Daily Papers

Open-vocabulary detection (OVD) aims to detect objects beyond a predefined set of categories. As a pioneering model incorporating the YOLO series into OVD, YOLO-World is well-suited for scenarios prioritizing speed and efficiency.However, its performance is hindered by its neck feature fusion mechanism, which causes the quadratic complexity and the limited guided receptive fields.To address these limitations, we present Mamba-YOLO-World, a novel YOLO-based OVD model employing the proposed MambaFusion Path Aggregation Network (MambaFusion-PAN) as its neck architecture. Specifically, we introduce an innovative State Space Model-based feature fusion mechanism consisting of a Parallel-Guided Selective Scan algorithm and a Serial-Guided Selective Scan algorithm with linear complexity and globally guided receptive fields. It leverages multi-modal input sequences and mamba hidden states to guide the selective scanning process.Experiments demonstrate that our model outperforms the original YOLO-World on the COCO and LVIS benchmarks in both zero-shot and fine-tuning settings while maintaining comparable parameters and FLOPs. Additionally, it surpasses existing state-of-the-art OVD methods with fewer parameters and FLOPs.

Diffusion model-based inverse problem solvers have demonstrated state-of-the-art performance in cases where the forward operator is known (i.e. non-blind). However, the applicability of the method to blind inverse problems has yet to be explored. In this work, we show that we can indeed solve a family of blind inverse problems by constructing another diffusion prior for the forward operator. Specifically, parallel reverse diffusion guided by gradients from the intermediate stages enables joint optimization of both the forward operator parameters as well as the image, such that both are jointly estimated at the end of the parallel reverse diffusion procedure. We show the efficacy of our method on two representative tasks -- blind deblurring, and imaging through turbulence -- and show that our method yields state-of-the-art performance, while also being flexible to be applicable to general blind inverse problems when we know the functional forms.

Pan-cancer screening in large-scale CT scans remains challenging for existing AI methods, primarily due to the difficulty of localizing diverse types of tiny lesions in large CT volumes. The extreme foreground-background imbalance significantly hinders models from focusing on diseased regions, while redundant focus on healthy regions not only decreases the efficiency but also increases false positives. Inspired by radiologists' glance and focus diagnostic strategy, we introduce GF-Screen, a Glance and Focus reinforcement learning framework for pan-cancer screening. GF-Screen employs a Glance model to localize the diseased regions and a Focus model to precisely segment the lesions, where segmentation results of the Focus model are leveraged to reward the Glance model via Reinforcement Learning (RL). Specifically, the Glance model crops a group of sub-volumes from the entire CT volume and learns to select the sub-volumes with lesions for the Focus model to segment. Given that the selecting operation is non-differentiable for segmentation training, we propose to employ the segmentation results to reward the Glance model. To optimize the Glance model, we introduce a novel group relative learning paradigm, which employs group relative comparison to prioritize high-advantage predictions and discard low-advantage predictions within sub-volume groups, not only improving efficiency but also reducing false positives. In this way, for the first time, we effectively extend cutting-edge RL techniques to tackle the specific challenges in pan-cancer screening. Extensive experiments on 16 internal and 7 external datasets across 9 lesion types demonstrated the effectiveness of GF-Screen. Notably, GF-Screen leads the public validation leaderboard of MICCAI FLARE25 pan-cancer challenge, surpassing the FLARE24 champion solution by a large margin (+25.6% DSC and +28.2% NSD).

Vision-language models (VLMs) can couple visual perception with open-ended clinical reasoning, making them attractive for computational histopathology. However, fine-tuning billions of parameters on scarce, expert-annotated pathology data is prohibitive, while in-context learning (ICL), which conditions the VLM on demonstrative image-text pairs without parameter updates, suffers from high sensitivity to which examples are selected and how the query is phrased, producing unreliable diagnostics. Existing selection strategies rely on query-dependent nearest-neighbour retrieval that ignores global data structure, require costly parameter updates, or disregard the joint vision-text embedding geometry of VLMs. We propose GAUC, a training-free coreset selection method operating directly in the pre-trained multimodal embedding space. GAUC jointly optimises three objectives: (1) a Maximum Mean Discrepancy term enforcing distributional fidelity between coreset and full dataset, (2) an Effective Mutual Information Difference regulariser bounding performance degradation under prompt paraphrases by exploiting the VLM's joint vision-text alignment, and (3) a predictive-variance penalty suppressing overconfident, unstable outputs. On CRC-100K and MHIST across multiple open-source VLM architectures, GAUC consistently improves accuracy, calibration, and prompt robustness over recent ICL selection methods and dataset-distillation baselines, all without a single gradient update.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Model selection/optimization in conformal inference is challenging, since it may break the exchangeability between labeled and unlabeled data. We study this problem in the context of conformal selection, which uses conformal p-values to select ``interesting'' instances with large unobserved labels from a pool of unlabeled data, while controlling the FDR in finite sample. For validity, existing solutions require the model choice to be independent of the data used to construct the p-values and calibrate the selection set. However, when presented with many model choices and limited labeled data, it is desirable to (i) select the best model in a data-driven manner, and (ii) mitigate power loss due to sample splitting. This paper presents OptCS, a general framework that allows valid statistical testing (selection) after flexible data-driven model optimization. We introduce general conditions under which OptCS constructs valid conformal p-values despite substantial data reuse and handles complex p-value dependencies to maintain finite-sample FDR control via a novel multiple testing procedure. We instantiate this general recipe to propose three FDR-controlling procedures, each optimizing the models differently: (i) selecting the most powerful one among multiple pre-trained candidate models, (ii) using all data for model fitting without sample splitting, and (iii) combining full-sample model fitting and selection. We demonstrate the efficacy of our methods via simulation studies and real applications in drug discovery and alignment of large language models in radiology report generation.

This study demonstrates that incorporating a consistency heuristic into the point-matching algorithm yerebakan2023hierarchical improves robustness in matching anatomical locations across pairs of medical images. We validated our approach on diverse longitudinal internal and public datasets spanning CT and MRI modalities. Notably, it surpasses state-of-the-art results on the Deep Lesion Tracking dataset. Additionally, we show that the method effectively addresses landmark localization. The algorithm operates efficiently on standard CPU hardware and allows configurable trade-offs between speed and robustness. The method enables high-precision navigation between medical images without requiring a machine learning model or training data.

We revisit the problem of large-scale bundle adjustment and propose a technique called Multidirectional Conjugate Gradients that accelerates the solution of the normal equation by up to 61%. The key idea is that we enlarge the search space of classical preconditioned conjugate gradients to include multiple search directions. As a consequence, the resulting algorithm requires fewer iterations, leading to a significant speedup of large-scale reconstruction, in particular for denser problems where traditional approaches notoriously struggle. We provide a number of experimental ablation studies revealing the robustness to variations in the hyper-parameters and the speedup as a function of problem density.

Vision-language foundation models (VLMs) show promise for diverse imaging tasks but often underperform on medical benchmarks. Prior efforts to improve performance include model finetuning, which requires large domain-specific datasets and significant compute, or manual prompt engineering, which is hard to generalize and often inaccessible to medical institutions seeking to deploy these tools. These challenges motivate interest in approaches that draw on a model's embedded knowledge while abstracting away dependence on human-designed prompts to enable scalable, weight-agnostic performance improvements. To explore this, we adapt the Declarative Self-improving Python (DSPy) framework for structured automated prompt optimization in medical vision-language systems through a comprehensive, formal evaluation. We implement prompting pipelines for five medical imaging tasks across radiology, gastroenterology, and dermatology, evaluating 10 open-source VLMs with four prompt optimization techniques. Optimized pipelines achieved a median relative improvement of 53% over zero-shot prompting baselines, with the largest gains ranging from 300% to 3,400% on tasks where zero-shot performance is low. These results highlight the substantial potential of applying automated prompt optimization to medical AI systems, demonstrating significant gains for vision-based applications requiring accurate clinical image interpretation. By reducing dependence on prompt design to elicit intended outputs, these techniques allow clinicians to focus on patient care and clinical decision-making. Furthermore, our experiments offer scalability and preserve data privacy, demonstrating performance improvement on open-source VLMs. We publicly release our evaluation pipelines to support reproducible research on specialized medical tasks, available at https://github.com/DaneshjouLab/prompt-triage-lab.

Currently, evaluating vision-language models (VLMs) in medical imaging tasks oversimplifies clinical reality by relying on pre-selected 2D images that demand significant manual labor to curate. This setup misses the core challenge of realworld diagnostics: a true clinical agent must actively navigate full 3D volumes across multiple sequences or modalities to gather evidence and ultimately support a final decision. To address this, we propose MEDOPENCLAW, an auditable runtime designed to let VLMs operate dynamically within standard medical tools or viewers (e.g., 3D Slicer). On top of this runtime, we introduce MEDFLOWBENCH, a full-study medical imaging benchmark covering multi-sequence brain MRI and lung CT/PET. It systematically evaluates medical agentic capabilities across viewer-only, tool-use, and open-method tracks. Initial results reveal a critical insight: while state-of-the-art LLMs/VLMs (e.g., Gemini 3.1 Pro and GPT-5.4) can successfully navigate the viewer to solve basic study-level tasks, their performance paradoxically degrades when given access to professional support tools due to a lack of precise spatial grounding. By bridging the gap between static-image perception and interactive clinical workflows, MEDOPENCLAW and MEDFLOWBENCH establish a reproducible foundation for developing auditable, full-study medical imaging agents.

Medical eye-tracking data is an important information source for understanding how radiologists visually interpret medical images. This information not only improves the accuracy of deep learning models for X-ray analysis but also their interpretability, enhancing transparency in decision-making. However, the current eye-tracking data is dispersed, unprocessed, and ambiguous, making it difficult to derive meaningful insights. Therefore, there is a need to create a new dataset with more focus and purposeful eyetracking data, improving its utility for diagnostic applications. In this work, we propose a refinement method inspired by the target-present visual search challenge: there is a specific finding and fixations are guided to locate it. After refining the existing eye-tracking datasets, we transform them into a curated visual search dataset, called GazeSearch, specifically for radiology findings, where each fixation sequence is purposefully aligned to the task of locating a particular finding. Subsequently, we introduce a scan path prediction baseline, called ChestSearch, specifically tailored to GazeSearch. Finally, we employ the newly introduced GazeSearch as a benchmark to evaluate the performance of current state-of-the-art methods, offering a comprehensive assessment for visual search in the medical imaging domain. Code is available at https://github.com/UARK-AICV/GazeSearch.

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We achieve this by training a neural network estimator that maps query locations to atlas coordinates via regression. Efficiency is improved by sparsely sampling the input, enabling response times of less than 1 ms without additional accelerator hardware. We demonstrate the utility of the algorithm in both CT and MRI modalities.

We investigate fine-tuning Vision-Language Models (VLMs) for multi-task medical image understanding, focusing on detection, localization, and counting of findings in medical images. Our objective is to evaluate whether instruction-tuned VLMs can simultaneously improve these tasks, with the goal of enhancing diagnostic accuracy and efficiency. Using MedMultiPoints, a multimodal dataset with annotations from endoscopy (polyps and instruments) and microscopy (sperm cells), we reformulate each task into instruction-based prompts suitable for vision-language reasoning. We fine-tune Qwen2.5-VL-7B-Instruct using Low-Rank Adaptation (LoRA) across multiple task combinations. Results show that multi-task training improves robustness and accuracy. For example, it reduces the Count Mean Absolute Error (MAE) and increases Matching Accuracy in the Counting + Pointing task. However, trade-offs emerge, such as more zero-case point predictions, indicating reduced reliability in edge cases despite overall performance gains. Our study highlights the potential of adapting general-purpose VLMs to specialized medical tasks via prompt-driven fine-tuning. This approach mirrors clinical workflows, where radiologists simultaneously localize, count, and describe findings - demonstrating how VLMs can learn composite diagnostic reasoning patterns. The model produces interpretable, structured outputs, offering a promising step toward explainable and versatile medical AI. Code, model weights, and scripts will be released for reproducibility at https://github.com/simula/PointDetectCount.

