medical imaging teams

Abstract: Three-dimensional multi-echo MRI provides rich anatomical and quantitative information, but repeated volumetric encoding prolongs acquisition and motivates k-space undersampling. Reconstructing undersampled multi-echo data requires exploiting shared anatomy while preserving echo-dependent signal variation; full-volume modeling also introduces substantial computational and memory demands. We propose MIGA, a scan-specific framework comprising shared anisotropic Gaussian geometry, a coordinate-conditioned multi-output amplitude network, and explicit echo-specific phase variables. The Gaussian geometry provides common spatial support across echoes, the implicit network models spatially structured amplitude variations, and the phase variables retain echo-specific complex signal information. All components are jointly optimized using only the acquired multi-coil k-space, requiring no fully sampled training data. Experiments showed that MIGA consistently outperformed the comparison methods across imaging tasks and acceleration factors, with larger improvements under stronger undersampling. MIGA also achieved a favorable quality-cost balance among the evaluated full-volume multi-echo methods. These results support the effectiveness of combining shared Gaussian geometry with implicit echo-dependent amplitude modeling for accelerated 3D multi-echo MRI reconstruction.

Abstract: Diffusion models are increasingly adapted from generation to conditional prediction, where a conditioning signal is combined with an evolving noisy representation of the target. In fully supervised segmentation, however, the conditioning image can already support direct target prediction, so endpoint performance alone establishes neither reliance on the added diffusion state nor a deterministic advantage over image-only prediction. For state reliance, we disrupt target-derived state content or correct image-state pairing during retraining of twelve published methods across three datasets, with ten matched seeds per setting. All 40 original-method comparisons whose evaluated-mask routes remained downstream of noised-quantity reconstruction exhibited state reliance, whereas all 30 comparisons with a segmentation-supervised bypass preserved reference performance. Rerouting five originally bypass-capable methods by forcing segmentation supervision through noise-to-mask reconstruction converted all 30 corresponding comparisons from preserved performance to state reliance. For deterministic utility, matched image-only counterparts achieved similar or better performance in 28 of 35 settings overall, including 16 of 20 whose native methods relied on both audited state properties. These results identify supervision path as a determinant of state reliance in the audited methods. Separately, matched image-only counterparts show that diffusion-specific computation often provides no deterministic endpoint advantage, including in methods that rely on the audited state properties. More generally, when conditioning already supports strong target prediction, diffusion-specific claims require additional evidence that the added state is used and that diffusion-specific computation improves the claimed capability beyond a matched condition-only counterpart.

Abstract: Three-dimensional fetal brain ultrasound offers non-ionizing, cost-effective imaging with rich spatial information for comprehensive anatomical assessment, yet its development remains limited by scarce data and annotations. In contrast, fetal brain magnetic resonance imaging has advanced further, supported by larger datasets and mature analysis methods. To leverage these resources, anatomical label maps provide a promising modality-invariant bridge for transferring knowledge from fetal brain magnetic resonance imaging to ultrasound. However, generating ultrasound images from label maps remains challenging because anatomy is tightly entangled with ultrasound appearance. To address this challenge, we separate anatomical correspondence learning from ultrasound appearance adaptation at both the data and model levels. Specifically, we propose the anatomy wavelet residual network, a two-stage framework combining wavelet diffusion and residual refinement. The first stage learns to generate volumes from label maps using atlas pairs in the wavelet domain, while the second stage learns bounded residual corrections from real clinical ultrasound in the image domain. This separation enables realistic synthesis with consistent preservation of normal and abnormal anatomy. Experiments on real fetal brain ultrasound show that our method outperforms representative synthesis methods, with normalized cross correlation of 0.518 versus 0.482 and Fréchet Inception Distance of 8.905 versus 13.319 for the strongest baseline. Beyond synthesis quality, volumes generated from fetal brain magnetic resonance imaging label maps also improve downstream segmentation, particularly for severe abnormal cases. Overall, these results highlight the potential of the proposed framework to leverage rich fetal brain magnetic resonance imaging resources for advancing three-dimensional ultrasound analysis.

Abstract: In classification-oriented adaptive sensing, posterior samples characterize uncertainty at the current measurement state and can serve two roles: they may guide the next sensing direction, while their class labels provide votes for the candidate classes and determine whether sensing should continue. We focus on the stopping layer that turns these votes into a declaration, without modifying the posterior sampler or sensing directions. A natural plug-in rule declares when the observed vote share exceeds a threshold. We show that this threshold is not itself a confidence guarantee: when the underlying vote mass equals the threshold, the plug-in rule declares about half the time. As alternatives, we calibrate a fixed-sample rule and a finite-horizon sequential rule to a prescribed false-declaration probability, and study exact curtailment, which stops a fixed-pool rule once its final verdict is forced. We then derive how one-round declaration probabilities determine posterior-sample cost and classification accuracy along a sensing path. On MNIST with DDRM and a fixed PCA-guided probe sequence, curtailment saves up to 62% of posterior samples. Among the evaluated rules at matched operating points, sequential stopping reduces the cost the most. At a high accuracy, that same sequential rule can trade more posterior samples for fewer measurements.

Abstract: Recent advances in diffusion models have enabled high-performance, instance-adaptive compressed sensing through posterior sampling, without task-specific policy training. Existing methods select sensing probes by maximizing total posterior signal variance and are therefore primarily reconstruction-driven. We introduce a classification-driven extension motivated by the closed-form posterior covariance of a class-conditional Gaussian mixture model, which decomposes into within-class and between-class uncertainty. Using calibrated soft classifier outputs, we estimate these uncertainty terms from diffusion posterior samples and propose a classification-oriented criterion for selecting the dominant sensing direction in the unmeasured subspace. Experiments on MNIST and CIFAR-10 compare the resulting classification accuracy, measurement cost, and reconstruction quality with those of reconstruction-oriented counterparts. The results identify regimes in which semantic posterior uncertainty yields a more favorable classification--measurement trade-off and quantify the associated reconstruction cost.

Abstract: Entropy minimization is a standard objective for test-time adaptation (TTA), but it can fail in imbalanced binary segmentation. Unlike image classification, dense segmentation aggregates thousands of pixel predictions, allowing the larger predicted class to dominate the update, pull minority predictions toward itself, and produce a degenerate mask as predictions saturate and their entropy gradients vanish. We theoretically establish this collapse in a shared-shift model. This analysis motivates Balanced-Anchor Prompt Adaptation (BAPA), which combines two complementary modules. The Class-Balanced Anchors (CBA) module selects high-confidence anchors separately from each predicted class and gives foreground and background equal total loss weight, preventing the larger region from dominating the update. Dynamic Prompt Adaptation (DPA) refreshes these anchors after each prediction update and optimizes only text-side prompt residuals while keeping the vision-language encoders frozen. This prompt-only update refines the foreground-background decision boundary without altering the pretrained dense visual representation. Across experiments from four domains, BAPA achieves the highest mean Dice among the evaluated methods. Factorized ablations further validate the complementary roles of CBA and DPA, supporting balanced prompt adaptation as an effective alternative to entropy minimization for test-time binary segmentation.

Abstract: Episodic test-time adaptation resets a frozen segmenter to source weights $M_0$ on each case and adapts for a fixed step count. A fixed horizon conflates a cohort-level question, how far to adapt, with an irreducibly per-case one, whether this case should be adapted at all. Cohort means hide that decision: on cross-vendor cardiac MRI the mean $Δ$Dice from adaptation is statistically indistinguishable from zero while 58.7% of cases are individually made worse. We quantify this harm as harmful accepted area (HA), the harmful fraction of the edited area a controller deploys. Held-out tuning gives a stronger baseline than a fixed horizon, but the budget it selects transfers on neither of the two main medical benchmarks, and no global budget can condition on the case. We show that prediction fragmentation---the disagreement geometry between $M_0$ and the adapted mask $M_k$---predicts HA with no labels or extra backward passes at decision time, comparably on three benchmarks (Spearman $ρ$ 0.50--0.60), at a quarter of gradient-norm's latency. A case-level router built on it cuts HA from 0.228 to 0.139 on a benchmark that took no part in its design, with the design frozen and only cut-points recalibrated there. On the cardiac benchmark the design was selected on, the router cuts HA from 0.129 to 0.013 at matched Dice and 1.10 deployed updates, against the retrospective-best budget found post hoc on evaluation labels, and reduces that 58.7% to 20.0%, an upper bound we quantify. Where the retained cases are not net-helped (as on prostate), the router still cuts HA but concedes accuracy, a boundary we report. Thresholds are fit once on a labeled split disjoint from evaluation; decisions use no labels or gradients. The template ports across architecture and domain (nnU-Net$\to$SegFormer, Cityscapes$\to$ACDC) with coordinate, thresholds and per-bucket actions instantiated per domain.

