view Longitudinal data to facilitate chest X-ray Report Generation, named MLRG. Specifically, we introduce a multi-view longitudinal contrastive learning method that integrates spatial information from current multi-view images and temporal information from longitudinal data. This method also utilizes the inherent spatiotemporal information of radiology reports to supervise the pre-training of visual and textual representations. Subsequently, we present a tokenized absence encoding technique to flexibly handle missing patient-specific prior knowledge, allowing the model to produce more accurate radiology reports based on available prior knowledge. Extensive experiments on MIMIC-CXR, MIMIC-ABN, and Two-view CXR datasets demonstrate that our MLRG outperforms recent state-of-the-art methods, achieving a 2.3% BLEU-4 improvement on MIMIC-CXR, a 5.5% F1 score improvement on MIMIC-ABN, and a 2.7% F1 RadGraph improvement on Two-view CXR.

Current knowledge distillation approaches in semantic segmentation tend to adopt a holistic approach that treats all spatial locations equally. However, for dense prediction, students' predictions on edge regions are highly uncertain due to contextual information leakage, requiring higher spatial sensitivity knowledge than the body regions. To address this challenge, this paper proposes a novel approach called boundary-privileged knowledge distillation (BPKD). BPKD distills the knowledge of the teacher model's body and edges separately to the compact student model. Specifically, we employ two distinct loss functions: (i) edge loss, which aims to distinguish between ambiguous classes at the pixel level in edge regions; (ii) body loss, which utilizes shape constraints and selectively attends to the inner-semantic regions. Our experiments demonstrate that the proposed BPKD method provides extensive refinements and aggregation for edge and body regions. Additionally, the method achieves state-of-the-art distillation performance for semantic segmentation on three popular benchmark datasets, highlighting its effectiveness and generalization ability. BPKD shows consistent improvements across a diverse array of lightweight segmentation structures, including both CNNs and transformers, underscoring its architecture-agnostic adaptability. The code is available at https://github.com/AkideLiu/BPKD.

This paper addresses the challenge of localization of anatomical landmarks in knee X-ray images at different stages of osteoarthritis (OA). Landmark localization can be viewed as regression problem, where the landmark position is directly predicted by using the region of interest or even full-size images leading to large memory footprint, especially in case of high resolution medical images. In this work, we propose an efficient deep neural networks framework with an hourglass architecture utilizing a soft-argmax layer to directly predict normalized coordinates of the landmark points. We provide an extensive evaluation of different regularization techniques and various loss functions to understand their influence on the localization performance. Furthermore, we introduce the concept of transfer learning from low-budget annotations, and experimentally demonstrate that such approach is improving the accuracy of landmark localization. Compared to the prior methods, we validate our model on two datasets that are independent from the train data and assess the performance of the method for different stages of OA severity. The proposed approach demonstrates better generalization performance compared to the current state-of-the-art.

The objective of Radiology Report Generation (RRG) is to automatically generate coherent textual analyses of diseases based on radiological images, thereby alleviating the workload of radiologists. Current AI-based methods for RRG primarily focus on modifications to the encoder-decoder model architecture. To advance these approaches, this paper introduces an Organ-Regional Information Driven (ORID) framework which can effectively integrate multi-modal information and reduce the influence of noise from unrelated organs. Specifically, based on the LLaVA-Med, we first construct an RRG-related instruction dataset to improve organ-regional diagnosis description ability and get the LLaVA-Med-RRG. After that, we propose an organ-based cross-modal fusion module to effectively combine the information from the organ-regional diagnosis description and radiology image. To further reduce the influence of noise from unrelated organs on the radiology report generation, we introduce an organ importance coefficient analysis module, which leverages Graph Neural Network (GNN) to examine the interconnections of the cross-modal information of each organ region. Extensive experiments an1d comparisons with state-of-the-art methods across various evaluation metrics demonstrate the superior performance of our proposed method.

Medical image retrieval is essential for clinical decision-making and translational research, relying on discriminative visual representations. Yet, current methods remain fragmented, relying on separate architectures and training strategies for 2D, 3D, and video-based medical data. This modality-specific design hampers scalability and inhibits the development of unified representations. To enable unified learning, we curate a large-scale hybrid-modality dataset comprising 867,653 medical imaging samples, including 2D X-rays and ultrasounds, RGB endoscopy videos, and 3D CT scans. Leveraging this dataset, we train M3Ret, a unified visual encoder without any modality-specific customization. It successfully learns transferable representations using both generative (MAE) and contrastive (SimDINO) self-supervised learning (SSL) paradigms. Our approach sets a new state-of-the-art in zero-shot image-to-image retrieval across all individual modalities, surpassing strong baselines such as DINOv3 and the text-supervised BMC-CLIP. More remarkably, strong cross-modal alignment emerges without paired data, and the model generalizes to unseen MRI tasks, despite never observing MRI during pretraining, demonstrating the generalizability of purely visual self-supervision to unseen modalities. Comprehensive analyses further validate the scalability of our framework across model and data sizes. These findings deliver a promising signal to the medical imaging community, positioning M3Ret as a step toward foundation models for visual SSL in multimodal medical image understanding.