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

Clinical decision-making relies heavily on understanding relative positions of anatomical structures and anomalies. Therefore, for Vision-Language Models (VLMs) to be applicable in clinical practice, the ability to accurately determine relative positions on medical images is a fundamental prerequisite. Despite its importance, this capability remains highly underexplored. To address this gap, we evaluate the ability of state-of-the-art VLMs, GPT-4o, Llama3.2, Pixtral, and JanusPro, and find that all models fail at this fundamental task. Inspired by successful approaches in computer vision, we investigate whether visual prompts, such as alphanumeric or colored markers placed on anatomical structures, can enhance performance. While these markers provide moderate improvements, results remain significantly lower on medical images compared to observations made on natural images. Our evaluations suggest that, in medical imaging, VLMs rely more on prior anatomical knowledge than on actual image content for answering relative position questions, often leading to incorrect conclusions. To facilitate further research in this area, we introduce the MIRP , Medical Imaging Relative Positioning, benchmark dataset, designed to systematically evaluate the capability to identify relative positions in medical images.

MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

Radiology report generation (RRG) is commonly formulated as a single-path generation task, where a multimodal large language model (MLLM) produces one decoded report as the final output. While recent progress has largely been driven by scaling training data, model capacity, and retrieval mechanisms, improving report quality at inference time remains underexplored. In this work, we observe that fixed radiology MLLMs often generate clinically stronger reports elsewhere in their candidate pool than the one selected by default decoding, suggesting that inference-time decision making remains an overlooked bottleneck. To address this, we propose Clinical Consensus Selection (CCS), a decoder-agnostic inference-time selection framework that samples multiple candidate reports and selects the one with the highest clinical consensus across the rollout pool. CCS unifies text-based utilities with a radiology-adapted utility computed by an image--report-trained multimodal embedder, which measures candidate agreement beyond surface-level textual similarity. Across three datasets and multiple radiology MLLMs, CCS consistently improves inference-time performance over single-path decoding and generic Best-of-N baselines, with particularly clear gains on clinical metrics. Further analysis shows that image-grounded utility forms a selection axis distinct from textual consensus and that substantial headroom remains for improving RRG at inference time.

Dynamic imaging addresses the recovery of a time-varying 2D or 3D object at each time instant using its undersampled measurements. In particular, in the case of dynamic tomography, only a single projection at a single view angle may be available at a time, making the problem severely ill-posed. In this work, we propose an approach, RED-PSM, which combines for the first time two powerful techniques to address this challenging imaging problem. The first, are partially separable models, which have been used to efficiently introduce a low-rank prior for the spatio-temporal object. The second is the recent Regularization by Denoising (RED), which provides a flexible framework to exploit the impressive performance of state-of-the-art image denoising algorithms, for various inverse problems. We propose a partially separable objective with RED and a computationally efficient and scalable optimization scheme with variable splitting and ADMM. Theoretical analysis proves the convergence of our objective to a value corresponding to a stationary point satisfying the first-order optimality conditions. Convergence is accelerated by a particular projection-domain-based initialization. We demonstrate the performance and computational improvements of our proposed RED-PSM with a learned image denoiser by comparing it to a recent deep-prior-based method known as TD-DIP. Although the main focus is on dynamic tomography, we also show the performance advantages of RED-PSM in a cardiac dynamic MRI setting.

Understanding radiologists' eye movement during Computed Tomography (CT) reading is crucial for developing effective interpretable computer-aided diagnosis systems. However, CT research in this area has been limited by the lack of publicly available eye-tracking datasets and the three-dimensional complexity of CT volumes. To address these challenges, we present the first publicly available eye gaze dataset on CT, called CT-ScanGaze. Then, we introduce CT-Searcher, a novel 3D scanpath predictor designed specifically to process CT volumes and generate radiologist-like 3D fixation sequences, overcoming the limitations of current scanpath predictors that only handle 2D inputs. Since deep learning models benefit from a pretraining step, we develop a pipeline that converts existing 2D gaze datasets into 3D gaze data to pretrain CT-Searcher. Through both qualitative and quantitative evaluations on CT-ScanGaze, we demonstrate the effectiveness of our approach and provide a comprehensive assessment framework for 3D scanpath prediction in medical imaging.

Executing multiple tasks simultaneously in medical image analysis, including segmentation, classification, detection, and regression, often introduces significant challenges regarding model generalizability and the optimization of shared feature representations. While Vision Foundation Models (VFMs) provide powerful general representations, full fine-tuning on limited medical data is prone to overfitting and incurs high computational costs. Moreover, existing parameter-efficient fine-tuning approaches typically adopt task-agnostic adaptation protocols, overlooking both task-specific mechanisms and the varying sensitivity of model layers during fine-tuning. In this work, we propose Task-Aware Prompting and Selective Layer Fine-Tuning (TAP-SLF), a unified framework for multi-task ultrasound image analysis. TAP-SLF incorporates task-aware soft prompts to encode task-specific priors into the input token sequence and applies LoRA to selected specific top layers of the encoder. This strategy updates only a small fraction of the VFM parameters while keeping the pre-trained backbone frozen. By combining task-aware prompts with selective high-layer fine-tuning, TAP-SLF enables efficient VFM adaptation to diverse medical tasks within a shared backbone. Results on the FMC_UIA 2026 Challenge test set, where TAP-SLF wins fifth place, combined with evaluations on the officially released training dataset using an 8:2 train-test split, demonstrate that task-aware prompting and selective layer tuning are effective strategies for efficient VFM adaptation.

The ODELIA Breast MRI Challenge 2025 addresses a critical issue in breast cancer screening: improving early detection through more efficient and accurate interpretation of breast MRI scans. Even though methods for general-purpose whole-body lesion segmentation as well as multi-time-point analysis exist, breast cancer detection remains highly challenging, largely due to the limited availability of high-quality segmentation labels. Therefore, developing robust classification-based approaches is crucial for the future of early breast cancer detection, particularly in applications such as large-scale screening. In this write-up, we provide a comprehensive overview of our approach to the challenge. We begin by detailing the underlying concept and foundational assumptions that guided our work. We then describe the iterative development process, highlighting the key stages of experimentation, evaluation, and refinement that shaped the evolution of our solution. Finally, we present the reasoning and evidence that informed the design choices behind our final submission, with a focus on performance, robustness, and clinical relevance. We release our full implementation publicly at https://github.com/MIC-DKFZ/MeisenMeister

Efficient, reliable and reproducible target volume delineation is a key step in the effective planning of breast radiotherapy. However, post-operative breast target delineation is challenging as the contrast between the tumor bed volume (TBV) and normal breast tissue is relatively low in CT images. In this study, we propose to mimic the marker-guidance procedure in manual target delineation. We developed a saliency-based deep learning segmentation (SDL-Seg) algorithm for accurate TBV segmentation in post-operative breast irradiation. The SDL-Seg algorithm incorporates saliency information in the form of markers' location cues into a U-Net model. The design forces the model to encode the location-related features, which underscores regions with high saliency levels and suppresses low saliency regions. The saliency maps were generated by identifying markers on CT images. Markers' locations were then converted to probability maps using a distance-transformation coupled with a Gaussian filter. Subsequently, the CT images and the corresponding saliency maps formed a multi-channel input for the SDL-Seg network. Our in-house dataset was comprised of 145 prone CT images from 29 post-operative breast cancer patients, who received 5-fraction partial breast irradiation (PBI) regimen on GammaPod. The performance of the proposed method was compared against basic U-Net. Our model achieved mean (standard deviation) of 76.4 %, 6.76 mm, and 1.9 mm for DSC, HD95, and ASD respectively on the test set with computation time of below 11 seconds per one CT volume. SDL-Seg showed superior performance relative to basic U-Net for all the evaluation metrics while preserving low computation cost. The findings demonstrate that SDL-Seg is a promising approach for improving the efficiency and accuracy of the on-line treatment planning procedure of PBI, such as GammaPod based PBI.

We present ENSAM (Equivariant, Normalized, Segment Anything Model), a lightweight and promptable model for universal 3D medical image segmentation. ENSAM combines a SegResNet-based encoder with a prompt encoder and mask decoder in a U-Net-style architecture, using latent cross-attention, relative positional encoding, normalized attention, and the Muon optimizer for training. ENSAM is designed to achieve good performance under limited data and computational budgets, and is trained from scratch on under 5,000 volumes from multiple modalities (CT, MRI, PET, ultrasound, microscopy) on a single 32 GB GPU in 6 hours. As part of the CVPR 2025 Foundation Models for Interactive 3D Biomedical Image Segmentation Challenge, ENSAM was evaluated on hidden test set with multimodal 3D medical images, obtaining a DSC AUC of 2.404, NSD AUC of 2.266, final DSC of 0.627, and final NSD of 0.597, outperforming two previously published baseline models (VISTA3D, SAM-Med3D) and matching the third (SegVol), surpassing its performance in final DSC but trailing behind in the other three metrics. In the coreset track of the challenge, ENSAM ranks 5th of 10 overall and best among the approaches not utilizing pretrained weights. Ablation studies confirm that our use of relative positional encodings and the Muon optimizer each substantially speed up convergence and improve segmentation quality.

Multi-modal brain tumor segmentation is critical for clinical diagnosis, and it requires accurate identification of distinct internal anatomical subregions. While the recent prompt-based segmentation paradigms enable interactive experiences for clinicians, existing methods ignore cross-modal correlations and rely on labor-intensive category-specific prompts, limiting their applicability in real-world scenarios. To address these issues, we propose a MSM-Seg framework for multi-modal brain tumor segmentation. The MSM-Seg introduces a novel dual-memory segmentation paradigm that synergistically integrates multi-modal and inter-slice information with the efficient category-agnostic prompt for brain tumor understanding. To this end, we first devise a modality-and-slice memory attention (MSMA) to exploit the cross-modal and inter-slice relationships among the input scans. Then, we propose a multi-scale category-agnostic prompt encoder (MCP-Encoder) to provide tumor region guidance for decoding. Moreover, we devise a modality-adaptive fusion decoder (MF-Decoder) that leverages the complementary decoding information across different modalities to improve segmentation accuracy. Extensive experiments on different MRI datasets demonstrate that our MSM-Seg framework outperforms state-of-the-art methods in multi-modal metastases and glioma tumor segmentation. The code is available at https://github.com/xq141839/MSM-Seg.

Precision medicine, such as patient-adaptive treatments assisted by medical image analysis, poses new challenges for segmentation algorithms in adapting to new patients, due to the large variability across different patients and the limited availability of annotated data for each patient. In this work, we propose a data-efficient segmentation algorithm, namely Part-aware Prompted Segment Anything Model (P^2SAM). Without any model fine-tuning, P^2SAM enables seamless adaptation to any new patients relying only on one-shot patient-specific data. We introduce a novel part-aware prompt mechanism to select multiple-point prompts based on the part-level features of the one-shot data, which can be extensively integrated into different promptable segmentation models, such as SAM and SAM 2. Moreover, to determine the optimal number of parts for each specific case, we propose a distribution-guided retrieval approach that further enhances the robustness of the part-aware prompt mechanism. P^2SAM improves the performance by +8.0% and +2.0% mean Dice score for two different patient-adaptive segmentation applications, respectively. In addition, P^2SAM also exhibits impressive generalizability in other adaptive segmentation tasks in the natural image domain, e.g., +6.4% mIoU within personalized object segmentation task. The code is available at: https://github.com/Zch0414/p2sam

Magnetic Resonance Imaging (MRI) is a critical medical imaging modality in clinical diagnosis and research, yet its complexity and heterogeneity pose challenges for automated analysis, particularly in scalable and generalizable machine learning applications. While foundation models have revolutionized natural language and vision tasks, their application to MRI remains limited due to data scarcity and narrow anatomical focus. In this work, we present Decipher-MR, a 3D MRI-specific vision-language foundation model trained on a large-scale dataset comprising 200,000 MRI series from over 22,000 studies spanning diverse anatomical regions, sequences, and pathologies. Decipher-MR integrates self-supervised vision learning with report-guided text supervision to build robust, generalizable representations, enabling effective adaptation across broad applications. To enable robust and diverse clinical tasks with minimal computational overhead, Decipher-MR supports a modular design that enables tuning of lightweight, task-specific decoders attached to a frozen pretrained encoder. Following this setting, we evaluate Decipher-MR across diverse benchmarks including disease classification, demographic prediction, anatomical localization, and cross-modal retrieval, demonstrating consistent performance gains over existing foundation models and task-specific approaches. Our results establish Decipher-MR as a scalable and versatile foundation for MRI-based AI, facilitating efficient development across clinical and research domains.

