Anatomy

Deep networks trained on structural MRI for Alzheimer's disease (AD) staging often reach reasonable accuracy while attending to anatomically irrelevant regions, and multimodal models that add clinical tables frequently rely on variables that were used to assign the diagnostic label in the first place. We study both issues with a deliberately lightweight slice-based encoder (ResNet18 with a one-layer Transformer over slices) on 1,075 baseline T1-weighted scans from ADNI-1. First, we use FastSurfer segmentations as an anatomical reference: YOLOv8 models trained on segmentation-derived labels localize Alzheimer-relevant structures with mAP_50 above 0.96, and a Grad-CAM comparison shows that the image-only classifier frequently attends to the skull, orbits and background. Second, we adapt a CLIP-style image - tabular contrastive framework and organize ADNIMERGE variables along a label-leakage spectrum. Fusion with cognitive scores yields 87.3% three-way accuracy, which we treat as a leakage-driven upper bound rather than an imaging result; fusion with regional volumes yields 73.0%. We observe that the choice of contrastive target changes what the image encoder learns: on MCI vs. CN, the image-only head reaches 52.4% when the encoder is aligned to cognitive scores and 73.8% when aligned to volumes, although no tabular input is used at inference. Third, restricting the input to a per-subject crop of the medial temporal lobe raises image-only three-way accuracy from 58.7% to 65.1%. All results come from single runs on a small balanced test set, and we report confidence intervals and the protocol differences that prevent direct comparison with published numbers.

Multimodal image registration is a key component of many clinical workflows, yet it remains challenging because corresponding anatomical structures often exhibit substantially different image intensities across modalities. In this work, we present a comprehensive benchmark of intra-patient 3D multimodal deformable registration methods across three datasets covering different anatomical regions and difficulty levels, including both synthetic deformation recovery and real clinical scenarios. We evaluate classical optimization-based approaches and modern learning-based methods, including recent deep learning and foundation models, using complementary metrics: Average Dice similarity coefficient (DSC), average 95th-percentile Hausdorff distance (HD95), and a modality-independent structural similarity measure based on the MIND self-similarity context (MIND-SSC). Results show high variability across datasets, with learning-based methods demonstrating superior performance on large synthetic benchmarks, while only limited improvements are observed in real pelvic registration. A key finding of this study is the consistent disagreement between geometric metrics (DSC, HD95) and image-based similarity metrics (MIND-SSC), highlighting that improved overlap does not necessarily imply better global multimodal correspondence. Furthermore, anatomy-guided approaches achieve the highest overlap scores but exhibit degraded performance outside of segmented regions, revealing a trade-off between label-driven alignment and global structural coherence. Overall, our results indicate that no current method achieves robust performance across anatomies and modalities. We demonstrate that intra-patient 3D multimodal registration requires multi-criteria evaluation, including deformation-based metrics, and remains an open problem.

Prequential adaptation of frozen tabular foundation models under temporal drift, with each label revealed only after prediction, helps some deployments and harms others, yet current practice does not predict which. We study the sources and limits of these gains. A diagnostic anatomy attributes gains to four recurring mechanisms under a streaming protocol that removes three optimistic biases and quantifies a fourth. Within an agnostic total-variation drift class, the target conditional is only partially identified: its identified-set diameter, the \emph{wall}, is irreducible from unlabeled data uniformly in sample size. A second, orthogonal $L^2$ projection wall quantifies what the frozen representation cannot express. Two canonical mechanism priors collapse the first wall. Under stated nuisance-rate conditions, the wall can be estimated from labeled historical windows at a $\sqrt N$ rate above the margin threshold $\gamma^\star=d_0/(2\alpha_s)$. At $\gamma=0$, the conditional lower-bound program depends on an open affinity estimate; the positive-margin lower branch also remains open. Semi-synthetic data illustrate the finite-sample mechanism with calibrated exponents. Stream-level proxies on eight industrial streams fall on the difficult side under a stated roughness bound, while the equality case $\gamma=\gamma^\star$ remains unresolved.

Robust medical image segmentation across imaging modalities is challenging because of large differences in appearance and intensity distributions. Models trained on a single modality often show substantial performance drops when applied to unseen domains. In this work, we develop a unified 3D pancreas segmentation framework that applies domain-adversarial learning to 4,604 heterogeneous CT and MRI scans to learn anatomical representations. A shared nnU-Net encoder-decoder is trained for whole-pancreas segmentation, with a latent domain discriminator encouraging CT-MRI feature alignment. The learned encoder is subsequently transferred to pancreatic head-body-tail segmentation using limited MRI-only subregion annotations. An average Dice score of 87.31% on the in-distribution test set and Dice scores ranging from 84.20% to 88.09% across external OOD datasets were achieved in whole pancreas segmentation. Dice scores of 80.53% on MRI and 83.05% on CT were achieved for downstream subregion segmentation, without using CT subregion annotations. These results demonstrate that a unified anatomical representation can support both cross-modality pancreas segmentation and label-efficient downstream transfer.

Three-dimensional ultrasound (US) is a safe, radiation-free complementary modality to CT and X-rays for longitudinal monitoring, yet its segmentation-derived partial point clouds are extremely artifact-laden. Consequently, it is challenging to recover a clean and complete anatomical structure from such US point clouds. In this paper, we present UBone3D, a novel framework based on physics-rectified conditional flow matching (CFM) that performs point cloud completion directly from partial US observations. UBone3D models deterministic physics artifacts (e.g., surface thickening, streaking, dropouts) via a simulated physics proxy, and introduces test-time physics rectification to steer the shape completion. At inference, the completion is jointly steered by two decoupled forces: (1) anatomical plausibility enforced by a CT-trained generative shape prior, BoneFM, and (2) physics consistency enforced by USimNet in the ultrasound formation space. Extensive experiments on simulated and in-vivo data demonstrate significant improvements in reconstruction accuracy and anatomical fidelity over existing baselines.

Sparse-view X-ray 3D reconstruction is essential for reducing radiation exposure, but recovering a density field from a handful of X-ray projections is severely ill-posed. Recently, 3D Gaussian Splatting has achieved state-of-the-art performance in sparse-view reconstruction by representing the volume using explicit, optimized primitives, but it requires dozens of projected views. With fewer views, reconstruction quality degrades severely since the explicit primitives are optimized freely without any anatomical information. Anatomical structures, in contrast, share similar geometry and density across a population. Their variations are bounded within a limited range that statistical shape models can capture. This paper proposes a shape-guided Gaussian splatting framework for sparse-view X-ray 3D reconstructions. Our contribution lies in driving Gaussian positions toward anatomically valid configurations, alongside atlas-based density regularization. Our method ensures anatomically consistent reconstruction and improves PSNR by 2.83 dB over a state-of-the-art Gaussian splatting baseline with as few as 5 views. Code Available: https://github.com/polyshape-lab/ShapeGuidedGaussian

Large language models act as strategic agents and models of human choice, yet choosing like a strategic agent does not mean computing like one. We recorded activations from four open-weight models --- dense and mixture-of-experts, including a matched base--instruct pair --- in one-shot play of 144 strict ordinal $2\times2$ games. We followed a prespecified incentive from prompt, through activations, to choice. Dense models mirrored the unadjusted human decline with game complexity. Incentive and choice were detectable in every model, but models differed in whether incentive reached the choice, aligned with it and, where tested, whether strengthening it shifted preference. The base and instruction-tuned Qwen2.5 models chose almost identically at baseline yet differed in whether incentive reached choice. Fixed decision cues were distinguishable internally but changed choices selectively. Similar behaviour can rest on different computation; post-training can reshape the path from represented incentive to decision while leaving behaviour and decodable information largely intact.

Deep learning models for CT scan analysis are often limited by the scarcity of precise pixel-level annotations, which require significant radiologist effort to produce. Training on scan-level labels alone reduces annotation requirements but introduces challenges: low supervision ratios and large input volumes make models prone to overfitting and shortcut learning. In this work, we investigate two complementary methods to address these challenges: multi-instance learning (MIL) and anatomical filtering. MIL divides CT volumes into 2D slice instances, enabling efficient 2D architectures with ImageNet pretraining rather than computationally demanding 3D models. Anatomical filtering uses Compass, our self-supervised body part regression model, to crop scans to pathology-relevant subregions without requiring segmentation masks. We evaluate two MIL frameworks - Attention-based MIL (ABMIL) and FocusMIL - on kidney tumor classification across one internal dataset (TUH) and two external datasets (KiTS23 and TCGA-KiRC). Our best models achieve F1 = 0.83 on the internal test set using only scan-level labels. We further show that anatomical filtering with the Compass model is critical for the out-of-distribution generalization of embedding-based ABMIL, while instance-based FocusMIL demonstrates greater inherent robustness to distribution shift. While evaluated on kidney tumors, we consider this a proof-of-concept for a broader weakly supervised CT classification pipeline applicable to other organs and pathologies.