Abstract: Magnetic Resonance Imaging (MRI) acquired at different field strengths exhibits pronounced variation in noise, resolution, homogeneity, and contrast, which limits comparability across acquisition settings and complicates downstream analysis. We address this with a unified conditional model for controllable field-to-field synthesis, built on the framework of conditional latent bridge matching. Our single model achieves highly competitive results across the validation phase for all three tasks of the MRIxFields2026 challenge without task-specific architectures or training. We achieve fast generation with only a single inference step, producing all modality and field-strength combinations for $30$ axial slices in under $90$ seconds, as well as cross-modality-strength translation for a full volume in under $70$ seconds, on a single NVIDIA A5000 GPU. We further provide extensive ablations regarding different components of our solution. Code: https://gitlab.com/siddharthsrivastava/mrixfields-2026

Abstract: Recent findings indicate that Vision Transformers settle into locally similar computational phases, implying a level of depthwise computational redundancy. However, existing methods to exploit this redundancy either fail to reduce inference compute or severely degrade model expressivity. In this work, we formalise a unified view of block redundancy that decouples the geometry from specific surrogate interventions. We then introduce Transformer-Within-Transformer (TWT), a post-hoc method that fuses contiguous groups of redundant layers into a single learned surrogate layer. TWT reduces parameter count and inference compute while remaining competitive with original models using half the depth on natural images, and in several downstream histopathology settings, TWT matches or even improves on the original baseline.

Abstract: We propose a new probabilistic model for general-purpose medical image registration that builds upon the mutual information registration criterion. It centers around a spatial interpolation technique that assumes latent voxel-wise correspondences between the images being registered. By exploiting these latent variables, we derive dedicated optimization and MCMC sampling techniques that only involve closed-form iterative updates. When applied to nonlinear registration, an efficient demons-like optimization algorithm is obtained that shows robust out-of-the-box performance across a variety of monomodal and multimodal registration tasks. We also demonstrate a corresponding sampler that can quantify, for the first time, uncertainty in multimodal registration scenarios with very high-dimensional 3D deformations. Our code, which we call BINDER (Bayesian INference for DEformable Registration), is freely available at https://github.com/ste93ste/BINDER.

Abstract: Accurate classification of brain disorders from neuroimaging data remains challenging because of substantial inter-subject heterogeneity and the complex multi-scale patterns present in functional connectivity and morphological representations. To address these challenges, we propose HyperAMS-Net, a deep learning framework for brain disorder classification using neuroimaging representations derived from resting-state functional MRI or structural MRI. HyperAMS-Net integrates adaptive multi-scale convolution, hypergraph attention, spatial-channel attention, and adaptive feature fusion. Specifically, adaptive multi-scale convolution learns data-driven weights over multiple receptive fields to capture complementary patterns at different scales. Hypergraph attention models higher-order dependencies among learned feature representations through node--hyperedge--node message passing, while spatial-channel attention enhances discriminative feature learning. Adaptive feature fusion further aggregates complementary information across parallel network branches. HyperAMS-Net is evaluated on three benchmark datasets spanning distinct brain disorders: ABIDE for autism spectrum disorder, REST-meta-MDD for major depressive disorder, and ADNI for Alzheimer's disease, using 5-fold stratified cross-validation. HyperAMS-Net achieves state-of-the-art performance across all evaluated datasets, attaining the highest accuracy and AUC among the compared methods. Ablation studies further demonstrate the contribution of each proposed component, with the largest performance degradation observed when hypergraph attention is removed.

Abstract: Recent innovations in deep learning have significantly enhanced the diagnosis of medical images, although they are based on the use of centralized data storage that pose severe threats to patient privacy and medical data security. To address this issue, this research proposes a Federated Learning (FL) model that is coupled with an optimized YOLOv8 network to detect the kidney stones on a computed tomography (CT) image and at the same time, protect privacy of the patients. The suggested system can help various medical organizations to jointly train a common model without exchanging the information about the patients. This is to ensure that data protection laws like GDPR and HIPAA are adhered to. The residual feature fusion and DropBlock regularization among other architectural improvements are also included in YOLOv8 to enhance detection robustness and minimize overfitting. Experimental analysis carried out on a distributed CT dataset demonstrated that the federated YOLOv8 model has a mAP at 50 of 0.733 and is able to keep the data confidential. Moreover, its lean design facilitates fast edge deployment and real-time inference across a clinical setting. Altogether, these findings indicate that Federated Learning is a safe and efficient solution to AI-assisted diagnosis in contemporary healthcare when combined with the use of sophisticated object detection models.

Abstract: Pathologists diagnose diseases by first locating suspicious tissue and then examining it at higher magnification, whereas self-supervised vision transformers (ViTs) allocate the same spatial resolution to every image region despite diagnostic evidence being sparse and spanning multiple biological scales. Recent pathology foundation models have substantially improved representation quality by scaling training data and model capacity, but largely retain uniform tokenization. We instead investigate whether pathology representations can be improved by learning where to allocate spatial resolution during self-supervised learning. To this end, we propose CRAFT (Coarse-to-fine Region-Adaptive Feature Tokenization), a DINO-based framework that learns image-dependent mixed-scale representations by using self-supervised attention to selectively refine informative regions while preserving coarse context, together with a symmetric cross-scale regularization objective that encourages complementary coarse and fine representations. Across CAMELYON16, TCGA-Lung subtype classification, and TCGA-LUAD survival prediction, CRAFT consistently outperforms comparable-scale self-supervised methods while requiring lower inference computation. Despite using only a compact 22M parameter backbone trained on comparatively small pathology datasets, CRAFT remains competitive with, and often surpasses, substantially larger pathology foundation models.

Abstract: Multiresolution hash encodings have recently enabled fast and high-fidelity implicit neural representations by storing multi-scale features in fixed-size hash tables along a geometric resolution schedule. However, the standard design is data-agnostic: different resolution levels receive identical hash-table capacity despite large differences in image frequency content. As a result, some levels experience severe hash collisions while others underutilize parameters, leading to inefficient capacity allocation. To address this issue, we propose Collision-Aware Resolution Adaptation (CARA), a method that assigns per-level resolutions by balancing the effective information load across hash levels. This adaptive allocation reduces capacity bottlenecks and improves parameter efficiency. In addition, we introduce an invertible pixel-shuffle transform that reduces hash load factors by redistributing spatial information, thereby mitigating collision-induced information loss without enlarging the hash tables. To support evaluation on extremely high-resolution data, we also curate, to the best of our knowledge, the first uncompressed whole-slide image dataset for academic research. Experiments on Kodak images, gigapixel natural images, and raw whole-slide images demonstrate that CARA consistently improves the fidelity-parameter trade-off. Our method matches state-of-the-art performance while using only $27.76%$ of the parameters, and achieves up to $6.11$ dB PSNR improvement at comparable parameter counts. Code is provided in the supplementary.

Abstract: Identifying isolated points is important in image processing applications such as medical imaging, astronomy and quality control management. Other domains, such as cybersecurity, also present challenges that can be framed as image processing problems. One example of particular interest is the identification of anomalous single nodes in spatially organised networks where groups of nodes in different regions share similar feature values. This task can involve both binary and more complex grayscale images. However, existing methods face limitations: template matching is infeasible for grayscale images, while 2nd order derivative based methods are highly sensitive to noise and require user-specified thresholds. To overcome these issues, a novel method is proposed for detecting meaningful single-pixel deviations in images. This approach modifies and extends a neuron model, originally designed for anomaly detection, to operate on spatially diameter limited receptive fields that incorporate excitatory and inhibitory regions. The result is a method that is free from user-specified thresholds and parameters, and can be applied to both binary and grayscale images, providing an effective, robust and efficient solution.

Abstract: Segment Anything Models provide reusable priors, yet they require user prompts and cannot support fully automatic instrument segmentation. Automatic prompting is difficult for thin, articulated, reflective, and partly occluded tools, where several configurations can be valid. We formulate automatic prompting as lightweight point-set planning and isolate the point source under a frozen pathway. To this end, we present SetPlanner, a 1.52M-parameter plug-in point-set planner for frozen SAM. The plug-in preserves SAM's point-prompt interface and enables reuse across backbones. SetPlanner plans complete unordered K-point sets from geometry-aware targets with a permutation-aware conditional flow. SAM decodes eight candidates; their consensus readout yields a ground-truth-free prediction. Across three endoscopic datasets, SetPlanner wins all six transfer routes over a LoRA-adapted system. Under our frozen-pathway protocol, SetPlanner reaches 0.934 Dice on Kvasir-Instrument and recovers 96% of a 44.4-point localization gap, while candidate disagreement ranks low-Dice cases at AUROC 0.969.

