Anatomical Priors

Foundation models hold promise for generalizable analysis of structural brain magnetic resonance imaging (MRI) across development, aging and disease. However, existing models are typically built through centralized pretraining on pooled data, despite privacy and governance constraints. Such pooling optimization can overemphasize cohort size and overlook complementary information from smaller, specialized cohorts. Here we present BrainFedFM, a structural brain MRI foundation model federatively pretrained on 164,707 three-dimensional scans drawn from diverse real-world data distributions and organized across 42 federated sites. BrainFedFM uses dual-priority federated pretraining, coupling spatial-priority masking at each site with site-priority aggregation at the server to emphasize informative anatomical regions locally and prioritize site contributions globally. Across 20 downstream datasets spanning 17 classification, regression and segmentation tasks, BrainFedFM achieved the state-of-the-art performance (mean rank 1.68, 50% gain) across seven models, including four centralized foundation models, while showing particularly consistent advantages in classification and regression and robustness across underrepresented populations. These findings demonstrate the generalizability of BrainFedFM and highlight federated pretraining as a practical strategy for developing neuroimaging foundation models from distributed data without pooling raw images.

Autonomous precision milling of biological structures is challenged by incomplete knowledge of target geometry, local material thickness, and critical internal boundaries. Subject-specific preoperative models can address geometric and thickness variations, but static models cannot determine boundary status encountered during execution, while repeated target-specific imaging limits scalability. This article presents an uncertainty-aware autonomous milling framework that assigns complementary roles to generic anatomical priors and active boundary perception. A generic anatomical prior provides conservative global guidance and is transformed through semantic-guided registration and hybrid vision-force calibration into robot-executable guidance for individual targets. As milling approaches uncertain boundaries, the robot actively probes the remaining structure and uses relative stiffness changes to estimate boundary status and structural detachability. A state-adaptive controller governs transitions between active perception and spatially selective incremental refinement, repeating this cycle until the termination criterion is satisfied. Hierarchical experiments on biological surrogates and in vivo mouse cranial window creation demonstrate accurate anatomical prior transfer, reliable boundary adaptation, and autonomous precision milling of biological structures.

While multimodal large language models (MLLMs) achieve remarkable performance on generic image captioning, they frequently suffer from structural hallucinations in human-centric scenarios. Accurately modeling human subjects is foundational for critical downstream applications, such as accurate avatar/video/image generation and fine-grained human action understanding. However, these tasks require highly precise subject-centered spatial grounding, such as distinguishing egocentric left/right laterality and maintaining correct anatomical-object bindings. Although catastrophic for structural integrity, these localized spatial inversions are often overshadowed by overall descriptive metrics in existing benchmarks. To systematically expose and quantify this bottleneck, we introduce SPACE (Subject-centric Poses, Appearance, and Characteristics Evaluation), a benchmark designed to evaluate subject-centered spatial understanding. On SPACE, we reveal that despite strong generic perception, current MLLMs consistently fail to ground descriptions in the subject's intrinsic frame of reference. To bridge this gap, we propose a specialized data construction and alignment pipeline. We first extract structured spatial hints from fine-grained body-part localization to guide a two-stage caption rewriting process, yielding highly spatially-faithful training data. Furthermore, we design a rubric-based reward for Group Relative Policy Optimization (GRPO) that explicitly penalizes structurally critical spatial errors during alignment. Extensive experiments on SPACE demonstrate our framework significantly improves human-centric caption quality, particularly in subject-centered spatial reasoning, achieving performance competitive with strong closed-source models. Our benchmark and code are available at https://github.com/JHang2020/SPACE-Eval.

Training deep learning-based medical image segmentation models is challenging with limited curated datasets. For AGITG TOPGEAR, a gastric cancer trial, the Clinical Target Volume (CTV) is complex and defined by multiple anatomical landmarks, making upfront training data preparation difficult for an automated contour QA segmentation model. We investigate anatomical priors, derived from surrounding organ segmentations, to provide spatial context and improve TOPGEAR CTV segmentation accuracy. We also evaluate active learning, iteratively expanding the training dataset by selecting cases expected to improve performance. One hundred TOPGEAR CT scans were retrospectively analyzed. An initial set of 10 expert-contoured cases was used to train an nnU-Net model. TotalSegmentator generated a voxel-wise anatomical prior map from surrounding structures as an additional input channel. Active learning was simulated over four iterations, selecting cases by model uncertainty and segmentation performance. All models used five-fold cross-validation for an ensemble uncertainty measure. Evaluation used a hold-out testing set of 50 cases. The anatomical prior improved CTV segmentation accuracy, increasing mean Dice Similarity Coefficient (DSC) from 0.84 to 0.86. Active learning similarly improved performance to 0.86, with greatest benefit in the final round. Combining the anatomical prior with active learning achieved the highest accuracy, with a DSC of 0.87. Model uncertainty correlated with DSC, supporting its use in identifying suboptimal predictions and guiding active learning. Anatomical priors and active learning each improved CTV segmentation accuracy and generalizability, with their combination achieving the best performance, supporting integration into segmentation model development for automated contour QA in radiotherapy clinical trials.