Given a K-vertex simplex in a d-dimensional space, suppose we measure n points on the simplex with noise (hence, some of the observed points fall outside the simplex). Vertex hunting is the problem of estimating the K vertices of the simplex. A popular vertex hunting algorithm is successive projection algorithm (SPA). However, SPA is observed to perform unsatisfactorily under strong noise or outliers. We propose pseudo-point SPA (pp-SPA). It uses a projection step and a denoise step to generate pseudo-points and feed them into SPA for vertex hunting. We derive error bounds for pp-SPA, leveraging on extreme value theory of (possibly) high-dimensional random vectors. The results suggest that pp-SPA has faster rates and better numerical performances than SPA. Our analysis includes an improved non-asymptotic bound for the original SPA, which is of independent interest.

Real-world medical image segmentation has tremendous long-tailed complexity of objects, among which tail conditions correlate with relatively rare diseases and are clinically significant. A trustworthy medical AI algorithm should demonstrate its effectiveness on tail conditions to avoid clinically dangerous damage in these out-of-distribution (OOD) cases. In this paper, we adopt the concept of object queries in Mask Transformers to formulate semantic segmentation as a soft cluster assignment. The queries fit the feature-level cluster centers of inliers during training. Therefore, when performing inference on a medical image in real-world scenarios, the similarity between pixels and the queries detects and localizes OOD regions. We term this OOD localization as MaxQuery. Furthermore, the foregrounds of real-world medical images, whether OOD objects or inliers, are lesions. The difference between them is less than that between the foreground and background, possibly misleading the object queries to focus redundantly on the background. Thus, we propose a query-distribution (QD) loss to enforce clear boundaries between segmentation targets and other regions at the query level, improving the inlier segmentation and OOD indication. Our proposed framework is tested on two real-world segmentation tasks, i.e., segmentation of pancreatic and liver tumors, outperforming previous state-of-the-art algorithms by an average of 7.39% on AUROC, 14.69% on AUPR, and 13.79% on FPR95 for OOD localization. On the other hand, our framework improves the performance of inlier segmentation by an average of 5.27% DSC when compared with the leading baseline nnUNet.

Magnetic Resonance Imaging can produce detailed images of the anatomy and physiology of the human body that can assist doctors in diagnosing and treating pathologies such as tumours. However, MRI suffers from very long acquisition times that make it susceptible to patient motion artifacts and limit its potential to deliver dynamic treatments. Conventional approaches such as Parallel Imaging and Compressed Sensing allow for an increase in MRI acquisition speed by reconstructing MR images from sub-sampled MRI data acquired using multiple receiver coils. Recent advancements in Deep Learning combined with Parallel Imaging and Compressed Sensing techniques have the potential to produce high-fidelity reconstructions from highly accelerated MRI data. In this work we present a novel Deep Learning-based Inverse Problem solver applied to the task of Accelerated MRI Reconstruction, called the Recurrent Variational Network (RecurrentVarNet), by exploiting the properties of Convolutional Recurrent Neural Networks and unrolled algorithms for solving Inverse Problems. The RecurrentVarNet consists of multiple recurrent blocks, each responsible for one iteration of the unrolled variational optimization scheme for solving the inverse problem of multi-coil Accelerated MRI Reconstruction. Contrary to traditional approaches, the optimization steps are performed in the observation domain (k-space) instead of the image domain. Each block of the RecurrentVarNet refines the observed k-space and comprises a data consistency term and a recurrent unit which takes as input a learned hidden state and the prediction of the previous block. Our proposed method achieves new state of the art qualitative and quantitative reconstruction results on 5-fold and 10-fold accelerated data from a public multi-coil brain dataset, outperforming previous conventional and deep learning-based approaches.

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

Robust estimation is essential in correspondence-based Point Cloud Registration (PCR). Existing methods using maximal clique search in compatibility graphs achieve high recall but suffer from exponential time complexity, limiting their use in time-sensitive applications. To address this challenge, we propose a fast and robust estimator, TurboReg, built upon a novel lightweight clique, TurboClique, and a highly parallelizable Pivot-Guided Search (PGS) algorithm. First, we define the TurboClique as a 3-clique within a highly-constrained compatibility graph. The lightweight nature of the 3-clique allows for efficient parallel searching, and the highly-constrained compatibility graph ensures robust spatial consistency for stable transformation estimation. Next, PGS selects matching pairs with high SC^2 scores as pivots, effectively guiding the search toward TurboCliques with higher inlier ratios. Moreover, the PGS algorithm has linear time complexity and is significantly more efficient than the maximal clique search with exponential time complexity. Extensive experiments show that TurboReg achieves state-of-the-art performance across multiple real-world datasets, with substantial speed improvements. For example, on the 3DMatch+FCGF dataset, TurboReg (1K) operates 208.22times faster than 3DMAC while also achieving higher recall. Our code is accessible at https://github.com/Laka-3DV/TurboReg{TurboReg}.

Vision-Language Models (VLMs) have shown impressive performance in vision tasks, but adapting them to new domains often requires expensive fine-tuning. Prompt tuning techniques, including textual, visual, and multimodal prompting, offer efficient alternatives by leveraging learnable prompts. However, their application to Vision-Language Segmentation Models (VLSMs) and evaluation under significant domain shifts remain unexplored. This work presents an open-source benchmarking framework, TuneVLSeg, to integrate various unimodal and multimodal prompt tuning techniques into VLSMs, making prompt tuning usable for downstream segmentation datasets with any number of classes. TuneVLSeg includes 6 prompt tuning strategies on various prompt depths used in 2 VLSMs totaling of 8 different combinations. We test various prompt tuning on 8 diverse medical datasets, including 3 radiology datasets (breast tumor, echocardiograph, chest X-ray pathologies) and 5 non-radiology datasets (polyp, ulcer, skin cancer), and two natural domain segmentation datasets. Our study found that textual prompt tuning struggles under significant domain shifts, from natural-domain images to medical data. Furthermore, visual prompt tuning, with fewer hyperparameters than multimodal prompt tuning, often achieves performance competitive to multimodal approaches, making it a valuable first attempt. Our work advances the understanding and applicability of different prompt-tuning techniques for robust domain-specific segmentation. The source code is available at https://github.com/naamiinepal/tunevlseg.

This paper introduces a novel one-stage end-to-end detector specifically designed to detect small lesions in medical images. Precise localization of small lesions presents challenges due to their appearance and the diverse contextual backgrounds in which they are found. To address this, our approach introduces a new type of pixel-based anchor that dynamically moves towards the targeted lesion for detection. We refer to this new architecture as GravityNet, and the novel anchors as gravity points since they appear to be "attracted" by the lesions. We conducted experiments on two well-established medical problems involving small lesions to evaluate the performance of the proposed approach: microcalcifications detection in digital mammograms and microaneurysms detection in digital fundus images. Our method demonstrates promising results in effectively detecting small lesions in these medical imaging tasks.

Traditional whole slide image (WSI) analysis methods typically rely on the multiple instance learning (MIL) paradigm, which extracts patch-level features at high magnification and aggregates them for slide-level prediction. However, such exhaustive patch-level processing is computationally expensive, severely limiting the efficiency and scalability of WSI analysis. To address this challenge, we propose PathCTM (a Pathology-oriented Continuous Thought Model) that enables token-efficient scale-space continuous reasoning for gigapixel WSIs. PathCTM formulates diagnostic inference as a dynamic sequential information pursuit. It progressively transitions from low-magnification global to high-magnification local inspection, and adaptively terminates inference when sufficient evidence is gathered to effectively bound decision uncertainty. Specifically, it uses conditional computation for dynamic scale switching with attention-guided region pruning, coupled with confidence-aware early stopping. Extensive experiments demonstrate that, compared with standard MIL-based methods, PathCTM reduces the number of required image patches by 95.95% and shortens inference time by approximately 95.62%, while maintaining AUC without degradation. Code is available at https://github.com/JSGe-AI/PathCTM.

Following the impressive development of LLMs, vision-language alignment in LLMs is actively being researched to enable multimodal reasoning and visual IO. This direction of research is particularly relevant to medical imaging because medical image analysis and generation consist of reasoning based on a combination of visual features and prior knowledge. Many recent works have focused on training adapter networks that serve as an information bridge between image processing networks and LLMs; but presumably, in order to achieve maximum reasoning potential of LLMs on visual information as well, visual and language features should be allowed to interact more freely. This is especially important in the medical domain because understanding and generating medical images such as chest X-rays (CXR) require not only accurate visual and language-based reasoning but also a more intimate mapping between the two modalities. Thus, taking inspiration from previous work on the transformer and VQ-GAN combination for bidirectional image and text generation, we build upon this approach and develop a method for instruction-tuning an LLM pre-trained only on text to gain vision-language capabilities for medical images. Specifically, we leverage a pretrained LLM's existing question-answering and instruction-following abilities to teach it to understand visual inputs by instructing it to answer questions about image inputs and, symmetrically, output both text and image responses appropriate to a given query by tuning the LLM with diverse tasks that encompass image-based text-generation and text-based image-generation. We show that our model, LLM-CXR, trained in this approach shows better image-text alignment in both CXR understanding and generation tasks while being smaller in size compared to previously developed models that perform a narrower range of tasks. The code is at https://github.com/hyn2028/llm-cxr.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

Subsampling is commonly used to mitigate costs associated with data acquisition, such as time or energy requirements, motivating the development of algorithms for estimating the fully-sampled signal of interest x from partially observed measurements y. In maximum-entropy sampling, one selects measurement locations that are expected to have the highest entropy, so as to minimize uncertainty about x. This approach relies on an accurate model of the posterior distribution over future measurements, given the measurements observed so far. Recently, diffusion models have been shown to produce high-quality posterior samples of high-dimensional signals using guided diffusion. In this work, we propose Active Diffusion Subsampling (ADS), a method for performing active subsampling using guided diffusion in which the model tracks a distribution of beliefs over the true state of x throughout the reverse diffusion process, progressively decreasing its uncertainty by choosing to acquire measurements with maximum expected entropy, and ultimately generating the posterior distribution p(x | y). ADS can be applied using pre-trained diffusion models for any subsampling rate, and does not require task-specific retraining - just the specification of a measurement model. Furthermore, the maximum entropy sampling policy employed by ADS is interpretable, enhancing transparency relative to existing methods using black-box policies. Experimentally, we show that ADS outperforms fixed sampling strategies, and study an application of ADS in Magnetic Resonance Imaging acceleration using the fastMRI dataset, finding that ADS performs competitively with supervised methods. Code available at https://active-diffusion-subsampling.github.io/.

Typical quantitative MRI (qMRI) methods estimate parameter maps after image reconstructing, which is prone to biases and error propagation. We propose a Nonlinear Conjugate Gradient (NLCG) optimizer for model-based T2/T1 estimation, which incorporates U-Net regularization trained in a scan-specific manner. This end-to-end method directly estimates qMRI maps from undersampled k-space data using mono-exponential signal modeling with zero-shot scan-specific neural network regularization to enable high fidelity T1 and T2 mapping. T2 and T1 mapping results demonstrate the ability of the proposed NLCG-Net to improve estimation quality compared to subspace reconstruction at high accelerations.