Recent radiology multi-modal language models have made substantial progress in chest X-ray report generation, visual question answering, and temporal reasoning. While longitudinal chest X-ray interpretation compares sequential examinations to describe change, visual grounding aims to connect clinical language with localized image evidence. Although longitudinal modeling and visual grounding have each advanced radiology language models, how localized visual evidence can support longitudinal interpretation remains under-explored. We introduce CheXGround, a region-grounded longitudinal chest X-ray language model that represents paired studies through corresponding anatomical regions. CheXGround extracts anatomical regions from current and prior radiographs, encodes them as temporally enhanced Region-of-Interest (ROI) tokens, and combines them with global temporal image context during generation. To connect these region tokens with clinical text, we propose Temporal Region--Phrase Alignment, a pretraining objective that aligns temporal anatomical representations with localized report phrases. We evaluate CheXGround on single-study and longitudinal Visual Question Answering (VQA), longitudinal findings generation, temporal grounded VQA, and anatomical grounding. Across these tasks, CheXGround improves clinical language quality, temporal reasoning, and localization accuracy over recent baselines. Our results suggest that organizing longitudinal evidence at the anatomical level is a strong representation for grounded radiology language modeling. Project page: https://adonaydem.github.io/chexground-website

3D brain MRI generation has made significant advances in medical imaging, simulation, and controllable anatomical analysis. However, existing generative models typically synthesize 3D volumes monolithically, often overlooking regional anatomical structures and limiting local controllability. To address these limitations, we introduce AnaDiffusion, an anatomically compositional latent diffusion framework that factorizes the generation process into distinct, anatomically meaningful regions, followed by part-to-whole assembly and global refinement. Our approach first trains part diffusion models to capture local structural priors. We then inject an assembled anatomical composite of the parts into the whole-brain latent representation and continue denoising. This mechanism enables the model to resolve global context while preserving the injected anatomy. As a result, AnaDiffusion produces both explicit part assets and a globally coherent volume, thereby enabling controllable part editing without requiring subject-specific dense segmentation maps at inference time while maintaining consistent part-to-whole brain structure. On the subject-disjoint ADNI test split, AnaDiffusion achieves the lowest FID across the whole brain, left and right hemispheres, cerebellar-brainstem complex, and seam regions. It also achieves the best cerebellar and second-best ventricular and brainstem absolute Cohen's d values among the evaluated methods. In localized editing experiments, paired MS-SSIM demonstrates high target transfer and off-target preservation, supporting controllable part replacement with minimal unintended anatomical alterations.

Automated lesion segmentation in whole-body PET/CT imaging can assist clinicians with cancer detection, staging, and treatment planning across radiotracers and cancer types. However, training lesion segmentation models that capture variations in lesion size, distribution, and appearance requires large annotated datasets, whose creation is both time- and expertise-intensive. As a result, models trained on limited labeled PET/CT data often lack the accuracy and generalizability needed for clinical use. We present FEEDS (Foundation model-Enabled Efficient Data Sampling), a label- and compute-efficient learning strategy that uses vision foundation model embeddings to select the most informative and diverse unlabeled cases for expert annotation. Unlike unsupervised, semi-supervised, and active learning approaches, FEEDS is a one-step training paradigm requiring only a limited, representative training set, making it label- and compute-efficient. We train and validate FEEDS using the AutoPET-III dataset. We test its accuracy and generalizability on three held-out sets: AutoPET-III, DeepPSMA, and an internal Dartmouth-Hitchcock Medical Center dataset. We evaluate clinical utility at the voxel, lesion, and anatomic region level to assess performance in high-risk areas and treatment planning utility. FEEDS outperforms random-sampling-based labeling, pseudolabel-based semi-supervised learning, and training with limited labeled data alone. It generalizes across all three test sets, FDG and PSMA tracers, and multiple diseases, matching fully-labeled (100%) training performance with 70% less annotation burden. FEEDS addresses the challenge of label scarcity in an automatic lesion segmentation framework by providing a practical approach for constructing representative and diverse annotation queues from large, unannotated clinical repositories.

Deep learning systems perform mainly within the 2D for a single image domain and take the face as a single-dimension representation, losing sight of the 3D anatomy of sheep and cross-landmark spatial relationships that are intrinsic to the clinically proven Sheep Pain Facial Expression Scale (SPFES). This paper presents the \textbf{3D Sheep Pain Facial Expression System (3D-SPFES)}, a novel, monocular depth-aware geometric graph neural network system that integrates each SPFES facial landmark, such as the ears, eyes, and nose, into 3D Euclidean space estimated from a single RGB camera by using VideoDepthAnything, thus preventing the need for specialized depth hardware. Each landmark node includes a feature vector containing its 3D spatial coordinates, estimated surface normal, and facial attribute class embedding. Edges linked to nodes are assigned weights based on an aggregate metric that combines both Euclidean distance and surface co-planarity in a 3D space. A Weighted Geometric Graph Neural Network (WG-GNN) studies this graph using $\mathcal{K} = 3$ geometry-aware message-passing layers enhanced by a scaled dot-product attention method that selectively enhances anatomically relevant inter-landmark messages. The resultant node embeddings are combined into $\mathcal{O} = 3$ pain-level clusters and integrated into a Normalized Pain Score (NPS) within the range of $[0, 100$ a confidence-weighted, SPFES-derived scoring method.

Patient motion remains a source of image degradation in brain MRI, leading to signal loss, blurring, and geometric distortion that compromise quantitative analysis. Existing deep learning methods for motion correction typically rely on paired clean-corrupted data or k-space acquisitions, which are rarely available in clinical settings. We propose SSRL-MAR, a motion artifact-aware unpaired representation learning framework for motion artifact reduction that requires neither paired training data nor explicit motion labels. SSRL-MAR employed a three-stage training strategy: (1) contrastive learning on 3D patches to extract motion representations by contrasting clean and synthetically corrupted images, (2) a motion artifact-aware synthesis network to generate motion artifacts from clean scans, and (3) a motion artifact-aware generator to restore clean volumes using the learned degrader for self-supervised supervision. On in-silico dataset, SSRL-MAR achieved PSNR 23.81dB, SSIM 91.55%, and NMSE 0.79%. On in-vivo MR-ART dataset, the pretrained model reduced motion distortion, and unsupervised domain adaptation further improved anatomical fidelity. Against a source-only supervised model trained on the same simulated pairs, SSRL-MAR improved PSNR by up to 2.0 dB on MR-ART after unsupervised domain adaptation, and remained within 0.25-0.47 dB of an oracle supervised model that requires real paired data unavailable in practice. At the milder motion level, volumetric error in structures such as the corpus callosum and ventricular system decreased by more than 50%, confirming improved neuroanatomical consistency. These results indicate that SSRL-MAR provides a robust and scalable image-domain solution for 3D brain MRI motion correction, enabling reliable structural quantification in large-scale neuroimaging studies without requiring prospectively acquired pairs or acquisition-specific calibration.

Magnetic field strength is a major source of domain shift in magnetic resonance imaging (MRI), affecting signal-to-noise ratio, tissue contrast, spatial detail, and the visibility of anatomical boundaries. The MRIxFields 2026 challenge investigates this problem through cross-field MRI translation across acquisitions at 0.1T, 1.5T, 3T, 5T, and 7T. Its three tasks, Any-to-7T, 0.1T-to-High, and Any-to-Any synthesis, require the generation of target-field image characteristics while preserving subject-specific anatomy. This problem is particularly challenging because paired acquisitions of the same subject across multiple field strengths are rarely available for training. We propose a 3D unpaired cross-field MRI translation framework based on field-conditioned content-style pretraining. The proposed framework first learns controllable field-to-field translation across all available field strengths by disentangling anatomical content from field-dependent contrast characteristics. The pretrained backbone is then adapted to task-specific target domains. Our model comprises a 3D content encoder, a 3D style encoder, a field-conditioned style generator, an AdaIN-modulated decoder, and a multi-field discriminator. Adversarial learning encourages realistic target-field appearance, while cycle-consistency, identity, content, style, and diversity constraints promote anatomical fidelity and controllable translation. We evaluate the proposed method on MRIxFields data spanning five field strengths and three MRI modalities. Experiments on paired test data demonstrate that the framework can adapt to the three challenge settings while preserving three-dimensional anatomical structure in the synthesized volumes. The implementation code is publicly available at https://github.com/Idea89560041/3D-MRI-Field-Translation.