Camera localization in bronchoscopy remains a challenging problem due to stringent accuracy requirements, real-time constraints, and limited training data. Compared to natural scenes, the confined anatomical structures demand millimeter-level precision, while intraoperative guidance necessitates low-latency inference. However, existing methods often fail to effectively exploit preoperative geometric priors, limiting their robustness and accuracy. To address these limitations, we propose a unified geometry-aware bronchoscope localization framework (GABL) that effectively fuses preoperative structural priors with paired intraoperative video to estimate 6-DoF camera poses. Specifically, to address visual ambiguity in complex airways, we propose a graph-guided coarse-to-fine localization scheme that effectively leverages structural priors for precise pose estimation. Furthermore, to mitigate pose jitter and bridge the visual-structural gap, we integrate a Transformer-based tracking model with a novel RGB-depth matching objective, jointly enforcing spatio-temporal and geometric consistency. Extensive experiments demonstrate that our method yields remarkable reductions of 8.37% and 31.76% in translation and rotation errors over the prior state-of-the-art, alongside 4 times inference speedup (33.6 FPS) for robust real-time bronchoscope localization. Project website: https://paulili08.github.io/GABL/.

Registration between cone-beam computed tomography (CBCT) and intraoral scans (IOS) is essential for patient-specific surgical planning. However, disparate imaging modalities, limited overlap, and large pose offsets make automated registration unreliable. Consequently, clinical registration remains dependent on conventional geometry pipelines and manual clinician adjustment. To address these challenges, we propose APCReg, an anatomical-prior-guided coarse-to-fine framework for global registration and reliability-controlled residual correction. Specifically, multi-view anatomical coarse registration (MACR) performs ordered orthogonal projection alignment (buccal, proximal, and occlusal) to decompose the six-degree-of-freedom search before three-dimensional refinement. Overlap-aware residual registration (OARR) combines shared KPConv features, a folded arch-length cue, overlap-gated cross-attention, and Sinkhorn matching. Finally, dental-arch-structured hypothesis selection evaluates diverse poses on held-out reliable correspondences, while a ground-truth-free coarse-retention guard conditionally retains a geometrically reliable coarse pose. On 60 held-out jaw pairs, APCReg achieves a submillimeter mean Chamfer distance of 0.87 mm and a Hausdorff distance of 2.92 mm under this evaluation protocol, and ranks first across the six reported metrics among the evaluated open-source baselines.

Learning transferable representations from CT-report pairs requires combining whole-volume context with anatomy-specific evidence. Existing methods typically emphasize either global CT-report alignment or fine-grained anatomy-level correspondence. Global alignment preserves broad study context but leaves the contribution of localized evidence implicit, whereas anatomy-level alignment explicitly grounds local findings but does not specify how independently represented evidence should interact, acquire study-level meaning, and contribute to a global CT representation. To address this gap, we propose SCOPE (Semantic Calibration Of comPosed Evidence), a framework for semantically calibrated evidence composition in CT vision-language learning. Under organ-specific report supervision, mask-guided queries with fixed anatomical identities extract context-aware organ evidence from shared, uncropped volumetric features, while an unrestricted global query retains access to whole-volume context. The global query then drives Local-Global Coupling to compose the organ evidence into a unified evidence representation. The composed evidence is subsequently calibrated using the diagnostic summary, providing study-level semantic supervision beyond local organ descriptions, and is finally integrated as a controlled residual into a context-preserving whole-volume representation aligned with the complete report. This progressive pathway connects localized evidence with study-level semantics without reducing the CT representation to a predefined set of organs. On CT-RATE and RadChestCT, SCOPE achieves macro AUCs of 85.0 and 72.2, respectively, outperforming the previous SOTA by 7.2 and 4.2, while also yielding substantial gains in linear probing and cross-modal retrieval. These results demonstrate the effectiveness of semantically calibrated evidence composition.

High-resolution 3D segmentation of hip and shoulder anatomy from CT and MRI is essential for surgical planning, yet frozen segmentation models often fail under domain shift. CNN-based expert models are fully automatic but lack adaptability, whereas promptable foundation models generalize better but require manual prompting. We present MedSAM2-Anatomy, a training-free inference-time optimization framework that improves frozen segmentation models without retraining or human interaction. A frozen expert model generates anatomical priors that are automatically converted into multiple prompt hypotheses for a frozen 3D foundation model. Candidate masks are fused while anatomically implausible priors are rejected. No model weights are updated and no manual prompts are required. TotalSegmentator and MedSAM2 are used as representative expert and foundation models, allowing the contribution of the inference policy to be isolated. Evaluation on the independent Balgrist-V0 CT and MRI cohorts shows that inference-time optimization increases median Dice from 0.71 to 0.92 on hip MRI and from 0.89 to 0.92 on shoulder CT, while reducing median HD95 on hip MRI from 22.0 mm to 5.0 mm. On public TotalSegmentator benchmarks, the expert model remains strongest, indicating that the optimal fusion strategy depends on the reliability of the expert prior. These results demonstrate that training-free inference-time optimization provides a practical strategy for improving frozen segmentation models without manual prompting.

