medical imaging developers

Abstract: State-of-the art approaches to retinal vessel segmentation typically require extensive annotations, a highly time-consuming process, reliant on clinical expertise. We present FPG-Seg, an annotation-free pipeline for retinal vessel segmentation combining classical vesselness filtering, Bayesian deep learning and topology-aware graph reconstruction to segment retinal vessel topology without manual labels. Tested across four widely used benchmark datasets for retinal vessel segmentation, FPG-Seg attains a clDice of $0.74{-}0.78$, representing $86{-}98\%$ of the performance of an equivalent fully-supervised baseline, despite using no manual annotations for training or hyperparameter tuning. As part of this work, we also provide, to our knowledge, the first performance benchmark of an annotation-free vessel segmentation method on FIVES.

Abstract: In this paper, we study the spectral compressed sensing problem of recovering a spectrally sparse signal from linear compressive measurements. Exploiting the low-rank Hankel structure associated with the signal, we formulate a nonconvex fixed-rank optimization problem with a Hankel regularization. We propose a Superfast Iterative Hard Thresholding (SIHT) algorithm, where each iteration consists of a tangent-space least-squares update followed by a fixed-rank hard thresholding projection. SIHT is the first nonconvex algorithm with provable quadratic convergence for spectral compressed sensing. For random Gaussian measurements, it achieves exact recovery in the noiseless case and stable recovery in the noisy case with near-optimal sample complexity. To efficiently implement SIHT, we develop a parameterized conjugate gradient method for solving the least-squares subproblem, endowing SIHT with state-of-the-art computational and memory efficiency. Numerical experiments are provided to validate our results.

Abstract: While foundation models and vision transformers (ViTs) have redefined visual representations, current active learning (AL) strategies for these backbones largely operate at the patch or region level, where annotation requirements remain high due to extensive pixel labeling. Extending ViT-based AL to the pixel-level, low-budget regime is uniquely challenging: with as little as one pixel query per image, a method must simultaneously identify the most informative locations and train a reliable decoder head from an extremely sparse signal. We introduce TEAL (Token-space Efficient Active Learning), the first pixel-level AL framework built around ViT representations. TEAL uses a frozen ViT backbone and performs diversity-based selection directly on its native token lattice, avoiding the artifacts introduced by interpolating token embeddings to dense pixel resolutions. Our framework applies a two-level MaxHerding strategy over multi-layer token descriptors to select representative candidates, followed by margin-based uncertainty refinement on a finer decoder grid. Across CamVid, Cityscapes, ADE20K, and Pascal Context, TEAL consistently outperforms previous baselines under extreme label scarcity, improving over the strongest baseline by up to +24.36 mIoU with a single labeled pixel (px) per image, and reaching up to 97% of fully supervised performance with just 10 px. To rigorously establish the source of the gains, we further show that the improvements persist when all baselines are equipped with the same DINOv3 backbone, demonstrating that coupling token-space selection with uncertainty refinement on the decoder grid makes ViT token geometry an effective foundation for extremely low-budget active segmentation.

Abstract: We present a generative surrogate for charged-current \(ν_μ\)-nucleus scattering that can be calibrated to measured differential cross sections without event-level experimental samples. Starting from a theoretical interaction model, we fine-tune the surrogate to a MicroBooNE measurement and show that this also improves the description of observables not used in the fit. The calibrated model can also be applied to measurements from different neutrino fluxes without retuning, while retaining event-level predictions of outgoing-muon kinematics. Our results show that experimental cross sections can directly constrain generative event models while preserving their applicability across different observables and beam configurations.

Abstract: Boundary delineation of anatomical structures in prostate MRI is often compromised by regional ambiguity. Automated segmentation methods relying on global overlap loss functions tend to be insensitive to surface deviations, leading to significant errors in ambiguous regions. Most existing uncertainty-aware methods treat uncertainty as a post-hoc quality indicator or prediction filter. We propose Contrastive Uncertainty Learning (CUL), a supervised framework that uses predictive uncertainty to directly guide representation learning. Using Monte Carlo Dropout, CUL identifies voxel-wise uncertainty and structures the embedding geometry accordingly: low-uncertainty, correctly predicted features form stable voxels while high-uncertainty or misclassified features are actively repelled, preventing feature collapse at difficult boundaries. We evaluate CUL on a 589-scan 3D prostate MRI multi-structure segmentation task (8 anatomical structures) using a ViT with UperNet decoder architecture. Average Dice ($83.38\%$) remains comparable to the baseline ($83.35\%$), while surface distance decreases significantly ($p<0.001$) across 6 of 8 anatomical structures. A hard-case analysis reveals a $22{\times}$ asymmetry between significantly improved and degraded cases ($18.8\%$ vs $0.9\%$). Ablation studies show that removing uncertainty-guided sample selection eliminates improvements for the transition zone, while replacing the contrastive objective with a boundary loss additionally removes bladder improvements, demonstrating that both uncertainty-guided sampling and the contrastive objective are essential for the observed gains. These findings demonstrate that the proposed uncertainty-guided representation learning is a useful mechanism for reducing the risk of extreme errors in safety-critical medical segmentation

Abstract: Dense cardiac dynamics are essential for assessing cardiac function, yet in practice clinicians often observe only extremely sparse measurements. However, recovering full dynamics from such sparsity is a highly ill-posed problem due to the lack of temporal cues. While auxiliary time-series signals like ECG provide physiological guidance, effectively exploiting them is challenging due to the cross-modal representation gap and phase misalignment. In this work, we present CardioFAD, a Focus--Align--Diffuse paradigm that reformulates sparse cardiac dynamic synthesis as a recoverability--alignability anchor discovery problem. Our core insight is that resolving extreme temporal ambiguity requires a compact set of anchor states that are both sufficient to recover the visual trajectory and reliable for ECG--visual alignment. We therefore learn motion-salient keyframes under two complementary principles: trajectory sufficiency, which preserves trajectory-critical intra-modal motion content, and anchor alignment, which promotes consistent inter-modal correspondence at these anchors. We implement the Focus and Align modules optimized by the two aspects. Diffuse then performs two-stage generation by first synthesizing keyframes and subsequently interpolating the remaining frames. Extensive experiments on cardiac MRI and echocardiography videos demonstrate superior visual quality, temporal coherence, and improved functional consistency under the extreme one-shot regime.

Abstract: Self-supervised anomaly detection is a promising paradigm for medical ultrasound, as normal images are often easier to obtain than exhaustive annotations of all possible pathologies. However, most existing evaluations are limited to a single anatomy or task, making it unclear whether models learn a robust notion of normal ultrasound appearance or only a source-specific representation. We introduce the SADUSI benchmark, a multi-source ultrasound dataset designed to train and evaluate anomaly detection methods across a broad range of anatomical regions, views, and acquisition protocols. The goal of SADUSI is to provide a diverse normal ultrasound distribution and a benchmark for visible structural anomalies that can be assessed from single images. We evaluate representative self-supervised anomaly detection methods and find that current approaches struggle in this setting. In particular, reconstruction-based diffusion methods such as AnoDDPM and DeCo-Diff achieve pixel-level AUROC values of 0.56-0.72 and maximum F1 scores of 0.10-0.26, indicating limited separation of pathology from normal image regions. Feature-based PatchCore variants perform better, reaching pixel-level AUROC values of 0.76-0.83, but remain limited with maximum F1 scores of 0.14-0.40. These findings suggest that broad multi-source ultrasound anomaly detection remains an open challenge and that SADUSI can serve as a resource for developing methods that generalize beyond anatomy-specific settings.

Abstract: Handcrafted preprocessing is widely employed in automated dermoscopic analysis to suppress imaging artifacts and enhance lesion visibility. Nevertheless, its actual contribution to modern real-time models remains unclear, particularly when evaluation protocols do not adequately control correlations among images of the same lesion. This study presents a leakage-controlled, lesion-disjoint evaluation of dermoscopic preprocessing and augmentation for joint multi-class lesion classification and instance segmentation using a fixed nano-scale YOLO26 segmentation model (YOLO26n-seg). From HAM10000 (10,015 images), quality control yields 10,013 valid image-mask pairs from 7,468 unique lesions, partitioned into mutually exclusive sets by lesion identity. With the architecture, resolution, training budget, and evaluation protocol held fixed, we compare minimally processed images plus online augmentation against offline class balancing, DullRazor-CLAHE preprocessing, and raw-processed hybrid views, over three random seeds. On the lesion-disjoint test set, the raw baseline achieves a mask mAP$_{50:95}$ of $0.5636 \pm 0.0234$, a Dice score of $0.9356 \pm 0.0024$, and a macro-F1 score of $0.6917 \pm 0.0202$. Offline augmentation does not improve the mean performance, while the combined and hybrid strategies reduce both class-aware segmentation and classification accuracy. At only 2.69 million parameters, the model runs at approximately 50 frames per second. Under a leakage-controlled, lesion-disjoint protocol with all non-input factors held fixed, minimally processed dermoscopic images combined with standard online augmentation deliver a better accuracy-efficiency trade-off than increasingly complex deterministic preprocessing, which yields no consistent joint benefit across three seeds on HAM10000.