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

Recent advances in vision language models (VLMs) have enabled broad progress in the general medical field. However, pathology still remains a more challenging subdomain, with current pathology specific VLMs exhibiting limitations in both diagnostic accuracy and reasoning plausibility. Such shortcomings are largely attributable to the nature of current pathology datasets, which are primarily composed of image description pairs that lack the depth and structured diagnostic paradigms employed by real world pathologists. In this study, we leverage pathology textbooks and real world pathology experts to construct high-quality, reasoning-oriented datasets. Building on this, we introduce Patho-R1, a multimodal RL-based pathology Reasoner, trained through a three-stage pipeline: (1) continued pretraining on 3.5 million image-text pairs for knowledge infusion; (2) supervised fine-tuning on 500k high-quality Chain-of-Thought samples for reasoning incentivizing; (3) reinforcement learning using Group Relative Policy Optimization and Decoupled Clip and Dynamic sAmpling Policy Optimization strategies for multimodal reasoning quality refinement. To further assess the alignment quality of our dataset, we propose PathoCLIP, trained on the same figure-caption corpus used for continued pretraining. Comprehensive experimental results demonstrate that both PathoCLIP and Patho-R1 achieve robust performance across a wide range of pathology-related tasks, including zero-shot classification, cross-modal retrieval, Visual Question Answering, and Multiple Choice Question. Our project is available at the Patho-R1 repository: https://github.com/Wenchuan-Zhang/Patho-R1.

Ultrasound (US) imaging exhibits substantial heterogeneity across anatomical structures and acquisition protocols, posing significant challenges to the development of generalizable analysis models. Most existing methods are task-specific, limiting their suitability as clinically deployable foundation models. To address this limitation, the Foundation Model Challenge for Ultrasound Image Analysis (FM\_UIA~2026) introduces a large-scale multi-task benchmark comprising 27 subtasks across segmentation, classification, detection, and regression. In this paper, we present the official baseline for FM\_UIA~2026 based on a unified Multi-Head Multi-Task Learning (MH-MTL) framework that supports all tasks within a single shared network. The model employs an ImageNet-pretrained EfficientNet--B4 backbone for robust feature extraction, combined with a Feature Pyramid Network (FPN) to capture multi-scale contextual information. A task-specific routing strategy enables global tasks to leverage high-level semantic features, while dense prediction tasks exploit spatially detailed FPN representations. Training incorporates a composite loss with task-adaptive learning rate scaling and a cosine annealing schedule. Validation results demonstrate the feasibility and robustness of this unified design, establishing a strong and extensible baseline for ultrasound foundation model research. The code and dataset are publicly available at https://github.com/lijiake2408/Foundation-Model-Challenge-for-Ultrasound-Image-Analysis{GitHub}.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Federated Learning (FL) is a rising approach towards collaborative and privacy-preserving machine learning where large-scale medical datasets remain localized to each client. However, the issue of data heterogeneity among clients often compels local models to diverge, leading to suboptimal global models. To mitigate the impact of data heterogeneity on FL performance, we start with analyzing how FL training influence FL performance by decomposing the global loss into three terms: local loss, distribution shift loss and aggregation loss. Remarkably, our loss decomposition reveals that existing local training-based FL methods attempt to reduce the distribution shift loss, while the global aggregation-based FL methods propose better aggregation strategies to reduce the aggregation loss. Nevertheless, a comprehensive joint effort to minimize all three terms is currently limited in the literature, leading to subpar performance when dealing with data heterogeneity challenges. To fill this gap, we propose a novel FL method based on global loss decomposition, called FedLD, to jointly reduce these three loss terms. Our FedLD involves a margin control regularization in local training to reduce the distribution shift loss, and a principal gradient-based server aggregation strategy to reduce the aggregation loss. Notably, under different levels of data heterogeneity, our strategies achieve better and more robust performance on retinal and chest X-ray classification compared to other FL algorithms. Our code is available at https://github.com/Zeng-Shuang/FedLD.