Abstract: Reference labels used to train medical image classification models are not always as certain as they may appear, and this uncertainty has implications on performance metrics. In this study, we propose a framework to analyze model performance for periventricular Fazekas score prediction that goes beyond conventional metrics. The Fazekas score is an ordinal visual rating scale used to assess the severity of white matter hyperintensities and is known to be affected by inter-rater variability. While the best Fazekas score prediction model achieved a Matthews correlation coefficient (MCC) of 0.70, performance varied across data splits and loss functions, making interpretation of model capabilities difficult. Rather than interpreting epistemic uncertainty of a model's prediction as an isolated scalar value, our approach of uncertainty mapping relates uncertainty to its position within the learned feature representation. This highlights regions of class-boundary transitions where cases appear more ambiguous and misclassifications are more likely. It also identifies potential label disagreement, including low-uncertainty misclassified cases that expert review found to be inconsistent with the original reference Fazekas score. Therefore, uncertainty mapping allows model behaviour to be examined in relation to class separation and potential model-label disagreement. Loss function choice also influenced the uncertainty profile, with some models showing clearer class separation and more localized uncertainty in ambiguous regions than others. These findings suggest that uncertainty mapping for Fazekas score predictions can support model interpretation and targeted dataset review when reference labels are affected by ambiguity/ inter-rater variability.

Abstract: Forecasting anatomical changes such as tumor growth and neurodegeneration is a challenging generative vision task. Morphological evolution is subtle relative to static anatomy, highly patient-specific, and inherently stochastic. Existing methods struggle with several issues: deterministic networks ignore biological stochasticity, while standard diffusion models require computationally prohibitive multi-pass sampling to quantify uncertainty. We propose MUMINS (Metadata-conditioned Uncertainty-aware Medical Image Next-state Synthesis), an efficient diffusion framework that jointly diffuses a baseline scan and its follow-up residual, summed to synthesize the follow-up scan, while concurrently predicting a spatial uncertainty map, in a single reverse diffusion process. Conditioned on the time interval and relevant metadata, it preserves fine-grained anatomy by dynamically re-injecting the baseline as a soft anchor at every denoising step, and a negative-log-likelihood head learns the uncertainty map to explicitly flag error-prone regions. Designed without organ-specific heuristics, the same architecture is reused across anatomies via separate, dataset-specific retraining. Extensive evaluations demonstrate that dataset-specific retraining of MUMINS matches or outperforms dedicated, domain-specific state-of-the-art methods on lung CT (PNG) and brain MRI (OASIS-3). Project page: https://github.com/aolivtous/MUMINS.

Abstract: Congenital heart disease (CHD) diagnosis and surgical planning often require patient-specific 3D anatomical models, but manual segmentation is labor-intensive, particularly in complex anatomies. Although deep-learning methods can automate this process, they are typically evaluated in-distribution, despite clinically relevant shifts in scanner, protocol, institution, population, and imaging modality. We present, to our knowledge, the first systematic evaluation of out-of-distribution (OOD) generalization in CHD segmentation, using ImageCHD as a held-out target cohort. We compare representative segmentation architectures under combined CT and CMR training, CT-only training, self-supervised pretraining, and limited target-domain adaptation. In-distribution performance proves to be a poor indicator of cross-cohort robustness: nnU-Net achieves the highest validation Dice (0.77) but falls to 0.51 on ImageCHD, while SwinUNETR generalizes substantially better, reaching 0.67 Dice. MAE and JEPA pretraining provide only modest additional benefit, suggesting that architecture contributes more to robustness than the tested pretraining strategies in this setting. When limited target-domain supervision is introduced, all SwinUNETR variants exceed 0.76 Dice with only 11 labeled ImageCHD cases. These findings demonstrate that conventional in-distribution evaluation can obscure clinically important generalization failures and support explicit cross-dataset testing as a key component of CHD segmentation evaluation.

Abstract: With the increasing deployment of deep neural networks in critical systems, such as medical diagnostics and autonomous vehicles, ensuring their interpretability is crucial to building trust in decision-making systems. In the field of explainable artificial intelligence, prototype-based reasoning has gained particular popularity, as it mimics human cognitive processes by explaining model decisions based on visual similarity under the looks like this paradigm. While this paradigm has been thoroughly investigated in the context of global image classification, the interpretability of dense predictions, particularly semantic segmentation, remains largely unexplored despite its immense importance in tasks requiring precise object localization. Existing prototype-based interpretable segmentation models rely on ante-hoc architectures, which entails significant limitations because they require costly training from scratch and modifications to the network structure, ultimately leading to a noticeable drop in predictive performance compared to standard black-box models. To address this issue, we propose PiPS (Post-hoc interpretable Prototypical Segmentation), the first fully post-hoc solution for generating prototypical explanations for semantic segmentation models. Our method enables the extraction of intuitive, spatially localized explanations from any pre-trained network without modification or fine-tuning, thereby preserving 100% of the model's original predictive performance. This approach opens a new avenue for the safe and cost-effective deployment of transparent systems in advanced computer vision tasks. Codebase available at https://github.com/gmum/PIPS.

Abstract: Recent advances in angiographic imaging have enabled longitudinal visualization of the microvasculature. Image processing pipelines based on vessel graphs are able to resolve subtle temporal changes at the level of individual blood vessels. However, current strategies for graph extraction, refinement, and matching are highly sensitive, with even minuscule differences in the underlying segmentation map resulting in substantially different vessel graphs. These artifacts severely inhibit the ability to accurately match sequential vessel graphs of the same subject over time. To address this problem, we propose a strategy that matches graphs before jointly refining them. Specifically, we perform an early matching after basic graph extraction before removing spurious bulges and merging junctions in both graphs using joint information. In experiments with complex retinal vessel graphs, we demonstrate that this strategy results in a higher matched area without graph fragmentation compared to separate or no refinement, respectively.

Abstract: Pediatric brain tumors are a leading cause of cancer-related mortality in children, and their small, rare, and often low-contrast subregions make accurate manual delineation challenging. Reliable automated segmentation is therefore needed to support diagnosis, treatment planning, and response assessment. Accordingly, we introduce NeuroTS-Net, a three-dimensional encoder-decoder convolutional neural network architecture for multi-class semantic segmentation that incorporates a dual-scale raw-detail stream, adaptive low-resolution context selection, and detail-preserving multipath downsampling. These components preserve fine intensity and boundary information while efficiently modeling broader tumor context. NeuroTS-Net was trained on the BraTS 2026 pediatric dataset without external data or pretrained weights and evaluated against nnU-Net and MedNeXt under the same experimental protocol. NeuroTS-Net outperformed the baseline methods, achieving whole-tumor and tumor-core Dice scores of 0.938 and 0.937 on the internal validation set and 0.927 and 0.926 on the official challenge validation set. The code is open-sourced at: https://github.com/maenstru56/NeuroTS.

Abstract: Brain tumor segmentation remains difficult because enhancing tumor (ET) has low contrast and overlaps surrounding tissue, while scanner and site variation causes domain shift. We propose DE-GAN, a contrast-enhancing conditional GAN that combines input-adaptive dynamic convolutions, style-aware feature mixing, and coordinate encoding to synthesize slice-adaptive FLAIR images. A label-guided, class-conditional target separates tumor-core (TC) and ET intensities while preserving anatomy. The generated FLAIR is concatenated with the original MR modalities and used to train a 3D U-Net. Across BraTS 2015, 2018, and 2019, DE-GAN improves segmentation over the baseline and static EnhGAN replacement on most reported TC/ET metrics, with the largest gains from retaining both original and enhanced FLAIR. Code and pretrained models are available at https://github.com/zkhansuri-ui/DE-GAN.