Automated grading of Lumbar Disc Degeneration is essential for the objective quantification of structural changes associated with low back pain. Observing that baseline models underperformed on our data, we propose a framework designed to overcome these limitations. First, we present the Cross-sequence Attention Spine (CrossSpine) framework, a novel architecture that employs a cross-sequence attention mechanism to adaptively fuse features from different MRI sequences at multiple spa- tial scales. Second, we contribute a meticulously curated dataset aimed at automated Pfirrmann grading. Finally, we introduce an IVD-aware classification technique that integrates anatomical disc-level information, enabling the model to learn level-specific degeneration priors. Our experi- ments demonstrate the superiority of this approach: CrossSpine achieved a relative improvement exceeding 125% in the Macro F1 score, while boosting the Mean AUPRC by 99% and the Mean AUROC by 36% com- pared to the baseline.

Prostate cancer diagnosis with multiparametric MRI (mpMRI) is commonly based on PI-RADS assessment or binary classification, which suffer from subjectivity and fail to capture clinically relevant pathological heterogeneity. To address this limitation, we construct a Prostate Cancer Histopathology Spectrum Dataset (PCa-HSD) and formulate a clinically meaningful four-class classification task, addressing the underrepresentation of benign lesions that are easily confounded with prostate cancer in existing datasets. We propose Language-guided Segmentation-assisted Diagnostic Transformer model (LSDT), which leverages zero-shot segmentation to provide anatomical priors and performs effective multi-modal slice fusion for classification. Our proposed method consistently improves accuracy across backbones, achieving the best average accuracy of 0.633 and JointRecall of 0.768 in five-fold cross-validation on a cohort of 344 patients. These results demonstrate that integrating pathology supervision and anatomical priors significantly enhances fine-grained prostate MRI classification and provides a more clinically relevant paradigm for risk stratification. Code will be made publicly available in a future revision.

Automatic voxel-level grounding of free-text findings in 3D chest Computed Tomography (CT) is critical for clinical interpretability. However, this task remains highly challenging due to the intricate spatial complexity of large 3D volumes and the heterogeneity of free-text findings. Existing end-to-end approaches often struggle to simultaneously learn the localized feature representations required for accurate 3D segmentation and the complex semantic understanding needed for text alignment, leading to suboptimal grounding performance. To overcome this fundamental limitation, we propose a novel decoupled framework that disentangles the problem into two specialized stages: (1) class-agnostic lesion segmentation and (2) text-volume reasoning. This structural separation allows the model to first extract candidate sub-volumes by localizing potential abnormalities. Subsequently, intensive cross-modal reasoning is performed to align these localized sub-volumes with free-text medical findings. To resolve the spatial ambiguities inherent in local regions, the reasoning module is augmented with explicit anatomical guidance, utilizing relative spatial coordinates and lung lobe priors. Evaluated on the ReXGroundingCT benchmark, our method achieves state-of-the-art performance in overall grounding quality on the official leaderboard. These results demonstrate that decoupling detection from reasoning is a highly effective paradigm for handling the complexity of 3D medical visual grounding. Our code is publicly available at https://github.com/khuhm/DAGG.

Medical image classification models are ideally expected to identify diagnostically relevant regions while making predictions, yet standard classification losses rarely provide spatial supervision. Explicit supervision via anatomical shape information, such as segmentation masks of task-relevant anatomy, has been shown to guide the network toward regions relevant to the target prediction. However, obtaining such masks incurs substantial manual annotation effort and computational overhead. With the advent of segmentation foundation models that exhibit strong localization of anatomical structures across diverse imaging modalities, we leverage this capability to extract anatomical shape priors without the burden of training a dedicated segmentation model. In this paper, we propose a new framework, Locus, an anatomical attention regularization framework that leverages pretrained segmentation foundation models to guide a classifier's attention toward diagnostically meaningful anatomical structures across diverse imaging modalities. Instead of enforcing pixel-wise alignment with the foundation-model-derived mask, we introduce a regularization term that adaptively balances attention between anatomical (foreground) and background regions, penalizing the classifier when background attention dominates. We validate Locus on eight diverse medical imaging datasets spanning dermoscopy, X-ray, histopathology, and cardiac MRI, showing consistent gains in classification performance alongside improved anatomically grounded attention.

Robotic ultrasound scanning in real clinical environments requires both high-level clinical workflow reasoning and low-level closed-loop execution. Physicians natural-language instructions often contain implicit anatomical targets, procedural logic, image-quality requirements, and safety constraints, while execution is affected by patient motion, contact variations, and target drift. We propose a fast and slow hierarchical embodied ultrasound system for safe and interpretable robotic ultrasound assistance. The Slow Brain performs intent parsing and stage-wise task planning with knowledge augmentation from an API and handbook corpus, and generates executable plans through task-graph construction and structured plan verification. The Fast Brain fuses multimodal feedback, including ultrasound images, robot pose and force states, and patient-motion information, to refine local actions and perform image-quality-guided recovery behaviors. The system further integrates a Safety Shield and a hierarchical escalation policy to constrain risky actions and trigger replanning or human confirmation under persistent failures or safety-bound violations. Experiments on planning evaluation, closed-loop execution under dynamic perturbations, and safety-mechanism validation demonstrate that the proposed hierarchical design improves task success rates while reducing safety violations.