Accurate landmark localization in medical images is a fundamental step for quantitative clinical measurement and downstream analysis. Existing localization methods have advanced, among which multi-stage refinement is a superior solution. Although this strategy mitigates the anatomical ambiguity inherent in single-stage global predictions, its high computational cost limits practical applicability. In this work, we propose a parameter-economic model, PPOC-LL, which leverages Prototype learning-based Progressive Offset Correction for Landmark Localization. Our contribution is three-fold. First, to drive coarse-to-fine landmark optimization, we introduce a multi-scale dynamic perception strategy for patch-level feature pyramid modeling. Second, to effectively handle anatomically similar patterns, we design a similarity-driven prototype learning mechanism that captures informative local semantics for robust offset prediction. Last, to stabilize the model learning and improve the overall performance, we incorporate a novel error-aware reliability regularization via tolerance-based balancing. We collected a large validation cohort, including two public and one private datasets spanning X-ray and ultrasound modalities, covering cephalometric, symphysis-fetal head, and fetal heart landmarks. Extensive experiments demonstrate that PPOC-LL achieves satisfactory performance with a favorable trade-off between accuracy and model complexity.

T2-weighted (T2w) brain MRI provides fluid-sensitive soft-tissue contrast that is important for neuro-oncology and radiotherapy planning. However, T2w scans are acquired with anisotropic voxels and appear blurred or stair-stepped on coronal and sagittal views, which obscures small structures and weakens any downstream 3D analysis. We propose VIPP-SR (View-Independent Patched Projection Super-Resolution), a cross-contrast guided super-resolution framework that restores the inter-plane resolution of an existing anisotropic T2w volume without an isotropic ground-truth T2w. VIPP-SR first trains a view-independent patched generator (VIP-GAN) to learn local T1c-to-T2w anatomical correspondence from high-resolution axial slices. The trained generator is then applied to axial, coronal, and sagittal views of the T1c volume to generate three orthogonal T2w estimates. Shape-preserving patching and deepest-skip removal reduce view-specific shortcuts, thereby constraining the generator to learn patch-local representations and enabling the zero-shot inter-plane transfer. Central to VIPP-SR, a projection-based optimization then enforces anatomical consistency across the three view-specific volumes, fusing them by balancing inter-plane self-consistency against per-view data fidelity. The generator is trained on BraTS-MET and evaluated on both the held-out BraTS-MET testing set and the BraTS-GLI cohort without retraining, assessing the cross-cohort generalizability. The results validate that VIPP-SR improves downstream segmentation over the real anisotropic T2w baseline, raising mean-label Dice from 0.330 to 0.465 on BraTS-MET and, zero-shot, from 0.473 to 0.563 on BraTS-GLI and ablation studies identify inter-plane self-consistency as the main source of the gain.

How a language model internally represents who is speaking, the Assistant, an assigned roleplay persona, or a narrated story character, remains underexplored. We study speaker representations using a dataset of user-expressed emotional text and corresponding model responses. We decompose three generation settings (Assistant, Roleplay, and Story) into sparse autoencoder features extracted at turn-boundary and pronoun-token positions and selected through a filtering pipeline for different depths. We characterize each surviving feature through its steering effects and activation distribution. Our main finding is that the Assistant and roleplay personas are not independent alternatives: personas retain the Assistant-associated feature core while progressively differentiating from it across layers, starting from operational machinery towards behavioral and stylistic features. Meanwhile, generated story characters lack the Assistant-associated core. Both Story and Roleplay can be distinguished from the Assistant with Immersive Simulation Mode. However, the Assistant can sometimes enter or slowly drift into it even in the default setting.

Four years after prompt injection was first identified in 2022, attacks are still predominantly documented as verbatim strings rather than structured exploits, despite advancing agent capabilities and threat actors embedding injections to subvert AI-assisted security analysis. This paper formalizes the structure of prompt-injection artifacts, enabling defenders, red teamers, and cyber threat intelligence (CTI) teams to label, compare, and mutate attacks without relying on fragile string matching. Because large language models compile varied natural-language realizations into identical executable actions, labeling must track attacker intent (tool targets, sinks, and effects) rather than surface wording. We propose a seven-component model (carrier, delivery vector, concealment, context-break, privilege escalation, payload, and return channel) consisting of five artifact fields and two environment fields. This framework unifies roles partially addressed by HOUYI's payload decomposition, the Promptware Kill Chain, and campaign taxonomies, while framing minimal jailbreak frameworks like ReNeLLM as projections onto a restricted subspace. We provide clear labeling rules, a logical analysis record mapping directly to industry CTI schemas, worked examples including EchoLeak (CVE-2025-32711) and an in-the-wild malware AI-evasion sample, and an illustrative agentic flowchart.

Registration-based Few-shot medical image segmentation (RFMIS) aims to generate pseudo-labels for unlabeled images by warping a labeled image through registration. However, existing methods primarily perform pixel-level optimization and inference in Euclidean space, treating anatomical structures as flat and disjoint. This neglect of inherent hierarchies degrades pseudo-label quality and weakens the discrimination of ambiguous regions, limiting the segmentation performance. To overcome this challenge, we propose a Hyperbolic Hierarchy-aware Aggregative Learning framework for RFMIS, termed H2AL, that enhances both deformation plausibility and anatomical discrimination for dual-task learning. Specifically, we introduce a Hyperbolic Hierarchy-aware Infusion (H2I) module, which leverages the hierarchical modeling capability of hyperbolic space to learn precise hierarchy-aware representations via transformation-guided supervised hyperbolic contrastive learning, and injects such hierarchical priors into Euclidean space through a gated infusion block while preserving semantic richness. Furthermore, we propose an end-to-end joint optimization algorithm by gradient aggregation, where the gradients from the registration and segmentation decoders, embedding semantic and hierarchical cues, are aggregated to update the shared encoder to promote collaborative learning across tasks. Extensive experiments on two anatomical regions, with five experimental settings, demonstrate the effectiveness and efficiency of our method in both registration and segmentation. The code is publicly available at https://github.com/JiamingCai469/H2AL.

Computed tomography (CT) is widely used for clinical diagnosis and longitudinal follow-up, yet automatically generating accurate and complete radiology reports from three-dimensional (3D) CT remains challenging. Existing methods improve fine-grained correspondence between images and text by modeling anatomical regions, but remain centered on the current examination. Consequently, patient-specific longitudinal changes within individual regions remain insufficiently modeled. Meanwhile, interval changes are often distributed across multiple anatomical regions, complicating a coherent assessment of the overall longitudinal state. We propose Anatomically Localized Temporal Evidence Representation (ALTER) to address these limitations. Global Prior Integration (GPI) incorporates the prior CT and report to establish historical context for the current examination. Regional Proxy Differencing (RPD) enables each current anatomical region to retrieve a historical proxy from a single shared encoding of the prior volume and to derive localized interval evidence. Interval Change Fusion (ICF) further combines current abnormality states with region-distributed differences, converting their joint representation into change-aware soft prompts that guide report generation. ALTER achieves state-of-the-art results on most evaluation metrics across the RadGenome-ChestCT validation and CTRG-Chest-548K test sets. Code and data preprocessing details are available at https://github.com/peytonkarlie/ALTER/tree/main.

High-fidelity 3D MRI synthesis requires both globally coherent anatomy and fine-grained voxel-level detail. Although latent diffusion makes volumetric generation tractable, its image autoencoder introduces a reconstruction bottleneck that can limit the fine detail recoverable in the final volume. We present VoxStruct3D, a voxel-space flow-matching framework that directly models full-resolution MRI volumes using a clean-data prediction objective. Its Volumetric Voxel Generator (VVG) combines factorized 3D patch embedding with overlapping upsampling, time-modulated residual refinement, and skip fusion, enabling neighboring tokens to jointly reconstruct shared voxel regions and suppress patch-boundary artifacts. To complement direct voxel-space modeling with an explicit anatomical prior, we further introduce a Structure-First, Image-Follows (SFIF) strategy. A frozen pretrained 3D medical encoder and a StructVAE extract compact structure tokens that preserve dominant anatomy, while a structure-leading schedule keeps their trajectory ahead of the image trajectory. Patch-Aligned RoPE spatially aligns the unequal token grids, and asymmetric attention enforces one-way guidance from structure to image. Experiments on pathological and healthy T1-weighted brain MRI datasets show that VoxStruct3D achieves the strongest overall performance across feature-distribution alignment, sample diversity, and perceptual quality, producing anatomically coherent and visually realistic volumes.

