Daily Papers

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.

UV map estimation is used in computer vision for detailed analysis of human posture or activity. Previous methods assign pixels to body model vertices by comparing pixel descriptors independently, without enforcing global coherence or plausibility in the UV map. We propose Pose-Constrained Continuous Surface Embeddings (PC-CSE), which integrates estimated 2D human pose into the pixel-to-vertex assignment process. The pose provides global anatomical constraints, ensuring that UV maps remain coherent while preserving local precision. Evaluation on DensePose COCO demonstrates consistent improvement, regardless of the chosen 2D human pose model. Whole-body poses offer better constraints by incorporating additional details about the hands and feet. Conditioning UV maps with human pose reduces invalid mappings and enhances anatomical plausibility. In addition, we highlight inconsistencies in the ground-truth annotations.

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.

In this work we address the problem of landmark-based segmentation for anatomical structures. We propose HybridGNet, an encoder-decoder neural architecture which combines standard convolutions for image feature encoding, with graph convolutional neural networks to decode plausible representations of anatomical structures. We benchmark the proposed architecture considering other standard landmark and pixel-based models for anatomical segmentation in chest x-ray images, and found that HybridGNet is more robust to image occlusions. We also show that it can be used to construct landmark-based segmentations from pixel level annotations. Our experimental results suggest that HybridGNet produces accurate and anatomically plausible landmark-based segmentations, by naturally incorporating shape constraints within the decoding process via spectral convolutions.

Recently, diffusion-based methods for monocular 3D human pose estimation have achieved state-of-the-art (SOTA) performance by directly regressing the 3D joint coordinates from the 2D pose sequence. Although some methods decompose the task into bone length and bone direction prediction based on the human anatomical skeleton to explicitly incorporate more human body prior constraints, the performance of these methods is significantly lower than that of the SOTA diffusion-based methods. This can be attributed to the tree structure of the human skeleton. Direct application of the disentangled method could amplify the accumulation of hierarchical errors, propagating through each hierarchy. Meanwhile, the hierarchical information has not been fully explored by the previous methods. To address these problems, a Disentangled Diffusion-based 3D Human Pose Estimation method with Hierarchical Spatial and Temporal Denoiser is proposed, termed DDHPose. In our approach: (1) We disentangle the 3D pose and diffuse the bone length and bone direction during the forward process of the diffusion model to effectively model the human pose prior. A disentanglement loss is proposed to supervise diffusion model learning. (2) For the reverse process, we propose Hierarchical Spatial and Temporal Denoiser (HSTDenoiser) to improve the hierarchical modeling of each joint. Our HSTDenoiser comprises two components: the Hierarchical-Related Spatial Transformer (HRST) and the Hierarchical-Related Temporal Transformer (HRTT). HRST exploits joint spatial information and the influence of the parent joint on each joint for spatial modeling, while HRTT utilizes information from both the joint and its hierarchical adjacent joints to explore the hierarchical temporal correlations among joints. Code and models are available at https://github.com/Andyen512/DDHPose

Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse clinical scenarios. Constraint by the high cost of collecting and labeling 3D medical data, most of the deep learning models to date are driven by datasets with a limited number of organs of interest or samples, which still limits the power of modern deep models and makes it difficult to provide a fully comprehensive and fair estimate of various methods. To mitigate the limitations, we present AMOS, a large-scale, diverse, clinical dataset for abdominal organ segmentation. AMOS provides 500 CT and 100 MRI scans collected from multi-center, multi-vendor, multi-modality, multi-phase, multi-disease patients, each with voxel-level annotations of 15 abdominal organs, providing challenging examples and test-bed for studying robust segmentation algorithms under diverse targets and scenarios. We further benchmark several state-of-the-art medical segmentation models to evaluate the status of the existing methods on this new challenging dataset. We have made our datasets, benchmark servers, and baselines publicly available, and hope to inspire future research. Information can be found at https://amos22.grand-challenge.org.

Learning spatial-temporal correspondences in cardiac motion from images is important for understanding the underlying dynamics of cardiac anatomical structures. Many methods explicitly impose smoothness constraints such as the L_2 norm on the displacement vector field (DVF), while usually ignoring biomechanical feasibility in the transformation. Other geometric constraints either regularize specific regions of interest such as imposing incompressibility on the myocardium or introduce additional steps such as training a separate network-based regularizer on physically simulated datasets. In this work, we propose an explicit biomechanics-informed prior as regularization on the predicted DVF in modeling a more generic biomechanically plausible transformation within all cardiac structures without introducing additional training complexity. We validate our methods on two publicly available datasets in the context of 2D MRI data and perform extensive experiments to illustrate the effectiveness and robustness of our proposed methods compared to other competing regularization schemes. Our proposed methods better preserve biomechanical properties by visual assessment and show advantages in segmentation performance using quantitative evaluation metrics. The code is publicly available at https://github.com/Voldemort108X/bioinformed_reg.

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/.

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.

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.

In 2015 we began a sub-challenge at the EndoVis workshop at MICCAI in Munich using endoscope images of ex-vivo tissue with automatically generated annotations from robot forward kinematics and instrument CAD models. However, the limited background variation and simple motion rendered the dataset uninformative in learning about which techniques would be suitable for segmentation in real surgery. In 2017, at the same workshop in Quebec we introduced the robotic instrument segmentation dataset with 10 teams participating in the challenge to perform binary, articulating parts and type segmentation of da Vinci instruments. This challenge included realistic instrument motion and more complex porcine tissue as background and was widely addressed with modifications on U-Nets and other popular CNN architectures. In 2018 we added to the complexity by introducing a set of anatomical objects and medical devices to the segmented classes. To avoid over-complicating the challenge, we continued with porcine data which is dramatically simpler than human tissue due to the lack of fatty tissue occluding many organs.

Parametric body models offer expressive 3D representation of humans across a wide range of poses, shapes, and facial expressions, typically derived by learning a basis over registered 3D meshes. However, existing human mesh modeling approaches struggle to capture detailed variations across diverse body poses and shapes, largely due to limited training data diversity and restrictive modeling assumptions. Moreover, the common paradigm first optimizes the external body surface using a linear basis, then regresses internal skeletal joints from surface vertices. This approach introduces problematic dependencies between internal skeleton and outer soft tissue, limiting direct control over body height and bone lengths. To address these issues, we present ATLAS, a high-fidelity body model learned from 600k high-resolution scans captured using 240 synchronized cameras. Unlike previous methods, we explicitly decouple the shape and skeleton bases by grounding our mesh representation in the human skeleton. This decoupling enables enhanced shape expressivity, fine-grained customization of body attributes, and keypoint fitting independent of external soft-tissue characteristics. ATLAS outperforms existing methods by fitting unseen subjects in diverse poses more accurately, and quantitative evaluations show that our non-linear pose correctives more effectively capture complex poses compared to linear models.