Image quality control is vital for a wide range of downstream applications. Deep learning-based image quality assessment methods typically train classifiers on dataset-specific quality labels, inheriting two limitations: (1) generalization is tied to the labeling criteria of the training set and (2) these methods cannot provide spatial feedback on where the quality is degraded, lacking explainability. In this work, we propose EFIQA, a framework that requires no quality-related supervision and produces spatial quality maps by design. Rather than learning what is degradation" from human-annotated labels, EFIQA learns what should be there" by leveraging anatomical priors. For fundus photography, we instantiate this as a two-stage approach, by first training an unsupervised anomaly detector via masked anatomical inpainting to identify regions of missing vasculature, and then distilling this prior knowledge into a shallow adapter mapping features of a frozen foundation model to precise quality maps. External-dataset evaluation demonstrates that this label-free approach with minimal adaptation achieves better performance and explainability compared with supervised methods across benchmarks with different quality criteria, highlighting its potential for real-world applications.

Detecting anatomical structures in surgical video is essential for intraoperative safety frameworks such as the Critical View of Myopectineal Orifice (CVMPO) in inguinal hernia repair. While prominent structures like the Cooper's Ligament and Triangle of Doom are reliably detected by standard methods, smaller structures such as the epigastric vessels remain challenging due to their visual ambiguity and intermittent visibility. We observe that the spatial relationship between structures is anatomically constrained, and propose a Gaussian Spatial Prior (GSP) module that encodes this relationship as a compact, parametric bias injected into the self-attention of a DAB-DETR decoder. The prior is computed offline from training annotations as a small set of frozen Gaussian parameters and recomputed at each decoder layer using the iteratively refined reference points. On a dataset of inguinal hernia repair videos with 5-fold cross-validation, GSP improves dependent class detection by $+33.5\%$ ($\text{AP}_{50}$) over DAB-DETR and $+53.9\%$ over YOLOv26, while also improving anchor detection by $+6.0\%$. These gains are statistically significant across all folds ($p=0.012$, paired $t-$test).

Dexterous robotic hands are usually formulated as high dimensional active control systems governed by degrees of freedom, actuation, and algorithms. Human hand dexterity, however, is partly encoded in the physical architecture of bones, ligaments, tendons, aponeuroses, and intrinsic muscles. This work describes that contribution as two linked forms of structural intelligence: structural prior generation, in which wrist to finger tenodesis, FDS/FDP routing, and the dorsal extensor hood transform low dimensional posture inputs into default grasp configurations and PIP to DIP coordination; and muscle mediated modulation, in which extrinsic muscles, lumbricals, and interossei regulate MCP posture, distal stability, fingertip force paths, and contact states around that default state. Based on this framework, MCR-Bionic Hand is developed as a 1:1 musculoskeletal biomimetic hand integrating a two row eight bone wrist, cross wrist tendons, anatomical flexor routing, volar plate and collateral ligament constraints, the dorsal extensor hood, and intrinsic muscle pathways within one body. Functional demonstrations and geometric mechanical models show that wrist posture induces multi joint pre shaping, the extensor hood maps PIP posture to a coupled DIP response, and intrinsic plus pathways modulate distal stability and fingertip action direction after grasp formation. Contact rich tasks, including coin rotation, pen transfer, dorsal coin flipping, and cube manipulation, show that MCR-Bionic links low dimensional state generation with fine post contact modulation. These results suggest that anatomical biomimetics is valuable not for visual similarity, but for identifying human hand structures that perform part of control.

Large-scale text-to-image foundation models have achieved remarkable visual realism, yet generating human images with correct anatomical structures remains challenging. Existing approaches enforce anatomical constraints through part-specific modules or localized loss weighting during supervised fine-tuning on high-quality human photos, but such datasets are limited and often provide ambiguous optimization signals due to confounding factors such as lighting, pose, and background. Preference-based alignment offers an alternative, but standard Direct Preference Optimization (DPO) treats all pixels equally and therefore fails to exploit the localized nature of anatomical artifacts. To address this, we propose the framework of Alignment via Synthetic Anatomical Preference (ASAP), which constructs controlled preference pairs through a localized degradation mechanism applied to high-fidelity human images. This mechanism performs a controlled experiment on images by introducing explicit anatomical errors in targeted regions while preserving the remaining content. With this mechanism, we create the Human Anatomical Preference (HAP) dataset with over 10K curated pairs for effective anatomical alignment of text-to-image human image generative models. To better leverage the locality of these controlled preference pairs, we introduce a localized and margin-bounded variant of DPO that prioritizes optimization in targeted anatomical regions while enforcing a finite preference margin to prevent over-optimization and preserve global semantics. We further introduce HAF-Bench, a benchmark for systematic evaluation of anatomical fidelity. Extensive experiments demonstrate that ASAP consistently reduces anatomical errors across multiple foundation models while maintaining overall image quality.