Abstract: Pretrained score-based diffusion models provide strong unconditional priors, yet enforcing measurement or physics consistency in inverse problems is often handled by heuristic guidance, intermittent projections, or task-specific conditional training, with limited guarantees of feasibility at the end of inference. We propose terminal-conditioned inversion for score-based SDE priors. Given a frozen Score-SDE prior and a task-defined terminal feasibility specification, we construct an associated backward stochastic differential equation whose adapted solution defines a principled inverse map from the terminal requirement to a prior state at a chosen noise level. Under standard regularity conditions, we establish existence and uniqueness of the adapted solution and obtain terminal consistency by construction. We further develop a practical neural BSDE solver that composes arbitrary pretrained diffusion priors with domain constraints without modifying the score-defined coefficients, producing an anchored prior state that enables neighborhood sampling for uncertainty characterization. Experiments on toy datasets validate stable terminal-conditioned inversion and distributionally consistent neighborhood sampling. As a real-world case study, we apply the framework to sparse-view CT reconstruction and achieve improved reconstruction quality over representative training-free baselines while satisfying strict measurement feasibility under the prescribed terminal specification. Project is available in: \href{https://laplacelab.github.io/BSDEDiffusion/}{https://laplace.center/icmlbsdeI/}

Abstract: Medical counterfactual generation modifies images to change model predictions for interpretability. However, existing diffusion-based approaches are often prohibitively slow and memory-intensive, making them difficult to apply in high-resolution settings. Moreover, existing masking strategies are tightly coupled with pixel-space representations, making them incompatible with latent-space diffusion editing. To address these challenges, we propose MedDiME, a latent-space classifier-guided diffusion framework that reduces computational and memory overhead while introducing a latent-compatible, gradient-driven adaptive masking mechanism for spatially precise medical counterfactual generation. Extensive experiments demonstrate that MedDiME achieves high-quality counterfactual generation with significant efficiency gains compared to prior classifier-guided diffusion baselines, achieving up to 40 times faster inference and 13 times lower peak GPU memory usage.

Abstract: Accurate PSMA PET/CT interpretation is central to prostate cancer management, yet existing PET/CT AI models typically address isolated tasks. We propose a unified PSMA PET/CT vision-language model for report generation, visual question answering, and lesion segmentation. The framework adopts an LLaVA-style architecture, comprising a PET/CT vision encoder, an MLP-Mixer projection module, a LoRA-tuned large language model, and a 3D segmentation branch. Training followed a four-stage strategy: vision encoder pretraining, projection-layer alignment, VLM fine-tuning, and final multitask tuning. Language tasks used 5,747 PSMA PET/CT datasets with paired reports, while segmentation used the PSMA subset of AutoPET. The model outperformed PET2REP and a CT-based baseline across standard report-generation metrics, improved performance across VQA question types, and achieved higher Dice and lesion-level overlap F1 than SegAnyPET and nnUNet. These results support the feasibility of a unified framework for structured, interactive, interpretable PSMA PET/CT analysis with voxel-level grounding within a single multitask model architecture.

Abstract: Vessel segmentation in X-ray coronary angiography (XCA) is a fundamental step for quantitative coronary analysis and subsequent assessment of coronary artery disease. However, accurate vessel segmentation remains challenging because of imaging noise, complex bifurcations, and the overlap of vessels and background structures, which can lead to disrupted vascular connectivity and missed small branches. In this work, we propose BSC-Net, a ResNet-U-Net-based framework tailored to improve small-vessel representation and repair vascular structural continuity. BSC-Net enhances small-vessel representation through targeted sampling and improves vascular structural continuity by integrating long-range contextual modeling and Edge-Informed Loss (EIL). BSC-Net was validated on two public XCA datasets, demonstrating state-of-the-art (SOTA) performance in coronary vessel segmentation with Dice and IoU scores of 77.8%/90.6% and 64.5%/83.0%, respectively. Furthermore, based on the obtained vessel segmentation, we performed automated quantitative coronary analysis and derived clinically relevant morphological and hemodynamic parameters, including stenosis ratio, time-to-peak, and relative propagation velocity. These results demonstrate that BSC-Net produces accurate vessel segmentation results with preserved vascular continuity for quantitative coronary assessment, enabling reliable downstream analysis and clinical evaluation of coronary artery disease.

Abstract: Accurate cell detection and classification are crucial for pathological analysis, directly affecting diagnostic accuracy and treatment planning. To capture complex cellular interactions beyond visual appearance within the tumor microenvironment, several approaches have employed graph neural networks to model spatial and relational patterns among cell nuclei, yielding promising results. However, these methods typically adopt a two-stage paradigm of visual extraction followed by relational modeling, which necessitates separate tuning for each stage, thereby increasing pipeline complexity and hindering end-to-end joint optimization. In this paper, we propose an end-to-end framework for cell detection and classification that jointly models patch-level visual representations and instance-level interactions, which incorporates a dynamic graph construction module and an instance-aware graph network. Specifically, the graph construction module dynamically builds the graph structure using learnable queries derived from patch-level features as cell instance representations, with adjacency defined by integrating feature similarity and spatial distances. The instance-aware graph network performs adaptive instance filtering and feature reorganization, aggregating them over the cell graph into a topological latent state for a selective state-space transition driven by visual cues, fusing appearance and relational evidence. When evaluated on multiple datasets with different staining protocols for cell and nucleus detection, our method significantly outperforms existing approaches in both detection and classification performance. The code will be released at https://github.com/RuochenLiu23/IGM.

Abstract: Medical volume visualization requires selecting regions of interest (ROIs) and carefully controlling their relative visual emphasis according to a given clinical intent. Implementing these decisions in conventional workflows demands substantial clinical and visualization expertise and often involves trial-and-error optimization. Recent agentic systems have introduced natural-language interaction and autonomous visualization operations but largely rely on MLLM-based inference throughout the workflow. Although MLLMs encode broad medical knowledge and provide strong reasoning capabilities, such inference may be suboptimal for medical volume visualization, potentially leading to clinically incomplete interpretations of user requests and unreliable ROI identification and visualization optimization. In this work, we present MedVA, an end-to-end neuro-symbolic agentic system for medical volume visualization that addresses these limitations through three complementary agents. The neuro-symbolic intent formulation agent refines MLLM-based interpretations of natural-language requests through symbolic reasoning over established clinical knowledge, which provides more complete, clinically grounded ROI specifications than MLLM-only reasoning. The multi-model ROI identification agent directly identifies semantically specified ROIs in the original volume by leveraging complementary large-scale pretrained medical segmentation models. The objective-driven visualization optimization agent explicitly evaluates ROI visibility and occlusion in the original volume using a volume-based visibility objective. Extensive agent-level and system-level evaluations across diverse medical datasets and interaction scenarios support the effectiveness of the individual agents. A formative user study further indicates high usability and practical value among users with different levels of expertise.

Abstract: Federated learning enables collaborative model development without centralizing patient data, but annotation reliability at participating institutions cannot always be assumed. In ophthalmic imaging, differences in disease prevalence and class composition can resemble changes caused by corrupted supervision. We introduce OCT-FedSIR, a reliability-aware spectral framework for federated OCT classification under client-dependent annotation noise and heterogeneous data distributions. OCT-FedSIR combines class-balanced spectral estimation, Stage-I logit adjustment, complementary spectral descriptors, selective spectral relabeling, and noise-aware federated optimization. We evaluated the framework on the Kermany, University of Illinois Chicago, and Wake Forest datasets under symmetric and structured asymmetric noise and three levels of non-IID heterogeneity. Across 117 experimental conditions, OCT-FedSIR achieved a mean accuracy of 86.73%, compared with 79.94% for RoFL and 78.75% for FedCorr. It correctly separated clients with original and corrupted annotations across all evaluated conditions, while the original FedSIR identification procedure was less robust, particularly under asymmetric noise. Spectral relabeling recovered 77.2% of corrupted annotations with 91.3% correction precision and a 3.5% false-correction rate. Retaining corrected clients outperformed spectral pruning by 9.30 percentage points on average. These findings show that annotation noise can often be identified and corrected without discarding informative client data.

Abstract: Purpose: To compare four multimodal large language models (MLLMs) with radiologists of varying expertise in breast density assessment, BI-RADS assessment, biopsy candidacy determination, and continuous malignancy probability estimation using digital mammography (DM) and contrast-enhanced mammography (CEM). Methods: This study included 179 women with paired DM/CEM examinations and reference standards. Four MLLMs (ChatGPT-5.2, Gemini-3.1 Pro, Sonnet-4.6, Muse Spark) interpreted images with and without masks; three radiologists interpreted non-masked images. Results: For binary density classification on DM, radiologist accuracies ranged from 55.81% to 78.60%, exceeding most MLLM values (62.33%-71.63%), while masks added limited benefit. Five-category BI-RADS accuracies were higher for radiologists on DM (56.74-67.44%) and CEM (62.33-82.79%) compared with MLLMs (DM 31.16-45.12%; CEM 40.00-55.81%). Binary biopsy-candidacy accuracies were likewise higher for radiologists (DM 85.12-89.77%; CEM 86.98-92.09%) than for MLLMs (DM 61.39-75.35%; CEM 69.30-82.79%), although CEM improved performance across all readers. Lesion masks substantially improved MLLM continuous malignancy-probability accuracies from 64.65%-71.63% to 72.56-78.60% on DM and from 67.91%-77.21% to 72.56%-81.86% on CEM, approaching radiologist ranges (DM 63.72-82.79%; CEM 81.86-88.84%). The corresponding AUCs for the top masked models overlapped those of the human readers. Overall, Muse Spark, followed by Sonnet-4.6, demonstrated the strongest performance among the MLLMs across domains. Conclusion: Radiologists generally outperformed MLLMs in categorical tasks, while selected masked models approached human performance for continuous malignancy probability estimation, suggesting a potential adjunctive role.