Injury to the cervical spinal cord can cause quadriplegia, impairing muscle function in all four limbs. People with impaired hand function and mobility encounter significant difficulties in carrying out essential self-care and household tasks. Despite the impairment of their neural drive, their volitional myoelectric activity is often partially preserved. High-density electromyography (HDEMG) can detect this myoelectric activity, which can serve as control inputs to assistive devices. Previous HDEMG-controlled robotic interfaces have primarily been limited to controlling table-mounted robot arms. These have constrained reach capabilities. Instead, the ability to control mobile manipulators, which have no such workspace constraints, could allow individuals with quadriplegia to perform a greater variety of assistive tasks, thus restoring independence and reducing caregiver workload. In this study, we introduce a non-invasive wearable HDEMG interface with real-time myoelectric hand gesture recognition, enabling both coarse and fine control over the intricate mobility and manipulation functionalities of an 8 degree-of-freedom mobile manipulator. Our evaluation, involving 13 participants engaging in challenging self-care and household activities, demonstrates the potential of our wearable HDEMG system to profoundly enhance user independence by enabling non-invasive control of a mobile manipulator.

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.

Sexual dimorphism is a critical factor in many biological and medical research fields. In biomechanics and bioengineering, understanding sex differences is crucial for studying musculoskeletal conditions such as temporomandibular disorder (TMD). This paper focuses on the association between the craniofacial skeletal morphology and temporomandibular joint (TMJ) related masticatory muscle attachments to discern sex differences. Data were collected from 10 male and 11 female cadaver heads to investigate sex-specific relationships between the skull and muscles. We propose a conditional cross-covariance reduction (CCR) model, designed to examine the dynamic association between two sets of random variables conditioned on a third binary variable (e.g., sex), highlighting the most distinctive sex-related relationships between skull and muscle attachments in the human cadaver data. Under the CCR model, we employ a sparse singular value decomposition algorithm and introduce a sequential permutation for selecting sparsity (SPSS) method to select important variables and to determine the optimal number of selected variables.

Significant advancements have been made in developing parametric models for digital humans, with various approaches concentrating on parts such as the human body, hand, or face. Nevertheless, connectors such as the neck have been overlooked in these models, with rich anatomical priors often unutilized. In this paper, we introduce HACK (Head-And-neCK), a novel parametric model for constructing the head and cervical region of digital humans. Our model seeks to disentangle the full spectrum of neck and larynx motions, facial expressions, and appearance variations, providing personalized and anatomically consistent controls, particularly for the neck regions. To build our HACK model, we acquire a comprehensive multi-modal dataset of the head and neck under various facial expressions. We employ a 3D ultrasound imaging scheme to extract the inner biomechanical structures, namely the precise 3D rotation information of the seven vertebrae of the cervical spine. We then adopt a multi-view photometric approach to capture the geometry and physically-based textures of diverse subjects, who exhibit a diverse range of static expressions as well as sequential head-and-neck movements. Using the multi-modal dataset, we train the parametric HACK model by separating the 3D head and neck depiction into various shape, pose, expression, and larynx blendshapes from the neutral expression and the rest skeletal pose. We adopt an anatomically-consistent skeletal design for the cervical region, and the expression is linked to facial action units for artist-friendly controls. HACK addresses the head and neck as a unified entity, offering more accurate and expressive controls, with a new level of realism, particularly for the neck regions. This approach has significant benefits for numerous applications and enables inter-correlation analysis between head and neck for fine-grained motion synthesis and 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.

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.

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.

Imposing known physical constraints, such as conservation laws, during neural network training introduces an inductive bias that can improve accuracy, reliability, convergence, and data efficiency for modeling physical dynamics. While such constraints can be softly imposed via loss function penalties, recent advancements in differentiable physics and optimization improve performance by incorporating PDE-constrained optimization as individual layers in neural networks. This enables a stricter adherence to physical constraints. However, imposing hard constraints significantly increases computational and memory costs, especially for complex dynamical systems. This is because it requires solving an optimization problem over a large number of points in a mesh, representing spatial and temporal discretizations, which greatly increases the complexity of the constraint. To address this challenge, we develop a scalable approach to enforce hard physical constraints using Mixture-of-Experts (MoE), which can be used with any neural network architecture. Our approach imposes the constraint over smaller decomposed domains, each of which is solved by an "expert" through differentiable optimization. During training, each expert independently performs a localized backpropagation step by leveraging the implicit function theorem; the independence of each expert allows for parallelization across multiple GPUs. Compared to standard differentiable optimization, our scalable approach achieves greater accuracy in the neural PDE solver setting for predicting the dynamics of challenging non-linear systems. We also improve training stability and require significantly less computation time during both training and inference stages.

We present a multilinear statistical model of the human tongue that captures anatomical and tongue pose related shape variations separately. The model is derived from 3D magnetic resonance imaging data of 11 speakers sustaining speech related vocal tract configurations. The extraction is performed by using a minimally supervised method that uses as basis an image segmentation approach and a template fitting technique. Furthermore, it uses image denoising to deal with possibly corrupt data, palate surface information reconstruction to handle palatal tongue contacts, and a bootstrap strategy to refine the obtained shapes. Our evaluation concludes that limiting the degrees of freedom for the anatomical and speech related variations to 5 and 4, respectively, produces a model that can reliably register unknown data while avoiding overfitting effects. Furthermore, we show that it can be used to generate a plausible tongue animation by tracking sparse motion capture data.

Machine learning models are often trained to predict the outcome resulting from a human decision. For example, if a doctor decides to test a patient for disease, will the patient test positive? A challenge is that historical decision-making determines whether the outcome is observed: we only observe test outcomes for patients doctors historically tested. Untested patients, for whom outcomes are unobserved, may differ from tested patients along observed and unobserved dimensions. We propose a Bayesian model class which captures this setting. The purpose of the model is to accurately estimate risk for both tested and untested patients. Estimating this model is challenging due to the wide range of possibilities for untested patients. To address this, we propose two domain constraints which are plausible in health settings: a prevalence constraint, where the overall disease prevalence is known, and an expertise constraint, where the human decision-maker deviates from purely risk-based decision-making only along a constrained feature set. We show theoretically and on synthetic data that domain constraints improve parameter inference. We apply our model to a case study of cancer risk prediction, showing that the model's inferred risk predicts cancer diagnoses, its inferred testing policy captures known public health policies, and it can identify suboptimalities in test allocation. Though our case study is in healthcare, our analysis reveals a general class of domain constraints which can improve model estimation in many settings.