Current fMRI decoders face a performance-fidelity trade-off where efficient ID encoders outperform geometrically faithful surface-based models. We argue this is partly driven by inefficient surface tokenization and the failure to use anatomy as a predictive signal. We present NeurIPS, a framework that improves surface-based decoding by reframing anatomical variation from a nuisance to a powerful inductive prior. NeurIPS unites two innovations: a Selective ROI Spherical Tokenizer (SRST) for efficient geometric encoding, and a Structure-Guided Mixture of Experts (SG-MoE) that explicitly models individual anatomy using cortical features. On the Natural Scenes Dataset, NeurIPS establishes a new state-of-the-art for surface decoders and achieves performance comparable to strong 1D baselines. This is achieved with unprecedented efficiency, as the model converges dramatically faster (10 vs. 600 epochs). This efficiency enables rapid adaptation to new subjects using only 20% of data and ensures robust scalability as the training cohort is expanded. Ablations provide causal evidence that these gains are driven by the model's use of cortical features, not by memorizing subject IDs. By leveraging anatomical priors, NeurIPS provides a principled and scalable path toward robust, generalizable brain decoding.

Accurate localization of myocardial infarction is essential for risk stratification. While LGE-MRI remains the gold standard, it is resource-intensive. Integrating cine MRI with ECG enables a more detailed representation of infarct properties. Existing inverse MI inference methods overlook realistic scar morphology and cardiac repolarization, reducing sensitivity to subtle ECG variations and interpretability of infarct-induced electrophysiological changes. In this paper, we propose a novel framework for noninvasive MI localization using cardiac digital twins. To bridge the domain gap between simulation and reality, we introduce an anatomy-aware stochastic infarct synthesis strategy to synthesize realistic, irregular scars with border zones, mimicking ischemic transmural progression. We then construct a virtual cohort to simulate QRS-T waveforms, capturing both depolarization and repolarization dynamics. Furthermore, we design a Physiology and Anatomy Aware Network (PAA-Net) that jointly encodes 3D myocardial geometry and multi-lead ECGs to infer infarct areas with varying localizations, sizes, spatial extents, and transmuralities. Experimental results demonstrate that our framework significantly outperforms existing methods in inverse inference, achieving Dice scores of 0.7391 and 0.5503 for scar and border zone segmentation, respectively, while further enhancing the interpretability of the ECG-infarct relationship. Our code will be released upon acceptance.

Whole-heart multi-compartment CT segmentation is clinically important, but standard CNNs do not explicitly enforce anatomical plausibility. Based on statistics derived from the training data, we evaluate whether lightweight explicit shape priors, implemented as shape-aware losses and spatial label distribution heatmap-guided U-Net variants, improve 3D cardiac segmentation on MM-WHS CT and WHS++. Across all experiments, a standard 3D U-Net surprisingly remained a very strong baseline, with handcrafted priors yielding at best marginal and inconsistent changes and often degrading performance. These results suggest that the baseline already captures substantial implicit anatomical regularities and that future gains will likely require more expressive learned priors rather than simple handcrafted anatomical shape constraints.

Retinal diagnosis is inherently bilateral: clinicians compare homologous structures across eyes (e.g., optic disc asymmetry), yet most deep models operate on monocular representations. We investigate whether explicit structural correspondence improves diagnosis, and propose Anatomy-Slot to operationalize this hypothesis. Anatomy-Slot introduces an unsupervised anatomical bottleneck by decomposing patch tokens into a set of emergent, structurally-coherent slots that correspond to anatomical regions, then aligning these slots across eyes via bidirectional cross-attention. On ODIR-5K with $n=10$ seeds, the method improves AUC by $4.2$ points over a matched ViT-L baseline (95% CIs; Wilcoxon signed-rank test, $W=0$, $p=0.002$). Pairing disruption and stress testing under Gaussian noise provide controlled tests of correspondence dependence and robustness under corruption. We further report quantitative optic disc grounding on REFUGE and cross-attention localization analysis. Beyond the reported gains, these results indicate that object-centric anatomical correspondence offers a principled path toward interpretable diagnostic systems aligned with clinical bilateral comparison.

Recent advances in 3D medical vision-language models have enabled joint reasoning over volumetric images and text, showing strong performance in medical visual question-answering (VQA) and report generation. Despite this progress, it remains unclear whether these models learn spatially grounded anatomy from 3D volumes or rely primarily on learned priors and language correlations. This uncertainty stems from the lack of systematic evaluation of semantic-spatial reasoning in volumetric medical VLMs for clinically reliable decision support. To address this gap, we introduce CT-SpatialVQA, a benchmark designed to evaluate semantic-spatial reasoning in 3D CT data. The benchmark comprises 9077 clinically grounded question-answer (QA) pairs derived directly from 1601 radiology reports and CT volumes, which are validated via a robust LLM-assisted pipeline with a 95% human consensus agreement rate. Our dataset requires explicit anatomical localization, laterality awareness, structural comparison, and 3D inter-structure relational reasoning. We also introduce a standardized evaluation protocol and benchmark eight 3D medical VLMs, finding severe degradation on semantic-spatial reasoning tasks, averaging 34% accuracy and often below random, highlighting the need for deeper integration of volumetric evidence for trustworthy clinical use.