Abstract: Training-free diffusion inverse solvers typically choose between local measurement guidance and costly clean-space posterior updates. Independent posterior refresh can improve global correction by sampling a clean conditional and re-noising it, but its practical realization requires probability-flow ODE integration and clean-space Markov chain Monte Carlo (MCMC). We propose Direct Conditional Transition Sampling (DCTS), a direct stochastic-flow approximation to the same ideal refresh target. Rather than explicitly drawing a clean sample, DCTS estimates the measurement-conditioned clean mean along a short inner path and transports Gaussian source noise directly to the next noisy state. A denoiser-compatible sufficient statistic and a covariance-scaled operator update enable this conditional-mean estimation. Experiments on four inverse problems demonstrate that DCTS achieves competitive reconstruction quality with up to $16.8\times$ speedups over competing methods.

Abstract: Deep learning-based spatio-temporal disease progression models commonly overlook the incubation period of progressive diseases, limiting the use of those models in early interventions, which are vital for not easily reversible diseases such as Alzheimer's. This is because, the existing deep learning based longitudinal disease-progression models are almost always run forward: from an observed baseline they predict future decline. In many clinical settings, however, imaging begins only after pathology is suspected or already visible, the earlier, healthier patient-specific reference was never acquired. To address this, we propose to study reverse disease progression prediction: given later diseased anatomy, reconstruct the unobserved healthier anatomy that preceded it. We use a two-stage model in which a frozen 3D vector-quantised autoencoder defines a compact discrete latent space, while a Neural Ordinary Differential Equation (ODE) learns continuous-time dynamics in that space. A recurrent encoder reads late observations in reverse temporal order, initialises the latent state, and the ODE is integrated backwards across the trajectory. On a controlled Morpho-MNIST benchmark with a sinusoidal perturbation, our model successfully recovered the unseen previous states from later observations of the non-monotonic trajectory. On longitudinal brain MRIs from Alzheimer's Disease Neuroimaging Initiative, at the task to recover the previous unseen trajectory towards healthy states of the patients from observed later diseased states, our model outperforms the baselines that uses copy-nearest and mean-observed, with positive disease-reversal scores in every diagnostic stratum. We hope that our work can provide insights and tools towards discovering the incubation periods from single-shot scans, and developing early interventions of diseases based on imaging.

Abstract: Many analytics tasks require secure computation over encrypted data. In particular, fine-grained data such as pixel-level images require higher precision, as every pixel can directly affect outcomes in tasks like tumor segmentation and anomaly detection. While Multi-Party Computation (MPC) is interactive, Differential Privacy (DP) protects only aggregate values, and Partially Homomorphic Encryption (PHE) lacks multiplicative support, none of them can efficiently handle fine-grained data analytics. Fully Homomorphic Encryption (FHE) uniquely enables arbitrary operations on encrypted pixels but remains computationally expensive, posing significant challenges for both software and hardware accelerators. We present PixCrypt, a caching-based acceleration mechanism for fine-grained fully homomorphic encryption. PixCrypt replaces expensive fresh ciphertext generation with cache retrieval and coefficient-level operations across CKKS, BFV, and BGV, while randomized reconstruction ensures that ciphertexts do not repeat. Its linear noise growth reduces the need for bootstrapping and lowers NTT load, improving hardware accelerator efficiency. This design yields up to 35x faster fine-grained encryption and maintains IND-CPA (Indistinguishability under Chosen Plaintext Attack) security. Experiments on five real-world pixel-level image processing tasks show that PixCrypt significantly improves the practicality of FHE for privacy-preserving analytics.

Abstract: We evaluated parameter-efficient fine-tuning (PEFT) of the Segment Anything Model (SAM) for liver tumor segmentation in abdominal CT of colorectal liver metastases. We compared Low-Rank Adaptation (LoRA), 4-bit Quantized LoRA (QLoRA), a convolutional adapter (Conv-Adapter), and our Directional Spectral Top-K adapter (DiSCo), training only adapters while freezing the SAM backbone. DiSCo derives spectral bases from singular value decomposition of row-normalized weights and learns rank-gated spectral coefficients, per-output magnitude offsets, and a spectral gain, with optional Top-K rank selection at inference and 0.14 M trainable parameters. We benchmarked five prompting regimes: no prompt, single-point, multi-point, and bounding boxes at intersection over union 0.50 and 0.75. Conv-Adapter and LoRA achieved the highest accuracy (overall Dice 0.793 and 0.792; single-point Dice 0.795 and 0.792; 95th-percentile Hausdorff distance (HD95) 32 mm). QLoRA was close (overall Dice 0.766; single-point Dice 0.768; HD95 36.41 mm), with 0.91 M trainable parameters, 120 ms latency, and 4.9 GB peak memory. DiSCo achieved the highest Dice per million trainable parameters (4.66), with overall Dice 0.653, single-point Dice 0.698, and HD95 49.53 mm. These results show an accuracy-efficiency trade-off and support PEFT for liver tumor segmentation with reduced adaptation costs when compute and labeled data are limited. Code: https://github.com/Ramtin-Mojtahedi/PEFT-SAM-Liver-CT

Abstract: Sparse-view computed tomography (CT) reduces radiation dose and acquisition time but remains severely ill-posed because incomplete projections poorly constrain null-space information. Existing learning-based methods often estimate this information in high-dimensional image space, conflate physical measurement errors with prediction errors, and depend on fixed discretizations. We propose SONAR, a Structure-Consistent Neural Operator for Null-Space-Aware Reconstruction. Instead of recovering the full null-space component, SONAR predicts a low-dimensional null-space-aware representation from the acquired projections as pseudo-measurements. It separates measurement and pseudo-measurement residuals, lifts them into the image domain through physics operators, and applies independent neural operators to constrain their structural effects, thereby accommodating admissible errors while suppressing unsupported structures. To support cross-discretization reconstruction, an anisotropic U-shaped neural operator models the periodic angular and nonperiodic detector dimensions using direction-dependent continuous supports, while image-domain neural operators re-discretize continuous kernels on target grids. These components form an optimization-inspired unrolled network. Experiments on simulated AAPM and clinical MARS photon-counting CT data demonstrate consistent improvements across seen and unseen view settings and unseen image resolutions. On AAPM dataset, SONAR improves PSNR by 1.87~dB at 62 views and by 7.63~dB under zero-shot transfer to a $512\times512$ grid over the strongest competing methods. SONAR also achieves the best overall performance in all clinical settings evaluated, demonstrating accurate, structurally reliable, and discretization-robust sparse-view CT reconstruction.

Abstract: Phase unwrapping is a key step in interferometric and coherent imaging, where the physical quantity of interest is carried by a phase that the instrument delivers only modulo 2*pi. The difficulty in two dimensions is to separate the jumps caused by wrapping from those produced by noise, by true discontinuities, by under-sampling or by decorrelation. Spatial-domain and frequency-domain methods have both been studied extensively, each with advantages the other lacks; hybrid schemes combining the two remain scarce. We propose a semi-global tile-based strategy in which every tile is unwrapped in the frequency domain, through the Discrete Cosine Transform (DCT) and the least squares (LS) formalism of Ghiglia et al., the tiles being merged spatially. Unwrapping and noise filtering are performed jointly, which regularizes an otherwise ill-posed inverse problem. An error stays confined to the tile in which it arose; the tiling artifacts are removed by averaging over every shift of the grid and over the symmetries of the square; and that average is weighted by the Poisson residual each pass leaves behind, so that a pass whose tile boundaries fell on a discontinuity does not impose its seam on the result. Experiments on synthetic and real data, against four reference algorithms from four distinct families and under six complementary metrics, show that the proposed method matches or improves on the state of the art. One of these metrics, a corrected cyclic re-wrap residual introduced here, needs no ground truth and therefore remains available on real acquisitions.