Accurate chest X-ray interpretation is inherently hierarchical. Clinical decisions depend not only on what abnormality is present but where it is situated, requiring reasoning from broad anatomical systems down to specific pathological findings. Yet existing automated systems largely treat this as a flat classification problem, failing to capture inter-level dependencies or enforce coherence between coarse and fine predictions. We propose CHASE (Classification with Hierarchical Analysis and Structured Enforcement), a unified single-stage framework that mirrors radiologists' coarse-to-fine reasoning through a clinically driven three-level taxonomy of 9 anatomical regions, 17 sub-regions, and 28 pathological findings. CHASE jointly optimizes multi-level supervision, cross-level probability alignment, and a hierarchy-violation penalty within a shared Vision Transformer backbone. This ensures that fine-grained findings are anatomically supported by their coarser-level context rather than predicted in isolation. Experiments demonstrate that CHASE outperforms flat and hierarchical baselines across all levels while achieving superior probabilistic hierarchy consistency, with level-wise attention maps confirming anatomically grounded predictions. Code is available at: https://github.com/yejix-ai/CHASE.

Deep learning models for medical image analysis typically apply a fixed amount of computation to every input, regardless of case difficulty. Anatomy-guided dual-stream architectures have been shown to improve diagnostic performance, but they evaluate both streams unconditionally, even on cases a single stream could already resolve confidently. We propose SecondOpinion, a framework in which a fast primary stream processes every case, while a second, anatomy-guided stream is invoked only when GateKeeper, a gating mechanism trained explicitly as a binary correctness classifier, judges that the primary stream's prediction needs additional scrutiny, much as a clinician might seek a second opinion on a difficult case. When activated, the two streams are combined through a lightweight cross-attention fusion module. We evaluate SecondOpinion on a unified five-class chest X-ray dataset and a pelvic fracture dataset, the latter including a held-out, harder subset of fractures that are invisible on X-ray but confirmed via CT. SecondOpinion matches or exceeds prior state-of-the-art performance on both tasks, while activating its anatomy-guided stream on only 9.23% of chest X-ray cases, rising to 24.12% on visible fractures and 45.71% on invisible fractures, an activation rate that tracks task difficulty directly. These results suggest that supervising a gating signal toward correctness, rather than relying on unsupervised confidence, allows a model to allocate anatomical reasoning where it is actually needed.

Head-and-neck (HN) proton therapy is highly sensitive to anatomical change over a 4-to-6-week course, as tumor shrinkage, weight loss, and setup variation can misposition the Bragg peak near critical organs such as the parotids, oral cavity, brainstem, and spinal cord, leading to target underdosing or organ-at-risk overdosing. Online adaptive proton therapy replans on the anatomy of the day, yet standard workflows rely on offline replanning that requires repeated CT acquisition and roughly a week of preparation, adding burden, cost, and delay. We investigate whether a patient's treatment-day anatomy can be predicted before image acquisition by transferring longitudinal change from a population database. We propose a digital-twin framework built on a pretrained foundation-model deformable registration network used without patient-specific training. A first registration aligns a prior patient's planning CT to the target and carries the prior's during-treatment quality assurance CT (QACT) into the target frame; a second registration estimates the prior's planning-to-QACT change, which is then applied to the target's own planning CT to synthesize predicted CTs (pdCTs) with propagated contours. Using 88 HN patients, each with a planning CT and three QACTs, we show that pdCTs better match treatment-day anatomy than the static planning CT. Compared with the planning CT alone, normalized cross-correlation improves by 22.8%, Dice for organs-at-risk by 20.2%, and CT-number error decreases by 23.4%. Gains are largest for patients with major anatomical change and negligible when anatomy is stable. This cross-patient motion transfer leverages the digital-twin concept to anticipate treatment-day anatomy, enabling personalized online adaptive proton therapy without repeated imaging.

Reliable pelvic bone segmentation (PBS) from CT is essential for robot-assisted pelvic trauma surgery, yet deploying a source-trained model to a new hospital suffers from severe performance degradation due to cross-center domain shifts. While test-time adaptation (TTA) enables online model adaptation without accessing source data, existing methods show limited effectiveness for PBS, facing challenges including boundary degradation, anatomical inconsistency under domain shifts, and voxel-level class imbalance. To address these challenges, we propose a novel closed-loop dynamic Reliability-Guided TTA framework (ReGA) for PBS. Specifically, we introduce a pseudo-label reliability criterion termed Segmentation Inference Consistency Evaluation (SICE), which jointly measures region overlap and boundary deviation via dropout-based ensemble predictions. Based on SICE, a trust-weighted refinement module adaptively updates features to mitigate boundary errors in pseudo-labels. Furthermore, a confidence-weighted region-level contrastive learning strategy is proposed to enforce anatomical consistency. Finally, ReGA follows the teacher-student (TS) scheme to alleviate voxel-level class imbalance. Experiments on three heterogeneous 3D pelvic CT datasets demonstrate that ReGA consistently outperforms state-of-the-art TTA methods, enabling effective adaptation of the source-trained PBS model to unseen clinical domains. The code is available at https://github.com/Ren-ling/ReGA.

Correspondence-based statistical shape modeling (SSM) is vital for population-level morphometric analysis, but conventional pipelines assume clean, fully registered surfaces. Real-world clinical photogrammetry scans are often noisy, partial, and cluttered, hindering the adoption of radiation-free surface imaging as a safe alternative to computed tomography (CT) for infant craniosynostosis. We present SCALP (Semi-supervised Correspondence via lAndmark Localization and sPectral warping), a two-stage framework that constructs consistent shape models directly from raw, imperfect surface scans. First, a semi-supervised Point Transformer leverages a small expert-annotated dataset alongside a large unlabeled cohort to accurately localize craniofacial landmarks with minimal annotation overhead. Second, these landmarks anchor a Laplace--Beltrami spectral deformation of an anatomical template, generating dense correspondences while naturally isolating the cranium from peripheral scanning clutter without manual preprocessing. Experiments on infant photogrammetry scans demonstrate that SCALP consistently outperforms state-of-the-art unsupervised point-cloud approaches, offering a clinically practical pathway toward objective, radiation-free head shape analysis.

Effective multi-organ segmentation in surgical data requires learning the intricate anatomical features and alleviating the challenge of class imbalance, which results from relatively lower proportions of small and limitedly exposed structures. Recent works on laparoscopic multi-organ segmentation focus on learning structure-specific features through class-specific decoder architectures and report favorable results. This work extends the decoder-focused architectures to investigate knowledge sharing in the cross-surgical domain. We utilize two datasets representing different surgical domains, rectal and cholecystectomy surgeries, to explore how surgical conceptual knowledge transfers under partially common anatomical representations. Additionally, we compare the feature adaptation for the encoder and decoder at different training stages to analyse the knowledge adaptation and retention in the network. Our results corroborate previous findings on decoder-specific architectures and demonstrate that the organ-specific decoder model (CEMD), fully fine-tuned after cross-domain pre-training, achieves the highest segmentation performance (62.4% dice) while converging substantially faster than training from scratch. However, we also find that class imbalance in surgical data remains a persistent challenge that transfer learning does not fully resolve for underrepresented anatomical structures.

Vision-language models (VLMs) are increasingly being evaluated for medical imaging, but many available benchmarks emphasize disease classification, report generation, or broad visual question answering rather than the spatial and anatomical reasoning required for radiology. We developed the Spatial Perception and Anatomical Reasoning in Clinical Radiology (SPARC-Rad) Benchmark, a manually curated multimodal benchmark dataset and evaluation pipeline for assessing these capabilities in radiology VLMs. SPARC-Rad includes 300 image-question pairs derived from healthy control imaging studies in The Cancer Imaging Archive (TCIA), spanning CT, MRI, and radiography across the abdomen, chest, breast, neuro, and musculoskeletal categories. Radiology trainees manually designed and annotated questions to evaluate anatomical identification, localization, laterality, regional recognition, device identification, and inter-structure spatial relationships. The evaluation pipeline supports standardized prompting, structured output collection, response normalization, LLM-as-judge grading, human quality review, binary correctness scoring, and subgroup analysis by modality, anatomy, and reasoning type. SPARC-Rad provides a reusable framework for evaluating whether VLMs can provide reasoning for radiologic anatomy as a spatial system, supporting future model development, failure-mode analysis, and pre-deployment assessment.

Fine-grained segmentation of auricular structures in CT is challenging because the ear occupies a small image region, cartilage boundaries are highly irregular, and interfaces between cartilage and surrounding soft tissues are often ambiguous. Clinical annotations may also include both composite structures containing cartilage and adjacent skin and their corresponding cartilage-only regions, producing nested and overlapping labels. We propose a world-model-based segmentation framework that enables iterative anatomical reasoning beyond conventional feed-forward prediction. Built on an encoder-decoder architecture, the framework introduces a deterministic recurrent state-space model into the intermediate latent space. Multi-scale encoder features and partially decoded representations are fused to form a structural observation that initializes the latent dynamics. During inference, the model performs a three-step latent rollout without ground-truth guidance. Hierarchical anatomical actions update the recurrent state and progressively refine the latent representation. The resulting latent trajectory is projected back into the decoder and combined with high-resolution features to produce the final segmentation. To learn reliable latent transitions, we introduce a balanced hierarchical action objective that addresses foreground sparsity, missing anatomical groups, and imbalance between add and remove operations. Extensive experiments show that the proposed framework consistently improves segmentation accuracy and reduces HD95 by more than 43% for small, irregular, and overlapping auricular structures in CT. These results demonstrate the effectiveness of latent world-model reasoning for challenging medical image segmentation.