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.

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.

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.

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

The integration of Computer-Assisted Diagnosis (CAD) with Large Language Models (LLMs) holds great potential in clinical applications, specifically in the roles of virtual family doctors and clinic assistants. However, current works in this field are plagued by limitations, specifically a restricted scope of applicable image domains and the provision of unreliable medical advice. This restricts their overall processing capabilities. Furthermore, the mismatch in writing style between LLMs and radiologists undermines their practical usefulness. To tackle these challenges, we introduce ChatCAD+, which is designed to be universal and reliable. It is capable of handling medical images from diverse domains and leveraging up-to-date information from reputable medical websites to provide reliable medical advice. Additionally, it incorporates a template retrieval system that improves report generation performance via exemplar reports. This approach ensures greater consistency with the expertise of human professionals. The source code is available at https://github.com/zhaozh10/ChatCAD.

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.

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.

When applying offline reinforcement learning (RL) in healthcare scenarios, the out-of-distribution (OOD) issues pose significant risks, as inappropriate generalization beyond clinical expertise can result in potentially harmful recommendations. While existing methods like conservative Q-learning (CQL) attempt to address the OOD issue, their effectiveness is limited by only constraining action selection by suppressing uncertain actions. This action-only regularization imitates clinician actions that prioritize short-term rewards, but it fails to regulate downstream state trajectories, thereby limiting the discovery of improved long-term treatment strategies. To safely improve policy beyond clinician recommendations while ensuring that state-action trajectories remain in-distribution, we propose Offline Guarded Safe Reinforcement Learning (OGSRL), a theoretically grounded model-based offline RL framework. OGSRL introduces a novel dual constraint mechanism for improving policy with reliability and safety. First, the OOD guardian is established to specify clinically validated regions for safe policy exploration. By constraining optimization within these regions, it enables the reliable exploration of treatment strategies that outperform clinician behavior by leveraging the full patient state history, without drifting into unsupported state-action trajectories. Second, we introduce a safety cost constraint that encodes medical knowledge about physiological safety boundaries, providing domain-specific safeguards even in areas where training data might contain potentially unsafe interventions. Notably, we provide theoretical guarantees on safety and near-optimality: policies that satisfy these constraints remain in safe and reliable regions and achieve performance close to the best possible policy supported by the data.

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.

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

The aim of this article is to introduce a new methodology for constructing morphings between shapes that have identical topology. This morphing is obtained by deforming a reference shape, through the resolution of a sequence of linear elasticity equations, onto the target shape. In particular, our approach does not assume any knowledge of a boundary parametrization. Furthermore, we demonstrate how constraints can be imposed on specific points, lines and surfaces in the reference domain to ensure alignment with their counterparts in the target domain after morphing. Additionally, we show how the proposed methodology can be integrated in an offline and online paradigm, which is useful in reduced-order modeling scenarii involving variable shapes. This framework facilitates the efficient computation of the morphings in various geometric configurations, thus improving the versatility and applicability of the approach. The methodology is illustrated on the regression problem of the drag and lift coefficients of airfoils of non-parameterized variable shapes.

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.

Recent advancements in Gaussian-based human body reconstruction have achieved notable success in creating animatable avatars. However, there are ongoing challenges to fully exploit the SMPL model's prior knowledge and enhance the visual fidelity of these models to achieve more refined avatar reconstructions. In this paper, we introduce AniGaussian which addresses the above issues with two insights. First, we propose an innovative pose guided deformation strategy that effectively constrains the dynamic Gaussian avatar with SMPL pose guidance, ensuring that the reconstructed model not only captures the detailed surface nuances but also maintains anatomical correctness across a wide range of motions. Second, we tackle the expressiveness limitations of Gaussian models in representing dynamic human bodies. We incorporate rigid-based priors from previous works to enhance the dynamic transform capabilities of the Gaussian model. Furthermore, we introduce a split-with-scale strategy that significantly improves geometry quality. The ablative study experiment demonstrates the effectiveness of our innovative model design. Through extensive comparisons with existing methods, AniGaussian demonstrates superior performance in both qualitative result and quantitative metrics.

In this paper, we introduce a method for reconstructing 3D humans from a single image using a biomechanically accurate skeleton model. To achieve this, we train a transformer that takes an image as input and estimates the parameters of the model. Due to the lack of training data for this task, we build a pipeline to produce pseudo ground truth model parameters for single images and implement a training procedure that iteratively refines these pseudo labels. Compared to state-of-the-art methods for 3D human mesh recovery, our model achieves competitive performance on standard benchmarks, while it significantly outperforms them in settings with extreme 3D poses and viewpoints. Additionally, we show that previous reconstruction methods frequently violate joint angle limits, leading to unnatural rotations. In contrast, our approach leverages the biomechanically plausible degrees of freedom making more realistic joint rotation estimates. We validate our approach across multiple human pose estimation benchmarks. We make the code, models and data available at: https://isshikihugh.github.io/HSMR/

We present SpineTrack, the first comprehensive dataset for 2D spine pose estimation in unconstrained settings, addressing a crucial need in sports analytics, healthcare, and realistic animation. Existing pose datasets often simplify the spine to a single rigid segment, overlooking the nuanced articulation required for accurate motion analysis. In contrast, SpineTrack annotates nine detailed spinal keypoints across two complementary subsets: a synthetic set comprising 25k annotations created using Unreal Engine with biomechanical alignment through OpenSim, and a real-world set comprising over 33k annotations curated via an active learning pipeline that iteratively refines automated annotations with human feedback. This integrated approach ensures anatomically consistent labels at scale, even for challenging, in-the-wild images. We further introduce SpinePose, extending state-of-the-art body pose estimators using knowledge distillation and an anatomical regularization strategy to jointly predict body and spine keypoints. Our experiments in both general and sports-specific contexts validate the effectiveness of SpineTrack for precise spine pose estimation, establishing a robust foundation for future research in advanced biomechanical analysis and 3D spine reconstruction in the wild.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

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.

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.

Stable diffusion models represent the state-of-the-art in data synthesis across diverse domains and hold transformative potential for applications in science and engineering, e.g., by facilitating the discovery of novel solutions and simulating systems that are computationally intractable to model explicitly. While there is increasing effort to incorporate physics-based constraints into generative models, existing techniques are either limited in their applicability to latent diffusion frameworks or lack the capability to strictly enforce domain-specific constraints. To address this limitation this paper proposes a novel integration of stable diffusion models with constrained optimization frameworks, enabling the generation of outputs satisfying stringent physical and functional requirements. The effectiveness of this approach is demonstrated through material design experiments requiring adherence to precise morphometric properties, challenging inverse design tasks involving the generation of materials inducing specific stress-strain responses, and copyright-constrained content generation tasks. All code has been released at https://github.com/RAISELab-atUVA/Constrained-Stable-Diffusion.