Accurate 3D brain MRI subtype classification benefits from both localized anatomical cues and long-range contextual reasoning. We present AGA3DNet, a report-grounded framework that incorporates brief anatomical phrases extracted from radiology reports as a soft anatomical prior channel and fuses it with a lightweight 3D CNN and multi-view xLSTM aggregation. Specifically, extracted anatomical phrases are mapped to atlas-defined regions and converted into smooth spatial priors using a signed-distance transform followed by Gaussian weighting, providing interpretable, anatomy-grounded guidance without requiring dense voxel annotations. We evaluate AGA3DNet on a retrospective institutional brain MRI cohort for abnormal subtype discrimination and compare against reproducible 3D classification baselines. AGA3DNet achieves improved overall balance across performance metrics and supports clinically interpretable localization through the prior channel. We discuss limitations related to single-cohort evaluation and the lack of large-scale public brain MRI datasets paired with radiology reports under broadly usable terms.

Clinicians trace cephalometric radiographs following a structured anatomical workflow, yet no prior system encodes this into computation. We present a five-phase anatomy-guided pipeline producing confidence-weighted spatial priors that shape HRNet-W32 training, achieving 1.04 mm mean radial error on 25 landmarks across 1,502 radiographs from 7+ imaging devices. A training x inference prior matrix isolates the mechanism: anatomical priors maintain a 1% validation-to-test gap versus 88% without priors (1.94 mm), despite identical validation convergence. The matrix establishes that all trained models are inference-independent, the expanded architecture alone provides no benefit, random priors yield partial but unstable improvement (1.72 mm), and only image-specific anatomically correct priors produce the 1.04 mm result -- functioning as a training-time regularizer requiring no automated prior generation at deployment. Five-fold cross-validation (p=0.0015), patient-level permutation testing (p<0.0001, n=151), quantified Grad-CAM analysis (88% vs. 74% in-zone activation, p<0.001), and clinical measurement validation (skeletal classification kappa=0.79-0.84, zero Class II<->III reversals, ICC>0.95) provide converging evidence. Cross-domain experiments on echocardiography, cervical spine, and hand radiography support the hypothesis that prior effectiveness scales with the spatial entropy of the landmark distribution.

Anatomical mesh segmentation requires models that operate directly on irregular surface geometry while remaining robust to arbitrary patient pose and mesh resolution variation. Existing task-specific mesh and point-cloud methods are not equivariant, and can degrade sharply under test-time perturbation, for example dropping by 25-26 IoU points on intraoral scan segmentation at $40^\circ$ tilt. We present EAMS, an Equivariant Anatomical Mesh Segmentor built on Equivariant Mesh Neural Networks (EMNN), and evaluate it across four clinically distinct tasks spanning edge-, vertex-, and face-level supervision. We combine intrinsic mesh descriptors with anatomy-aware priors, including PCA-derived frames for dental arches and liver surfaces, and augment message passing to provide lightweight global context. Across intracranial aneurysm and intraoral segmentation, EAMS variants are competitive with specialized baselines on unperturbed inputs while remaining stable under geometric perturbations, and on liver surfaces they expose a favorable trade-off between canonical-pose accuracy and rotation robustness. These results show that a lightweight ($<2$M parameters) equivariant framework can deliver robust anatomical mesh segmentation across diverse supervision types without task-specific architectures.

Brain MRI foundation models learn rich representations of anatomy, but interpreting what clinical information they encode remains an open problem. Standard sparse autoencoders (SAEs) suffer from severe feature collapse in deep transformer layers, and in Alzheimer's disease (AD) research, aging confounds nearly every clinical variable, making naive annotation unreliable. We propose GeoSAE, a geometry-guided SAE framework that uses the foundation model's learned manifold structure to prevent feature collapse and annotates each surviving feature via age-deconfounded partial correlations. Applied to ~14k T1-weighted MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Australian Imaging biomarkers and Lifestyle (AIBL) datasets, GeoSAE identifies a compact, fully interpretable feature set that predicts mild cognitive impairment (MCI)-to-AD conversion (AUC 0.746) using only 2% of the embedding dimensions, while comorbidity-annotated features achieve only chance-level performance. The identified features replicate across cohorts without retraining (r=0.97) and localize to neuroanatomically distinct regions consistent with Braak staging. This shows that geometry-guided SAEs can extract interpretable, biomarkers from frozen brain MRI foundation models.

High-precision medical diagnosis relies not only on static imaging features but also on the implicit diagnostic memory experts instantly invoke during image interpretation. We pinpoint a fundamental cognitive misalignment in medical VLMs caused by discrete tokenization, leading to quantization loss, long-range information dissipation, and missing case-adaptive expertise. To bridge this gap, we propose ours, a framework for latent diagnostic memory evolution that simulates the experiential invocation of clinicians by dynamically synthesizing implicit diagnostic memories within the model's hidden stream. Specifically, it begins with a Meta Query for Prior Memorization mechanism, where learnable probes retrieve structured priors from an anatomical prior encoder to generate condensed implicit memories. To ensure clinical fidelity, we introduce Causal Counterfactual Refinement (CCR), which leverages reinforcement learning and counterfactual rewards derived from region-level feature masking to quantify the causal contribution of each memory, thereby pruning redundancies and aligning latent representations with diagnostic logic. This evolutionary process culminates in Intrinsic Memory Transition (IMT), a privileged-autonomous dual-branch paradigm that internalizes teacher-branch diagnostic patterns into the student-branch via full-vocabulary divergence alignment. Comprehensive empirical evaluations across multiple datasets demonstrate that ours, by transferring external expertise into endogenous parameters, significantly outperforms existing state-of-the-art methods, particularly chain-of-thought paradigms, in diagnostic accuracy. The code is available at https://github.com/zhcz328/MedSynapse-V.