Abstract: Flow matching approaches to imaging inverse problems commonly incorporate measurements in two ways. Conditioning-based approaches supply measurement-derived information as a network input, often through concatenation, while inference-guided approaches combine an unconditional velocity field with a separate data-consistency update. In these common formulations, the forward model is not explicitly enforced within the learned conditional velocity field. We propose a principled parametrization of the measurement-conditional velocity field to solve inverse problems. Under linear interpolation, we express the conditional velocity $v(x_t,t,y)$ in terms of the posterior mean $E[x_1 | x_t,y]$, and characterize that mean as the unique minimizer of a variational objective whose data-consistency term is explicit. We further prove that the velocity field defines a probability flow from the source distribution to the measurement-conditioned posterior. Splitting the variational objective yields a conditional velocity parameterization with operator-dependent data-consistency updates, which we train end-to-end under the flow-matching objective, with no additional guidance at inference. Our method achieves state-of-the-art PSNR with $50\times$ fewer function evaluations than the strongest flow baseline. Varying the sampling steps provides test-time control over the distortion-perception trade-off without retraining.

Abstract: Modelling how a disease progresses over time requires longitudinal imaging cohorts, which are scarce and small, whereas cross-sectional data -- one image per participant -- is abundant. Self-supervised pre-training on such data offers a way to bridge this gap, but it is unclear which strategy best supports progression modelling, or how that answer depends on the amount of labelled longitudinal data. We study this for age-related macular degeneration (AMD), pre-training encoders on the large cross-sectional NAKO cohort and predicting time to late AMD on the longitudinal AREDS dataset. We compare in-house self-supervised encoders against a general-purpose (DINOv2) and a domain-specific (RETFound) foundation model, across contrastive, masked-autoencoding, and self-distillation objectives, under frozen and fine-tuned protocols, and across labelled training sets from 100 to 32,250 examples. Which model performs best depends on how the encoder is used. When the encoder is frozen and labels are few -- the regime typical of longitudinal cohorts -- pre-trained representations reach clinically reasonable discrimination from a few hundred labelled samples, while models trained from scratch do not; this advantage fades under fine-tuning. Transfer is governed by the self-supervision objective rather than corpus scale or domain match, so that an encoder pre-trained on a modest cross-sectional cohort matches or exceeds a far larger in-domain foundation model. Together, these results offer a practical recipe for building progression models where longitudinal data is scarce: a frozen self-supervised encoder with a lightweight survival head.

Abstract: Ultra-widefield (UWF) swept-source optical coherence tomography angiography (SS-OCTA) enables large-area retinal vascular imaging, yet vessel segmentation at this scale lacks dedicated public benchmarks and comprehensive evaluation for quantitative vascular analysis. We introduce WOIVES, to our knowledge the first publicly available UWF SS-OCTA vessel-segmentation dataset, comprising 206 eyes from 152 participants with a 24x20mm^2 field of view. WOIVES spans emmetropia to high myopia and provides soft probability vessel annotations. We further propose PG-Mamba, a visual state space model that enhances conventional directional scans with two complementary polar-coordinate scan orders. An auxiliary Dynamic FOV Gating module performs spatial modulation at the bottleneck. PG-Mamba outperformed seven competitive approaches on broad segmentation metrics under cross-validation. It achieved the lowest median absolute errors for vessel density, fractal dimension, and vessel length density. WOIVES is publicly available on Zenodo (DOI: 10.5281/zenodo.21904672), and the PG-Mamba code is available at https://github.com/syb1234567/PG-Mamba.

Abstract: Post-treatment MRI in patients with glioma provides serial observations for updating patient-specific tumor-state proxy estimates, but variable appearances and trajectories complicate forecasting. We formulate forecasting as an observation-aware digital-twin update in which an intermediate observation anchors the patient-specific state. Among 203 patients and 594 follow-up time points, a predefined no-new-treatment criterion retained 120 of 236 candidate triplets, split into 81/24/15 training/validation/test triplets at the patient level. Each time point was represented by a continuous voxel-wise tumor-state proxy map in [0,1] derived from MRI lesion labels. A SegMamba-based single-step forecaster predicted update proposals from multimodal source-state tensors. Observation-Anchored Selective Assimilation (OASA) retained the observed intermediate proxy as the state anchor and selectively applied updates through a validation-selected tiered case-level rule and voxel-wise soft gate. We compared initial-scan forecasting, rollout without assimilation, latest-observation persistence, direct prediction, OASA, OASA + calibration, and morphological dilation. Checkpoints, OASA rules, and calibration thresholds were selected using validation data only. Across three seeds on 15 held-out test triplets, OASA maintained Dice at $τ$ = 0.2 comparable to persistence (0.6071 $\pm$ 0.0025 vs. 0.6070) while yielding numerically higher Dice at $τ$ = 0.5 (0.4269 $\pm$ 0.0079 vs. 0.3981), with a small RMSE increase. Calibration increased Dice at $τ$ = 0.2 to 0.6178 $\pm$ 0.0025, increased false-positive (FP) support (11,836$\rightarrow$18,663), and reduced false-negative (FN) support (22,107$\rightarrow$17,536). This reflects near-threshold support calibration rather than improved biological predictive capability. Code is publicly available at https://github.com/jsudg436/longitudinal-proxy-forecasting.

Abstract: Accurate segmentation of colorectal liver metastases (CRLM) in contrast-enhanced computed tomography (CT) is important for response assessment, surgical planning, and follow-up. We propose two parameter-efficient spectral adapters for the Segment Anything Model (SAM): the Directional Spectral Adapter (DiSECT) and Spectral Instance-Guided Adapter (SiGA). DiSECT uses singular value decomposition of frozen weights to constrain residual updates to leading spectral directions, while SiGA adds global and input-conditioned gating through a multilayer perceptron. We evaluate these methods on 446 contrast-enhanced CT volumes (355 training, 91 testing) and compare them with LoRA, QLoRA, convolutional adapters (CAD), and a 3D nnU-Net baseline. Experiments consider single-point, three-point, bounding-box, and no-prompt regimes. SiGA achieves the best single-point performance with a Dice score of 0.77, IoU of 0.69, and HD95 of 35.39 mm. Under no-prompt inference, SiGA reaches 0.76 Dice, 0.68 IoU, and 46.76 mm HD95, comparable to the nnU-Net baseline (0.758 Dice). DiSECT uses only 0.14 million trainable parameters. These results show that spectral adapters can efficiently adapt SAM for CRLM segmentation while retaining strong accuracy with limited trainable parameters.

Abstract: Brain metastases exhibit high inter-lesion variability in size, enhancement pattern, and post-treatment appearance, making volumetric segmentation of both pre- and post-treatment cases the central challenge of the BraTS 2026 Task 1 (Brain Metastases). We build a pragmatic pipeline on a 5-fold nnU-Net ResEnc-L ensemble, in which each fold is trained independently for 1,000 epochs with the standard Dice + cross-entropy loss on 1,296 four-modality training cases. This ensemble is followed by a rule-based post-processing cascade tuned for the lesion-wise Dice similarity coefficient (LW-DSC), a detection-oriented metric that behaves very differently from the traditional global Dice. The final pipeline reaches an LW-DSC of 0.733 / 0.751 / 0.713 / 0.549 on the enhancing tumour (ET), tumour core (TC), whole tumour (WT), and resection cavity (RC) sub-regions on the official validation leaderboard. Rather than trusting these leaderboard gains, we audit every post-processing stage with a five-fold out-of-fold (OOF) analysis with no model-training leakage over all 1,296 training cases, scored with the official BraTS evaluation code (BraTS_evaluation): it confirms two stages as robust, per-fold-consistent improvements while the third improves only the leaderboard and does not reproduce out-of-fold. We further provide a mechanistic analysis of the LW-DSC metric that explains why recall-recovering post-processing carries low risk whereas component deletion does not, and we report thirteen negative results spanning loss engineering, alternative backbones, and inference-time settings, several of which run counter to widely held intuitions. Source code is released under Apache-2.0 at https://github.com/hornbeamliu/brats2026-met.

Abstract: Reliable non-rigid point cloud correspondences are important for deformable anatomical registration, embodied perception and manipulation, and dynamic 3D reconstruction. Coarse-to-fine methods reduce computational cost by selecting the top-\(K\) coarse regions. However, this pruning may remove weak but correct hypotheses and restrict fine matching to an incomplete search space. We present \paper, a two-stage generative solver that maintains the complete soft matching matrix at both coarse and high resolutions. Stage~I uses denoising diffusion to estimate a global matching matrix in the compact coarse-resolution space. We then lift this matrix to high resolution while preserving its hierarchy. The lifted matrix is rank-bounded and block-constant. Stage~II refines it through a conditional transport bridge. We implement the bridge with two types of dynamics: a deterministic endpoint-parameterized conditional Flow Matching (CFM) ODE and a stochastic Brownian-bridge SDE inspired by Schrödinger bridges. Both variants share the lifted source, a time-conditioned transformer, and a matching-matrix endpoint predictor. Experiments on 4DMatch and 4DLoMatch show that both variants produce more accurate correspondences than the compared methods and improve downstream registration, with larger gains in low-overlap cases. They also improve cross-dataset generalization on CAPE and DeepDeform without target-domain adaptation while using the same deformation solver.