Abstract: Gastric adenocarcinoma (GA) is a leading cause of cancer-related mortality worldwide, and accurate histopathological subtype classification from whole-slide images (WSIs) is essential for effective treatment planning. While multimodal approaches that integrate pathology report text with WSIs can improve classification, existing methods often depend on computationally expensive transformer architectures and large language models. We propose a multimodal knowledge distillation (MKD) framework that combines a pretrained WSI image encoder and a clinical text encoder using Low-Rank Multimodal Fusion (LMF) to efficiently model cross-modal interactions during training. Each WSI is represented as a bag of patches paired with a slide-level diagnostic caption. The teacher model learns fused image-text representations for subtype classification, while the student model distills this knowledge to enable accurate image-only inference. We evaluate our method on the PatchGastric benchmark dataset and achieve at least 3.35% higher mean accuracy than state-of-the-art approaches, without relying on transformer-based fusion, multi-task learning, or large language models. The source code is available at https://github.com/helomelo1/MKD-LMF.

Abstract: We introduce a sampling approach for energy- and score-based generative models that requires no gradient evaluations of the model. Replacing the drift term that would normally contain the score $\nabla_\mathbf{x} \log p_θ(\bf{x})$ with a high-frequency dithered cosine of the model's \textit{value}, $\sqrt{αω}\,\cos(ωt + k \log p_θ(\bf{x}))$, produces, in the high-frequency averaging limit, Langevin Markov chain Monte Carlo for energy-based models and the reverse-time SDE of score-based diffusion. We prove that trajectories of the dithered Itô SDE converge to those of the target SDE, driven by the same Brownian motion, uniformly on compact time intervals in probability, by an averaging argument that extends bounded extremum seeking (ES) to Itô processes, with an explicit $O(ω^{-1/2})$ mean-square rate under global bounds. The approach is not confined to smooth targets: it extends to $C^{1,1}$ energies with discontinuous curvature (without ellipticity requirement) and to Sobolev energies whose Hessians exist only off measure zero sets; for Lipschitz energies with gradient kinks the averaged limit remains well posed; the Krylov-Röckner integrability class is the boundary of provability. The approach provides a hard \textit{a priori} bound on the per-step update rate and applies to explicitly time-varying targets on finite horizons. Gradient-free pixel-space sampling is not competitive with well-tuned backpropagation-based samplers at practical evaluation budgets; the regime where the approach offers an advantage is latent-space sampling when the model is a black box and the target drifts in time. We demonstrate latent-space tracking for time-varying images on CelebA-HQ ($256{\times}256$) from limited 1D projection measurements and latent-space EBM sampling on CIFAR-10.

Abstract: Machine learning (ML) has emerged as a promising approach for improving diffusion MRI (dMRI) tractography, a task that remains limited by the intrinsic tension between local diffusion information and global anatomical plausibility. In this work, we systematically evaluate recurrent neural networks (RNNs) and Transformer models for iterative tractography, with particular attention to training strategies, input representations (including convolutional neural network (CNN)-based embeddings and end-of-sequence (EOS) tokens), and hyperparameter selection. We introduce a generation-validation phase enabling supervision at the streamline level during training, allowing supervision despite the mismatch between local loss functions and global streamline quality. Using the ISMRM2015 tractography challenge dataset, our models achieve the highest reported performance to date. Through controlled experiments, we quantify the impact of missing bundles, noisy or imperfect training streamlines, and invalid fibers in the training set. Finally, we demonstrate the applicability of our best-performing models for in vivo data from the Tractoinferno database. Overall, our results highlight both the potential and the limits of sequence-based deep learning models such as Transformers and RNNs for tractography, and emphasize the need for improved phantoms and evaluation methods for in vivo validation. We provide takeaways and recommendations for future researchers training and validating sequence-based supervised methods for tractography.

Abstract: Generative super-resolution models can turn portable 64 mT MRI into images that look like 3T scans, and the field evaluates them with PSNR, SSIM, and pixelwise uncertainty, most often on pairs built by synthetically degrading high-field images. Prior work acknowledges that these models hallucinate and that the problem is ill posed, but to our knowledge no study measures how much information about the individual subject the real low-field scan actually contains. We measure it. Using paired 64 mT and 3T scans of the same subjects from three public datasets, and a measurement protocol validated on tests whose correct answer is known in advance, we find that, judged over the whole brain, real 64 mT scans carry structure specific to the individual only down to approximately 3 to 4 mm half-pitch in plane, and coarser still through plane. Standard synthetic degradations preserve subject information roughly 1 mm beyond this ceiling, so models trained and benchmarked on synthetic pairs are evaluated on information that real scanners never record. We then test trained diffusion models and a publicly released external model on real paired acquisitions; 24 trained runs of five architectures (GAN, diffusion, and transformer families) give the coverage of the audit. On every subject where faithfulness can be measured, fine output detail is no more correlated with the subject's own 3T scan than with a stranger's, while sample-variance uncertainty does not distinguish fabricated structure from reconstruction difficulty. Because PSNR and SSIM score resemblance to a reference rather than whether detail belongs to the subject, a benchmark scored by them cannot tell recovery from fabrication. Code for the measurement protocol will be released so that recoverability claims can be tested for newer models.

Abstract: We benchmarked vision-language models (VLMs) on the decisions annotators take when inspecting electron microscopy images in connectomics: synapse detection (presence and polarity) and proofreading (split errors and merge errors). For synapse detection, we evaluated 19 open and 2 closed models across various architectures and sizes under zero-shot, four-shot in-context learning and LoRA settings, against specialist models, on datasets constructed by us using public resources. For proofreading, we evaluated 3 open and 2 closed models on the ConnectomeBench2 dataset, with cross-species transfer from fly and mouse to human and zebrafish. Most models were at chance zero-shot; a few examples helped mainly the closed and largest open ones. LoRA on a few thousand labels brought open models level with specialist models. When evaluated on unseen species, the best adapted VLMs outperformed specialist models trained on the same data in identifying merge errors. The project will be publicly available upon acceptance.

Abstract: Whole slide image classification is a fundamental task in computational pathology, where patch representation quality directly affects downstream aggregation and slide-level discriminability. Pathology foundation models are widely adopted as frozen feature extractors for WSI classification; however, their fixed encoders may produce representations insufficiently adapted to target-specific tissue patterns and discriminative cues. Fine-tuning can improve target adaptation, but introduces a trade-off between pathology-specific representation capacity and adaptation efficiency, particularly in data-scarce settings. To address this, we propose a pathology role-guided mixture-of-experts feed-forward network (MoE-FFN) framework for efficient encoder-level representation learning. We design a two-stage training paradigm to establish and adapt pathology-aware expert specialization. In source-domain expert initialization, pathology-specific priors are distilled from a frozen Virchow2 teacher into a lightweight DINOv2-small student, while role prototypes serve as weak pathological anchors to encourage distinct expert functions. MoE-FFN blocks are introduced into selected high-level transformer layers to provide transformation diversity for heterogeneous pathological patterns. In target-domain adaptation, the initialized experts are refined through asymmetric prototype-guided optimization, enhancing task-relevant positive evidence and separating confusable hard negatives. The resulting encoder extracts offline patch representations that can be directly integrated with standard MIL aggregators. Experiments on the public BRACS dataset and a private PAROTID WSI dataset across five representative backbones demonstrate consistent improvements over the strongest baseline.