This paper presents a comprehensive evaluation of GPT-4V's capabilities across diverse medical imaging tasks, including Radiology Report Generation, Medical Visual Question Answering (VQA), and Visual Grounding. While prior efforts have explored GPT-4V's performance in medical image analysis, to the best of our knowledge, our study represents the first quantitative evaluation on publicly available benchmarks. Our findings highlight GPT-4V's potential in generating descriptive reports for chest X-ray images, particularly when guided by well-structured prompts. Meanwhile, its performance on the MIMIC-CXR dataset benchmark reveals areas for improvement in certain evaluation metrics, such as CIDEr. In the domain of Medical VQA, GPT-4V demonstrates proficiency in distinguishing between question types but falls short of the VQA-RAD benchmark in terms of accuracy. Furthermore, our analysis finds the limitations of conventional evaluation metrics like the BLEU scores, advocating for the development of more semantically robust assessment methods. In the field of Visual Grounding, GPT-4V exhibits preliminary promise in recognizing bounding boxes, but its precision is lacking, especially in identifying specific medical organs and signs. Our evaluation underscores the significant potential of GPT-4V in the medical imaging domain, while also emphasizing the need for targeted refinements to fully unlock its capabilities.

We present MInDI-3D (Medical Inversion by Direct Iteration in 3D), the first 3D conditional diffusion-based model for real-world sparse-view Cone Beam Computed Tomography (CBCT) artefact removal, aiming to reduce imaging radiation exposure. A key contribution is extending the "InDI" concept from 2D to a full 3D volumetric approach for medical images, implementing an iterative denoising process that refines the CBCT volume directly from sparse-view input. A further contribution is the generation of a large pseudo-CBCT dataset (16,182) from chest CT volumes of the CT-RATE public dataset to robustly train MInDI-3D. We performed a comprehensive evaluation, including quantitative metrics, scalability analysis, generalisation tests, and a clinical assessment by 11 clinicians. Our results show MInDI-3D's effectiveness, achieving a 12.96 (6.10) dB PSNR gain over uncorrected scans with only 50 projections on the CT-RATE pseudo-CBCT (independent real-world) test set and enabling an 8x reduction in imaging radiation exposure. We demonstrate its scalability by showing that performance improves with more training data. Importantly, MInDI-3D matches the performance of a 3D U-Net on real-world scans from 16 cancer patients across distortion and task-based metrics. It also generalises to new CBCT scanner geometries. Clinicians rated our model as sufficient for patient positioning across all anatomical sites and found it preserved lung tumour boundaries well.

Radiologists play a crucial role by translating medical images into medical reports. However, the field faces staffing shortages and increasing workloads. While automated approaches using vision-language models (VLMs) show promise as assistants, they require exceptionally high accuracy. Most current VLMs in radiology rely solely on supervised fine-tuning (SFT). Meanwhile, in the general domain, additional preference fine-tuning has become standard practice. The challenge in radiology lies in the prohibitive cost of obtaining radiologist feedback. We propose a scalable automated preference alignment technique for VLMs in radiology, focusing on chest X-ray (CXR) report generation. Our method leverages publicly available datasets with an LLM-as-a-Judge mechanism, eliminating the need for additional expert radiologist feedback. We evaluate and benchmark five direct alignment algorithms (DAAs). Our results show up to a 57.4% improvement in average GREEN scores, a LLM-based metric for evaluating CXR reports, and a 9.2% increase in an average across six metrics (domain specific and general), compared to the SFT baseline. We study reward overoptimization via length exploitation, with reports lengthening by up to 3.2x. To assess a potential alignment tax, we benchmark on six additional diverse tasks, finding no significant degradations. A reader study involving four board-certified radiologists indicates win rates of up to 0.62 over the SFT baseline, while significantly penalizing verbosity. Our analysis provides actionable insights for the development of VLMs in high-stakes fields like radiology.

Accurate prostate cancer diagnosis remains challenging. Even when using MRI, radiologists exhibit low specificity and significant inter-observer variability, leading to potential delays or inaccuracies in identifying clinically significant cancers. This leads to numerous unnecessary biopsies and risks of missing clinically significant cancers. Here we present prostate vision contrastive network (ProViCNet), prostate organ-specific vision foundation models for Magnetic Resonance Imaging (MRI) and Trans-Rectal Ultrasound imaging (TRUS) for comprehensive cancer detection. ProViCNet was trained and validated using 4,401 patients across six institutions, as a prostate cancer detection model on radiology images relying on patch-level contrastive learning guided by biopsy confirmed radiologist annotations. ProViCNet demonstrated consistent performance across multiple internal and external validation cohorts with area under the receiver operating curve values ranging from 0.875 to 0.966, significantly outperforming radiologists in the reader study (0.907 versus 0.805, p<0.001) for mpMRI, while achieving 0.670 to 0.740 for TRUS. We also integrated ProViCNet with standard PSA to develop a virtual screening test, and we showed that we can maintain the high sensitivity for detecting clinically significant cancers while more than doubling specificity from 15% to 38% (p<0.001), thereby substantially reducing unnecessary biopsies. These findings highlight that ProViCNet's potential for enhancing prostate cancer diagnosis accuracy and reduce unnecessary biopsies, thereby optimizing diagnostic pathways.

Understanding human visual attention on a scene over time has applications in domains such as interface design and inferring cognitive states. Modeling visual scanpaths has historically relied on specialized architectures with hand-crafted priors. While these architectures can model fixation sequences, their rigid structural biases restrict easy extendability and flexible conditioning. For instance, integrating task-specific instructions or adapting to distinct viewer identities requires custom, disjoint architectural additions. We frame scanpath prediction purely as a discrete sequence modeling task. By mapping coordinates into a text vocabulary, we leverage the pretrained representations of Vision-Language Models. This framing absorbs diverse factors of variation: simple prompting allows for global conditioning, such as providing viewer identities to capture personalized biases, or task-specific objectives like visual search. The framework can also integrate per-fixation attributes, such as individual fixation durations, alongside spatial locations. The autoregressive alignment enables the scalable, exact computation of per-fixation log-likelihoods, directly equivalent to the commonly used Information Gain (IG) metric. Our model, DeepGaze3.5-VL, establishes a new state-of-the-art across multiple datasets, achieving 2.18 bits of IG on MIT1003, a 46% improvement over DeepGaze III. This advantage persists even when baselines use identical high-capacity vision encoders. Beyond predictive performance, our generative framework serves as a powerful computational tool for direct behavioral interventions, allowing for controlled in-silico simulations that would be experimentally difficult or impossible to conduct in vivo. We demonstrate this ability by performing controlled interventions on the durations of pre-saccadic fixations, recovering known oculomotor phenomena purely from data.

The Iterative Closest Point (ICP) algorithm and its variants are a fundamental technique for rigid registration between two point sets, with wide applications in different areas from robotics to 3D reconstruction. The main drawbacks for ICP are its slow convergence as well as its sensitivity to outliers, missing data, and partial overlaps. Recent work such as Sparse ICP achieves robustness via sparsity optimization at the cost of computational speed. In this paper, we propose a new method for robust registration with fast convergence. First, we show that the classical point-to-point ICP can be treated as a majorization-minimization (MM) algorithm, and propose an Anderson acceleration approach to speed up its convergence. In addition, we introduce a robust error metric based on the Welsch's function, which is minimized efficiently using the MM algorithm with Anderson acceleration. On challenging datasets with noises and partial overlaps, we achieve similar or better accuracy than Sparse ICP while being at least an order of magnitude faster. Finally, we extend the robust formulation to point-to-plane ICP, and solve the resulting problem using a similar Anderson-accelerated MM strategy. Our robust ICP methods improve the registration accuracy on benchmark datasets while being competitive in computational time.

Current evaluation protocols for Vision-Language Models (VLMs) in Radiology Report Generation (RRG) rely on report-level metrics that measure lexical overlap or aggregate clinical correctness. However, such metrics do not test whether individual diagnostic statements stem from the actual pathological evidence visible in the image. This allows models to achieve competitive scores by exploiting learned priors or spurious correlations, a failure mode we refer to as vision shortcut. We introduce SHOVIR, a benchmark for evaluating vision shortcut behavior in RRG. SHOVIR extends two spatially annotated chest X-ray datasets, MIMIC-CXR and PadChest-GR, with per-box CheXpert labels, and defines image-level and disease-level occlusion experiments that contrast baseline performance on clean images against localized, region-specific perturbations. Comparing predictions across these conditions isolates two failure modes at the disease-class level: direct shortcuts, where a finding persists after its visual evidence is removed, and contextual shortcuts, where detection degrades once co-occurring pathologies are occluded despite the target region remaining intact. Benchmarking eight state-of-the-art VLMs, we find that shortcut behavior varies substantially across architectures and datasets. Models achieving the highest baseline report quality do not necessarily rank highest in spatial grounding, revealing that clinically fluent generation can coexist with shallow reliance on visual evidence. These findings expose a blind spot in current RRG evaluation and motivate region-aware assessment protocols.

Surgical scene segmentation is critical in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, referring surgical segmentation is emerging, given its advantage of providing surgeons with an interactive experience to segment the target object. However, existing methods are limited by low efficiency and short-term tracking, hindering their applicability in complex real-world surgical scenarios. In this paper, we introduce ReSurgSAM2, a two-stage surgical referring segmentation framework that leverages Segment Anything Model 2 to perform text-referred target detection, followed by tracking with reliable initial frame identification and diversity-driven long-term memory. For the detection stage, we propose a cross-modal spatial-temporal Mamba to generate precise detection and segmentation results. Based on these results, our credible initial frame selection strategy identifies the reliable frame for the subsequent tracking. Upon selecting the initial frame, our method transitions to the tracking stage, where it incorporates a diversity-driven memory mechanism that maintains a credible and diverse memory bank, ensuring consistent long-term tracking. Extensive experiments demonstrate that ReSurgSAM2 achieves substantial improvements in accuracy and efficiency compared to existing methods, operating in real-time at 61.2 FPS. Our code and datasets will be available at https://github.com/jinlab-imvr/ReSurgSAM2.

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

The emergence of large multimodal models has unlocked remarkable potential in AI, particularly in pathology. However, the lack of specialized, high-quality benchmark impeded their development and precise evaluation. To address this, we introduce PathMMU, the largest and highest-quality expert-validated pathology benchmark for LMMs. It comprises 33,573 multimodal multi-choice questions and 21,599 images from various sources, and an explanation for the correct answer accompanies each question. The construction of PathMMU capitalizes on the robust capabilities of GPT-4V, utilizing approximately 30,000 gathered image-caption pairs to generate Q\&As. Significantly, to maximize PathMMU's authority, we invite six pathologists to scrutinize each question under strict standards in PathMMU's validation and test sets, while simultaneously setting an expert-level performance benchmark for PathMMU. We conduct extensive evaluations, including zero-shot assessments of 14 open-sourced and three closed-sourced LMMs and their robustness to image corruption. We also fine-tune representative LMMs to assess their adaptability to PathMMU. The empirical findings indicate that advanced LMMs struggle with the challenging PathMMU benchmark, with the top-performing LMM, GPT-4V, achieving only a 51.7\% zero-shot performance, significantly lower than the 71.4\% demonstrated by human pathologists. After fine-tuning, even open-sourced LMMs can surpass GPT-4V with a performance of over 60\%, but still fall short of the expertise shown by pathologists. We hope that the PathMMU will offer valuable insights and foster the development of more specialized, next-generation LLMs for pathology.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

The integration of artificial intelligence (AI) with radiology marks a transformative era in medicine. Vision foundation models have been adopted to enhance radiologic imaging analysis. However, the distinct complexities of radiologic 2D and 3D radiologic data pose unique challenges that existing models, pre-trained on general non-medical images, fail to address adequately. To bridge this gap and capitalize on the diagnostic precision required in radiologic imaging, we introduce Radiologic Contrastive Language-Image Pre-training (RadCLIP): a cross-modal vision-language foundational model that harnesses Vision Language Pre-training (VLP) framework to improve radiologic image analysis. Building upon Contrastive Language-Image Pre-training (CLIP), RadCLIP incorporates a slice pooling mechanism tailored for volumetric image analysis and is pre-trained using a large and diverse dataset of radiologic image-text pairs. The RadCLIP was pre-trained to effectively align radiologic images with their corresponding text annotations, creating a robust vision backbone for radiologic images. Extensive experiments demonstrate RadCLIP's superior performance in both uni-modal radiologic image classification and cross-modal image-text matching, highlighting its significant promise for improving diagnostic accuracy and efficiency in clinical settings. Our Key contributions include curating a large dataset with diverse radiologic 2D/3D radiologic image-text pairs, a slice pooling adapter using an attention mechanism for integrating 2D images, and comprehensive evaluations of RadCLIP on various radiologic downstream tasks.