The ASNR-MICCAI BraTS Local Synthesis (Inpainting) task asks for the anatomically plausible completion of healthy brain tissue within a masked region of a T1-weighted MRI, providing a tumor-free anatomical reference for downstream analysis. As the task is scored by distortion metrics (SSIM, PSNR, MSE), we build a deterministic regression model and focus on giving it inductive biases tailored to inpainting. Our network follows the U-DiT principle of performing self-attention on a downsampled token grid: a volumetric encoder-decoder imports long-range context through a downsampled global self-attention block with three-dimensional rotary position embeddings, while convolutions and skip connections preserve high-frequency detail. Two ideas drive our results. First, we constrain the attention so that occluded ("void") tokens attend only to known-healthy tokens of the same volume, with a learned bias toward each query's contralateral homologue, forcing the completion to be inferred from observed anatomy rather than from other unknown regions. Second, we add a contralateral-symmetry input that supplies the mirrored healthy hemisphere as a patient-specific prior; since the brain is approximately bilaterally symmetric and lesions are typically unilateral, this prior improves the distortion metrics at matched structural similarity. On the official BraTS-2026 validation leaderboard our submission reaches a mean healthy-region SSIM of $0.864$, PSNR of $24.7$,dB and MSE of $4.6{\times}10^{-3}$ over $219$ cases. We further analyse the residual smoothness inherent to distortion-optimal regression and discuss its implications for anatomical realism.

CT vision-language foundation models have demonstrated promising performance across downstream tasks, but are typically trained with whole-volume representations that dilute fine-grained anatomical signals. Fine-grained vision-language pre-training addresses this by aligning anatomy-level visual features with anatomy-specific text, but in doing so discards the global context that whole-volume models provide. Furthermore, existing fine-grained approaches train from scratch, making them computationally expensive. We introduce Anatomy Contextualized Adaptation (ACA), a lightweight framework that adapts frozen CT foundation model representations for anatomy-level vision-language alignment while enhancing global contextualization. ACA uses TotalSegmentator to decompose CT volumes into anatomy-level embeddings, which are refined via a transformer that captures cross-anatomy relationships, and aligned to both per-anatomy and scan-level text extracted from radiology reports. Evaluated on Merlin and CT-RATE, ACA consistently outperforms both the frozen foundation model baselines and existing fine-grained methods in zero-shot finding classification, while requiring less than one hour of training once embeddings are cached. The attention weights learned by ACA's inter-anatomy transformer additionally indicate plausible cross-anatomy context routing. Altogether, these results support ACA as a lightweight approach for adapting CT foundation models to anatomically grounded vision-language alignment while preserving and enhancing global anatomical context.

Medical image visualization requires volumetric rendering algorithms that preserve anatomical fidelity while maintaining high rendering speeds. To address the high computational cost of large volumetric datasets, we propose a Gaussian-based volumetric representation for efficient visualization of dense medical volumes without compromising structural and radiometric details. We optimize the proposed representation using Monte Carlo volumetric estimation, which enables training on a highly sparse subset of voxels while maintaining consistency with the dense volumetric objective. In addition, we introduce a curriculum learning strategy that progressively incorporates structured slice-based sampling during training. Sparse voxel samples provide an early global coverage of the volume, while slice samples capture spatially correlated regions that aid geometric structure and texture continuity. This combination enables the Gaussian representation to learn anatomical details of various structures and corresponding textures from sparse supervision while significantly reducing the computational cost associated with dense voxel processing. The learned representation supports slice-based rendering methods such as shear-warp volume rendering, enabling efficient visualization of multimodal medical datasets including MRI and Cryosection volumes while preserving anatomical structures. Using sparse supervision, our method achieves up to 43.86 FPS rendering with a compression ratio of 11.31:1.

Tracheostomy requires precise localization of the tracheal incision site; however, conventional manual palpation is subjective and often unreliable, while ultrasound utility remains operator-dependent. This work presents a learning-based framework for hierarchical tracheal anatomy understanding, designed specifically for ultrasound-guided robotic systems. We propose a two-stage perception pipeline integrating a YOLOv8n localization backbone with a sparse, prompt-optimized SAM2 decoder to achieve high-fidelity segmentation from sparse surgical annotations. Our hybrid training strategy, bridging curated laboratory data with unconstrained sequences, ensures clinical robustness. Experimental benchmarks demonstrate that this decoupled architecture effectively balances generalization, precision, and efficiency. The YOLOv8n and SAM2 framework achieves a consistent Mean Dice Similarity Coefficient (DSC) of 0.777 across both controlled and generalized domains. This significantly outperforms U-Net baselines, which often suffer from anatomical fragmentation and performance degradation (Generalization DSC $\le$ 0.494). By constraining mask decoding to targeted, sparse regions of interest, our model achieves a throughput of 6.92 FPS, which is vital for closed-loop robotic teleoperation. This study confirms that a robust hierarchical understanding of tracheal anatomy can be derived by coupling lightweight localization with foundation-scale visual models. Our framework establishes a scalable foundation for standardized, autonomous surgical assistance, effectively navigating the variability of real-world ultrasound to enhance the safety and precision of robotic-assisted tracheostomy.

Quantitative drug-induced sleep endoscopy (DISE) requires reliable airway boundaries at specific anatomical levels. Pixel-level DISE annotations are scarce, and manual contouring limits the scalability of quantitative assessment. To address this limitation, we developed ASTRA-Net for known-plane DISE segmentation with limited real annotations. Stage 1 aligned intermediate ConvNeXt-Base representations from 14,250 unlabeled virtual endoscopy frames derived from computed tomography and real DISE frames. Virtual images were used only for feature alignment. Stage 2 fine-tuned four independent UNet++ decoders on 401 real annotated frames. Structured zero-mask supervision constrained incompatible plane outputs and invalid frames. Six alignment configurations used maximum mean discrepancy, domain adversarial learning, or both objectives. On a hold-out evaluation set of 100 frames, the five-model MMD-only segmentation ensemble achieved a mean Dice of 0.8927, with a 95% image-level bootstrap interval of 0.8631 to 0.9160. The mean intersection over union was 0.8239. A classification- enabled variant of the same alignment configuration reached a restricted four-plane top-1 accuracy of 0.92 on the same hold-out frames. These results indicate that ASTRA-Net can support frame-level, plane-specific DISE boundary delineation when real annotations are limited.

We present a privacy-preserving framework for synthetic lung CT slice generation developed for the Image-CLEFmed GANs 2026 challenge. The approach combines Optimal Transport Conditional Flow Matching with privacy-oriented training and a post-generation "Supervisor" pipeline that filters generated candidates in learned geometric latent spaces using autoencoder embeddings, Determinantal Point Processes, and Stein Kernel Thinning. Official results show a strong realism-privacy trade-off, with the best-performing model achieving a Privacy Preservation Score of 0.549 and competitive visual fidelity with an FID of 0.3290. While the proposed geometric filtering substantially reduces nearest-neighbor memorization and membership-inference leakage, persistent patient re-identification scores indicate that preventing direct image copying is not sufficient to remove deeper patient-specific anatomical identity, highlighting an important frontier for future privacy-preserving medical image generation.

Diffusion Magnetic Resonance Imaging (dMRI) is a powerful tool for probing brain microstructure, but clinical acquisitions are often limited by low out-of-plane resolution, resulting in degraded structural information and reduced utility for advanced analysis. We introduce SIINR (Structurally Informed Implicit Neural Representations), a general framework for super-resoltion of clinical dMRI datasets while quantifying uncertainty in the reconstructed outputs. SIINR utilizes a supervised 3D U-net as a prior and combines it with a self-supervised implicit neural representation (INR) that fuses the high-resolution prior and the original low-resolution data. The INR enables joint modeling across spatial and angular domains, enforces data consistency, and provides analytic approximate posterior distributions for downstream uncertainty quantification. We validate the framework on a diverse set of open-access dMRI datasets, demonstrating that SIINR outperforms standard interpolation methods in both quantitative error metrics and qualitative anatomical fidelity. Experiments on clinical cases, including subjects with multiple sclerosis and brain lesions, illustrate the framework its ability to propagate intensity changes and flag uncertain regions in challenging scenarios. SIINR is flexible, modular, and can be adapted to different upsampling ratios and downstream tasks, providing a principled approach for enhancing clinical dMRI and supporting robust interpretation of derived neuroimaging metrics.