Abstract: Vision-language (VL) pretraining using paired chest X-ray (CXR) images and radiology reports has shown strong potential for medical image understanding. However, existing methods often remain dependent on task-specific finetuning because radiology reports are lengthy, clinically dense, and difficult to align with simple zero-shot prompts. Recent sentence-level approaches partially address this limitation using clinical phrases extracted by large language models (LLMs), but they largely overlook the intrinsic characteristics of radiology discourse. In particular, limited positive-pair diversity constrains further gains, while clinically equivalent sentences frequently recur across patients, creating false negatives in contrastive learning. To address these issues, we propose SentZero, an enhanced sentence-centric VL pretraining framework for zero-shot, multi-task CXR analysis. SentZero introduces LLM-based abstract-level sentence structuring and mapping to expand positive-pair diversity, together with an additional loss term to mitigate false negatives. We further introduce sentence-conditioned residual modulation of visual embeddings, enabling visual features to adapt to the semantic characteristics of each input sentence. Across diverse downstream tasks and datasets, SentZero improves zero-shot generalization and outperforms prior multi-task zero-shot methods.

Abstract: Conventional reflectance photoplethysmography (PPG) typically reduces tissue optical responses to one or a few detector channels. Matrix Pinhole Image Sensing (MAPIS) instead simultaneously samples multiple aperture-dependent optical signals. We analyzed 44 recordings of 30 seconds each from a single MAPIS device to characterize the spatial relationships among DC intensity, pulsatile AC, perfusion index (PI), and temporal coherence across Red and infrared channels. AC increased sublinearly with DC at both wavelengths, resulting in higher PI toward lower-DC apertures, consistent with a first-order relative path-sensitivity interpretation. A second counterintuitive spatial trend was observed in temporal coherence: lower-DC and lower-AC apertures exhibited higher autocorrelation and greater cardiac-periodic spectral concentration. IR signals also showed consistently higher temporal coherence than corresponding Red signals. These observations demonstrate that multi-aperture PPG resolves reproducible spatial relationships among optical intensity, fractional pulsatile sensitivity, and waveform coherence that are largely averaged together in conventional single-channel PPG. The present study establishes within-device relationships and motivates controlled studies of the underlying photon-path mechanisms.

Abstract: Weakly-supervised thoracic disease detection in chest X-rays (CXR) is challenging due to subtle appearances and complex anatomical overlap, motivating anatomy-aware modeling for improved localization. However, prior anatomy-aware methods typically rely on coarse region proxies or static spatial priors, which may restrict dynamic instance discovery and limit precise localization of small abnormalities. We propose Anatomy-Structured Hierarchical Multiple Instance Learning (ASH-MIL), a framework that introduces parallel anatomy-structured observation branches (cardiac, pulmonary, and agnostic) combined with hierarchical MIL aggregation. Anatomical priors are injected as soft spatial biases into decoder cross-attention, enabling anatomically grounded evidence maps without disease bounding-box supervision. Instance localization is derived directly from MIL-weighted cross-attention maps without bounding box supervision. Experiments on CXR8 and cross-domain MIMIC-CXR held-out sets demonstrate consistent improvements over prior weakly-supervised and anatomy-aware approaches, particularly under stricter localization criteria. Our code is available at https://github.com/jn-kim/ash-mil.

Abstract: In recent years, bilevel optimization has been widely used in a variety of machine learning tasks. However, prior bilevel optimization algorithms generally require the computation of second-order information, which limits their practical scalability. Only recently has a first-order paradigm for bilevel optimization been established, attaining near-optimal theoretical guarantees for solving bilevel optimization problems. In this paper, we propose ABO-Med, a scalable instantiation of this paradigm for few-shot learning, by incorporating it into the model-agnostic meta-learning (MAML) framework and tailoring it to medical image classification. We also introduce Medical Adaptive RandomAugment (MedRAug), a modality-aware augmentation strategy designed for medical images. Theoretically, ABO-Med establishes the optimality of MAML-type meta-learning approaches. Empirically, ABO-Med outperforms prior baselines on several public medical datasets, with gains of 1.99% to 18.76%, while MedRAug further improves the average accuracy by 2.20% to 6.34%. Additional cross-domain experiments, augmentation ablation studies, backbone ablation studies, and training efficiency analysis further validate the effectiveness and efficiency of the proposed method.

Abstract: Endoscopic scene reconstruction requires modeling tissue motion and temporal appearance while recovering fine surface detail. Deformable Gaussian models provide explicit trajectories, but their fixed colour coefficients lack a dedicated temporal representation for photometric changes. We propose Endo-TSR, which augments deformable Gaussian splatting with bounded Fourier colour residuals and independent translation residuals on shared temporal frequencies. The colour residuals capture local appearance changes, while a Matérn spectral prior regularises motion corrections. Multi-scale Laplacian supervision guides tissue-detail recovery during joint image fitting. Extensive experiments on the EndoNeRF and StereoMIS datasets demonstrate state-of-the-art rendering quality, with the highest PSNR across all evaluated sequences. Ablation studies show that temporal appearance yields the largest PSNR gain among the tested component additions, while appearance and detail supervision jointly improve rendering with fixed Gaussian counts.

Abstract: Plug-and-Play (PnP) methods solve imaging inverse problems by incorporating deep denoisers into iterative optimization algorithms. Although practical implementations often decrease the denoiser noise level $σ$ along iterations, most existing convergence analyses assume a fixed denoiser. In this work, we establish convergence guarantees for a broad family of Plug-and-Play algorithms with annealed noise level, spanning deterministic methods (RED--GD and PnP--PGD) and stochastic methods (SNORE, equivariant RED, and a variant of PnP--Flow). For each method, we identify an explicit, nonconvex objective associated with the terminal denoising level and prove asymptotic stationarity of the iterates with respect to this objective. Our analysis does not prescribe any decay rate for the noise schedule, and our assumptions cover both learned gradient-step denoisers and exact MMSE denoisers. Overall, our theoretical results bridge the gap between existing PnP convergence theory and the decreasing-denoising practices used by state-of-the-art image restoration methods. We empirically demonstrate the benefits of such schedules and illustrate the predicted convergence behavior on several imaging inverse problems, including inpainting, super-resolution, demosaicing and tomography.

Abstract: Vision-language models (VLMs) have shown increasing potential for medical image understanding, yet their capabilities in ophthalmic imaging remain insufficiently characterized. Existing ophthalmic datasets are typically designed for individual diseases or specialized tasks, making it difficult to systematically evaluate whether VLMs can move beyond disease recognition toward comparative reasoning and fine-grained spatial grounding. We introduce EyeVQA, a unified visual question answering benchmark for comprehensive evaluation of ophthalmic VLMs. EyeVQA is constructed from 21 available ophthalmic datasets and contains 20,000 question-answer pairs spanning six disease groups and seven question types: Single-Choice, Multi-Select, Variable-Select, True-False, Ranking, Point Location, and Bounding Box. Gold answers are deterministically derived from source-provided diagnoses, severity grades, clinical findings, segmentation masks, bounding boxes, and anatomical landmarks, enabling reproducible evaluation without relying on model-generated annotations. Notably, 44.5% of the questions require reasoning across multiple images, extending evaluation beyond conventional single-image medical VQA. We benchmark fourteen representative general-purpose, scientific, and medically specialized VLMs under a unified zero-shot protocol. The best-performing model only achieves an overall score of 62.8, while substantial gaps remain in spatial grounding and cross-task generalization. These results highlight the limitations of current VLMs in comprehensive ophthalmic visual understanding and establish EyeVQA as a diagnostic benchmark for developing more reliable and spatially grounded ophthalmic multimodal models. The project page is available at https://github.com/PKUTHM/EyeVQA.

Abstract: Pathology vision-language models (VLMs) are conventionally evaluated by accuracy, but accuracy alone does not measure evidence use: it may conflate dataset contamination, prior knowledge, and image evidence. In a motivating study of lymph-node metastasis prediction, we found that most public pathology VLMs showed minimal differences when changing from feeding the models with whole-slide images, an annotated lesion, or no image at all. To better understand the specific features leveraged by these models, this paper presents two contributions aimed at disentangling these factors. First, we present CleanSlide, a TCGA-based VQA benchmark designed to eliminate image- and question-side contamination. It contains 149K audited multiple-choice questions over 9,985 slides, with patient- and tissue-source-disjoint splits. Every question is audited for option shortcuts, stem leakage, cross-split duplication, and blind solvability. Second, we propose Pair-DPO, a preference loss over counterfactual slide pairs from the same question and source. By controlling for shared confounding factors, Pair-DPO cancels out the question-attributable signal and leaves image evidence as the source of preference. Specifically, each pair consists of two real slides with opposite, verified findings, introducing neither editing artifacts nor unverified labels for diffuse or graded features such as invasion, necrosis, and tumor grade. Experiments show that our method gains 15.29% from image evidence on the CleanSlide, compared with 2.81% for the best published model. On the external CPTAC and BCNB cohorts, our method achieves accuracies of 57.6% and 59.0%, outperforming all other evaluated models by 9.7% and 3.4%, respectively. We will release the benchmark and code.