As dental caries appear as subtle, low-contrast lesions in intraoral imaging, existing deep learning models face significant challenges in the early detection of caries. While recent Transformer-based detectors have shown promising results in natural images, they often fail to capture the domain-specific anatomical priors crucial for dental caries detection. In this paper, we propose Caries-DETR, a specialized Transformer framework for caries detection in intraoral images. A Tooth Structure-aware Query Initialization (TSQI) is designed, leveraging large-scale intraoral photograph pre-training and a structure perception branch (SPB) to integrate high-frequency structural priors, guiding the model to focus on anatomically significant lesion areas. Furthermore, we design a Lesion-aware Dynamic Loss Refinement (LDLR) to implement quality-driven hard mining through adaptive loss reweighting based on lesion size, anatomical relevance, and prediction quality, optimizing detection for subtle lesions. Extensive experiments on two public datasets (i.e., AlphaDent and DentalAI) demonstrate that Caries-DETR achieves a state-of-the-art performance compared to existing methods and exhibits good generalization and robustness. Code and data at https://github.com/XuefenLiu-SZU/Caries-DETR}{https://github.com/XuefenLiu-SZU/Caries-DETR.

Segmentation is central to clinical diagnosis and monitoring, yet the reliability of modern foundation models in medical imaging still depends on the availability of precise prompts. The Segment Anything Model (SAM) offers powerful zero-shot capabilities, although it collapses under the weak, generic, and noisy prompts that dominate real clinical workflows. In practice, annotations such as centerline points are coarse and ambiguous, often drifting across neighboring anatomy and misguiding SAM toward inconsistent or incomplete masks. We introduce SPD, a Saliency-Guided Prompt Distillation framework that converts these unreliable cues into robust guidance. SPD first learns data-driven anatomical priors through a lightweight saliency head to obtain confident localization maps. These priors then drive Contextual Prompt Distillation, which validates and enriches noisy prompts using cues from anatomically adjacent slices, producing a consensus prompt set that matches the behavior of expert reasoning. A Pairwise Slice Consistency objective further enforces local anatomical coherence during segmentation. Experiments on four challenging MRI and CT benchmarks demonstrate that SPD consistently outperforms existing SAM adaptations and supervised baselines, delivering large gains in both region-based and boundary-based metrics. SPD provides a practical and principled path toward reliable foundation model deployment in clinical environments where only imperfect prompts are available.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder and a major cause of dementia. Structural MRI is widely used to analyze AD-related brain atrophy; however, most deep learning methods rely on computationally expensive 3D convolutional neural networks (CNNs), limiting deployment in resource-constrained settings. This work introduces two main contributions. First, we propose a pipeline that converts T1-weighted MRI into anatomically informed 2D point clouds using Anatomical Priority Sampling (APS), producing ADNI-2DPC, the first neuroanatomically labeled MRI-derived point cloud dataset. Second, we present NeuroAPS-Net, a lightweight geometric deep learning model that incorporates anatomical priors via region-aware feature encoding and ROI token aggregation. Experiments on ADNI-2DPC demonstrate that NeuroAPS-Net achieves competitive classification accuracy while significantly reducing inference latency and GPU memory compared to state-of-the-art point cloud methods. These results highlight the potential of anatomically guided point cloud learning as an efficient and interpretable alternative to voxel-based CNNs for AD classification.

Deploying AI-based anomaly detection across diverse clinical imaging settings remains challenging because most existing methods rely on modality-specific architectures, anatomical priors, or extensive retraining, limiting their use as general-purpose screening tools. One-class classification (OCC) offers a label-efficient alternative by training exclusively on normal data, but conventional two-stage pipelines fit a density estimator directly on raw pretrained embeddings, leaving substantial discriminative structure in the latent space unexploited. We introduce a training-free, modality-agnostic framework that inserts an explicit manifold-refinement stage between feature extraction and anomaly scoring. Empirical density weights, estimated via a UMAP-derived neighborhood graph, guide an iterative shift of embeddings toward locally dense regions, compacting normal samples, leaving anomalies relatively isolated prior to Gaussian density estimation and Mahalanobis-based scoring. This refinement introduces no additional trainable parameters and no architectural modification, allowing it to be layered onto any pretrained encoder. Evaluated on the MedIAnomaly benchmark across seven datasets spanning five imaging modalities (X-ray, MRI, fundus, dermatoscopy, histopathology), the framework achieves the best AUC on four datasets and the best Average Precision on five datasets among methods evaluated in the benchmark, outperforming specialized reconstruction and diffusion-based methods with a single fixed hyperparameter configuration across all modalities. These results demonstrate that meaningful gains can be achieved through post-hoc geometric refinement of existing representations rather than bespoke encoders, offering a practical and scalable AI screening framework for real-world, multi-modality clinical workflows where retraining and abnormal-case annotation are costly or infeasible.