This paper explores the problem of collision-free motion generation for manipulators by formulating it as a global motion optimization problem. We develop a parallel optimization technique to solve this problem and demonstrate its effectiveness on massively parallel GPUs. We show that combining simple optimization techniques with many parallel seeds leads to solving difficult motion generation problems within 50ms on average, 60x faster than state-of-the-art (SOTA) trajectory optimization methods. We achieve SOTA performance by combining L-BFGS step direction estimation with a novel parallel noisy line search scheme and a particle-based optimization solver. To further aid trajectory optimization, we develop a parallel geometric planner that plans within 20ms and also introduce a collision-free IK solver that can solve over 7000 queries/s. We package our contributions into a state of the art GPU accelerated motion generation library, cuRobo and release it to enrich the robotics community. Additional details are available at https://curobo.org

Many modern iterative solvers for large-scale tomographic reconstruction incur two major computational costs per iteration: expensive forward/adjoint projections to update the data fidelity term and costly proximal computations for the regulariser, often done via inner iterations. This paper studies for the first time the application of methods that couple randomised skipping of the proximal with variance-reduced subset-based optimisation of data-fit term, to simultaneously reduce both costs in challenging tomographic reconstruction tasks. We provide a series of experiments using both synthetic and real data, demonstrating striking speed-ups of the order 5x--20x compared to the non-skipped counterparts which have been so far the standard approach for efficiently solving these problems. Our work lays the groundwork for broader adoption of these methods in inverse problems.

Online surgical phase recognition (SPR) underpins context-aware operating-room systems and requires committing to a prediction at every frame from past context alone. Surgical video poses three demands that natural-video recognizers do not jointly address: procedures span tens of thousands of frames, time flows non-uniformly as long routine stretches are punctuated by brief phase-defining transitions, and the visual domain is narrow so backbone features are strongly correlated across channels. Existing recognizers either let per-frame cost grow with elapsed length, or hold cost bounded but advance state at a uniform rate with channel-independent dynamics, leaving the latter two demands unaddressed. We present SurgicalMamba, a causal SPR model built on Mamba2's structured state-space duality (SSD) that holds per-frame cost at O(d). It introduces three SSD-compatible components, each targeting one demand: a dual-path SSD block that separates long- and short-term regimes at the level of recurrent state; intensity-modulated stepping, a continuous-time time-warp that adapts the slow path's effective rate to phase-relevant information; and state regramming, a per-chunk Cayley rotation that opens cross-channel mixing in the otherwise axis-aligned SSM recurrence. The learned rotation planes inherit a phase-aligned structure without any direct supervision, offering an interpretable internal signature of surgical workflow. Across seven public SPR benchmarks, SurgicalMamba reaches state-of-the-art accuracy and phase-level Jaccard under strict online evaluation: 94.6%/82.7% on Cholec80 (+0.7 pp/+2.2 pp over the strongest prior) and 89.5%/68.9% on AutoLaparo (+1.7 pp/+2.0 pp), at 119 fps on a single GPU. Ablations isolate the contribution of each component. The code is publicly available at https://github.com/sukjuoh/Surgical-Mamba.

Current vision-language models (VLMs) in medicine are primarily designed for categorical question answering (e.g., "Is this normal or abnormal?") or qualitative descriptive tasks. However, clinical decision-making often relies on quantitative assessments, such as measuring the size of a tumor or the angle of a joint, from which physicians draw their own diagnostic conclusions. This quantitative reasoning capability remains underexplored and poorly supported in existing VLMs. In this work, we introduce MedVision, a large-scale dataset and benchmark specifically designed to evaluate and improve VLMs on quantitative medical image analysis. MedVision spans 22 public datasets covering diverse anatomies and modalities, with 30.8 million image-annotation pairs. We focus on three representative quantitative tasks: (1) detection of anatomical structures and abnormalities, (2) tumor/lesion (T/L) size estimation, and (3) angle/distance (A/D) measurement. Our benchmarks show that current off-the-shelf VLMs perform poorly on these tasks. However, with supervised fine-tuning on MedVision, we significantly enhance their performance across detection, T/L estimation, and A/D measurement, demonstrating reduced error rates and improved precision. This work provides a foundation for developing VLMs with robust quantitative reasoning capabilities in medical imaging. Code and data are available at https://medvision-vlm.github.io.

The rapid progress of multimodal large language models (MLLMs) has led to increasing interest in agent-based systems. While most prior work in medical imaging concentrates on automating routine clinical workflows, we study an underexplored yet clinically significant setting: distinguishing visually hard-to-separate diseases in a zero-shot setting. We benchmark representative agents on two imaging-only proxy diagnostic tasks, (1) melanoma vs. atypical nevus and (2) pulmonary edema vs. pneumonia, where visual features are highly confounded despite substantial differences in clinical management. We introduce a multi-agent framework based on contrastive adjudication. Experimental results show improved diagnostic performance (an 11-percentage-point gain in accuracy on dermoscopy data) and reduced unsupported claims on qualitative samples, although overall performance remains insufficient for clinical deployment. We acknowledge the inherent uncertainty in human annotations and the absence of clinical context, which further limit the translation to real-world settings. Within this controlled setting, this pilot study provides preliminary insights into zero-shot agent performance in visually confounded scenarios.

3D reconstruction techniques have widely been used for digital documentation of archaeological fragments. However, efficient digital capture of fragments remains as a challenge. In this work, we aim to develop a portable, high-throughput, and accurate reconstruction system for efficient digitization of fragments excavated in archaeological sites. To realize high-throughput digitization of large numbers of objects, an effective strategy is to perform scanning and reconstruction in batches. However, effective batch-based scanning and reconstruction face two key challenges: 1) how to correlate partial scans of the same object from multiple batch scans, and 2) how to register and reconstruct complete models from partial scans that exhibit only small overlaps. To tackle these two challenges, we develop a new batch-based matching algorithm that pairs the front and back sides of the fragments, and a new Bilateral Boundary ICP algorithm that can register partial scans sharing very narrow overlapping regions. Extensive validation in labs and testing in excavation sites demonstrate that these designs enable efficient batch-based scanning for fragments. We show that such a batch-based scanning and reconstruction pipeline can have immediate applications on digitizing sherds in archaeological excavations. Our project page: https://jiepengwang.github.io/FIRES/.

Sampling-based motion planners (SBMPs) are effective for planning with complex kinodynamic constraints in high-dimensional spaces, but they still struggle to achieve real-time performance, which is mainly due to their serial computation design. We present Kinodynamic Parallel Accelerated eXpansion (Kino-PAX), a novel highly parallel kinodynamic SBMP designed for parallel devices such as GPUs. Kino-PAX grows a tree of trajectory segments directly in parallel. Our key insight is how to decompose the iterative tree growth process into three massively parallel subroutines. Kino-PAX is designed to align with the parallel device execution hierarchies, through ensuring that threads are largely independent, share equal workloads, and take advantage of low-latency resources while minimizing high-latency data transfers and process synchronization. This design results in a very efficient GPU implementation. We prove that Kino-PAX is probabilistically complete and analyze its scalability with compute hardware improvements. Empirical evaluations demonstrate solutions in the order of 10 ms on a desktop GPU and in the order of 100 ms on an embedded GPU, representing up to 1000 times improvement compared to coarse-grained CPU parallelization of state-of-the-art sequential algorithms over a range of complex environments and systems.

Medical image segmentation poses challenges due to domain gaps, data modality variations, and dependency on domain knowledge or experts, especially for low- and middle-income countries (LMICs). Whereas for humans, given a few exemplars (with corresponding labels), we are able to segment different medical images even without exten-sive domain-specific clinical training. In addition, current SAM-based medical segmentation models use fine-grained visual prompts, such as the bounding rectangle generated from manually annotated target segmentation mask, as the bounding box (bbox) prompt during the testing phase. However, in actual clinical scenarios, no such precise prior knowledge is available. Our experimental results also reveal that previous models nearly fail to predict when given coarser bbox prompts. Considering these issues, in this paper, we introduce a domain-aware selective adaptation approach to adapt the general knowledge learned from a large model trained with natural images to the corresponding medical domains/modalities, with access to only a few (e.g. less than 5) exemplars. Our method mitigates the aforementioned limitations, providing an efficient and LMICs-friendly solution. Extensive experimental analysis showcases the effectiveness of our approach, offering potential advancements in healthcare diagnostics and clinical applications in LMICs.

Radiologists rely on eye movements to navigate and interpret medical images. A trained radiologist possesses knowledge about the potential diseases that may be present in the images and, when searching, follows a mental checklist to locate them using their gaze. This is a key observation, yet existing models fail to capture the underlying intent behind each fixation. In this paper, we introduce a deep learning-based approach, RadGazeIntent, designed to model this behavior: having an intention to find something and actively searching for it. Our transformer-based architecture processes both the temporal and spatial dimensions of gaze data, transforming fine-grained fixation features into coarse, meaningful representations of diagnostic intent to interpret radiologists' goals. To capture the nuances of radiologists' varied intention-driven behaviors, we process existing medical eye-tracking datasets to create three intention-labeled subsets: RadSeq (Systematic Sequential Search), RadExplore (Uncertainty-driven Exploration), and RadHybrid (Hybrid Pattern). Experimental results demonstrate RadGazeIntent's ability to predict which findings radiologists are examining at specific moments, outperforming baseline methods across all intention-labeled datasets.

Magnetic Resonance Imaging (MRI) is a critical tool in modern medical diagnostics, yet its prolonged acquisition time remains a critical limitation, especially in time-sensitive clinical scenarios. While undersampling strategies can accelerate image acquisition, they often result in image artifacts and degraded quality. Recent diffusion models have shown promise for reconstructing high-fidelity images from undersampled data by learning powerful image priors; however, most existing approaches either (i) rely on unsupervised score functions without paired supervision or (ii) apply data consistency only as a post-processing step. In this work, we introduce a conditional denoising diffusion framework with iterative data-consistency correction, which differs from prior methods by embedding the measurement model directly into every reverse diffusion step and training the model on paired undersampled-ground truth data. This hybrid design bridges generative flexibility with explicit enforcement of MRI physics. Experiments on the fastMRI dataset demonstrate that our framework consistently outperforms recent state-of-the-art deep learning and diffusion-based methods in SSIM, PSNR, and LPIPS, with LPIPS capturing perceptual improvements more faithfully. These results demonstrate that integrating conditional supervision with iterative consistency updates yields substantial improvements in both pixel-level fidelity and perceptual realism, establishing a principled and practical advance toward robust, accelerated MRI reconstruction.

Multimodal MRI provides critical complementary information for accurate brain tumor segmentation. However, conventional methods struggle when certain modalities are missing due to issues such as image quality, protocol inconsistencies, patient allergies, or financial constraints. To address this, we propose a robust single-modality parallel processing framework that achieves high segmentation accuracy even with incomplete modalities. Leveraging Holder divergence and mutual information, our model maintains modality-specific features while dynamically adjusting network parameters based on the available inputs. By using these divergence- and information-based loss functions, the framework effectively quantifies discrepancies between predictions and ground-truth labels, resulting in consistently accurate segmentation. Extensive evaluations on the BraTS 2018 and BraTS 2020 datasets demonstrate superior performance over existing methods in handling missing modalities.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

Brain MRI scans are often found in four modalities, consisting of T1-weighted with and without contrast enhancement (T1ce and T1w), T2-weighted imaging (T2w), and Flair. Leveraging complementary information from these different modalities enables models to learn richer, more discriminative features for understanding brain anatomy, which could be used in downstream tasks such as anomaly detection. However, in clinical practice, not all MRI modalities are always available due to various reasons. This makes missing modality generation a critical challenge in medical image analysis. In this paper, we propose SLaM-DiMM, a novel missing modality generation framework that harnesses the power of diffusion models to synthesize any of the four target MRI modalities from other available modalities. Our approach not only generates high-fidelity images but also ensures structural coherence across the depth of the volume through a dedicated coherence enhancement mechanism. Qualitative and quantitative evaluations on the BraTS-Lighthouse-2025 Challenge dataset demonstrate the effectiveness of the proposed approach in synthesizing anatomically plausible and structurally consistent results. Code is available at https://github.com/BheeshmSharma/SLaM-DiMM-MICCAI-BraTS-Challenge-2025.