Abstract: The classical method of Kaczmarz, introduced in 1937, is a textbook iterative method for solving linear systems $A x = b.$ Despite its widespread use, particularly in the context of solving inverse problems where it is commonly included in software packages within Matlab, Python, and Julia, the precise characterization of convergence has long been deemed difficult to obtain. While different bounds on convergence rates have been established, they are largely unsatisfying as they cannot explain the classical, cyclic-update method's efficient convergence in practice. In this work, we obtain a tight characterization of convergence of the classical Kaczmarz method, establishing both linear and sublinear convergence bounds. The worst-case tight (i.e., exactly attained by some instances in the considered family) bounds are expressed in terms of a fixed matrix that depends only on $A,$ but are not fully interpretable in terms of the matrix spectrum and row correlations, which had been observed to have an impact on convergence. We thus provide relaxations of these bounds that are fully expressible in terms of matrix row norms, row correlations, rank, and extremal positive singular values. The provided relaxed bounds explain one-cycle convergence in special cases where the matrix rows are all either parallel or orthogonal to each other. We further argue that the dependence on different parameters appearing in the bounds is necessary and within a small constant factor of the best attainable in the worst case. Finally, our bounds explain why the classical cyclic update is faster than the randomized one when matrix rows are weakly correlated, which is often observed in inverse problems where the cyclic method is used.

Abstract: Native-latent guidance is a recent paradigm for solving inverse problems with latent diffusion models. It replaces repeated evaluations of the image-space forward model, each requiring a decoder pass, with efficient guidance computed using a learned latent-space surrogate. However, existing methods apply guidance uniformly across latent dimensions, ignoring that measurements are informative only along certain directions and that the reliability of model predictions varies across inputs and timesteps. We propose ANaLOG, a framework for efficient uncertainty-aware guidance with pretrained latent diffusion models. ANaLOG models uncertainty by learning an anisotropic, input- and time-dependent covariance that is integrated into the guidance mechanism to emphasize reliable directions and downweight uncertain ones. We theoretically analyze this framework in a linear model setting and prove that anisotropic, uncertainty-aware weighting is necessary for correct sampling, whereas isotropic guidance induces sampling errors. Experiments across five challenging inverse problems show that ANaLOG improves perceptual reconstruction quality over existing methods while preserving efficiency.

Abstract: Ordinal acne severity grading requires distinguishing visually similar neighboring grades while jointly weighing holistic facial appearance and localized lesion burden - evidence that most existing approaches collapse into a single opaque representation. We introduce CG-HAF, a global-local fusion framework that instead keeps this evidence explicit: averaged holistic severity probabilities from independently trained classifiers are combined with structured lesion-burden descriptors from an object detector (lesion count, detection confidence, lesion area) into a compact representation, from which a lightweight, interpretable classifier produces the final grade. On a widely used benchmark, this fusion yields a clear, statistically supported improvement over global-evidence-only baselines, with the largest gains on the most severe cases. Testing on an independent dataset with a different grading standard shows that strong within-dataset performance does not transfer automatically, and a follow-up diagnostic attributes much of this gap to mismatched grading criteria rather than detection failure alone. These findings support interpretable global-local fusion as an effective strategy for ordinal acne grading while highlighting criterion alignment as key to cross-dataset portability, with a further illustration of how the resulting severity signal can support transparent, non-diagnostic decision-making in skincare applications.

Abstract: Recent fMRI foundation models differ substantially in the spatial scale at which they represent brain activity. ROI- and connectivity-based models are efficient but coarse, whereas voxel-level models preserve fine-grained spatial structure but require specialized 3D/4D architectures and costly fMRI-specific pretraining. We ask how effectively an image-pretrained encoder can reuse the spatial organization of cortical activity. Motivated by evidence that macroscale brain activity is strongly constrained by brain geometry, we introduce FlatClip, a frozen-encoder surface-level baseline that renders cortical activity as geometry-aware flatmap sequences and reuses a frozen SigLIP2 image encoder with only a lightweight downstream probe. Across resting-state benchmarks, FlatClip serves as a competitive middle-ground representation, outperforming ROI-level baselines on HCP and ADNI tasks while remaining weaker on PPMI and below the strongest voxel-level models overall. On visual-fMRI decoding, restricting the input to visual or NSD-provided task-active cortex improves performance, highlighting the value of task-relevant cortical coverage. Spatial perturbation controls reduce the predictive performance of flatmap features under both retrained and fixed readouts, and anatomy-linked arrangements consistently outperform vertex permutations across three colormaps. Together, these results position surface-level flatmap sequences as a practical middle-ground baseline between ROI and voxel models, and support the utility of anatomy-linked spatial organization for reusing image-pretrained features. Code is available at https://github.com/OneMore1/FlatClip.

Abstract: Split Gibbs sampling enables diffusion posterior inference for general nonlinear inverse problems by decoupling prior and likelihood computations, allowing a pretrained diffusion prior to be reused across measurement models. However, its likelihood update often relies on iterative MCMC, which can hinder parallelization, require algorithm-specific tuning, and incur substantial computational cost. In this work, we propose a learning-based framework to replace this MCMC step by reformulating both Gibbs updates as Gaussian denoising problems and implementing them through ODE diffusion. The prior step reuses a pretrained denoiser, while the likelihood denoiser exploits known likelihood structure through a lightweight deep-unfolded network. Experiments on nonlinear phase retrieval demonstrate the effectiveness of the proposed method as an alternative to MCMC-based split Gibbs at lower likelihood-update cost.

Abstract: Survival research in pancreatic ductal adenocarcinoma (PDAC) is limited by the scarcity of datasets linking whole-slide histology with clinical, molecular, and long-term outcome data. We present a retrospective single-centre cohort of 302 patients who underwent PDAC resection at University Medical Center Gottingen. The dataset comprises 446 H&E whole-slide images, clinicopathological variables, targeted sequencing data for 154 patients, and overall-survival outcomes. During follow-up, 253 patients died, and the median follow-up was 76 months. To establish initial reference values, we evaluated fourteen survival-prediction configurations using identical five-repetition Monte Carlo cross-validation partitions. Ridge Cox regression using numeric clinicopathological variables achieved a mean concordance of $0.649 \pm 0.042$ and $0.652 \pm 0.046$ after adding KRAS and TP53 mutation status. The image-only attention model achieved $0.603 \pm 0.030$, while multimodal fusion achieved $0.619 \pm 0.025$, the highest concordance among the neural models. These results establish promising initial benchmarks for future research using this pancreas-specific multimodal dataset, paving the way for external validation.

Abstract: Supervised synthetic CT (sCT) generation is commonly trained and evaluated as voxel-wise regression against registered reference CT images. In practice, MRI-CT and CBCT-CT pairs are aligned through registration procedures that leave residual misalignments. These residuals are not independent intensity noise but spatially coherent geometric discrepancies that act as structured label noise. We investigate how this registration-induced bias affects supervised MRI-to-CT and CBCT-to-CT synthesis on 1,784 paired patients covering five anatomical regions. Voxel-wise scores strongly depend on the consistency between the registration used to build the training targets and the one used for evaluation: models score best when both conventions match, showing that networks partly learn the geometric convention of the registration pipeline and that standard metrics reward it. Training on more anatomically consistent registrations reduces prediction variability and improves out-of-distribution robustness, and CT-only controls show that registration alone produces metric errors in the range of top challenge submissions. To mitigate the limits of voxel-wise supervision, we introduce a perceptual loss computed in the feature space of a pretrained Segment Anything encoder. Compared with MAE-only and VGG-based objectives, it improves downstream segmentation and yields sharper, more structurally coherent sCT. Perceptual and voxel-wise metrics disagree under imperfect alignment and agree when the evaluation geometry is reliable. These results identify registration-induced bias as a central confounder in supervised sCT generation and argue for complementing voxel-wise agreement with anatomy-oriented evaluation criteria.