Active sampling for accelerated MRI must distribute a tight sampling budget across spatial frequencies that carry very different kinds of information. Low frequencies hold most of the anatomical context; high frequencies carry the fine details that drive pathology assessment. Existing active samplers either treat both regions identically or restrict the action space to entire Cartesian rows, which forces a poor compromise at high acceleration. We propose HieraSample, a task-driven framework built around this hierarchy. A cosine-annealed curriculum lowers the acceleration factor from 20x to 4x across 80 acquisition steps while keeping a fully-sampled low-frequency disk at every step; a Mamba-based policy then picks individual high-frequency coordinates from features extracted by dual disease and severity classifiers. The reward is the per-sample reduction in class-weighted cross-entropy after each action, so a positive reward corresponds directly to a more confident correct prediction. On the fastMRI+ knee benchmark, HieraSample matches the fully-sampled oracle on ACL diagnosis from 4x to 10x acceleration, and improves on a recent Cartesian baseline by as much as 20.4 AUC points on ACL severity.

Lung ultrasound (LUS) is a bedside tool for assessing pulmonary edema in patients at risk due to heart failure or impaired kidney function. However, automated LUS analysis remains challenging because of speckle noise, imaging artifacts, and operator-dependent acquisition variability. In this work, we present a deep learning framework for multi-class LUS video classification that explores two components: hierarchy-aware training, and anatomy-guided learning. Starting from a strong baseline, we introduce hierarchical training strategies and then introduce pleural line mask supervision to guide model attention toward anatomically relevant regions. We study four clinically relevant classes--healthy, B-lines, consolidations, and mixed B-lines with consolidations--using an open-access dataset of 1,886 videos from 219 patients, evaluated with patient-level five-fold cross-validation. Results show that hierarchy-aware training improves pathological separation relative to flat classification, while mask-guided attention supervision achieves the highest mean macro-F1 of 65.7% and produces more localized attention patterns. Transfer experiments on the external COVID-BLUeS dataset further show competitive and parameter-efficient adaptation while preserving pleural-focused attention behavior. These findings suggest that combining clinically structured objectives with anatomy-guided supervision is a practical approach to robust, interpretable LUS video analysis. Code and model implementations are available at https://github.com/Alya-Almsouti/LUS-video-classification.

Single-stream autoregressive decoding of large language models is bound by memory bandwidth: each generated token requires one full forward pass through the target model, and successive passes cannot be parallelized. Speculative decoding restructures this computation: a small draft model proposes $K$ tokens autoregressively, the target model scores all of them in one batched pass, and a rejection-sampling rule provably preserves the target model's output distribution. We present a from-scratch, device-agnostic (CUDA/MPS/CPU) implementation and an empirical study across five draft/target backend configurations on a consumer Apple-silicon laptop. Distribution equivalence is verified at three levels, culminating in a two-sample test over roughly 9,200 real-model tokens per method ($χ^2 = 162.5$, dof $= 200$, $p = 0.976$) and exact greedy-sequence agreement. The best configuration reaches a measured $1.61\times$ wall-clock speedup at $K=6$, on an acceptance profile declining from 69.7% at $K=1$ to 37.8% at the optimum, while three of five configurations decelerate, either because the draft fails to out-speed a small target or because the quantized Metal backend executes "parallel" verification serially, an effect we isolate and quantify. The failures are as instructive as the successes: speculative decoding pays off only when verification is genuinely batch-parallel and the draft/target latency gap is real.

Automated chest CT report generation remains challenging because clinically faithful reporting requires both whole-volume understanding and accurate description of localized anatomical findings. Here we developed and retrospectively evaluated MonteRET, a region-aware retrieval-enhanced framework for generating chest CT findings sections. MonteRET integrates global CT features with region-level anatomical representations, retrieves clinically relevant knowledge using predicted medical conditions and region-level vision-language alignment, and refines initial reports through a knowledge-guided report rewriting agent. We trained our model on a public cohort with 24,128 CT scans from RadGenome-ChestCT. We evaluated MonteRET on the public RadGenome-ChestCT test set of 1,564 CT scans and an external cohort of 82 CT scans from NewYork-Presbyterian/Weill Cornell Medical Center. MonteRET improved report quality, semantic similarity, and clinical efficacy compared with a matched baseline and several state-of-the-art methods. Gains were most pronounced for recall, suggesting fewer omitted findings. Human expert evaluation by radiology residents also favored MonteRET.

Life-limiting congenital anomalies require accurate prenatal diagnosis for appropriate clinical decision-making. Prenatal ultrasound (US) examinations involve multiple anatomical planes, and diagnosis depends on identifying anatomical planes and selecting diagnostically relevant planes for each anomaly. Existing automated methods either rely on plane-level annotations or aggregate heterogeneous images without explicitly modeling these diagnostic capabilities. We propose AnomExpert, a prototype-driven framework for prenatal US anomaly diagnosis using only case-level supervision. AnomExpert introduces learnable plane prototypes to organize unordered images into latent representations corresponding to anatomical planes without requiring plane annotations. A disease-aware sparse selection mechanism further selects diagnostically relevant planes for each anomaly. Experiments on a multi-center dataset of 3,654 cases show that AnomExpert consistently outperforms nine representative multi-instance learning methods. Using a ViT-small backbone, it achieves 86.9% accuracy and 84.2% F1-score while maintaining parameter efficiency. These findings indicate that modeling anatomical plane identification and disease-specific plane selection improves weakly supervised multi-plane prenatal US anomaly classification. The code is available at https://github.com/TIanCat/AnomExpert.

Biomedical imaging data exhibit substantial acquisition variability, where identical biological structures can appear markedly different due to differences in imaging devices, acquisition protocols, sites, and reconstruction settings. Consequently, learned representations often entangle underlying biological information with acquisition-dependent appearance, limiting interpretability, generalisation, and clinical deployment. We show that these sources of variation can be disentangled by jointly modelling medical images and acquisition metadata. Using large-scale clinical brain MRI data as a case study, we learn representations that disentangle anatomical structure from contrast-dependent appearance. The resulting framework enables the organisation of heterogeneous imaging protocols, sequence understanding, the detection of image-metadata inconsistencies and imaging artifacts, while preserving biologically relevant anatomical features across diverse acquisitions. Building on these disentangled representations, it further supports generative and translational capabilities, performing both metadata-conditioned synthesis of realistic 3D brain MRIs and anatomy-preserving harmonisation for cross-modality and cross-site adaptation. Our findings demonstrate that acquisition variability is a structured component of the imaging process that can be modeled, audited, synthesised, and controlled, establishing a foundation for acquisition-aware representation learning in large-scale biomedical imaging.

We present Spectral Consistent Flow (SC-Flow), a 3D medical image translation framework with a single function evaluation (1-NFE) in the latent space. This approach reformulates medical image translation as a stochastic Brownian bridge process that directly constructs a mapping between source and target modalities by predicting the support regularized mean velocity field. To mitigate modality entanglement, over-smoothing, and artifacts induced by the implicit low-pass modulation of the latent average velocity, we introduce a Spectral Consistency Corrector that dynamically regularizes the evolution of the power spectral density via learnable frequency-domain gain modulation. This mechanism establishes an explicit bridge between spatial textures and spectral energy flow, enabling the model to recover fine-grained anatomical fidelity while maintaining global structural coherence. Extensive experiments on four datasets demonstrate that SC-Flow delivers significantly more accurate, consistent, and robust performance across various translation scenarios.

Prompt-free adaptation of the Segment Anything Model (SAM) has emerged as a promising paradigm for automatic medical image segmentation. Existing methods mainly focus on prompt generation, while overlooking that prompt quality is fundamentally constrained by the expressiveness of anatomical representations. However, deterministic prototypes or semantic tokens are insufficient to jointly capture global anatomical priors, intra-structure diversity, and local structural reliability. To address this limitation, we propose the Hierarchical Probabilistic Representation (HPR) framework, which learns complementary anatomical representations through Distributional Anatomical Representation (DAR), Multi-component Anatomical Representation (MAR), and Local Reliability Representation (LRR), and integrates their predictions via Hierarchical Prediction Fusion (HPF) while remaining compatible with the original SAM decoder. Experiments on the Synapse, LA, and PROMISE12 datasets demonstrate that HPR-SAM achieves state-of-the-art performance on Synapse and the best performance under few-shot settings on LA and PROMISE12, validating the effectiveness of the proposed hierarchical probabilistic representation learning framework for prompt-free medical image segmentation. Code is available at https://anonymous.4open.science/r/HPR-SAM-E4AF.