Regardless of the particular task we want them to perform in an environment, there are often shared safety constraints we want our agents to respect. For example, regardless of whether it is making a sandwich or clearing the table, a kitchen robot should not break a plate. Manually specifying such a constraint can be both time-consuming and error-prone. We show how to learn constraints from expert demonstrations of safe task completion by extending inverse reinforcement learning (IRL) techniques to the space of constraints. Intuitively, we learn constraints that forbid highly rewarding behavior that the expert could have taken but chose not to. Unfortunately, the constraint learning problem is rather ill-posed and typically leads to overly conservative constraints that forbid all behavior that the expert did not take. We counter this by leveraging diverse demonstrations that naturally occur in multi-task settings to learn a tighter set of constraints. We validate our method with simulation experiments on high-dimensional continuous control 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.

Organ at risk (OAR) segmentation is a critical process in radiotherapy treatment planning such as head and neck tumors. Nevertheless, in clinical practice, radiation oncologists predominantly perform OAR segmentations manually on CT scans. This manual process is highly time-consuming and expensive, limiting the number of patients who can receive timely radiotherapy. Additionally, CT scans offer lower soft-tissue contrast compared to MRI. Despite MRI providing superior soft-tissue visualization, its time-consuming nature makes it infeasible for real-time treatment planning. To address these challenges, we propose a method called SegReg, which utilizes Elastic Symmetric Normalization for registering MRI to perform OAR segmentation. SegReg outperforms the CT-only baseline by 16.78% in mDSC and 18.77% in mIoU, showing that it effectively combines the geometric accuracy of CT with the superior soft-tissue contrast of MRI, making accurate automated OAR segmentation for clinical practice become possible. See project website https://steve-zeyu-zhang.github.io/SegReg

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>99.0%/97.3%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

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.

Increased effort during use of the paretic arm and hand can provoke involuntary abnormal synergy patterns and amplify stiffness effects of muscle tone for individuals after stroke, which can add difficulty for user-controlled devices to assist hand movement during functional tasks. We study how volitional effort, exerted in an attempt to open or close the hand, affects resistance to robot-assisted movement at the finger level. We perform experiments with three chronic stroke survivors to measure changes in stiffness when the user is actively exerting effort to activate ipsilateral EMG-controlled robot-assisted hand movements, compared with when the fingers are passively stretched, as well as overall effects from sustained active engagement and use. Our results suggest that active engagement of the upper extremity increases muscle tone in the finger to a much greater degree than through passive-stretch or sustained exertion over time. Potential design implications of this work suggest that developers should anticipate higher levels of finger stiffness when relying on user-driven ipsilateral control methods for assistive or rehabilitative devices for stroke.

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.

This work studies the challenge of transfer animations between characters whose skeletal topologies differ substantially. While many techniques have advanced retargeting techniques in decades, transfer motions across diverse topologies remains less-explored. The primary obstacle lies in the inherent topological inconsistency between source and target skeletons, which restricts the establishment of straightforward one-to-one bone correspondences. Besides, the current lack of large-scale paired motion datasets spanning different topological structures severely constrains the development of data-driven approaches. To address these limitations, we introduce Motion2Motion, a novel, training-free framework. Simply yet effectively, Motion2Motion works with only one or a few example motions on the target skeleton, by accessing a sparse set of bone correspondences between the source and target skeletons. Through comprehensive qualitative and quantitative evaluations, we demonstrate that Motion2Motion achieves efficient and reliable performance in both similar-skeleton and cross-species skeleton transfer scenarios. The practical utility of our approach is further evidenced by its successful integration in downstream applications and user interfaces, highlighting its potential for industrial applications. Code and data are available at https://lhchen.top/Motion2Motion.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

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/

Methods and datasets for human pose estimation focus predominantly on side- and front-view scenarios. We overcome the limitation by leveraging synthetic data and introduce RePoGen (RarE POses GENerator), an SMPL-based method for generating synthetic humans with comprehensive control over pose and view. Experiments on top-view datasets and a new dataset of real images with diverse poses show that adding the RePoGen data to the COCO dataset outperforms previous approaches to top- and bottom-view pose estimation without harming performance on common views. An ablation study shows that anatomical plausibility, a property prior research focused on, is not a prerequisite for effective performance. The introduced dataset and the corresponding code are available on https://mirapurkrabek.github.io/RePoGen-paper/ .

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.

Learning 3D shape representation with dense correspondence for deformable objects is a fundamental problem in computer vision. Existing approaches often need additional annotations of specific semantic domain, e.g., skeleton poses for human bodies or animals, which require extra annotation effort and suffer from error accumulation, and they are limited to specific domain. In this paper, we propose a novel self-supervised approach to learn neural implicit shape representation for deformable objects, which can represent shapes with a template shape and dense correspondence in 3D. Our method does not require the priors of skeleton and skinning weight, and only requires a collection of shapes represented in signed distance fields. To handle the large deformation, we constrain the learned template shape in the same latent space with the training shapes, design a new formulation of local rigid constraint that enforces rigid transformation in local region and addresses local reflection issue, and present a new hierarchical rigid constraint to reduce the ambiguity due to the joint learning of template shape and correspondences. Extensive experiments show that our model can represent shapes with large deformations. We also show that our shape representation can support two typical applications, such as texture transfer and shape editing, with competitive performance. The code and models are available at https://iscas3dv.github.io/deformshape

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.

We introduce MURA, a large dataset of musculoskeletal radiographs containing 40,561 images from 14,863 studies, where each study is manually labeled by radiologists as either normal or abnormal. To evaluate models robustly and to get an estimate of radiologist performance, we collect additional labels from six board-certified Stanford radiologists on the test set, consisting of 207 musculoskeletal studies. On this test set, the majority vote of a group of three radiologists serves as gold standard. We train a 169-layer DenseNet baseline model to detect and localize abnormalities. Our model achieves an AUROC of 0.929, with an operating point of 0.815 sensitivity and 0.887 specificity. We compare our model and radiologists on the Cohen's kappa statistic, which expresses the agreement of our model and of each radiologist with the gold standard. Model performance is comparable to the best radiologist performance in detecting abnormalities on finger and wrist studies. However, model performance is lower than best radiologist performance in detecting abnormalities on elbow, forearm, hand, humerus, and shoulder studies. We believe that the task is a good challenge for future research. To encourage advances, we have made our dataset freely available at https://stanfordmlgroup.github.io/competitions/mura .