Abstract: We investigate the expected reconstruction risk of trigonometric polynomial models under different sampling schemes. Through numerical experiments, we observe that when the sampling nodes $\{t_l\}_{l=1}^m$ are i.i.d. random variables uniformly distributed over $[0,1)$, the associated structured random matrix $\pmb{A} \in \mathbb{C}^{m \times N}$ with $A_{l,k} = e^{2π\mathrm{i} kt_l}, k \in Γ= \{-q, \dots, q\}, N = 2q+1$ frequently becomes nearly singular or severely ill-conditioned. As a consequence, the expected reconstruction risk exhibits divergent behavior. In contrast, when the sampling nodes $t_l$ are either equidistant points or small random perturbations of an equidistant grid, the expected reconstruction risk undergoes a sharp phase transition at the interpolation threshold $m=N$. To better understand the underlying mechanisms behind these different phenomena, we characterize the expected reconstruction risk through the spectral quantity $\sum_{i=1}^{r} \frac{1}{σ_i^2(\pmb{A})}$, where $σ_i(\pmb{A})$ denotes the singular values of the sampling matrix. Based on this spectral representation, we theoretically prove that the expected reconstruction risk diverges under uniformly distributed random sampling. Furthermore, we derive an explicit formula for the expected reconstruction risk in the equidistant sampling case and establish upper and lower bounds for the expected reconstruction risk under jittered sampling.

Abstract: Textual descriptions can reduce ambiguity in medical image segmentation by specifying the finding and location to be delineated. Existing text-guided methods mainly improve where image and language features interact but generally retain a single learned update pathway across all image-text pairs. We propose MRSeg, a parameter-efficient framework that uses each image-text pair to route the adaptation of visual and textual features before dense prediction. Frozen ConvNeXt-Tiny and PubMedBERT encoders provide multiscale visual features and clinical text tokens. A joint router uses the deepest visual feature and pooled text to predict a sparse mixture over low-rank adapter bases. The resulting route is shared across separate adapter banks for two visual scales and text, coordinating their adaptation while keeping the feature-specific parameters separate. Region Bridge uses text-derived queries to aggregate dense visual tokens into latent regions, refines these regions through self-attention and text cross-attention, and redistributes the refined information back to the feature maps. Finally, a multiscale decoder combines refined semantic features with shallow image evidence. On QaTa-COV19 and MosMedData+, MRSeg achieves 90.90/83.32 and 81.53/68.82 Dice/mIoU, respectively, with 7.11M trainable parameters and 7.60 GFLOPs. Code: https://github.com/maklachur/MRSeg.

Abstract: While various multimodal methods combining imaging and tabular data for Alzheimer's disease (AD) diagnosis were proposed, they are often limited in generalization across cohorts. In-context learning (ICL) has demonstrated excellent generalization performances and high flexibility in foundational tabular models such as TabPFN. To extend TabPFN's ICL to multimodal AD analysis, the main obstacle is that TabPFN is meta-trained on synthetic tabular priors that do not naturally match the statistical structure of image-derived features. We propose M$^2$PFN, an end-to-end framework that turns this tabular foundation model into a multimodal AD predictor. M$^2$PFN (i) performs differentiable inference through TabPFN's transformer, back-propagating task gradients into 3D-MRI and tabular encoders; (ii) aligns the two modalities into a shared subspace, via disentanglement and a contrastive objective, matched to the ICL engine's prior; and (iii) folds in a frozen tabular-only prediction through a learnable gated shortcut. Because the ICL engine stays frozen, its in-context mechanism is preserved for test-time generalization, while end-to-end training shapes the encoders into features it can exploit. On ADNI ($n=2240$, three-class CN/MCI/AD), M$^2$PFN attains $65.55\%$ macro-F1 and $82.21\%$ macro-AUC, surpassing a comprehensive set of unimodal and multimodal baselines. By swapping only the head for a TabPFN regressor, the same architecture regresses baseline MMSE on a $1250$-subject sub-cohort to test MAE $1.743$, outperforming every multimodal baseline. On two external cohorts (OASIS-3 and SCAN) with no retraining, M$^2$PFN achieves the best AUC and the lowest MMSE MAE across all baselines, and transfers even when the cognitive instrument changes.

Abstract: Pathology foundation models (PFMs) have transformed computational pathology through powerful representation learning from histopathological images. PFMs provide rich, discriminative representations for whole slide image (WSI) analysis, enabling tasks such as slide-level classification under multiple instance learning (MIL). However, these representations may also encode non-biological signals associated with acquisition centers, potentially introducing spurious shortcuts into downstream predictions. In this work, we evaluate center-associated robustness in WSI classification using a controlled training setting with increasing class-center correlations quantified by Cramér's V. We benchmark six PFMs across four datasets and two MIL aggregators, while evaluating ComBat as a robustification strategy. We further introduce the Area Under the Cramér's V Curve (AUCC) to jointly capture absolute classification performance and its degradation as spurious correlation increases. Results show that center-related information encoded by PFMs propagates to WSI-level predictions, with robustness depending on both the PFM representation and MIL aggregation strategy. Additionally, ComBat harmonization does not provide consistent robustness gains across datasets.

Abstract: Breast image classification requires local detail and global tissue context, yet these cues can weaken as representations deepen. We present M3D-Net, a mammography encoder that hierarchically coordinates multi-scale coordinate attention, bounded dynamic feature reuse, and differential attention through resolution-aware operator placement. Within-stage retrieval preserves access to earlier features, coordinate-aware aggregation integrates local and global context, and differential attention operates at coarse resolutions. We evaluate image-only classification on AISSLab mammography and an adapted image--clinical model on BrEaST ultrasound. Against EdgeNeXt, RepViT, and TransXNet, the proposed implementations achieve the highest recorded validation accuracy and late-training accuracy, with the lowest endpoint cross-entropy loss. Validation accuracies reach 97.78\% and 80.39\%, respectively. These results support further evaluation of hierarchical coordination across breast imaging settings; repeated-seed, component-controlled, and independent evaluations remain necessary.

Abstract: The annotation used to select a segmentation threshold is part of the evaluation protocol, yet its effect is easily conflated with model quality. We examine this choice for retinal vessel segmentation using all 28 CHASE DB1 images and both human annotations. A fixed seven-fold protocol keeps both eyes of each of the 14 subjects together. Random forests and Extra Trees are fitted against observer 1 with three random seeds, yielding 42 fits. Five threshold policies share identical score maps: fixed 0.50, observer-1 tuning, observer-2 tuning, mean-observer tuning, and maximin tuning of the per-image lower observer Dice. For random forests, maximin changes the threshold in 19 of 21 fits, but worst-observer Dice decreases from 70.53 percent to 70.45 percent. The paired difference is -0.073 percentage points, with a conditional subject-bootstrap 95 percent interval of [-0.384, 0.238]. Extra Trees shows the same direction. Identical observer-1-tuned random-forest masks score 73.66 percent against observer 1 and 71.06 percent against observer 2. The results support explicit reporting of both the threshold-selection reference and evaluation reference; they do not support an accuracy benefit from maximin tuning in this cohort. All splits, raw predictions, metrics and code are supplied. AI assistance is disclosed.

Abstract: Latent diffusion models now dominate medical image generation, and every such pipeline rests on a \emph{tokenizer} that compresses images into the latent codes for image generation to operate on. Thereby, the tokenizer choice bounds every downstream task from reconstruction fidelity and generation quality to the representations available for downstream analysis. Yet, medical imaging pipelines routinely utilize tokenizers from natural imaging on the hypothesis that their behavior carries over. However, this is an assumption never tested in the medical imaging regime, where datasets are orders of magnitude smaller and images exhibit far lower inter-sample variance. We present a systematic evaluation of medical image tokenizers evaluating thirty configurations across ten model families on twelve datasets at three compression factors, spanning reconstruction, generation, latent geometry, downstream classification, and memorization. We find that (1) performance on image reconstruction and generation strongly correlate, unlike prior reports on natural images; (2) modern tokenizers use nearly all of their codebook entries, but still leave most of the latent space unused; (3) training-set memorization is mild and is further suppressed by stronger latent space compression; and (4) discrete quantization can largely preserve downstream classification, with lookup-free schemes being the main exception.