Vision Transformers rely on positional embeddings and class tokens that encode fixed spatial priors. While effective for natural images, these priors may hinder generalization when spatial layout is weakly informative or inconsistent, a frequent condition in medical imaging and edge-deployed clinical systems. We introduce ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer), a compact Vision Transformer that removes both positional embeddings and the [CLS] token, achieving permutation invariance through global average pooling over patch representations. The term "Zero-token" specifically refers to removing the dedicated [CLS] aggregation token and positional embeddings; patch tokens remain unchanged and are processed normally. Adaptive residual projections preserve training stability in compact configurations while maintaining a strict parameter budget. Evaluation is performed across seven MedMNIST datasets spanning binary and multi-class tasks under a strict few-shot protocol (50 samples per class, fixed hyperparameters, five random seeds). The empirical analysis demonstrates regime-dependent behavior: ZACH-ViT (0.25M parameters, trained from scratch) achieves its strongest advantage on BloodMNIST and remains competitive with TransMIL on PathMNIST, while its relative advantage decreases on datasets with strong anatomical priors (OCTMNIST, OrganAMNIST), consistent with the architectural hypothesis. These findings support the view that aligning architectural inductive bias with data structure can be more important than pursuing universal benchmark dominance. Despite its minimal size and lack of pretraining, ZACH-ViT achieves competitive performance while maintaining sub-second inference times, supporting deployment in resource-constrained clinical environments. Code and models are available at https://github.com/Bluesman79/ZACH-ViT.

Lung diseases represent a significant global health challenge, with Chest X-Ray (CXR) being a key diagnostic tool due to their accessibility and affordability. Nonetheless, the detection of pulmonary lesions is often hindered by overlapping bone structures in CXR images, leading to potential misdiagnoses. To address this issue, we developed an end-to-end framework called BS-LDM, designed to effectively suppress bone in high-resolution CXR images. This framework is based on conditional latent diffusion models and incorporates a multi-level hybrid loss-constrained vector-quantized generative adversarial network which is crafted for perceptual compression, ensuring the preservation of details. To further enhance the framework's performance, we introduce offset noise and a temporal adaptive thresholding strategy. These additions help minimize discrepancies in generating low-frequency information, thereby improving the clarity of the generated soft tissue images. Additionally, we have compiled a high-quality bone suppression dataset named SZCH-X-Rays. This dataset includes 818 pairs of high-resolution CXR and dual-energy subtraction soft tissue images collected from a partner hospital. Moreover, we processed 241 data pairs from the JSRT dataset into negative images, which are more commonly used in clinical practice. Our comprehensive experimental and clinical evaluations reveal that BS-LDM excels in bone suppression, underscoring its significant clinical value.

Computed Tomography (CT) scan, which produces 3D volumetric medical data that can be viewed as hundreds of cross-sectional images (a.k.a. slices), provides detailed anatomical information for diagnosis. For radiologists, creating CT radiology reports is time-consuming and error-prone. A visual question answering (VQA) system that can answer radiologists' questions about some anatomical regions on the CT scan and even automatically generate a radiology report is urgently needed. However, existing VQA systems cannot adequately handle the CT radiology question answering (CTQA) task for: (1) anatomic complexity makes CT images difficult to understand; (2) spatial relationship across hundreds slices is difficult to capture. To address these issues, this paper proposes CT-Agent, a multimodal agentic framework for CTQA. CT-Agent adopts anatomically independent tools to break down the anatomic complexity; furthermore, it efficiently captures the across-slice spatial relationship with a global-local token compression strategy. Experimental results on two 3D chest CT datasets, CT-RATE and RadGenome-ChestCT, verify the superior performance of CT-Agent.

Large language models (LLMs) trained with next-word-prediction have achieved success as clinical foundation models. Representations from these language backbones yield strong linear probe performance across biomedical tasks, suggesting that patient semantics emerge from next-token prediction at scale. However, this paradigm treats patients as a document to be summarized rather than a dynamical system to be simulated; a patient's trajectory emerges from their state evolving under interventions and time, requiring models that simulate dynamics rather than predict tokens. To address this, we introduce SMB-Structure, a world model for structured EHR that grounds a joint-embedding prediction architecture (JEPA) with next-token prediction (SFT). SFT grounds our model to reconstruct future patient states in token space, while JEPA predicts those futures in latent space from the initial patient representation alone, forcing trajectory dynamics to be encoded before the next state is observed. We validate across two large-scale cohorts: Memorial Sloan Kettering (23,319 oncology patients; 323,000+ patient-years) and INSPECT (19,402 pulmonary embolism patients). Using a linear probe evaluated at multiple points along the disease trajectory, we demonstrate that our training paradigm learns embeddings that capture disease dynamics not recoverable by autoregressive baselines, enabling SMB-Structure to achieve competitive performance on complex tasks characterized by high patient heterogeneity. Model weights are available at https://huggingface.co/standardmodelbio/SMB-v1-1.7B-Structure.