Ultrasound (US) is a widely used medical imaging modality due to its real-time capabilities, non-invasive nature, and cost-effectiveness. Robotic ultrasound can further enhance its utility by reducing operator dependence and improving access to complex anatomical regions. For this, while deep reinforcement learning (DRL) and imitation learning (IL) have shown potential for autonomous navigation, their use in complex surgical tasks such as anatomy reconstruction and surgical guidance remains limited -- largely due to the lack of realistic and efficient simulation environments tailored to these tasks. We introduce SonoGym, a scalable simulation platform for complex robotic ultrasound tasks that enables parallel simulation across tens to hundreds of environments. Our framework supports realistic and real-time simulation of US data from CT-derived 3D models of the anatomy through both a physics-based and a generative modeling approach. Sonogym enables the training of DRL and recent IL agents (vision transformers and diffusion policies) for relevant tasks in robotic orthopedic surgery by integrating common robotic platforms and orthopedic end effectors. We further incorporate submodular DRL -- a recent method that handles history-dependent rewards -- for anatomy reconstruction and safe reinforcement learning for surgery. Our results demonstrate successful policy learning across a range of scenarios, while also highlighting the limitations of current methods in clinically relevant environments. We believe our simulation can facilitate research in robot learning approaches for such challenging robotic surgery applications. Dataset, codes, and videos are publicly available at https://sonogym.github.io/.

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.

Using Quadrics as the object representation has the benefits of both generality and closed-form projection derivation between image and world spaces. Although numerous constraints have been proposed for dual quadric reconstruction, we found that many of them are imprecise and provide minimal improvements to localization.After scrutinizing the existing constraints, we introduce a concise yet more precise convex hull-based algebraic constraint for object landmarks, which is applied to object reconstruction, frontend pose estimation, and backend bundle adjustment.This constraint is designed to fully leverage precise semantic segmentation, effectively mitigating mismatches between complex-shaped object contours and dual quadrics.Experiments on public datasets demonstrate that our approach is applicable to both monocular and RGB-D SLAM and achieves improved object mapping and localization than existing quadric SLAM methods. The implementation of our method is available at https://github.com/tiev-tongji/convexhull-based-algebraic-constraint.

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.

Generating accurate 3D reconstructions from endoscopic video is a promising avenue for longitudinal radiation-free analysis of sinus anatomy and surgical outcomes. Several methods for monocular reconstruction have been proposed, yielding visually pleasant 3D anatomical structures by retrieving relative camera poses with structure-from-motion-type algorithms and fusion of monocular depth estimates. However, due to the complex properties of the underlying algorithms and endoscopic scenes, the reconstruction pipeline may perform poorly or fail unexpectedly. Further, acquiring medical data conveys additional challenges, presenting difficulties in quantitatively benchmarking these models, understanding failure cases, and identifying critical components that contribute to their precision. In this work, we perform a quantitative analysis of a self-supervised approach for sinus reconstruction using endoscopic sequences paired with optical tracking and high-resolution computed tomography acquired from nine ex-vivo specimens. Our results show that the generated reconstructions are in high agreement with the anatomy, yielding an average point-to-mesh error of 0.91 mm between reconstructions and CT segmentations. However, in a point-to-point matching scenario, relevant for endoscope tracking and navigation, we found average target registration errors of 6.58 mm. We identified that pose and depth estimation inaccuracies contribute equally to this error and that locally consistent sequences with shorter trajectories generate more accurate reconstructions. These results suggest that achieving global consistency between relative camera poses and estimated depths with the anatomy is essential. In doing so, we can ensure proper synergy between all components of the pipeline for improved reconstructions that will facilitate clinical application of this innovative technology.

This work puts forth a new optimal design formulation for planar elastic membranes. The goal is to minimize the membrane's compliance through choosing the material distribution described by a positive Radon measure. The deformation of the membrane itself is governed by the convexified F\"{o}ppl's model. The uniqueness of this model lies in the convexity of its variational formulation despite the inherent nonlinearity of the strain-displacement relation. It makes it possible to rewrite the optimization problem as a pair of mutually dual convex variational problems. In the primal problem a linear functional is maximized with respect to displacement functions while enforcing that point-wisely the strain lies in an unbounded closed convex set. The dual problem consists in finding equilibrated stresses that are to minimize a convex integral functional of linear growth defined on the space of Radon measures. The pair of problems is analysed: existence and regularity results are provided, together with the system of optimality criteria. To demonstrate the computational potential of the pair, a finite element scheme is developed around it. Upon reformulation to a conic-quadratic & semi-definite programming problem, the method is employed to produce numerical simulations for several load case scenarios.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

Since the introduction of TotalSegmentator CT, there is demand for a similar robust automated MRI segmentation tool that can be applied across all MRI sequences and anatomic structures. In this retrospective study, a nnU-Net model (TotalSegmentator) was trained on MRI and CT examinations to segment 80 anatomic structures relevant for use cases such as organ volumetry, disease characterization, surgical planning and opportunistic screening. Examinations were randomly sampled from routine clinical studies to represent real-world examples. Dice scores were calculated between the predicted segmentations and expert radiologist reference standard segmentations to evaluate model performance on an internal test set, two external test sets and against two publicly available models, and TotalSegmentator CT. The model was applied to an internal dataset containing abdominal MRIs to investigate age-dependent volume changes. A total of 1143 examinations (616 MRIs, 527 CTs) (median age 61 years, IQR 50-72) were split into training (n=1088, CT and MRI) and an internal test set (n=55; only MRI), two external test sets (AMOS, n=20; CHAOS, n=20; only MRI), and an internal aging-study dataset of 8672 abdominal MRIs (median age 59 years, IQR 45-70) were included. The model showed a Dice Score of 0.839 on the internal test set and outperformed two other models (Dice Score, 0.862 versus 0.759; and 0.838 versus 0.560; p<.001 for both). The proposed open-source, easy-to-use model allows for automatic, robust segmentation of 80 structures, extending the capabilities of TotalSegmentator to MRIs of any sequence. The ready-to-use online tool is available at https://totalsegmentator.com, the model at https://github.com/wasserth/TotalSegmentator, and the dataset at https://zenodo.org/records/14710732.