Abstract: Confocal Laser Endomicroscopy (CLE) provides real-time, cellular-resolution optical biopsy but has a narrow field of view, which image mosaicing can extend to provide anatomical context. Because of line-by-line acquisition, probe motion, and probe-tissue interaction, frame alignment generally requires a non-linear transformation whose accuracy is difficult to quantify: flexible transformation models can fit intensity features and noise, so appearance-based metrics such as Normalized Cross-Correlation (NCC) can improve without a genuine gain in geometric accuracy. We therefore establish a dataset of 132 frame pairs across fourteen pCLE sequences from 4 patients with manually annotated landmark correspondences, so that Target Registration Error (TRE) can serve as a geometrically grounded complement to NCC. We assess the effect of progressively increasing the transformation model's degrees of freedom, from translation to Thin Plate Spline (TPS), and of six feature-matching backends spanning classical (Shi-Tomasi, Lucas-Kanade) and learned (SuperPoint, SuperGlue, LightGlue, LoFTR, RoMa) approaches. Translation and rigid models prove insufficient under tissue deformation, while TPS with random sampling achieves the strongest landmark-derived alignment of the evaluated configurations; among the learned matchers, used without fine-tuning, only RoMa offers a robust, if modest, advantage over other methods. At the sequence level, pairwise registration quality proved an unreliable predictor of final mosaic quality, so mosaic quality must be evaluated directly rather than inferred from pairwise metrics.

Abstract: Monocular colonoscopic 3D reconstruction is important for surgical robotic colonoscopy, but remains challenging due to weak texture, specular reflections, limited view overlap, and non-rigid tissue motion. Conventional multi-view 3D reconstruction methods rely on stable correspondences and approximate rigidity, which are often violated in colonoscopy. Existing endoscopic methods often rely on domain-specific supervision, whereas there are not enough in-vivo labeled data available to adapt geometry foundation models to clinical colonoscopy. We present Colon3R, a cross-domain semi-supervised framework built on pretrained VGGT that transfers coupled camera, depth, and pointmap geometry from labeled phantom and simulated data to unlabeled in-vivo colonoscopy without requiring target-domain geometric annotations. Unlike source-only fine-tuning, which learns only from phantom and simulated data, Colon3R directly exploits unlabeled in-vivo video through teacher-derived cross-view supervision. Our proposed hierarchical quasi-rigid reliability selects reliable supervision at the sequence, directed-pair, and pixel levels, while source-preserving adaptation retains the learned coupled geometry during target-domain adaptation. Extensive experiments demonstrate that our method achieves superior overall performance over state-of-the-art approaches in depth, pointmap, and camera pose estimation. Qualitative comparisons on real in-vivo colonoscopy further show substantially more complete and geometrically consistent reconstructions than competing methods under clinical domain shift. The code will be public available after the paper is accepted.

Abstract: Automated grading of conjunctival photographs could reduce the cost and variability of trachoma prevalence surveys, but the relative value of modern pretrained visual representations, lightweight feature adaptation, and training-objective design has not been established under a common protocol. This study presents a controlled evaluation for binary classification of Trachomatous Inflammation-Follicular (TF) versus Normal using 1,546 images from the public UCSF/Lietman collection. Images are processed using the OPTED pipeline for zero-shot tarsal-conjunctiva segmentation, alignment, cropping, and standardization. We first compare six pretrained backbones using a common classification pipeline and then evaluate four lightweight adaptation mechanisms on DINOv2 ViT-B/14. Under stratified five-fold cross-validation, DINOv2 with Efficient Channel Attention (ECA) and focal-plus-center loss achieved 91.66 +/- 0.97% accuracy, 90.69 +/- 1.10% macro-F1, and 96.06 +/- 0.71% AUC. ECA introduces only five learnable parameters while matching the performance of substantially larger alternatives. Objective ablation further showed that ECA did not consistently improve plain DINOv2 across loss functions; the lowest-variance 91.66% accuracy was obtained with cross-entropy plus center loss. Overall, the fine-tuned DINOv2 representation provided most of the predictive performance, while ECA offered a highly parameter-efficient refinement whose effect depended on the training objective. The resulting workflow provides a reproducible benchmark for active trachoma image classification.

Abstract: Referring surgical video instrument segmentation (RSVIS) aims at segmenting the instrument in a surgical video, given a textual description. Despite recent progress, current models are trained and assessed on relatively small-scale benchmarks, hindering the development of more general RSVIS. In addition, existing benchmarks support only the single-target expression that refers to one instrument in the video, while overlooking multi-target and no-target referring expressions, restricting the applicability of RSVIS in practical scenarios. Addressing these issues, we propose LD-RSVIS, a new benchmark aiming to facilitate more robust and general RSVIS. Specifically, LD-RSVIS consists of 3,536 surgical videos with 1.09 million frames and covers a broad set of 30 instrument classes from 25 various procedures. By including abundant videos and classes, LD-RSVIS could benefit large-scale training and evaluation of more general RSVIS methods. Besides, unlike existing datasets, LD-RSVIS offers diverse referring settings, including no-target, single-target, and multi-target expressions, which enables the development of more practical RSVIS models in real applications. In order to ensure high-quality annotations, all videos in LD-RSVIS are manually labeled with multiple rounds of inspection and refinement. To our knowledge, LD-RSVIS is the largest and most diverse benchmark for RSVIS. To analyze LD-RSVIS and to provide comparison for future research, we evaluate 12 representative methods, and the results reveal that more efforts are required for improvements. To encourage future research, we present a simple yet effective RSVIS method, dubbed Cascade-RSVIS, that first mines target-specific cues using the complementary multi-cue text information and then employs such cues and textual information for segmentation, achieving promising performance. Our benchmark and code will be released.

Abstract: Multimodal survival models can combine complementary prognostic information from whole-slide images and genomic profiles, but effective fusion remains challenging amid external cohort shift and computational complexity. To address these challenges, we propose MIST, multimodal survival prediction with genomic-guided histology attention. MIST represents genomic features as tokens and allows them to query compact foundation-model-derived histology context tokens before survival prediction. This design enriches molecular information with histology context rather than merging separately encoded modalities only at the final stage. Training combines discrete-time survival prediction with genomic feature masking, WSI dropout, and paired WSI-genomics contrastive alignment. Across four external evaluations in colon, renal, lung, and glioblastoma cohorts, MIST improves external C-index over standard fusion baselines in the primary comparisons. These results support genomic-guided histology attention as a compact and effective strategy for multimodal oncology outcome prediction. Our code is available at https://github.com/samiyavuuz/MIST .

Abstract: Hereditary polyposis syndromes can be precursor lesions to colorectal cancer and are associated with a broad spectrum of extracolonic tumors. Early identification and accurate classification of these syndromes are essential for timely diagnosis, individualized patient management, and targeted surveillance strategies for affected families. However, public endoscopic datasets are largely organized around the individual sporadic polyp, and none links the polyposis phenotype to histopathology and germline findings at the patient level. Here, we present ERCPMP-Gx, an endoscopic, histopathological, and genomic dataset developed to support the application of artificial intelligence (AI) in the recognition, characterization, and classification of colorectal polyposis. Most procedures were performed using the Olympus EVIS X1 system with white-light endoscopy (WLE), narrow-band imaging (NBI), magnifying NBI (M-NBI), and NBI with near focus modes, yielding 160 images and accompanying video clips. Approximately eighty percent of cases represent clinically and/or genetically confirmed hereditary polyposis syndromes (PG), including familial adenomatous polyposis (FAP), Peutz-Jeghers syndrome (PJS), juvenile polyposis syndrome (JPS), and ganglioneuroma syndrome (GNS), while the remaining twenty percent comprise non-hereditary polyps and polyp-mimicking lesions with overlapping morphological features (Non-PG), included to support differential classification. Each released record is linked, where available, to standardized endoscopic annotations, representative histopathology, and clinically reported germline findings, forming an AI-ready, patient-level annotation framework. The dataset is publicly accessible at Mendeley (https://doi.org/10.17632/nzyfc544bx.2). For the latest updates and further information, readers are referred to the DataBioX website: https://databiox.com.

Abstract: We train neural networks on synthesized frames to approach the optimum Bayes estimator for dense emitter localization. The result justifies the future work on training neural networks to achieve high-throughput large-FOV super spatiotemporal resolution SMLM.

Abstract: Medical image segmentation supports quantitative clinical analysis and computer-aided diagnosis. Recent methods for medical image segmentation have improved both local feature representation and volumetric context modeling. However, existing methods still strug- gle to efficiently model cross-slice relations in anisotropic volumet- ric images, limiting segmentation consistency and accuracy. This pa- per proposes G^2RA-Net, a medical image segmentation framework that combines graph-based cross-slice relation modeling with atten- tion gating. Graph-Based Slice Relationship Modeling (GSRM) cap- tures anatomical dependencies across consecutive slices by repre- senting each slice as a graph node and propagating semantic con- text through graph message passing. The Cross-Slice Attention Gate (CSAG) then selects relevant neighboring context and emphasizes target anatomical regions through attention-guided feature modula- tion. Experiments on brain MRI and abdominal CT datasets demon- strate that G^2RA-Net outperforms representative methods in seg- mentation accuracy and boundary quality. Ablation studies further validate the proposed design.