Abstract: Adapting natural-image foundation models like DINOv3 to multi-modal medical imaging is challenging due to the significant domain gap between natural color images and multi-channel medical scans. We present a unified, patch-based framework that processes raw multimodal imaging through training-free registration, automated localization, and mask-filtered patch extraction. This architecture culminates in a hierarchical strategy that aggregates patch-level insights into subject-level diagnostics. Using liver fibrosis staging as a case study, we evaluate four patch-level feature representations: handcrafted Radiomics features, learned ResNet features, pre-trained foundation model SAM-Med2D features, and frozen DINOv3 features. To ensure a controlled comparison, all models utilize the same lightweight MLP head and are evaluated across both rigid and deformable registration settings. Our training protocol focuses on mild fibrosis (S1) and cirrhosis (S4) classes only, enabling a single classifier to address both substantial fibrosis detection and cirrhosis staging. Evaluated via 10 random train (90%)/ test (10%) splits on 360 subjects from the CARE 2025 Liver Track 4 cohort, our DINOv3-based framework significantly outperforms all baselines, achieving the best classification accuracy of 78.4% for S1 and 75.8% for S4.

Abstract: No Free Lunch theorem implies that any performance gains achieved by a classifier on a particular image distribution are necessarily offset by a loss of performance over the set of all possible problems; thus, no single model is universally optimal. Selecting the most suitable classifier for image datasets is a critical yet challenging task due to the intrinsic complexity and diversity of images. This paper proposes a meta-learning framework that leverages a comprehensive set of meta-features capturing dataset complexity to predict classifier performance without exhaustive training. By extracting and selecting features using methods such as autoencoders, pre-trained networks, and dimensionality reduction techniques, we train regression models to efficiently estimate classifier accuracies. Additionally, clustering techniques are employed to group classifiers with similar performance patterns, simplifying the recommendation process. The datasets used span a wide range of concepts, including nature, animals, numbers, motorcycles, medical images, and human bodies, to ensure broad generalization. Evaluated on 56 diverse image datasets, our approach achieves an average ranking prediction accuracy exceeding 86%, demonstrating its effectiveness in guiding model selection. This scalable and interpretable framework provides a practical solution to improve classification performance while reducing computational costs.

Abstract: Diffeomorphic image registration is central to medical image analysis, enabling anatomically consistent alignment across subjects. Most learning-based diffeomorphic methods model autonomous ODEs(ordinary differential equations) by parameterizing a stationary velocity field and recovering deformations via scaling-and-squaring. While non-autonomous ODEs with time-dependent velocities increase expressiveness, existing approaches rely on numerical integration to implicitly enforce flow structure that entangles model expressiveness with discretization accuracy. We propose a framework to directly learn the continuous-time solution of a non-autonomous ODE formulated as a two-parameterflow map. By enforcing cocycle consistency, a fundamental structural property of time-varying flows, we learn the flow maps without time discretization and velocity integration during training. The framework recovers diffeomorphic mappings at inference using a small number of compositions. Our proposed framework seamlessly incorporates standard registration backbones and improves alignment accuracy consistently across nine datasets while preserving diffeomorphic structure. Notably, the proposed method achieves an average Dice improvement of 2.1% on brain MRI benchmarks, a 12% TRE reduction on lung CT, and a 2.6% Dice gain on cardiac MRI and ultrasound datasets.

Abstract: fMRI foundation models increasingly aggregate heterogeneous data across brain states, cohorts, and acquisition settings, yet pretraining domains are commonly treated as a flat mixture and downstream tasks are adapted independently. We study whether measured learning relations can organize both stages without modifying the backbone. During pretraining, a lightweight Brain-DiT proxy estimates difficulty and directed facilitation across ten fMRI domains, yielding a priority-guided cumulative domain curriculum combined with high-to-low-noise timestep scheduling and joint consolidation. During adaptation, controlled first- and higher-order transfer across fifteen tasks constructs a directed taskonomy, from which budgeted integer programming (BIP) selects directly supervised source tasks and target-specific routes. The joint priority-domain and high-to-low-timestep curriculum reduces v-NMSE, PSD-NMSE, and FC-MSE by 6.5%, 16.3%, and 10.5%, respectively, relative to uniform sampling over both dimensions, and shows strong downstream performance across six in- and out-of-domain tasks. The taskonomy reveals asymmetric, target-dependent transfer, while exploratory sealed-test evaluation shows larger descriptive gains for BIP policies when higher-order route spaces are available than for matched random controls. Together, these findings support organizing fMRI pretraining and adaptation by measured learning relations rather than treating domains and tasks as independent flat sets.

Abstract: 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

Abstract: Cancer segmentation models can fail silently, generating plausible but incorrect masks that risk missed findings or unnecessary biopsies. A critical question arises: Do AI models "know" when they are wrong, and if so, can we use the signal to predict their own failures? Humans do have a "Feeling of Error" (FOE): a spontaneous sense of unease that flags a potential error during thinking. We investigate whether cancer segmentation models exhibit an analogous internal signal. Unlike output-level cues (e.g., prediction confidence or uncertainty), which offer no insight into why a failure occurs and suffer from a sensitivity-quality tradeoff where high detection sensitivity could degrade overall segmentation quality. We instead propose to capture the model's FOE from its inner workings. Using mechanistic interpretability tools, specifically Sparse Autoencoders, we decompose internal neural activations into a dictionary of human-interpretable concepts and show that failure cases exhibit a distinct latent signature: fewer active concepts with lower activation magnitudes compared to successful segmentation. By training a classifier on these concept activations, we achieve accurate failure detection along with explanations for the model's mistakes. Experiments on prostate, pancreatic, and brain cancer segmentation demonstrate that our approach outperforms output-based methods in failure detection while preserving segmentation quality.

Abstract: Preoperative evaluation of trigeminal neuralgia (TN) often requires joint interpretation of structural MRI, which depicts the trigeminal nerve and surrounding cisternal anatomy, and time-of-flight MRA, which highlights vascular structures. Although MRI-MRA fusion is clinically attractive for visualizing neurovascular compression, this task is poorly captured by conventional whole-brain registration evaluation because the clinically relevant target is a small trigeminal ROI, vessel annotations are partial and clinically focused, local TOF-MRA contrast is variable, and field-of-view mismatch can limit deformable alignment. We formulate TN MRI-MRA fusion as an ROI-centered neurovascular registration-evaluation problem and construct a benchmark from 149 patients with clinician-annotated bilateral trigeminal ROIs. Six representative registration pipelines were evaluated using local image-based metrics, segmentation-derived vessel-localization metrics, prediction-volume analysis, and contrast- and FOV-stratified comparisons. Conventional evaluation summaries were often misleading: local image similarity, vessel-background separability, and downstream vessel localization did not co-rank methods; one-sided vessel distances were strongly affected by predicted vessel extent under partial annotations; and local MRA contrast determined when vessel-separability metrics were informative. Deformable refinement provided only a small, FOV-dependent benefit over affine alignment, while reader review showed that locally favorable vessel distances could coexist with globally implausible registrations. These findings indicate that TN MRI-MRA registration should be evaluated as a local, vessel-aware, contrast-sensitive, and FOV-aware visualization task rather than as generic multimodal brain registration. Our code is publicly available at https://github.com/jhuldr/TN-Reg-Benchmark.

Abstract: Semantic segmentation on very-high-resolution images remains challenging due to the high computational cost and the difficulty of capturing fine-grained details. We propose CoordFormer, a novel coordinate-based architecture for semantic segmentation that predicts labels at arbitrary spatial locations through a Coordinate Decoder equipped with a Localized Cross-Attention mechanism. The decoder combines coordinate embeddings with high-resolution local patch features and interacts with global tokens extracted from a downsampled image processed by a ViT foundation encoder, enabling rich semantic context while preserving pixel-level precision. This design enables flexible inference at arbitrary resolutions while keeping memory low on very-high-resolution inputs, and supports an efficient semantic-edge-focused strategy that concentrates computation along boundaries, maintaining fine-grained accuracy while reducing latency and computational cost. CoordFormer achieves state-of-the-art performance on MaSS13K and outperforms comparably sized and higher-parameter methods on DIS5K and KPIs, demonstrating its effectiveness for high-quality, very-high-resolution semantic segmentation.