Medical image analysis is critical yet challenged by the need of jointly segmenting organs or tissues, and numerous instances for anatomical structures and tumor microenvironment analysis. Existing studies typically formulated different segmentation tasks in isolation, which overlooks the fundamental interdependencies between these tasks, leading to suboptimal segmentation performance and insufficient medical image understanding. To address this issue, we propose a Co-Seg++ framework for versatile medical segmentation. Specifically, we introduce a novel co-segmentation paradigm, allowing semantic and instance segmentation tasks to mutually enhance each other. We first devise a spatio-temporal prompt encoder (STP-Encoder) to capture long-range spatial and temporal relationships between segmentation regions and image embeddings as prior spatial constraints. Moreover, we devise a multi-task collaborative decoder (MTC-Decoder) that leverages cross-guidance to strengthen the contextual consistency of both tasks, jointly computing semantic and instance segmentation masks. Extensive experiments on diverse CT and histopathology datasets demonstrate that the proposed Co-Seg++ outperforms state-of-the-arts in the semantic, instance, and panoptic segmentation of dental anatomical structures, histopathology tissues, and nuclei instances. The source code is available at https://github.com/xq141839/Co-Seg-Plus.

Breast cancer is one of the most common causes of death among women worldwide. Early detection helps in reducing the number of deaths. Automated 3D Breast Ultrasound (ABUS) is a newer approach for breast screening, which has many advantages over handheld mammography such as safety, speed, and higher detection rate of breast cancer. Tumor detection, segmentation, and classification are key components in the analysis of medical images, especially challenging in the context of 3D ABUS due to the significant variability in tumor size and shape, unclear tumor boundaries, and a low signal-to-noise ratio. The lack of publicly accessible, well-labeled ABUS datasets further hinders the advancement of systems for breast tumor analysis. Addressing this gap, we have organized the inaugural Tumor Detection, Segmentation, and Classification Challenge on Automated 3D Breast Ultrasound 2023 (TDSC-ABUS2023). This initiative aims to spearhead research in this field and create a definitive benchmark for tasks associated with 3D ABUS image analysis. In this paper, we summarize the top-performing algorithms from the challenge and provide critical analysis for ABUS image examination. We offer the TDSC-ABUS challenge as an open-access platform at https://tdsc-abus2023.grand-challenge.org/ to benchmark and inspire future developments in algorithmic research.

Predicting human gaze scanpaths is crucial for understanding visual attention, with applications in human-computer interaction, autonomous systems, and cognitive robotics. While deep learning models have advanced scanpath prediction, most existing approaches generate averaged behaviors, failing to capture the variability of human visual exploration. In this work, we present ScanDiff, a novel architecture that combines diffusion models with Vision Transformers to generate diverse and realistic scanpaths. Our method explicitly models scanpath variability by leveraging the stochastic nature of diffusion models, producing a wide range of plausible gaze trajectories. Additionally, we introduce textual conditioning to enable task-driven scanpath generation, allowing the model to adapt to different visual search objectives. Experiments on benchmark datasets show that ScanDiff surpasses state-of-the-art methods in both free-viewing and task-driven scenarios, producing more diverse and accurate scanpaths. These results highlight its ability to better capture the complexity of human visual behavior, pushing forward gaze prediction research. Source code and models are publicly available at https://aimagelab.github.io/ScanDiff.

Magnetic resonance imaging (MRI) super-resolution is vital for improving diagnostic accessibility, yet most methods treat it as a deterministic mapping from a fixed low-resolution input to a high-resolution target. This overlooks a key property of MRI acquisition physics: spatial resolution and signal-to-noise ratio (SNR) are inherently coupled, making any given low-resolution scan merely one of many possible realizations under varying acquisition trade-offs. We rethink MRI super-resolution as a physics-aware reconstruction problem, in which the goal is to identify the optimal resolution-SNR configuration and then super-resolve it to obtain high-quality MRI results. A key implication of this formulation is that MRI resolution becomes dynamic rather than fixed. To handle such resolution-heterogeneous inputs, we adapt 2D Gaussian Splatting (2D GS) to MRI by formulating reconstruction as a coordinate-based, resolution-agnostic rendering problem. To further enhance fidelity, we introduce three innovations: (1) a prior-aware Gaussian representation that combines an Anatomical Structure Prior for tissue-specific kernel initialization with an Imaging System Prior that captures hardware characteristics via a covariance dictionary; (2) a physics-constrained signal modeling scheme that predicts intrinsic tissue parameters (proton density rho and effective relaxation rate R2) and synthesizes intensities through governing physical equations, ensuring biophysically plausible contrast; and (3) a meta-learning framework that alleviates paired-data scarcity by pretraining on simulated data and adapting to real-world conditions. Extensive experiments on dynamic-resolution datasets and standard benchmarks demonstrate that our method achieves state-of-the-art performance, highlighting its strong potential for clinical deployment.

Planning long-horizon robot manipulation requires making discrete decisions about which objects to interact with and continuous decisions about how to interact with them. A robot planner must select grasps, placements, and motions that are feasible and safe. This class of problems falls under Task and Motion Planning (TAMP) and poses significant computational challenges in terms of algorithm runtime and solution quality, particularly when the solution space is highly constrained. To address these challenges, we propose a new bilevel TAMP algorithm that leverages GPU parallelism to efficiently explore thousands of candidate continuous solutions simultaneously. Our approach uses GPU parallelism to sample an initial batch of solution seeds for a plan skeleton and to apply differentiable optimization on this batch to satisfy plan constraints and minimize solution cost with respect to soft objectives. We demonstrate that our algorithm can effectively solve highly constrained problems with non-convex constraints in just seconds, substantially outperforming serial TAMP approaches, and validate our approach on multiple real-world robots. Project website and code: https://cutamp.github.io

Determining whether two sets of images belong to the same or different distributions or domains is a crucial task in modern medical image analysis and deep learning; for example, to evaluate the output quality of image generative models. Currently, metrics used for this task either rely on the (potentially biased) choice of some downstream task, such as segmentation, or adopt task-independent perceptual metrics (e.g., Fréchet Inception Distance/FID) from natural imaging, which we show insufficiently capture anatomical features. To this end, we introduce a new perceptual metric tailored for medical images, FRD (Fréchet Radiomic Distance), which utilizes standardized, clinically meaningful, and interpretable image features. We show that FRD is superior to other image distribution metrics for a range of medical imaging applications, including out-of-domain (OOD) detection, the evaluation of image-to-image translation (by correlating more with downstream task performance as well as anatomical consistency and realism), and the evaluation of unconditional image generation. Moreover, FRD offers additional benefits such as stability and computational efficiency at low sample sizes, sensitivity to image corruptions and adversarial attacks, feature interpretability, and correlation with radiologist-perceived image quality. Additionally, we address key gaps in the literature by presenting an extensive framework for the multifaceted evaluation of image similarity metrics in medical imaging -- including the first large-scale comparative study of generative models for medical image translation -- and release an accessible codebase to facilitate future research. Our results are supported by thorough experiments spanning a variety of datasets, modalities, and downstream tasks, highlighting the broad potential of FRD for medical image analysis.

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

Adapting CLIP to vertical domains is typically approached by novel fine-tuning strategies or by continual pre-training (CPT) on large domain-specific datasets. Yet, data itself remains an underexplored factor in this process. We revisit this task from a data-centric perspective: Can effective data selection substitute for large-scale datasets in CPT? We introduce CHIPS (Curvature-aware Hybrid Influence in Projection Subspace), which assigns each image-text pair a utility score that integrates three complementary factors aligned with three goals: faithfulness via a curvature-aware, Newton-style alignment computed in CLIP's end-point subspace; scalability via an InfoNCE-aware curvature estimator with Johnson-Lindenstrauss (JL) sketching; and retention via a selection-aware relevance weight combined with learnability to balance target adaptation against general-domain preservation. We justify this design theoretically by proving a lower-bound guarantee on the proxy's correlation with full-parameter alignment and by characterizing the bias-variance trade-offs introduced by curvature mixing and JL sketching. We evaluate CHIPS empirically across various settings: 1) CHIPS attains state-of-the-art performance among selection baselines on 17 medical benchmarks, matches full-dataset CPT with 30% of the data, and outperforms half-dataset CPT using only 10%; 2) on 31 general-domain benchmarks, CHIPS yields the smallest performance drop under 10-30% data-retention budgets. Code, data, and checkpoints will be released.

Intraoperative registration of real-time ultrasound (iUS) to preoperative Magnetic Resonance Imaging (MRI) remains an unsolved problem due to severe modality-specific differences in appearance, resolution, and field-of-view. To address this, we propose a novel 3D cross-modal keypoint descriptor for MRI-iUS matching and registration. Our approach employs a patient-specific matching-by-synthesis approach, generating synthetic iUS volumes from preoperative MRI. This enables supervised contrastive training to learn a shared descriptor space. A probabilistic keypoint detection strategy is then employed to identify anatomically salient and modality-consistent locations. During training, a curriculum-based triplet loss with dynamic hard negative mining is used to learn descriptors that are i) robust to iUS artifacts such as speckle noise and limited coverage, and ii) rotation-invariant. At inference, the method detects keypoints in MR and real iUS images and identifies sparse matches, which are then used to perform rigid registration. Our approach is evaluated using 3D MRI-iUS pairs from the ReMIND dataset. Experiments show that our approach outperforms state-of-the-art keypoint matching methods across 11 patients, with an average precision of 69.8%. For image registration, our method achieves a competitive mean Target Registration Error of 2.39 mm on the ReMIND2Reg benchmark. Compared to existing iUS-MR registration approaches, our framework is interpretable, requires no manual initialization, and shows robustness to iUS field-of-view variation. Code, data and model weights are available at https://github.com/morozovdd/CrossKEY.

Medical Image Quality Assessment (IQA) serves as the first-mile safety gate for clinical AI, yet existing approaches remain constrained by scalar, score-based metrics and fail to reflect the descriptive, human-like reasoning process central to expert evaluation. To address this gap, we introduce MedQ-Bench, a comprehensive benchmark that establishes a perception-reasoning paradigm for language-based evaluation of medical image quality with Multi-modal Large Language Models (MLLMs). MedQ-Bench defines two complementary tasks: (1) MedQ-Perception, which probes low-level perceptual capability via human-curated questions on fundamental visual attributes; and (2) MedQ-Reasoning, encompassing both no-reference and comparison reasoning tasks, aligning model evaluation with human-like reasoning on image quality. The benchmark spans five imaging modalities and over forty quality attributes, totaling 2,600 perceptual queries and 708 reasoning assessments, covering diverse image sources including authentic clinical acquisitions, images with simulated degradations via physics-based reconstructions, and AI-generated images. To evaluate reasoning ability, we propose a multi-dimensional judging protocol that assesses model outputs along four complementary axes. We further conduct rigorous human-AI alignment validation by comparing LLM-based judgement with radiologists. Our evaluation of 14 state-of-the-art MLLMs demonstrates that models exhibit preliminary but unstable perceptual and reasoning skills, with insufficient accuracy for reliable clinical use. These findings highlight the need for targeted optimization of MLLMs in medical IQA. We hope that MedQ-Bench will catalyze further exploration and unlock the untapped potential of MLLMs for medical image quality evaluation.