Abstract: Gromov--Wasserstein optimal transport (GW-OT) extends classical optimal transport by introducing structure-aware transport cost. This is particularly relevant for spatial transcriptomics, where dynamical reconstruction should preserve tissue structure in addition to matching expression patterns. While static formulations have been widely used for such structure-aware alignment, a general dynamic formulation for reconstructing continuous trajectories is still missing. We introduce Travelling Pair Dynamical Alignment and Trajectory Estimation (TP-DATE), a theoretical and computational framework to generalize GW-OT dynamically in a simulation-free manner. We formulate a broad class of static and dynamic Quadratic-form OT (QOT) through path actions and prove the static dynamic equivalence. We further develop travelling-pair flow matching, which allows interacting conditional paths and marginalizes their interactions into a single vector field. On synthetic and real spatial transcriptomics data, TP-DATE better preserves spatial structure and improves continuous 3D dynamics reconstruction.

Abstract: Long-range infrared imaging frequently confronts dense target clusters whose diffraction-limited signatures merge into a single indistinguishable blob, concealing the number, sub-pixel positions, and radiant intensities of the underlying sources. While deep learning has advanced general object detection, resolving such Closely-Spaced Infrared Small Targets (CSIST) remains largely unexplored, owing to a systemic infrastructure void and a fundamental paradigm mismatch. The dominant formulation, which reduces unmixing to a blind, discrete sub-pixel separation, is inherently insufficient: without semantic guidance, the ill-posed inverse problem admits ambiguous solutions plagued by false and missed detections, while grid-based discretization locks predictions onto fixed lattice centers, chaining precision to prohibitively expensive grid refinement. We argue that CSIST unmixing should instead be informed and continuous. To ground this paradigm shift, we establish the first comprehensive open-source ecosystem for the field, comprising the large-scale CSIST-100K benchmark, a tailored metric suite, and the GrokCSO toolkit. Upon this foundation, we propose DISTA-Net++, which anchors a dynamic deep unfolding backbone with two synergistic mechanisms: a Count-Guided Prior that injects the global target count as an explicit semantic constraint to regularize the solution space, and a Continuous Coordinate Rectification that regresses off-grid offsets to decouple localization accuracy from grid resolution. Extensive experiments validate our paradigm: even under the most economical 3x division, DISTA-Net++ surpasses 7x-division state-of-the-art methods by 16.15% in CSO-mAP and 62.96% in count accuracy at merely one-sixth of their computation, demonstrating that unmixing precision need not be purchased with finer discretization. The complete ecosystem is available at https://github.com/GrokCV/GrokDet.

Abstract: Query-based segmentation methods have shown promising potential for surgical instrument segmentation and recognition, which is essential for scene understanding and downstream tasks in computer assisted surgery. However, most existing approaches predominantly rely on per-frame predictions and overlook cross-frame temporal priors as well as temporal-consistency constraints. This limitation often leads to unstable query representations and suboptimal category recognition. In this paper, we propose TEDi, a Temporal memory-Enhanced and Denoising transformer for surgical instrument segmentation that addresses these is sues through Memory Search Enhancement and Temporal Consistency Denoising. The former introduces a query-level memory bank and a memory search enhancement encoder to retrieve discriminative representations from historical frames, enriching current-frame features. The latter constructs a temporally consistent reference as a cross-frame semantic anchor to suppress temporally unstable predictions and promote semantic coherence across frames. Extensive experiments on two benchmark datasets, EndoVis 2017 and EndoVis 2018, demonstrate that TEDi consistently outperforms state-of-the-art methods, highlighting its potential to further advance computer-assisted surgery. Our code is available at github.com/argon-xixi/TEDi.

Abstract: Unpaired cross-modal distillation transfers grade structure from histopathology into a micro-ultrasound (micro-US) encoder by aligning a pooled needle-region embedding to a frozen histopathology teacher under grade-group correspondence alone. A single objective is thereby required to serve two distinct functions: rendering patch features discriminative of tissue state, and selecting which patches enter the pooled representation. We decouple them. Weak spatial supervision derived from percentage involvement, recorded routinely at biopsy, constrains the predicted proportion of malignant tissue within each core, acting on the encoder features independently of the alignment objective. The alignment loss then operates on features that differ across a core, and attention concentrates on a subset of patches rather than remaining near-uniform. On 7,166 biopsy cores from 811 patients across seven centers under patient-level 5-fold cross-validation, the method reaches 67.1 macro AUC and 68.5 csPCa AUC, against 61.2 and 52.8 for the existing unpaired alignment method and 63.1 and 62.6 for the strongest unimodal baselines. Ablation against existing attention regularizers designed to prevent attention-uniformity collapse shows that such regularizers do not substitute for label-derived supervision: they constrain the attention distribution, whereas the signal required acts on the features that attention reads.

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

Abstract: High-frequency ultrasound (HFUS) enables noninvasive visualization of superficial skin structures, but automated skin-layer analysis is limited by the scarcity of densely annotated data. Existing real HFUS datasets commonly provide annotations for superficial targets such as the epidermis and subepidermal low-echogenic band (SLEB), while dense labels for deeper structures such as dermis, subcutaneous tissue, fascia, and muscle are rarely available. We propose a physics-guided synthetic HFUS generation framework for skin layer segmentation. The framework constructs multilayer acoustic skin phantoms, assigns layer dependent acoustic properties, and uses k-Wave simulation to generate paired synthetic HFUS images, dense layer masks, and simulation metadata. To evaluate whether the generated data provide transferable supervision, we use it for downstream segmentation pretraining and fine-tune the models on real Mendeley HFUS data. Synthetic pretraining followed by real fine-tuning achieved real-domain performance comparable to real-only training and improved mean Dice/IoU in three of four evaluated trainable architectures. These results suggest that physics-guided synthetic HFUS images contain transferable anatomical and textural cues for real-domain skin layer segmentation, although further reduction of the synthetic-real appearance gap is needed to enable greater gains. The code and data are available at: https://github.com/Finn-02/synthetic-hfus-skin-layer-segmentation.

Abstract: Accurate identification of end-diastole (ED) and end-systole (ES) in echocardiography underpins the quantification of ventricular function, yet manual selection of these key frames is subjective and introduces clinically significant inter-operator variability. Recent self-supervised methods either prescribe strict periodic trajectories or learn an unconstrained low-dimensional motion subspace from reconstruction or registration objectives. The former offers interpretability but imposes restrictive assumptions on temporal progression, whereas the latter leaves cardiac phase implicit and ED/ES must be recovered through post-hoc geometric processing of the learned trajectory. We translate the physiological observation that cardiac phase is a one-dimensional signal into a prior by constraining the latent motion component to a single-parameter latent orbit, i.e., a global linear trajectory in latent space indexed by a bounded scalar phase variable. Mapping this variable through a sinusoidal nonlinearity yields an oscillatory motion signal with consistent temporal ordering, enabling direct identification of ED and ES from the learned phase signal. This inductive bias allows the model to capture an interpretable representation of the cardiac cycle, while maintaining flexibility to capture irregular heartbeats. Trained on EchoNet-Dynamic without annotations, our minimal single-parameter cardiac phase model learns an effective latent orbit, significantly improves upon the previous state of the art in ED localisation and matches it in ES localisation while using a more constrained representation and fewer training epochs. This demonstrates that a principled physiological inductive bias can match or exceed the performance of more complex representations. Code is available at: https://github.com/BonniciJ/OrbitalEcho/

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

Abstract: Segmenting bruises is a challenging task in medical imaging due to limited data and annotations, diffuse boundaries, and highly variable appearance. In this work, we propose BruNet, a segmentation framework that combines a ViT-based visual encoder (a self-supervised DINOv3 or a pretrained LingBot-Vision backbone) with a SAM-based mask decoder. BruNet is trained on the HAM10000 skin lesion dataset and evaluated on a separate bruise dataset without additional fine-tuning. Although a small number of prior studies have explored machine learning and computer vision for bruise analysis, existing work has primarily focused on detection, classification, or colour analysis rather than pixel-level localisation. To the best of our knowledge, this is the first study to address automatic bruise segmentation. Our results show that BruNet outperforms CNN-based models, state-of-the-art segmentation models, ChatGPT-4o/5-assisted SAM2 zero-shot baselines, and the medical-oriented MedSAM model, demonstrating strong cross-domain generalisation to bruise segmentation.