Multi-view reasoning in coronary X-ray angiography is inherently a cross-projection geometric problem, yet automated report generation in this setting remains largely unexplored. The 3D vascular topology leads to projection-dependent branch overlap and foreshortening, rendering single-view modeling fundamentally incomplete and unstable for lesion localization and stenosis grading. Although multi-view fusion appears promising, learning anatomically consistent fusion from real angiograms is impeded by a critical limitation: cross-view alignment is unobservable and cannot be explicitly supervised. Consequently, conventional fusion relies on implicit correlations rather than verified anatomical correspondence. We address this by reformulating multi-view stenosis reporting as an alignment-constrained aggregation problem. A controllable synthetic angiography generation strategy is introduced to expose geometry-derived patch-level correspondence supervision unavailable in real data. An anatomy-correspondence module learns cross-view correspondence matrices that explicitly align auxiliary features within the main-view coordinate space prior to fusion, thereby constraining evidence aggregation to anatomically consistent regions. Experiments on synthetic data and zero-shot transfer to real angiograms show that this alignment-constrained design improves correspondence consistency and structured stenosis reporting compared to single-view modeling and conventional multi-view fusion methods. The code will be publicly available upon publication.

Due to the scarcity of expert-annotated data, Semi-Supervised Medical Image Segmentation (SSMIS) has emerged as a promising approach. Many anatomical structures in medical images exhibit significant intra-class heterogeneity, with different regions showing heterogeneous intensity patterns within the same structure. However, existing methods inadequately exploit this intensity-manifested intra-class heterogeneity, resulting in uniform structural representations and imprecise segmentation. Furthermore, the scarcity of labeled data makes it more difficult to effectively capture such complex heterogeneity. To address this, we propose Multiple Prototype Contrastive Learning (MPCL), an SSMIS framework that possesses better diversity and better precision. It consists of three novel designs: First, we provide structural representations with better diversity and propose Intensity-aligned Heterogeneous Prototype Generation (IHPG) that effectively models intra-class heterogeneity by generating multiple prototypes aligned with intensity characteristics. Second, we further enhance more diverse structural representations and build a solid foundation for more precise segmentation through Prototypical Space Optimization (PSO) that systematically optimizes a more discriminative and generalizable prototypical space. Finally, we achieve segmentation results with better precision through Dual-branch Knowledge Alignment (DKA) that efficiently promotes intra-class heterogeneity knowledge transfer from prototypical space to the segmentation network. Extensive experiments on three medical image datasets with significant intra-class heterogeneity demonstrate that MPCL significantly outperforms existing methods, especially under extremely limited labeled data.

Radiology is vital to modern healthcare, but rising imaging demand and persistent workforce shortages strain reporting capacity and clinical workflows. Automated radiology report generation has the potential to support radiologists and help alleviate this burden; however, existing retrieval-based methods remain rigid, lack explicit anatomical grounding, and do not account for longitudinal disease progression or available clinical context. In this work, we introduce STAR3, a multimodal, spatio-temporal, attentive retrieval framework for radiology report generation that aligns region-level anatomical information with clinical indications and longitudinal changes across chest X-ray studies. Our framework employs an object detector to identify anatomically meaningful regions and retrieves semantically relevant report sentences conditioned on both current clinical context and changes observed between prior and current examinations. This design enables anatomically and temporally grounded report generation that better reflects clinical reporting practice. Experiments on the MIMIC-CXR dataset demonstrate that STAR3 outperforms current retrieval-based approaches on retrieval, NLP and clinical metrics, highlighting the value of conditioning retrieval anatomically, temporally and clinically for advancing automated radiology report generation.

Positron emission tomography (PET) provides essential functional information for disease assessment, however reducing injected activity or acquisition time produces low-dose (LD) PET with stronger count dependent noise and less reliable uptake quantification. Diffusion models offer a promising solution for PET denoising by progressively recovering high-dose (HD) PET images from LD inputs. However, LD-to-HD PET denoising is still challenging due to insufficient anatomical guidance, unstable multi-scale feature propagation, and uncertain frequency domain uptake recovery. We propose AnF-DiffPET, an anatomy- and frequency-guided diffusion framework for computed tomography (CT) conditioned LD PET denoising. The framework integrates Anatomical-Frequency Guidance (AFG), Multi-Scale Cross-Transformer Reconstruction (MSCTR), and Frequency-Contrastive Hard Mining (FCHM) to enhance anatomy aware feature modulation and frequency domain consistency during denoising. Experimental results across four PET/CT datasets show that the proposed method improves image fidelity, anatomical consistency, and quantitative fidelity over representative CNN-based, GAN-based, transformer-based, and diffusion-based methods. The code and trained models will be publicly released upon acceptance.

Image-guided therapies, including radiotherapy, biopsy and deep brain stimulation, rely on real-time targeting of anatomical structures. However, in the presence of motion, imaging latencies create a temporal misalignment between observed and true anatomy, compromising treatment accuracy. Artificial intelligence-based frameworks have increasingly been presented to close this latency gap, but leading personalised models can fail due to a lack of stable anatomical grounding. Foundation models can provide grounded behaviour, but they do not adapt to real-time, individual patient dynamics. Here we introduce a closed-loop coupling framework that synergises patient-specific temporal prediction with continuous segmentation-based anatomical interpretation from a foundation model. A personalised model predicts future anatomy to compensate for system latency, while a streaming foundation model provides anatomical supervision used to continuously update the temporal predictor in real time during treatment. We validate the framework using a digital phantom and intrafraction magnetic resonance imaging (MRI) from patients undergoing MRI-guided radiotherapy. For a prediction horizon of 400 ms, the proposed method improves anatomical prediction and reduces dosimetric error compared with existing approaches, within clinically relevant latency constraints. These results establish closed-loop coupling as a general strategy for real-time image-guided intervention.

Computational models of the human heart are widely used to study electromechanical and fluid-dynamical cardiac function and to support applications such as in silico clinical trials. However, most studies remain limited to single or patient-specific anatomies, restricting the inclusion of population-level variability required for uncertainty quantification. A key challenge is translating medical-image segmentations, which may contain artifacts, mesh defects or disjoint domains, into topologically coherent geometries suitable for multiphysics simulations. In this work, we present a semi-automatic pipeline that converts CT-based segmentations into simulation-ready cardiac meshes within a few minutes while preserving anatomical and topological consistency. Building on modern deep learning segmentation methods, the framework incorporates a template-based registration stage to regularize artifacts and enforce mesh-quality constraints. A Chamfer-distance morphing strategy deforms a high-quality template toward each segmented heart, matching individual chambers while preserving topology. The resulting meshes are watertight, isotopological, and endowed with consistent point-to-point correspondence. The pipeline is validated on 58 healthy cardiac CT scans, including all cardiac chambers and proximal vessel segments. The resulting meshes can be represented in a unified shape space, enabling the construction of a statistical shape model of the heart and major vessels. Principal Component Analysis shows that a low-dimensional latent space efficiently captures population variability, while Gaussian Mixture Modeling enables synthetic anatomy generation. Overall, the proposed framework (released open-source) provides a pathway from raw segmentations to simulation-ready cardiac geometries, enabling anatomically consistent virtual cohorts for large-scale in silico studies.

Developing robust artificial intelligence models for 4D (3D + time) medical imaging is constrained by limited annotated data, inter-device domain shifts, and privacy restrictions. To address this, we propose a 4D controllable generative framework for anatomically consistent data augmentation. A semi-supervised variational autoencoder learns a compact latent representation of anatomical volumes while jointly predicting aligned segmentation masks in a unified framework. Anatomical structure is then disentangled from temporal dynamics through a cascaded latent diffusion model (LDM). A static LDM generates subject-specific anatomy conditioned on clinical priors (diagnosis and volumes measures) and a subsequent motion LDM estimates residual latent motions, ensuring strict temporal coherence across the 4D sequence. The proposed approach was evaluated on cine cardiac MRI as a representative 4D imaging application. Experiments across multiple datasets demonstrate high controllability of static anatomy (Pearson r > 0.8) and strong temporal coherence (FVD = 288.08). In cross-vendor generalization experiments, augmenting training sets with synthetic 4D sequences significantly improves downstream segmentation performance. Using nnU-Net, the proposed augmentation strategy improves the average Dice score by 1.4% and reduces the Hausdorff Distance by 3.0mm compared to training on real data alone, for the left ventricle, Dice improves by 2.8% with a 5.4mm reduction in boundary error. Overall, this framework provides a scalable and controllable solution for 4D medical image synthesis, supporting the development of more robust models with limited annotations and cross-vendor variability. Code available on https://github.com/cyiheng/4DCardiacMRISynthesis.