Accurate and generalizable object segmentation in ultrasound imaging remains a significant challenge due to anatomical variability, diverse imaging protocols, and limited annotated data. In this study, we propose a prompt-driven vision-language model (VLM) that integrates Grounding DINO with SAM2 to enable object segmentation across multiple ultrasound organs. A total of 18 public ultrasound datasets, encompassing the breast, thyroid, liver, prostate, kidney, and paraspinal muscle, were utilized. These datasets were divided into 15 for fine-tuning and validation of Grounding DINO using Low Rank Adaptation (LoRA) to the ultrasound domain, and 3 were held out entirely for testing to evaluate performance in unseen distributions. Comprehensive experiments demonstrate that our approach outperforms state-of-the-art segmentation methods, including UniverSeg, MedSAM, MedCLIP-SAM, BiomedParse, and SAMUS on most seen datasets while maintaining strong performance on unseen datasets without additional fine-tuning. These results underscore the promise of VLMs in scalable and robust ultrasound image analysis, reducing dependence on large, organ-specific annotated datasets. We will publish our code on code.sonography.ai after acceptance.

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

We introduce Medal S, a medical segmentation foundation model that supports native-resolution spatial and textual prompts within an end-to-end trainable framework. Unlike text-only methods lacking spatial awareness, Medal S achieves channel-wise alignment between volumetric prompts and text embeddings, mitigating inaccuracies from resolution mismatches. By preserving full 3D context, it efficiently processes multiple native-resolution masks in parallel, enhancing multi-class segmentation performance. A lightweight 3D convolutional module enables precise voxel-space refinement guided by both prompt types, supporting up to 243 classes across CT, MRI, PET, ultrasound, and microscopy modalities in the BiomedSegFM dataset. Medal S offers two prompting modes: a text-only mode, where model predictions serve as spatial prompts for self-refinement without human input, and a hybrid mode, incorporating manual annotations for enhanced flexibility. For 24-class segmentation, parallel spatial prompting reduces inference time by more than 90% compared to sequential prompting. We propose dynamic resampling to address target-patch ratio imbalance, extending SAT and nnU-Net for data augmentation. Furthermore, we develop optimized text preprocessing, a two-stage inference strategy, and post-processing techniques to improve memory efficiency, precision, and inference speed. On the five-modality average on the validation set, Medal S outperforms SAT with a DSC of 75.44 (vs. 69.83), NSD of 77.34 (vs. 71.06), F1 of 38.24 (vs. 24.88), and DSC TP of 65.46 (vs. 46.97). Medal S achieves excellent performance by harmonizing spatial precision with semantic textual guidance, demonstrating superior efficiency and accuracy in multi-class medical segmentation tasks compared to sequential prompt-based approaches. Medal S will be publicly available at https://github.com/yinghemedical/Medal-S.

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf/

Various tasks in data science are modeled utilizing the variational regularization approach, where manually selecting regularization parameters presents a challenge. The difficulty gets exacerbated when employing regularizers involving a large number of hyperparameters. To overcome this challenge, bilevel learning can be employed to learn such parameters from data. However, neither exact function values nor exact gradients with respect to the hyperparameters are attainable, necessitating methods that only rely on inexact evaluation of such quantities. State-of-the-art inexact gradient-based methods a priori select a sequence of the required accuracies and cannot identify an appropriate step size since the Lipschitz constant of the hypergradient is unknown. In this work, we propose an algorithm with backtracking line search that only relies on inexact function evaluations and hypergradients and show convergence to a stationary point. Furthermore, the proposed algorithm determines the required accuracy dynamically rather than manually selected before running it. Our numerical experiments demonstrate the efficiency and feasibility of our approach for hyperparameter estimation on a range of relevant problems in imaging and data science such as total variation and field of experts denoising and multinomial logistic regression. Particularly, the results show that the algorithm is robust to its own hyperparameters such as the initial accuracies and step size.

High-resolution segmentation is critical for precise disease diagnosis by extracting fine-grained morphological details. Existing hierarchical encoder-decoder frameworks have demonstrated remarkable adaptability across diverse medical segmentation tasks. While beneficial, they usually require the huge computation and memory cost when handling large-size segmentation, which limits their applications in foundation model building and real-world clinical scenarios. To address this limitation, we propose a holistically efficient framework for high-resolution medical image segmentation, called HER-Seg. Specifically, we first devise a computation-efficient image encoder (CE-Encoder) to model long-range dependencies with linear complexity while maintaining sufficient representations. In particular, we introduce the dual-gated linear attention (DLA) mechanism to perform cascaded token filtering, selectively retaining important tokens while ignoring irrelevant ones to enhance attention computation efficiency. Then, we introduce a memory-efficient mask decoder (ME-Decoder) to eliminate the demand for the hierarchical structure by leveraging cross-scale segmentation decoding. Extensive experiments reveal that HER-Seg outperforms state-of-the-arts in high-resolution medical 2D, 3D and video segmentation tasks. In particular, our HER-Seg requires only 0.59GB training GPU memory and 9.39G inference FLOPs per 1024times1024 image, demonstrating superior memory and computation efficiency. The code is available at https://github.com/xq141839/HER-Seg.

Similarity search finds application in specialized database systems handling complex data such as images or videos, which are typically represented by high-dimensional features and require specific indexing structures. This paper tackles the problem of better utilizing GPUs for this task. While GPUs excel at data-parallel tasks, prior approaches are bottlenecked by algorithms that expose less parallelism, such as k-min selection, or make poor use of the memory hierarchy. We propose a design for k-selection that operates at up to 55% of theoretical peak performance, enabling a nearest neighbor implementation that is 8.5x faster than prior GPU state of the art. We apply it in different similarity search scenarios, by proposing optimized design for brute-force, approximate and compressed-domain search based on product quantization. In all these setups, we outperform the state of the art by large margins. Our implementation enables the construction of a high accuracy k-NN graph on 95 million images from the Yfcc100M dataset in 35 minutes, and of a graph connecting 1 billion vectors in less than 12 hours on 4 Maxwell Titan X GPUs. We have open-sourced our approach for the sake of comparison and reproducibility.

Off-resonance artifacts in magnetic resonance imaging (MRI) are visual distortions that occur when the actual resonant frequencies of spins within the imaging volume differ from the expected frequencies used to encode spatial information. These discrepancies can be caused by a variety of factors, including magnetic field inhomogeneities, chemical shifts, or susceptibility differences within the tissues. Such artifacts can manifest as blurring, ghosting, or misregistration of the reconstructed image, and they often compromise its diagnostic quality. We propose to resolve these artifacts by lifting the 2D MRI reconstruction problem to 3D, introducing an additional "spectral" dimension to model this off-resonance. Our approach is inspired by recent progress in modeling radiance fields, and is capable of reconstructing both static and dynamic MR images as well as separating fat and water, which is of independent clinical interest. We demonstrate our approach in the context of PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI acquisitions, which are popular for their robustness to motion artifacts. Our method operates in a few minutes on a single GPU, and to our knowledge is the first to correct for chemical shift in gradient echo PROPELLER MRI reconstruction without additional measurements or pretraining data.

Text-conditioned generative models for volumetric medical imaging provide semantic control but lack explicit anatomical guidance, often resulting in outputs that are spatially ambiguous or anatomically inconsistent. In contrast, structure-driven methods ensure strong anatomical consistency but typically assume access to ground-truth annotations, which are unavailable when the target image is to be synthesized. We propose a retrieval-augmented approach for Text-to-CT generation that integrates semantic and anatomical information under a realistic inference setting. Given a radiology report, our method retrieves a semantically related clinical case using a 3D vision-language encoder and leverages its associated anatomical annotation as a structural proxy. This proxy is injected into a text-conditioned latent diffusion model via a ControlNet branch, providing coarse anatomical guidance while maintaining semantic flexibility. Experiments on the CT-RATE dataset show that retrieval-augmented generation improves image fidelity and clinical consistency compared to text-only baselines, while additionally enabling explicit spatial controllability, a capability inherently absent in such approaches. Further analysis highlights the importance of retrieval quality, with semantically aligned proxies yielding consistent gains across all evaluation axes. This work introduces a principled and scalable mechanism to bridge semantic conditioning and anatomical plausibility in volumetric medical image synthesis. Code will be released.

We introduce a deep learning image segmentation framework that is extremely robust to missing imaging modalities. Instead of attempting to impute or synthesize missing data, the proposed approach learns, for each modality, an embedding of the input image into a single latent vector space for which arithmetic operations (such as taking the mean) are well defined. Points in that space, which are averaged over modalities available at inference time, can then be further processed to yield the desired segmentation. As such, any combinatorial subset of available modalities can be provided as input, without having to learn a combinatorial number of imputation models. Evaluated on two neurological MRI datasets (brain tumors and MS lesions), the approach yields state-of-the-art segmentation results when provided with all modalities; moreover, its performance degrades remarkably gracefully when modalities are removed, significantly more so than alternative mean-filling or other synthesis approaches.

Medical image and video segmentation is a critical task for precision medicine, which has witnessed considerable progress in developing task or modality-specific and generalist models for 2D images. However, there have been limited studies on building general-purpose models for 3D images and videos with comprehensive user studies. Here, we present MedSAM2, a promptable segmentation foundation model for 3D image and video segmentation. The model is developed by fine-tuning the Segment Anything Model 2 on a large medical dataset with over 455,000 3D image-mask pairs and 76,000 frames, outperforming previous models across a wide range of organs, lesions, and imaging modalities. Furthermore, we implement a human-in-the-loop pipeline to facilitate the creation of large-scale datasets resulting in, to the best of our knowledge, the most extensive user study to date, involving the annotation of 5,000 CT lesions, 3,984 liver MRI lesions, and 251,550 echocardiogram video frames, demonstrating that MedSAM2 can reduce manual costs by more than 85%. MedSAM2 is also integrated into widely used platforms with user-friendly interfaces for local and cloud deployment, making it a practical tool for supporting efficient, scalable, and high-quality segmentation in both research and healthcare environments.

The Segment Anything Model (SAM) has demonstrated outstanding adaptation to medical image segmentation but still faces three major challenges. Firstly, the huge computational costs of SAM limit its real-world applicability. Secondly, SAM depends on manual annotations (e.g., points, boxes) as prompts, which are laborious and impractical in clinical scenarios. Thirdly, SAM handles all segmentation targets equally, which is suboptimal for diverse medical modalities with inherent heterogeneity. To address these issues, we propose an Efficient Self-Prompting SAM for universal medical image segmentation, named ESP-MedSAM. We devise a Multi-Modal Decoupled Knowledge Distillation (MMDKD) strategy to distil common image knowledge and domain-specific medical knowledge from the foundation model to train a lightweight image encoder and a modality controller. Further, they combine with the additionally introduced Self-Patch Prompt Generator (SPPG) and Query-Decoupled Modality Decoder (QDMD) to construct ESP-MedSAM. Specifically, SPPG aims to generate a set of patch prompts automatically and QDMD leverages a one-to-one strategy to provide an independent decoding channel for every modality. Extensive experiments indicate that ESP-MedSAM outperforms state-of-the-arts in diverse medical imaging segmentation takes, displaying superior zero-shot learning and modality transfer ability. Especially, our framework uses only 31.4% parameters compared to SAM-Base.

Recent advances in Large Vision-Language Models (LVLMs) have shown strong potential for multi-modal radiological reasoning, particularly in tasks like diagnostic visual question answering (VQA) and radiology report generation. However, most existing approaches for 3D CT analysis largely rely on static, single-pass inference. In practice, clinical interpretation is a dynamic, tool-mediated workflow where radiologists iteratively review slices and use measurement, radiomics, and segmentation tools to refine findings. To bridge this gap, we propose CT-Flow, an agentic framework designed for interoperable volumetric interpretation. By leveraging the Model Context Protocol (MCP), CT-Flow shifts from closed-box inference to an open, tool-aware paradigm. We curate CT-FlowBench, the first large-scale instruction-tuning benchmark tailored for 3D CT tool-use and multi-step reasoning. Built upon this, CT-Flow functions as a clinical orchestrator capable of decomposing complex natural language queries into automated tool-use sequences. Experimental evaluations on CT-FlowBench and standard 3D VQA datasets demonstrate that CT-Flow achieves state-of-the-art performance, surpassing baseline models by 41% in diagnostic accuracy and achieving a 95% success rate in autonomous tool invocation. This work provides a scalable foundation for integrating autonomous, agentic intelligence into real-world clinical radiology.