Abstract: Uncertainty estimation for medical vision--language models (VLMs) using conformal prediction has gained increasing attention due to its distribution-free coverage guarantees. However, standard conformal prediction relies on exchangeability between calibration and test data and typically requires a sufficiently large calibration set to obtain reliable coverage. These assumptions are difficult to satisfy in few-shot transfer settings, where only a small labeled support set is available to adapt a pretrained VLM to a new medical task, while an unlabeled query set is used for evaluation. Supervised fine-tuning on the support set changes the model parameters and consequently shifts the nonconformity score distribution, breaking exchangeability between calibration and query samples and leading to unreliable coverage under distribution shift. Existing transductive conformal adaptation methods often preserve validity by avoiding supervised updates. While this helps maintain conformal assumptions, it underutilizes the scarce labeled support data and limits task adaptation, which is the primary objective in few-shot learning. In this setting, conformal prediction should serve as an uncertainty estimation layer that supports the adapted model, rather than preventing adaptation itself. To this end, we propose AlignCP, a framework that reconciles supervised few-shot adaptation with conformal uncertainty estimation under non-exchangeability. AlignCP learns a reweighted calibration distribution that reduces the score-level discrepancy between the labeled support set and the unlabeled query set. By aligning the one-dimensional nonconformity score distributions, AlignCP aims to close the coverage gap induced by adaptation without requiring query labels.

Abstract: Trochlear dysplasia (TD) is an abnormality of the femoral trochlea associated with anterior knee pain and patellar instability. The sulcus angle (SA) is used to assess trochlear morphology, but it is typically measured on a single axial MR slice with no clear guidance on which to select, making it sensitive to slice selection and landmark placement. We propose an automatic framework for continuous SA profiling from super-resolved MR volumes. Clinically acquired axial, coronal, and sagittal MR scans are combined using implicit neural representations to reconstruct a high-resolution volume. SA measurements are computed across the trochlear region using two landmark detection U-Net models. The approach was evaluated on the public fastMRI dataset and a small in-house cohort of patients with TD. Compared with conventional manual single-slice SA measurements, the proposed automated method yielded a mean absolute error of 11.6$^\circ$ while providing continuous characterization of trochlear morphology. Population-level analysis demonstrated distinct mean SA profiles between the public cohort and the in-house TD cohort, highlighting the potential of profile-based assessment to characterize TD. By reducing reliance on a single manually selected axial slice, the proposed framework extends conventional SA assessment to a continuous profile-based description of trochlear morphology without additional imaging, while remaining conceptually linked to current clinical assessment. Further validation is required. The code is available: https://github.com/wehrlimi/SA_Profile.

Abstract: Out-of-distribution (OOD) detection is crucial for safe deployment of medical AI systems, where domain shifts arise across institutions, acquisition protocols, and patient populations. VLMs enable zero-shot OOD detection by embedding images into a language-aligned latent space, where cross-modal similarity serves as a non-parametric confidence signal for identifying in-distribution samples. Yet existing methods rely almost exclusively on final-layer embeddings, implicitly assuming that the deepest representations are universally optimal. We first show that this assumption does not hold in medical imaging: intermediate layers provide complementary OOD signals, and the optimal representational depth depends on the respective image modality. While prior work selects layer combinations via entropy minimization of normalized histograms, we demonstrate that single-resolution entropy estimation is highly sensitive to binning choices, leading to performance variations of up to 19.3% AUROC. To address this instability, we propose a multi-resolution entropy estimation strategy that aggregates histogram statistics across multiple discretization scales, enabling robust and stable intermediate-layer selection. Across two medical OOD benchmarks, namely MIDOG and OASIS, covering distinct imaging modalities, diverse shift types, and different VLM backbones, our method consistently outperforms state-of-the-art approaches, offering a lightweight and stable solution for zero-shot OOD detection.

Abstract: Because dense frame-level annotation of colonoscopy videos is costly, we propose WSPolypNet, a weakly supervised framework for polyp localization using only video-level labels. WSPolypNet employs a 3D convolutional neural network trained with video-level supervision to generate class activation maps (CAMs), which identify candidate polyp regions without requiring frame-level spatial annotations. The CAM-derived localization cues are further enhanced using a multi-view strategy and provided to MedSAM2 as point prompts. MedSAM2 then propagates segmentation masks across the video, refining the coarse localization cues according to polyp boundaries. WSPolypNet achieved CorLoc scores of 47.80%, 43.68%, and 35.01% at IoU thresholds of 0.3, 0.5, and 0.7, respectively, compared with 36.87%, 33.72%, and 27.94% in the single-view setting. For small polyps, the multi-view strategy improved CorLoc@0.5 from 16.01% to 30.97%. The framework also achieved a recall of 94.51%. These results demonstrate the potential of weakly supervised spatiotemporal learning to substantially reduce spatial annotation requirements for polyp localization in colonoscopy videos.

Abstract: Deep learning has achieved state-of-the-art performance in echocardiographic video segmentation, with an increasing number of models incorporating temporal information. However, quantitative evaluation of temporal explainability remains largely unexplored. We propose a quantitative framework for evaluating Grad-CAM explanations using four complementary metrics measuring temporal consistency, saliency motion, anatomical overlap, and temporal overlap. Using EchoNet-Dynamic, we compare a baseline 2D U-Net with ConvLSTM U-Net models trained across multiple temporal strides. While segmentation performance remained comparable across all models, intermediate ConvLSTM explanations exhibited substantially lower saliency consistency and greater centroid motion than final prediction explanations. Temporal Bottleneck explanations were significantly more stable than Encoder Bottleneck explanations across all strides, while final ConvLSTM Decoder3 explanations were broadly comparable to those of the 2D U-Net. Importantly, conventional frame-wise explanation metrics cannot determine whether variation in intermediate explanations reflects meaningful temporal feature evolution or explanation instability. These findings establish a preliminary quantitative framework for temporal explainability and motivate temporal-aware XAI methods that explicitly account for evolving representations in medical video models.

Abstract: Segmentation of complex structures in X-ray tomographic data is a fundamental task in biomedical research, but it often requires large amounts of precisely annotated data, making fully supervised approaches costly and difficult to scale. In this study, weakly supervised deep learning is investigated as a strategy to reduce annotation effort while maintaining accurate segmentation. A two-dimensional convolutional neural network based on the nnU-Net framework was adapted to a weak supervision setting using sparse dot-based annotations, complemented by a limited number of fully segmented images. The approach was evaluated on high-resolution microCT slices of rat kidneys, targeting the segmentation of renal glomeruli, which are small, low-contrast anatomical structures. Results indicate that weak supervision provides a meaningful learning signal, enabling reliable localization of glomeruli even in the absence of dense labels. Incorporating a small set of high-quality annotations substantially improves segmentation performance, approaching that of a fully supervised model. These findings highlight the potential of weakly supervised learning as an annotation-efficient strategy for the analysis of complex structures in X-ray tomographic data, and suggest that alternative loss formulations tailored to sparse annotations may further enhance performance.

Abstract: Basal Cell Carcinoma (BCC) is the most common type of skin cancer, accounting for nearly 80% of skin cancer di- agnoses. Its optimal clinical management is guided by the distinct histopathologic subtype, with aggressive variants requiring more drastic measures. In current clinical practice, subtyping relies on skin biopsies, a procedure both costly and invasive. In this paper, we conduct a preliminary investigation into using deep learning for BCC subtyping, solely from a single dermatoscopic image of the lesion. Given the limited data at our disposal, we employ pre-trained vision transformers (ViTs), a state-of-the-art family of models highly effective for challenging downstream tasks with limited labeled data. Through repeated stratified k-fold cross-validation, we demonstrate that ViTs can achieve superior performance (AUC 0.784 on a dataset of 1271 dermatoscopic images of various BCC subtypes) over standard CNN-based baselines as well as previously-reported human reader perfor- mance, on the task of differentiating aggressive BCCs from other subtype families. These initial findings highlight the potential of combining deep learning and dermatoscopy to provide a biopsy- free alternative for BCC subtyping, thus aiding in improving treatment planning and patient outcomes.