Intracranial aneurysms are often asymptomatic until rupture, which carries high mortality. Rupture risk assessment and treatment planning depend on both aneurysm morphology and anatomical location, yet existing automated methods remain limited to binary detection without fine-grained anatomical classification or multi-class segmentation. We present a multi-task framework that simultaneously performs multi-label classification, multi-class aneurysm segmentation, and multi-class vessel segmentation across 13 anatomical locations and four imaging modalities (CTA, MRA, T2, T1-post). Our two-stage approach combines a fast 2D tri-axial Region of Interest (ROI) extraction method with a 3D multi-task nnU-Net backbone. A dual-decoder design mitigates the extreme volume imbalance between aneurysm and vessel classes, while cross-attention pooling and modality-specific auxiliary heads improve feature learning across heterogeneous inputs. Our two-fold ensemble achieved 2nd place in the RSNA 2025 Intracranial Aneurysm Detection challenge. Code, model weights, and a 3D Slicer plugin are publicly available.

3D/2D registration serves as a cornerstone technique in surgical navigation. Traditional iterative optimization algorithms suffer from low efficiency and high failure rates in intraoperative settings. Deep learning-based methods reformulate registration from iterative optimization to a regression problem that maps image appearance features to spatial pose, typically achieving improved real-time performance and accuracy. However, such learnable methods are confined to memory-driven retrieval of specific pose features rather than understanding the task of image alignment itself, which limits their generalization in complex scenarios. We propose LayersReg, a pioneering regression paradigm that endows the model with 3D anatomical awareness and searches for the correct pose in a progressive, layer-by-layer manner. Inspired by the iterative pose-searching optimization criterion of classical registration, LayersReg searches for correlations between the moving and fixed images in feature space, capturing the trend of pixel flow and thereby converging iteratively toward the correct spatial pose transformation. We further design a coupling of node-wise regression with the progressive registration framework to enhance the model's perception of spatial pose changes. Experimental results demonstrate that under large offsets and multimodality conditions, LayersReg achieves high accuracy on both X-ray/CT registration (0.68°, 1.41 mm) and slice localization (0.73°, 1.55 mm) tasks, outperforming existing state-of-the-art methods while meeting the intraoperative demands for precision and real-time capability.

The objective of this paper is to improve radiological gradings measured on MRIs of spines, by resampling scans so that the new view planes are better aligned with the target anatomy than the original sparse images. To this end, we adapt 3D Gaussian Splatting to form a volumetric reconstruction starting from sparse anisotropic MRIs, and imaging planes aligned with the anatomy relevant for clinical evaluation are then sampled and rendered. The novel view plane is optimal for diagnostic radiological grading of the target anatomy, whereas the original MRI is not. The resampled scans are then used to predict ordinal severity grades of localised stenosis conditions in spinal MRIs. We compare our method against Voxel Interpolation resampling, which takes the average of inverse-distance weighted nearest neighbour intensities for each target coordinate. Experiments show that across all stenosis conditions, resampled scans using Gaussian Splatting produce more accurate stenosis gradings compared to the raw scans which do not include the complete anatomy in-plane, as well as images resampled using Voxel Interpolation.

Color fundus photography (CFP) is the most common ophthalmic imaging modality for large-scale screening. However, it is highly susceptible to degradations, making robust fundus image quality assessment (FIQA) crucial. The criteria for what constitutes high-quality at the image level vary across clinical tasks, making FIQA dependent on expert knowledge. This motivated the development of automated methods and datasets. While existing datasets aim to standardize image-level quality, their criteria often differ. Furthermore, image-level labels preclude the quantitative evaluation of localized degradations, which is essential for trustworthy FIQA. We argue that pixel-level FIQA based on anatomical visibility represents a more task-agnostic, explainable approach. In this work, we introduce FunPiQ, the first FIQA benchmark to provide pixel-level quality annotations. In addition, we propose EFIQA-CP, an explainable-by-design (EBD) method that uses quality pseudo-labels based on anatomical visibility to train a CNN via Non-Negative Positive-Unlabeled learning. Extensive evaluations of classification methods with post-hoc explanations, anomaly detection methods, and EBD methods demonstrate the superior performance of the last and, particularly, of EFIQA-CP.

The physical anastylosis of collapsed architectural monuments -- the meticulous reassembly of fallen stone elements into their original structural configuration -- represents one of the most intellectually demanding challenges in conservation science. Traditional approaches depend heavily on expert archaeologist judgement and manual block-by-block correspondence, a process that is both labour-intensive and inherently subjective. Inspired by the combinatorial complexity of this problem as manifested in the game of Jenga, we present Jenga Inverse Predictor , a GPU-accelerated deep learning framework that addresses structural anastylosis as an inverse prediction task. Given an image of a collapsed block assembly, JIP-2 reconstructs the most probable prior tower configuration by: (1) implementing a complete rigid-body physics engine with OBB/SAT collision detection and a Projected Gauss-Seidel (PGS) contact solver accelerated with Numba JIT and CuPy CUDA; (2) applying the analytical force thresholds of Ziglar (CMU, 2006) -- F_app = 3mu_smg (Y-axis, torque-free) and F_app = 4mu_smg (X-axis, torque risk) -- over three friction levels (mu_s in {0.25, 0.40, 0.60}) across 450 simulated episodes; (3) training a dual-stream ResNet-18 that injects a friction one-hot vector and jointly predicts block removal count, per-position removal probabilities, centre-of-mass imbalance, and Ziglar torque risk; and (4) generating a smooth 3-D video of the block-by-block reverse reconstruction. We discuss implications for computer-assisted anastylosis at the UNESCO Maya site of Uxmal, Yucatan, and provide a detailed technical description of the full pipeline, architecture, and loss formulation.

Accurate recognition of anatomical structures is essential for safe and effective minimally invasive surgery (MIS), yet it remains underexplored in surgical computer vision due to limited annotated data and methods tailored primarily to natural scenes. In this work, we present a combined dataset and model framework to advance anatomy-aware perception in MIS. First, we introduce ATLAS-120k, a large-scale clip-level semantic segmentation dataset comprising over 120,000 annotated frames from 100 surgical videos spanning 14 procedures and multiple modalities, including laparoscopic and robot-assisted surgery. The dataset captures substantial procedural variability and was created using a scalable annotation pipeline that integrates expert manual labeling, automated propagation, iterative refinement, and surgeon verification to ensure high-quality annotations. Second, we propose ATLAS (Anatomy Recognition with Context Learning using Foundation Representations), a video semantic segmentation model specifically designed for surgical anatomy recognition. Unlike conventional approaches that emphasize object tracking, ATLAS leverages foundation-model embeddings together with lightweight temporal reasoning to incorporate contextual cues such as procedure type, surgical phase, and short-term visual memory. This design enables temporally consistent and accurate predictions while maintaining real-time feasibility. Together, the dataset and model establish a practical foundation for robust surgical scene understanding and support the development of clinically applicable guidance systems for minimally invasive surgery. The models, dataset annotations and annotation platform are publicly available at: https://github.com/TimJaspers0801/ATLAS.

Medical image re-identification (MedReID) enables longitudinal patient linkage but remains vulnerable to shortcut learning and often produces decisions that clinicians cannot audit against named anatomy. We propose Graph-of-Differences (GoD), which grounds identity comparisons in explicit anatomical structure. Each image is represented as an anatomy graph whose nodes correspond to named anatomical regions; given an image pair, soft node correspondence is established, and differences are computed over matched anatomy. A graph-level difference alignment objective ties these anatomy-matched differences to the global backbone difference, ensuring the retrieval signal is anchored in homologous structures rather than arbitrary spatial tokens. Explanations are defined over named graph nodes and quantitatively audited via node insertion/deletion tests, replacing unstable pixel heatmaps with verifiable structure-level evidence. On internal benchmarks, GoD improves Rank-1 by +7.1 pp on fundus and +3.1 pp on CXR over a strong frozen-backbone baseline, with further gains on zero-shot external transfers confirming that anatomy grounding improves both accuracy and generalization. Code is available at https://github.com/GenMI-Lab/GoD.git.

Accurate segmentation of thin, tortuous anatomical structures, such as retinal vessels, cerebral vasculature, and facial wrinkles, remains challenging due to low contrast, frequent discontinuities, and severe class imbalance. Although recent convolutional and Transformer-based models have improved performance, they often yield fragmented predictions and fail to recover fine branches. We propose CSWinUNETR, a general-purpose backbone for 2D and 3D thin-structure segmentation. It employs cross-shaped stripe self-attention to model long-range principal-axis context and incorporates cyclic shifts to enhance information exchange across stripes. To better preserve fine-grained details, we further introduce a detail-enhanced multi-scale self-attention module that aggregates contextual features from multi-resolution representations. In addition, we propose sparse-control dynamic snake convolution, which reconstructs reliable dense curvilinear kernels from sparsely predicted control points to better follow tortuous geometry. Extensive experiments on four benchmarks across ophthalmology, neurovascular imaging, and dermatology demonstrate that CSWinUNETR consistently outperforms state-of-the-art methods without task-specific post-processing or topology-aware losses. The code is available at https://github.com/labhai/CSWinUNETR.

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.