The skeleton of a digital image is a compact representation of its topology, geometry, and scale. It has utility in many computer vision applications, such as image description, segmentation, and registration. However, skeletonization has only seen limited use in contemporary deep learning solutions. Most existing skeletonization algorithms are not differentiable, making it impossible to integrate them with gradient-based optimization. Compatible algorithms based on morphological operations and neural networks have been proposed, but their results often deviate from the geometry and topology of the true medial axis. This work introduces the first three-dimensional skeletonization algorithm that is both compatible with gradient-based optimization and preserves an object's topology. Our method is exclusively based on matrix additions and multiplications, convolutional operations, basic non-linear functions, and sampling from a uniform probability distribution, allowing it to be easily implemented in any major deep learning library. In benchmarking experiments, we prove the advantages of our skeletonization algorithm compared to non-differentiable, morphological, and neural-network-based baselines. Finally, we demonstrate the utility of our algorithm by integrating it with two medical image processing applications that use gradient-based optimization: deep-learning-based blood vessel segmentation, and multimodal registration of the mandible in computed tomography and magnetic resonance images.

Instance level detection and segmentation of thoracic diseases or abnormalities are crucial for automatic diagnosis in chest X-ray images. Leveraging on constant structure and disease relations extracted from domain knowledge, we propose a structure-aware relation network (SAR-Net) extending Mask R-CNN. The SAR-Net consists of three relation modules: 1. the anatomical structure relation module encoding spatial relations between diseases and anatomical parts. 2. the contextual relation module aggregating clues based on query-key pair of disease RoI and lung fields. 3. the disease relation module propagating co-occurrence and causal relations into disease proposals. Towards making a practical system, we also provide ChestX-Det, a chest X-Ray dataset with instance-level annotations (boxes and masks). ChestX-Det is a subset of the public dataset NIH ChestX-ray14. It contains ~3500 images of 13 common disease categories labeled by three board-certified radiologists. We evaluate our SAR-Net on it and another dataset DR-Private. Experimental results show that it can enhance the strong baseline of Mask R-CNN with significant improvements. The ChestX-Det is released at https://github.com/Deepwise-AILab/ChestX-Det-Dataset.

Spine-related diseases have high morbidity and cause a huge burden of social cost. Spine imaging is an essential tool for noninvasively visualizing and assessing spinal pathology. Segmenting vertebrae in computed tomography (CT) images is the basis of quantitative medical image analysis for clinical diagnosis and surgery planning of spine diseases. Current publicly available annotated datasets on spinal vertebrae are small in size. Due to the lack of a large-scale annotated spine image dataset, the mainstream deep learning-based segmentation methods, which are data-driven, are heavily restricted. In this paper, we introduce a large-scale spine CT dataset, called CTSpine1K, curated from multiple sources for vertebra segmentation, which contains 1,005 CT volumes with over 11,100 labeled vertebrae belonging to different spinal conditions. Based on this dataset, we conduct several spinal vertebrae segmentation experiments to set the first benchmark. We believe that this large-scale dataset will facilitate further research in many spine-related image analysis tasks, including but not limited to vertebrae segmentation, labeling, 3D spine reconstruction from biplanar radiographs, image super-resolution, and enhancement.

Recent AI-based scoliosis screening methods primarily rely on large-scale silhouette datasets, often neglecting clinically relevant postural asymmetries-key indicators in traditional screening. In contrast, pose data provide an intuitive skeletal representation, enhancing clinical interpretability across various medical applications. However, pose-based scoliosis screening remains underexplored due to two main challenges: (1) the scarcity of large-scale, annotated pose datasets; and (2) the discrete and noise-sensitive nature of raw pose coordinates, which hinders the modeling of subtle asymmetries. To address these limitations, we introduce Scoliosis1K-Pose, a 2D human pose annotation set that extends the original Scoliosis1K dataset, comprising 447,900 frames of 2D keypoints from 1,050 adolescents. Building on this dataset, we introduce the Dual Representation Framework (DRF), which integrates a continuous skeleton map to preserve spatial structure with a discrete Postural Asymmetry Vector (PAV) that encodes clinically relevant asymmetry descriptors. A novel PAV-Guided Attention (PGA) module further uses the PAV as clinical prior to direct feature extraction from the skeleton map, focusing on clinically meaningful asymmetries. Extensive experiments demonstrate that DRF achieves state-of-the-art performance. Visualizations further confirm that the model leverages clinical asymmetry cues to guide feature extraction and promote synergy between its dual representations. The dataset and code are publicly available at https://zhouzi180.github.io/Scoliosis1K/.

The end-to-end nature of neural machine translation (NMT) removes many ways of manually guiding the translation process that were available in older paradigms. Recent work, however, has introduced a new capability: lexically constrained or guided decoding, a modification to beam search that forces the inclusion of pre-specified words and phrases in the output. However, while theoretically sound, existing approaches have computational complexities that are either linear (Hokamp and Liu, 2017) or exponential (Anderson et al., 2017) in the number of constraints. We present a algorithm for lexically constrained decoding with a complexity of O(1) in the number of constraints. We demonstrate the algorithms remarkable ability to properly place these constraints, and use it to explore the shaky relationship between model and BLEU scores. Our implementation is available as part of Sockeye.

Despite the recent successes of deep learning, such models are still far from some human abilities like learning from few examples, reasoning and explaining decisions. In this paper, we focus on organ annotation in medical images and we introduce a reasoning framework that is based on learning fuzzy relations on a small dataset for generating explanations. Given a catalogue of relations, it efficiently induces the most relevant relations and combines them for building constraints in order to both solve the organ annotation task and generate explanations. We test our approach on a publicly available dataset of medical images where several organs are already segmented. A demonstration of our model is proposed with an example of explained annotations. It was trained on a small training set containing as few as a couple of examples.

2D keypoints are commonly used as an additional cue to refine estimated 3D human meshes. Current methods optimize the pose and shape parameters with a reprojection loss on the provided 2D keypoints. Such an approach, while simple and intuitive, has limited effectiveness because the optimal solution is hard to find in ambiguous parameter space and may sacrifice depth. Additionally, divergent gradients from distal joints complicate and deviate the refinement of proximal joints in the kinematic chain. To address these, we introduce Kinematic-Tree Rotation (KITRO), a novel mesh refinement strategy that explicitly models depth and human kinematic-tree structure. KITRO treats refinement from a bone-wise perspective. Unlike previous methods which perform gradient-based optimizations, our method calculates bone directions in closed form. By accounting for the 2D pose, bone length, and parent joint's depth, the calculation results in two possible directions for each child joint. We then use a decision tree to trace binary choices for all bones along the human skeleton's kinematic-tree to select the most probable hypothesis. Our experiments across various datasets and baseline models demonstrate that KITRO significantly improves 3D joint estimation accuracy and achieves an ideal 2D fit simultaneously. Our code available at: https://github.com/MartaYang/KITRO.