Three-dimensional (3D) medical image enhancement, including denoising and super-resolution, is critical for clinical diagnosis in CT, PET, and MRI. Although diffusion models have shown remarkable success in 2D medical imaging, scaling them to high-resolution 3D volumes remains computationally prohibitive due to lengthy diffusion trajectories over high-dimensional volumetric data. We observe that in conditional enhancement, strong anatomical priors in the degraded input render dense noise schedules largely redundant. Leveraging this insight, we propose a sparse voxel-space diffusion framework that trains and samples on a compact set of uniformly subsampled timesteps. The network predicts clean data directly on the data manifold, supervised in velocity space for stable gradient scaling. A lightweight Structure-aware Trajectory Modulation (STM) module recalibrates time embeddings at each network block based on local anatomical content, enabling structure-adaptive denoising over the shared sparse schedule. Operating directly in voxel space, our framework preserves fine anatomical detail without lossy compression while achieving up to $10\times$ training acceleration. Experiments on four datasets spanning CT, PET, and MRI demonstrate state-of-the-art performance on both denoising and super-resolution tasks. Our code is publicly available at: https://github.com/mirthAI/sparse-3d-diffusion.

Demographic attributes can be predicted from medical images, raising concerns about bias in clinical AI systems. In X-ray imaging, acquisition characteristics have been shown to contribute substantially to this predictability. Whether the same holds in brain MRI remains unclear, as anatomical variation and acquisition-dependent contrast are deeply entangled in the image formation process, obscuring the origins of demographic signal. To address this, we propose a controlled framework based on disentangled representation learning, decomposing brain MRI into anatomy-focused representations that suppress acquisition influence and contrast embeddings that capture acquisition-dependent characteristics. Training predictive models for age, sex, and race on full images, anatomical representations, and contrast embeddings allows us to quantify the relative contributions of structure and acquisition to the demographic signal. Across three datasets and multiple MRI sequences, demographic predictability is found to be driven primarily by anatomical variation, with anatomy-focused representations largely preserving the performance of models trained on raw images. Contrast embeddings retain a weaker signal that is dataset-specific and does not generalise across sites. These findings suggest that effective mitigation must explicitly account for the primarily anatomical and secondarily acquisition-dependent origins of demographic signal, ensuring that any bias reduction generalizes robustly across domains.

Brain tumors induce complex structural deformations that obscure the patient' s original neuroanatomy, making it difficult to distinguish tumor-induced changes from inherent anatomical variability. Reconstructing a subject-specific pseudo-healthy brain can provide a critical reference for such analysis, but this task is inherently counterfactual, as paired pre-tumor scans and explicit healthy guidance are unavailable. We propose BrainNormalizer, a diffusion-based framework for subject-specific pseudo-healthy brain MRI reconstruction that enables anatomy-informed reconstruction without requiring paired data or explicit healthy references. The framework learns anatomical priors and edge-based structural conditioning through a two-stage training strategy consisting of inpainting-based diffusion fine-tuning and ControlNet-based edge conditioning. At inference, counterfactual pseudo-healthy reconstruction is achieved through a deliberate misalignment strategy, where tumorous inputs are paired with non-tumorous prompts and mirrored contralateral edge maps. This allows subject-specific anatomical guidance to be constructed from the patient's own anatomy, enabling anatomically consistent pseudo-healthy reconstruction that preserves individual structural characteristics. Experiments on the BraTS2020 dataset demonstrate that BrainNormalizer achieves improved distributional realism, symmetry-based structural consistency, and reduced false positive detection compared to existing methods. These results indicate that the proposed framework provides a principled approach for subject-specific counterfactual reconstruction and supports downstream analysis of tumor-induced deformation.

Medical landmark detection usually requires accurate expert annotations, which are laborious and difficult to scale across anatomical regions. In this work, we study an extreme annotation-efficient setting where only a single annotated template image is available. We propose SGB-Match, a structure-guided coarse-to-fine self-supervised matching framework for one-shot medical landmark detection. The framework first learns dense anatomical correspondence from unlabeled augmented image pairs, and then transfers the landmark definition from the annotated template to each target image through feature matching. Different from standard contrastive correspondence learning, where negative candidates are penalized by a structure-agnostic rule, we introduce a structure-guided bias into the contrastive objective. The bias is constructed from relative distance and edge-aware anatomical cues, and explicitly reweights the negative gradients: nearby structure-relevant candidates are weakly repelled, while distant or structure-irrelevant negatives are strongly suppressed. As a result, the learned feature space better preserves local anatomical structures around template landmarks and reduces confusing responses from repeated textures. We further adopt a global-to-local design, where a global encoder provides coarse landmark localization and a local encoder refines the prediction in a cropped region. Extensive experiments on four 2D radiological landmark datasets demonstrate that SGB-Match achieves strong one-shot performance across both public and newly collected datasets and consistently benefits from both structure-guided bias and two-stage refinement.