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

Cross-entropy loss has long been the standard choice for training deep neural networks, yet it suffers from interpretability limitations, unbounded weight growth, and inefficiencies that can contribute to costly training dynamics. The harmonic loss is a distance-based alternative grounded in Euclidean geometry that improves interpretability and mitigates phenomena such as grokking, or delayed generalization on the test set. However, the study of harmonic loss remains narrow: only Euclidean distance is explored, and no systematic evaluation of computational efficiency or sustainability was conducted. We extend harmonic loss by systematically investigating a broad spectrum of distance metrics as replacements for the Euclidean distance. We comprehensively evaluate distance-tailored harmonic losses on both vision backbones and large language models. Our analysis is framed around a three-way evaluation of model performance, interpretability, and sustainability. On vision tasks, cosine distances provide the most favorable trade-off, consistently improving accuracy while lowering carbon emissions, whereas Bray-Curtis and Mahalanobis further enhance interpretability at varying efficiency costs. On language models, cosine-based harmonic losses improve gradient and learning stability, strengthen representation structure, and reduce emissions relative to cross-entropy and Euclidean heads. Our code is available at: https://anonymous.4open.science/r/rethinking-harmonic-loss-5BAB/.

Cancer progression arises from interactions across multiple biological layers, especially beyond morphological and across molecular layers that remain invisible to image-only models. To capture this broader biological landscape, we present EXAONE Path 2.5, a pathology foundation model that jointly models histologic, genomic, epigenetic and transcriptomic modalities, producing an integrated patient representation that reflects tumor biology more comprehensively. Our approach incorporates three key components: (1) multimodal SigLIP loss enabling all-pairwise contrastive learning across heterogeneous modalities, (2) a fragment-aware rotary positional encoding (F-RoPE) module that preserves spatial structure and tissue-fragment topology in WSI, and (3) domain-specialized internal foundation models for both WSI and RNA-seq to provide biologically grounded embeddings for robust multimodal alignment. We evaluate EXAONE Path 2.5 against six leading pathology foundation models across two complementary benchmarks: an internal real-world clinical dataset and the Patho-Bench benchmark covering 80 tasks. Our framework demonstrates high data and parameter efficiency, achieving on-par performance with state-of-the-art foundation models on Patho-Bench while exhibiting the highest adaptability in the internal clinical setting. These results highlight the value of biologically informed multimodal design and underscore the potential of integrated genotype-to-phenotype modeling for next-generation precision oncology.

Recent progress in 3D object generation has been fueled by the strong priors offered by diffusion models. However, existing models are tailored to specific tasks, accommodating only one modality at a time and necessitating retraining to change modalities. Given an image-to-3D model and a text prompt, a naive approach is to convert text prompts to images and then use the image-to-3D model for generation. This approach is both time-consuming and labor-intensive, resulting in unavoidable information loss during modality conversion. To address this, we introduce XBind, a unified framework for any-to-3D generation using cross-modal pre-alignment techniques. XBind integrates an multimodal-aligned encoder with pre-trained diffusion models to generate 3D objects from any modalities, including text, images, and audio. We subsequently present a novel loss function, termed Modality Similarity (MS) Loss, which aligns the embeddings of the modality prompts and the rendered images, facilitating improved alignment of the 3D objects with multiple modalities. Additionally, Hybrid Diffusion Supervision combined with a Three-Phase Optimization process improves the quality of the generated 3D objects. Extensive experiments showcase XBind's broad generation capabilities in any-to-3D scenarios. To our knowledge, this is the first method to generate 3D objects from any modality prompts. Project page: https://zeroooooooow1440.github.io/.

Cardiac MRI, crucial for evaluating heart structure and function, faces limitations like slow imaging and motion artifacts. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on MICCAI. CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techniques, physical modeling, and model complexity, thereby providing valuable insights for further developments in this field.

Counterfactual medical image generation effectively addresses data scarcity and enhances the interpretability of medical images. However, due to the complex and diverse pathological features of medical images and the imbalanced class distribution in medical data, generating high-quality and diverse medical images from limited data is significantly challenging. Additionally, to fully leverage the information in limited data, such as anatomical structure information and generate more structurally stable medical images while avoiding distortion or inconsistency. In this paper, in order to enhance the clinical relevance of generated data and improve the interpretability of the model, we propose a novel medical image generation framework, which generates independent pathological and structural features based on causal disentanglement and utilizes text-guided modeling of pathological features to regulate the generation of counterfactual images. First, we achieve feature separation through causal disentanglement and analyze the interactions between features. Here, we introduce group supervision to ensure the independence of pathological and identity features. Second, we leverage a diffusion model guided by pathological findings to model pathological features, enabling the generation of diverse counterfactual images. Meanwhile, we enhance accuracy by leveraging a large language model to extract lesion severity and location from medical reports. Additionally, we improve the performance of the latent diffusion model on long-tailed categories through initial noise optimization.