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.

We introduce a novel dataset designed to benchmark the physical and spatial reasoning capabilities of Large Language Models (LLM) based on topology optimization, a method for computing optimal material distributions within a design space under prescribed loads and supports. In this dataset, LLMs are provided with conditions such as 2D boundary, applied forces and supports, and must reason about the resulting optimal material distribution. The dataset includes a variety of tasks, ranging from filling in masked regions within partial structures to predicting complete material distributions. Solving these tasks requires understanding the flow of forces and the required material distribution under given constraints, without access to simulation tools or explicit physical models, challenging models to reason about structural stability and spatial organization. Our dataset targets the evaluation of spatial and physical reasoning abilities in 2D settings, offering a complementary perspective to traditional language and logic benchmarks.

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.

Background: Recent advances in large language models highlight the need for high-quality multilingual medical datasets. While Japan leads globally in CT scanner deployment and utilization, the lack of large-scale Japanese radiology datasets has hindered the development of specialized language models for medical imaging analysis. Objective: To develop a comprehensive Japanese CT report dataset through machine translation and establish a specialized language model for structured finding classification. Additionally, to create a rigorously validated evaluation dataset through expert radiologist review. Methods: We translated the CT-RATE dataset (24,283 CT reports from 21,304 patients) into Japanese using GPT-4o mini. The training dataset consisted of 22,778 machine-translated reports, while the validation dataset included 150 radiologist-revised reports. We developed CT-BERT-JPN based on "tohoku-nlp/bert-base-japanese-v3" architecture for extracting 18 structured findings from Japanese radiology reports. Results: Translation metrics showed strong performance with BLEU scores of 0.731 and 0.690, and ROUGE scores ranging from 0.770 to 0.876 for Findings and from 0.748 to 0.857 for Impression sections. CT-BERT-JPN demonstrated superior performance compared to GPT-4o in 11 out of 18 conditions, including lymphadenopathy (+14.2%), interlobular septal thickening (+10.9%), and atelectasis (+7.4%). The model maintained F1 scores exceeding 0.95 in 14 out of 18 conditions and achieved perfect scores in four conditions. Conclusions: Our study establishes a robust Japanese CT report dataset and demonstrates the effectiveness of a specialized language model for structured finding classification. The hybrid approach of machine translation and expert validation enables the creation of large-scale medical datasets while maintaining high quality.

Recent advancements in prompt-based medical image segmentation have enabled clinicians to identify tumors using simple input like bounding boxes or text prompts. However, existing methods face challenges when doctors need to interact through natural language or when position reasoning is required - understanding spatial relationships between anatomical structures and pathologies. We present PRS-Med, a framework that integrates vision-language models with segmentation capabilities to generate both accurate segmentation masks and corresponding spatial reasoning outputs. Additionally, we introduce the MMRS dataset (Multimodal Medical in Positional Reasoning Segmentation), which provides diverse, spatially-grounded question-answer pairs to address the lack of position reasoning data in medical imaging. PRS-Med demonstrates superior performance across six imaging modalities (CT, MRI, X-ray, ultrasound, endoscopy, RGB), significantly outperforming state-of-the-art methods in both segmentation accuracy and position reasoning. Our approach enables intuitive doctor-system interaction through natural language, facilitating more efficient diagnoses. Our dataset pipeline, model, and codebase will be released to foster further research in spatially-aware multimodal reasoning for medical applications.

Industry standards require medical device manufacturers to perform implant-induced artefact testing in phantoms at a pre-clinical stage to define the extent of artefacts that can be expected during MRI. Once a device is commercially available, studies on volunteers, cadavers or patients are performed to investigate implant-induced artefacts and artefact reduction methods more in-depth. This study describes the design and evaluation of a realistic head phantom for pre-clinical implant-induced artefact testing in a relevant environment. A case study is performed where a state-of-the-art piezoelectric bone conduction implant is used in the 1.5 T and 3 T MRI environments. Images were acquired using clinical and novel metal artefact reducing (MARS) sequences at both field strengths. Artefact width and length were measured in a healthy volunteer and compared with artefact sizes obtained in the phantom. Artefact sizes are reported that are similar in shape between the phantom and a volunteer, yet with dimensions differing up to 20% between both. When the implant magnet is removed, the artefact size can be reduced below a diameter of 5 cm, whilst the presence of an implant magnet and splint creates higher artefacts up to 20 cm in diameter. Pulse sequences have been altered to reduce the scan time up to 7 minutes, while preserving the image quality. These results show that the anthropomorphic phantom can be used at a preclinical stage to provide clinically relevant images, illustrating the impact of the artefact on important brain structures.

Data scarcity is a common obstacle in medical research due to the high costs associated with data collection and the complexity of gaining access to and utilizing data. Synthesizing health data may provide an efficient and cost-effective solution to this shortage, enabling researchers to explore distributions and populations that are not represented in existing observations or difficult to access due to privacy considerations. To that end, we have developed a multi-task self-attention model that produces realistic wearable activity data. We examine the characteristics of the generated data and quantify its similarity to genuine samples with both quantitative and qualitative approaches.

The dominant paradigm for neural text generation is left-to-right decoding from autoregressive language models. Constrained or controllable generation under complex lexical constraints, however, requires foresight to plan ahead feasible future paths. Drawing inspiration from the A* search algorithm, we propose NeuroLogic A*esque, a decoding algorithm that incorporates heuristic estimates of future cost. We develop efficient lookahead heuristics that are efficient for large-scale language models, making our method a drop-in replacement for common techniques such as beam search and top-k sampling. To enable constrained generation, we build on NeuroLogic decoding (Lu et al., 2021), combining its flexibility in incorporating logical constraints with A*esque estimates of future constraint satisfaction. Our approach outperforms competitive baselines on five generation tasks, and achieves new state-of-the-art performance on table-to-text generation, constrained machine translation, and keyword-constrained generation. The improvements are particularly notable on tasks that require complex constraint satisfaction or in few-shot or zero-shot settings. NeuroLogic A*esque illustrates the power of decoding for improving and enabling new capabilities of large-scale language models.

Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

Multimodal large language models (MLLMs) have achieved significant success in the general field of image processing. Their emerging task generalization and freeform conversational capabilities can greatly facilitate medical diagnostic assistance, helping patients better understand their conditions and enhancing doctor-patient trust. Computed Tomography (CT) is a non-invasive imaging technique used to capture the internal mechanisms of a patient's condition and is widely utilized. However, in past research, the complex textural features of this imaging data have made accurate interpretation by algorithms challenging, impeding the performance of general LLMs in diagnostic assistance. To address this, we developed OrthoDoc, a MLLM designed for CT diagnostics. OrthoDoc is trained on 120,000 CT images and diagnostic reports and includes a Retrieval-Augmented Generation (RAG) module capable of effectively mitigating model hallucinations. This module is informed by extensive medical literature, textbooks, and explanatory data. Thus, OrthoDoc not only processes complex CT images but also stores, understands, and reasons over medical knowledge and language. In extensive experiments, OrthoDoc outperforms commercial models led by GPT-4, demonstrating superior diagnostic capabilities and accuracy. Specifically, OrthoDoc significantly surpasses existing models in the diagnosis of common orthopedic conditions such as fractures, arthritis, and tumors. Additionally, OrthoDoc exhibits robust generalization and stability when handling rare and complex cases.

Unlike in language or vision, one of the fundamental challenges in robot learning is the lack of access to vast data resources. We can further break down the problem into (1) data sparsity from the angle of data representation and (2) data scarcity from the angle of data quantity. In this thesis, I will discuss selected works on two domains: (1) tactile sensing and (2) rehabilitation robots, which are exemplars of data sparsity and scarcity, respectively. Tactile sensing is an essential modality for robotics, but tactile data are often sparse, and for each interaction with the physical world, tactile sensors can only obtain information about the local area of contact. I will discuss my work on learning vision-free tactile-only exploration and manipulation policies through model-free reinforcement learning to make efficient use of sparse tactile information. On the other hand, rehabilitation robots are an example of data scarcity to the extreme due to the significant challenge of collecting biosignals from disabled-bodied subjects at scale for training. I will discuss my work in collaboration with the medical school and clinicians on intent inferral for stroke survivors, where a hand orthosis developed in our lab collects a set of biosignals from the patient and uses them to infer the activity that the patient intends to perform, so the orthosis can provide the right type of physical assistance at the right moment. My work develops machine learning algorithms that enable intent inferral with minimal data, including semi-supervised, meta-learning, and generative AI methods.

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/.

Large language models can produce creative and diverse responses. However, to integrate them into current developer workflows, it is essential to constrain their outputs to follow specific formats or standards. In this work, we surveyed 51 experienced industry professionals to understand the range of scenarios and motivations driving the need for output constraints from a user-centered perspective. We identified 134 concrete use cases for constraints at two levels: low-level, which ensures the output adhere to a structured format and an appropriate length, and high-level, which requires the output to follow semantic and stylistic guidelines without hallucination. Critically, applying output constraints could not only streamline the currently repetitive process of developing, testing, and integrating LLM prompts for developers, but also enhance the user experience of LLM-powered features and applications. We conclude with a discussion on user preferences and needs towards articulating intended constraints for LLMs, alongside an initial design for a constraint prototyping tool.

In daily life, humans utilize hands to manipulate objects. Modeling the shape of objects that are manipulated by the hand is essential for AI to comprehend daily tasks and to learn manipulation skills. However, previous approaches have encountered difficulties in reconstructing the precise shapes of hand-held objects, primarily owing to a deficiency in prior shape knowledge and inadequate data for training. As illustrated, given a particular type of tool, such as a mug, despite its infinite variations in shape and appearance, humans have a limited number of 'effective' modes and poses for its manipulation. This can be attributed to the fact that humans have mastered the shape prior of the 'mug' category, and can quickly establish the corresponding relations between different mug instances and the prior, such as where the rim and handle are located. In light of this, we propose a new method, CHORD, for Category-level Hand-held Object Reconstruction via shape Deformation. CHORD deforms a categorical shape prior for reconstructing the intra-class objects. To ensure accurate reconstruction, we empower CHORD with three types of awareness: appearance, shape, and interacting pose. In addition, we have constructed a new dataset, COMIC, of category-level hand-object interaction. COMIC contains a rich array of object instances, materials, hand interactions, and viewing directions. Extensive evaluation shows that CHORD outperforms state-of-the-art approaches in both quantitative and qualitative measures. Code, model, and datasets are available at https://kailinli.github.io/CHORD.

It is crucial for large language models (LLMs) to follow instructions that involve multiple constraints. However, it is an unexplored area to enhance LLMs' ability to follow soft constraints. To bridge the gap, we initially design a pipeline to construct datasets with high-quality outputs automatically. Additionally, to fully utilize the positive and negative samples generated during the data construction process, we choose Direct Preference Optimization (DPO) as the training method. Furthermore, taking into account the difficulty of soft constraints indicated by the number of constraints, we design a curriculum learning training paradigm based on the constraint quantity. We experimentally evaluate the effectiveness of our methods in improving LLMs' soft constraint following ability and analyze the factors driving the improvements.The datasets and code are publicly available at https://github.com/Rainier-rq/FollowSoftConstraint.

Estimating human pose and shape from monocular images is a long-standing problem in computer vision. Since the release of statistical body models, 3D human mesh recovery has been drawing broader attention. With the same goal of obtaining well-aligned and physically plausible mesh results, two paradigms have been developed to overcome challenges in the 2D-to-3D lifting process: i) an optimization-based paradigm, where different data terms and regularization terms are exploited as optimization objectives; and ii) a regression-based paradigm, where deep learning techniques are embraced to solve the problem in an end-to-end fashion. Meanwhile, continuous efforts are devoted to improving the quality of 3D mesh labels for a wide range of datasets. Though remarkable progress has been achieved in the past decade, the task is still challenging due to flexible body motions, diverse appearances, complex environments, and insufficient in-the-wild annotations. To the best of our knowledge, this is the first survey to focus on the task of monocular 3D human mesh recovery. We start with the introduction of body models and then elaborate recovery frameworks and training objectives by providing in-depth analyses of their strengths and weaknesses. We also summarize datasets, evaluation metrics, and benchmark results. Open issues and future directions are discussed in the end, hoping to motivate researchers and facilitate their research in this area. A regularly updated project page can be found at https://github.com/tinatiansjz/hmr-survey.

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

This paper introduces an approach to endow generative diffusion processes the ability to satisfy and certify compliance with constraints and physical principles. The proposed method recast the traditional sampling process of generative diffusion models as a constrained optimization problem, steering the generated data distribution to remain within a specified region to ensure adherence to the given constraints. These capabilities are validated on applications featuring both convex and challenging, non-convex, constraints as well as ordinary differential equations, in domains spanning from synthesizing new materials with precise morphometric properties, generating physics-informed motion, optimizing paths in planning scenarios, and human motion synthesis.