Abstract: Pancreatic tumor segmentation in 3D CT volumes is challenged by extreme scale variability across both the pancreas and tumor, and highly irregular tumor morphology. While recent advances have pushed segmentation performance, existing methods do not explicitly address these challenges and come at the cost of excessive computational complexity, limiting their practicality in resource-constrained clinical environments. We propose TRIUNE-Net, a lightweight unified architecture that harmonizes scale, shape, and efficiency through three synergistic innovations. A multi-scale context aggregation module with stage-adaptive dilated convolutions enables the model to reason across the broad range of anatomical scales present in both organs. A serial linear-deformable attention mechanism combines large effective receptive fields with shapeadaptive deformable convolutions to capture irregular, non-convex tumor morphologies. Finally, an information-preserving downsampling module replaces conventional max pooling entirely, retaining all spatial information while adding negligible parameters, preventing small tumors from being discarded before they can be recognized. On both the MSD Pancreas and NVD Pancreas datasets, TRIUNE-Net achieves state-of-theart results with only 5.86 M parameters and no external pre-training, outperforming all baselines across all key tumor metrics. Specifically, it surpasses the next-best model by 0.45% in tumor Dice, 6.0 points in F1 score, 6.6 points in sensitivity, and 3.4 points in precision, simultaneously reflecting its ability to suppress both missed tumors and false alarms in clinically realistic conditions. Our code is available at: https://github.com/abdora-ai/TRIUNE-Net

Abstract: Generative diffusion models have emerged as a class of powerful techniques for various imaging applications, including but not limited to synthesis, reconstruction, and segmentation. Despite their success, current generative models pose two key limitations. First, they primarily rely on image intensity and texture information, with limited attention to underlying object geometry. As a result, they do not guarantee geometric or topological consistency during the generation process, which is a crucial requirement for high-stakes domains such as computational anatomy, biology, and robotics, where preserving object structure is critical. Second, existing models fail to explicitly learn or represent shape changes in the generative process. Such deformation dynamics remain occluded within network parameters; hence leaving the transformation process uninterpretable and physically uninformed. To address these challenges, we introduce IGG (Image Generation informed by Geodesic dynamics), a novel framework that integrates topology-preserving geodesic principles into the diffusion-based generative process. In contrast to conventional methods that operate in image intensity space, IGG learns and synthesizes diverse samples within geodesic deformation spaces, where geometric object changes are learned as smooth and invertible smooth mappings from a given template/source image. Our code is publicly available at https://github.com/nellie689/IGG.

Abstract: Reconstructing a three-dimensional left-ventricular (LV) endocardial surface from cardiac magnetic resonance (CMR) data is challenging when supervision is available on only a small number of axial slices. Through-plane geometry is weakly constrained, and automatically generated two-dimensional masks can propagate segmentation errors into the recovered shape. We present MR-RS-SDFR, a per-case implicit signed distance field (SDF) framework that reconstructs a continuous LV surface from a CMR volume and sparse axial weak masks. The method first builds a cross-slice SDF initialization from axial and longitudinal geometric cues and then refines the field using two complementary signals: MRI edge-field normal alignment, which provides an image-derived boundary cue independent of the weak masks, and differentiable reslice Dice and contour consistency, which preserve agreement with the observed planes. We evaluate three weak-mask generators -- LOO TransUNet, LOO nnU-Net, and an off-the-shelf Medical SAM3 model used without MM-WHS-specific training or fine-tuning -- and five sparsity levels from 4 to 64 axial planes. In the sparse-16 setting, final MR-RS-SDFR reconstruction reaches 0.928 Dice and 3.80mm HD95 with Medical SAM3 masks. The upstream generators do not exhibit a single common ranking across 2D and dense 3D segmentation, and nnU-Net- and Medical-SAM3-driven sparse reconstruction achieve the same mean final Dice despite different upstream error profiles. Across all three sparse-16 mask sources, MR-RS-SDFR is numerically better than protocol-matched full GHD+DVS in both Dice and HD95. Final Dice improves markedly from sparse-4 to sparse-16 and then saturates at the reported precision through sparse-64. These results support MRI-guided per-case SDF refinement as a reconstruction strategy that remains effective across weak-mask generators and supervision densities.

Abstract: Shortcut learning denotes the widespread situation in which a classifier exploits spurious correlations rather than diagnostic features. Existing mitigation strategies mostly aim to learn shortcut-invariant representations; their empirical success is limited and they cannot be applied to classifiers using frozen foundation model encoders. We propose to reframe shortcut learning as fundamentally a calibration problem: unconstrained learning implicitly calibrates each shortcut group to its training set disease prevalence, rendering the resulting classifier necessarily over-confident in one group and under-confident in the other. Building on this insight, we prevalence-equalize calibration between shortcut groups through two encoder-agnostic methods, an in-processing regularizer and a post-hoc prevalence-equalized recalibration step. Across chest-drain-pneumothorax benchmarks on CheXpert and SIIM-ACR, spanning fine-tuned CNNs and frozen foundation-model backbones, both methods substantially outperform all baselines. Post-hoc recalibration of a standard ERM-trained DenseNet raises misaligned-group AUROC from 0.23 to 0.73, indicating that shortcut reliance degrades the classification head rather than the underlying representation. Besides two new state-of-the-art shortcut mitigation approaches, our findings more fundamentally connect shortcut learning to calibration theory and algorithmic fairness.

Abstract: Uncertainty arising from inter-observer variability in medical image segmentation plays an important role in developing treatment plans. Research in this area is inhibited by the lack of multiple annotations for large-scale medical datasets, especially for volumetric data, which suffers from additional scaling and computational complexity challenges. Flow matching has emerged as a powerful framework for generative modelling and has also been demonstrated to maintain strong performance when working with latent representations of images. In this work, we introduce a latent-to-latent flow technique for stochastic segmentation of medical volumes via encoded representations of both the image and label space. We evaluate our method on two challenging applications covering delineation uncertainty for radiotherapy planning and multiple organ structure segmentation, improving efficiency up to 14x compared with full resolution models while maintaining clinically relevant performance.

Abstract: 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.

Abstract: X-ray projection radiography is a non-invasive imaging technique used in medical diagnostics and industrial inspection. The simulation of X-ray projections is commonly used to optimise acquisition protocols and improve image quality before performing costly scans. Classical photon transport simulations that include realistic X-ray scattering physics are computationally expensive because they require the sampling of a large number of distinct scattering paths. This limits the practical exploration of parameter spaces such as beam energy. Quantum computing offers the potential to solve high-dimensional problems faster by making use of quantum properties such as superposition. This work introduces a discrete-time quantum walk algorithm that simulates the transport of X-ray photons through heterogeneous volumes. It approximates the physics of X-ray projection radiography, including processes such as photoelectric absorption and higher-order scattering, including Compton and Rayleigh scattering. The quantum walk encodes all admissible photon paths into a single quantum state, enabling all scattering histories to be propagated simultaneously via the superposition principle. This quantum state representation enables flexible readout of various imaging modalities, including the primary, i.e., unscattered, image, or images exclusively containing Rayleigh and Compton scattering of specified orders. A quantitative comparison with classically computed reference simulations shows that the proposed quantum walk accurately reproduces radiographic projections, given the limitations of the underlying physical model. These results indicate that quantum circuits for X-ray transport can produce accurate radiographic images and imply that, as quantum hardware scales up, these algorithms could outperform classical Monte Carlo-based approaches in large-scale, scatter-aware virtual imaging studies.

Abstract: Accurate segmentation of pulmonary lesions is essential for effective clinical diagnosis and treatment strategies. Existing segmentation approaches often lack task-specific semantic guidance, as text-based annotations typically offer coarse localization of lesions, leading to inadequate delineation of lesion boundaries and poor performance on small-scale lesions. To address this, we propose CGSM, a Concept-Guided Segmentation Model that integrates LLM-generated and clinically reviewed concepts into the segmentation process. Specifically, we design a Concept-Visual Alignment Module (CVAM) to activate relevant tokens within the concepts that align with visual features, enhancing the interaction between textual and visual information. In addition, we introduce a Concept Modulated Decoder (CM-Decoder), which uses concepts from CVAM as modulation signals to facilitate the adaptive fusion of image and text features, improving the segmentation accuracy. Extensive experiments on two public datasets show that CGSM achieves state-of-the-art performance, with results of 91.59% Dice and 84.49% mIoU on the QaTa-COV19 dataset, demonstrating its effectiveness in pulmonary lesion segmentation.