Medical image restoration (MedIR) aims to recover high-quality medical images from their low-quality counterparts. Recent advancements in MedIR have focused on All-in-One models capable of simultaneously addressing multiple different MedIR tasks. However, due to significant differences in both modality and degradation types, using a shared model for these diverse tasks requires careful consideration of two critical inter-task relationships: task interference, which occurs when conflicting gradient update directions arise across tasks on the same parameter, and task imbalance, which refers to uneven optimization caused by varying learning difficulties inherent to each task. To address these challenges, we propose a task-adaptive Transformer (TAT), a novel framework that dynamically adapts to different tasks through two key innovations. First, a task-adaptive weight generation strategy is introduced to mitigate task interference by generating task-specific weight parameters for each task, thereby eliminating potential gradient conflicts on shared weight parameters. Second, a task-adaptive loss balancing strategy is introduced to dynamically adjust loss weights based on task-specific learning difficulties, preventing task domination or undertraining. Extensive experiments demonstrate that our proposed TAT achieves state-of-the-art performance in three MedIR tasks--PET synthesis, CT denoising, and MRI super-resolution--both in task-specific and All-in-One settings. Code is available at https://github.com/Yaziwel/TAT.

Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of high clinical relevance because diagnostic decisions often depend on rating of objects rather than e.g. pixels. For this task, the cumbersome and iterative process of method configuration constitutes a major research bottleneck. Recently, nnU-Net has tackled this challenge for the task of image segmentation with great success. Following nnU-Net's agenda, in this work we systematize and automate the configuration process for medical object detection. The resulting self-configuring method, nnDetection, adapts itself without any manual intervention to arbitrary medical detection problems while achieving results en par with or superior to the state-of-the-art. We demonstrate the effectiveness of nnDetection on two public benchmarks, ADAM and LUNA16, and propose 11 further medical object detection tasks on public data sets for comprehensive method evaluation. Code is at https://github.com/MIC-DKFZ/nnDetection .

Rare cancers comprise 20-25% of all malignancies but face major diagnostic challenges due to limited expert availability-especially in pediatric oncology, where they represent over 70% of cases. While pathology vision-language (VL) foundation models show promising zero-shot capabilities for common cancer subtyping, their clinical performance for rare cancers remains limited. Existing multi-instance learning (MIL) methods rely only on visual features, overlooking cross-modal knowledge and compromising interpretability critical for rare cancer diagnosis. To address this limitation, we propose PathPT, a novel framework that fully exploits the potential of vision-language pathology foundation models through spatially-aware visual aggregation and task-specific prompt tuning. Unlike conventional MIL, PathPT converts WSI-level supervision into fine-grained tile-level guidance by leveraging the zero-shot capabilities of VL models, thereby preserving localization on cancerous regions and enabling cross-modal reasoning through prompts aligned with histopathological semantics. We benchmark PathPT on eight rare cancer datasets(four adult and four pediatric) spanning 56 subtypes and 2,910 WSIs, as well as three common cancer datasets, evaluating four state-of-the-art VL models and four MIL frameworks under three few-shot settings. Results show that PathPT consistently delivers superior performance, achieving substantial gains in subtyping accuracy and cancerous region grounding ability. This work advances AI-assisted diagnosis for rare cancers, offering a scalable solution for improving subtyping accuracy in settings with limited access to specialized expertise.

Medical imaging artificial intelligence has achieved strong performance in isolated image interpretation, but remains poorly aligned with radiological practice, where diagnosis and follow-up rely on comparison across prior studies and analogous reference cases. Here we formulate radiological comparison as an entity-aware cross-image reasoning problem and introduce a framework that supports both reference-case retrieval and temporal comparative interpretation. We construct MedReCo-DB, a large-scale comparative imaging resource derived from routine image-report pairs, comprising more than 690,000 images from over 160,000 patients across eight institutions, four countries and seven imaging modalities. Reports are decomposed into anatomical structures, abnormal findings and pathological conditions to provide supervision for entity-conditioned retrieval and comparative visual question answering. Using this resource, we develop MedReCo, an entity-aware visual encoder for controllable retrieval of clinically analogous cases, and MedReCo-VLM, a vision--language extension for generative interpretation of interval change. Across internal, external and cross-center evaluations, MedReCo achieved the highest Recall@1 in all 12 internal retrieval settings and improved external retrieval by a mean of 6.0 percentage points. In clinically confusable differential groups, it consistently outperformed the strongest baselines. MedReCo-VLM achieved the best performance across all comparative generation evaluations and improved longitudinal follow-up accuracy by 14.5-46.5 percentage points on chest radiographs and 13.0-27.9 percentage points on CT. These findings suggest that entity-aware comparative reasoning can be learned from routine clinical data at scale and may provide a more clinically aligned foundation for medical imaging AI.

Ultrasound imaging has become the preferred imaging modality for early cancer screening due to its advantages of non-ionizing radiation, low cost, and real-time imaging capabilities. However, conventional ultrasound diagnosis heavily relies on physician expertise, presenting challenges of high subjectivity and low diagnostic efficiency. Vision-language models (VLMs) offer promising solutions for this issue, but existing general-purpose models demonstrate limited knowledge in ultrasound medical tasks, with poor generalization in multi-organ lesion recognition and low efficiency across multi-task diagnostics. To address these limitations, we propose EchoVLM, a vision-language model specifically designed for ultrasound medical imaging. The model employs a Mixture of Experts (MoE) architecture trained on data spanning seven anatomical regions. This design enables the model to perform multiple tasks, including ultrasound report generation, diagnosis and visual question-answering (VQA). The experimental results demonstrated that EchoVLM achieved significant improvements of 10.15 and 4.77 points in BLEU-1 scores and ROUGE-1 scores respectively compared to Qwen2-VL on the ultrasound report generation task. These findings suggest that EchoVLM has substantial potential to enhance diagnostic accuracy in ultrasound imaging, thereby providing a viable technical solution for future clinical applications. Source code and model weights are available at https://github.com/Asunatan/EchoVLM.

In this work, we address the TrackRAD2025 challenge of real-time tumor tracking in cine-MRI sequences of the thoracic and abdominal regions under strong data scarcity constraints. Two complementary strategies were explored: (i) unsupervised registration with the IMPACT similarity metric and (ii) foundation model-based segmentation leveraging SAM 2.1 and its recent variants through prompt-based interaction. Due to the one-second runtime constraint, the SAM-based method was ultimately selected. The final configuration used SAM2.1 b+ with mask-based prompts from the first annotated slice, fine-tuned solely on the small labeled subset from TrackRAD2025. Training was configured to minimize overfitting, using 1024x1024 patches (batch size 1), standard augmentations, and a balanced Dice + IoU loss. A low uniform learning rate (0.0001) was applied to all modules (prompt encoder, decoder, Hiera backbone) to preserve generalization while adapting to annotator-specific styles. Training lasted 300 epochs (~12h on RTX A6000, 48GB). The same inference strategy was consistently applied across all anatomical sites and MRI field strengths. Test-time augmentation was considered but ultimately discarded due to negligible performance gains. The final model was selected based on the highest Dice Similarity Coefficient achieved on the validation set after fine-tuning. On the hidden test set, the model reached a Dice score of 0.8794, ranking 6th overall in the TrackRAD2025 challenge. These results highlight the strong potential of foundation models for accurate and real-time tumor tracking in MRI-guided radiotherapy.

Automatic analysis of the enormous sets of images is a critical task in life sciences. This faces many challenges such as: algorithms are highly parameterized, significant human input is intertwined, and lacking a standard meta-visualization approach. This paper proposes an alternative iterative approach for optimizing input parameters, saving time by minimizing the user involvement, and allowing for understanding the workflow of algorithms and discovering new ones. The main focus is on developing an interactive visualization technique that enables users to analyze the relationships between sampled input parameters and corresponding output. This technique is implemented as a prototype called Veni Vidi Vici, or "I came, I saw, I conquered." This strategy is inspired by the mathematical formulas of numbering computable functions and is developed atop ImageJ, a scientific image processing program. A case study is presented to investigate the proposed framework. Finally, the paper explores some potential future issues in the application of the proposed approach in parameter space analysis in visualization.

Solving the inverse problem is the key step in evaluating the capacity of a physical model to describe real phenomena. In medical image computing, it aligns with the classical theme of image-based model personalization. Traditionally, a solution to the problem is obtained by performing either sampling or variational inference based methods. Both approaches aim to identify a set of free physical model parameters that results in a simulation best matching an empirical observation. When applied to brain tumor modeling, one of the instances of image-based model personalization in medical image computing, the overarching drawback of the methods is the time complexity for finding such a set. In a clinical setting with limited time between imaging and diagnosis or even intervention, this time complexity may prove critical. As the history of quantitative science is the history of compression, we align in this paper with the historical tendency and propose a method compressing complex traditional strategies for solving an inverse problem into a simple database query task. We evaluated different ways of performing the database query task assessing the trade-off between accuracy and execution time. On the exemplary task of brain tumor growth modeling, we prove that the proposed method achieves one order speed-up compared to existing approaches for solving the inverse problem. The resulting compute time offers critical means for relying on more complex and, hence, realistic models, for integrating image preprocessing and inverse modeling even deeper, or for implementing the current model into a clinical workflow.

Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.

Accurate classification of computed tomography (CT) images is essential for diagnosis and treatment planning, but existing methods often struggle with the subtle and spatially diverse nature of pathological features. Current approaches typically process images uniformly, limiting their ability to detect localized abnormalities that require focused analysis. We introduce UGPL, an uncertainty-guided progressive learning framework that performs a global-to-local analysis by first identifying regions of diagnostic ambiguity and then conducting detailed examination of these critical areas. Our approach employs evidential deep learning to quantify predictive uncertainty, guiding the extraction of informative patches through a non-maximum suppression mechanism that maintains spatial diversity. This progressive refinement strategy, combined with an adaptive fusion mechanism, enables UGPL to integrate both contextual information and fine-grained details. Experiments across three CT datasets demonstrate that UGPL consistently outperforms state-of-the-art methods, achieving improvements of 3.29%, 2.46%, and 8.08% in accuracy for kidney abnormality, lung cancer, and COVID-19 detection, respectively. Our analysis shows that the uncertainty-guided component provides substantial benefits, with performance dramatically increasing when the full progressive learning pipeline is implemented. Our code is available at: https://github.com/shravan-18/UGPL

Segment Anything Model (SAM) has gained significant attention because of its ability to segment a variety of objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we provide an extensive evaluation of SAM 2's ability to segment both 2D and 3D medical images. We collect 18 medical imaging datasets, including common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. We consider two evaluation pipelines of SAM 2: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former is only applicable to 3D modalities, while the latter applies to both 2D and 3D modalities. We learn that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc.

Recent advances in generative vision-language models (VLMs) have exciting potential implications for AI in radiology, yet VLMs are also known to produce hallucinations, nonsensical text, and other unwanted behaviors that can waste clinicians' time and cause patient harm. Drawing on recent work on direct preference optimization (DPO), we propose a simple method for modifying the behavior of pretrained VLMs performing radiology report generation by suppressing unwanted types of generations. We apply our method to the prevention of hallucinations of prior exams, addressing a long-established problem behavior in models performing chest X-ray report generation. Across our experiments, we find that DPO fine-tuning achieves a 3.2-4.8x reduction in lines hallucinating prior exams while maintaining model performance on clinical accuracy metrics. Our work is, to the best of our knowledge, the first work to apply DPO to medical VLMs, providing a data- and compute- efficient way to suppress problem behaviors while maintaining overall clinical accuracy.

Large-scale Visual Instruction Tuning (VIT) has become a key paradigm for advancing the performance of vision-language models (VLMs) across various multimodal tasks. However, training on the large-scale datasets is computationally expensive and inefficient due to redundancy in the data, which motivates the need for multimodal data selection to improve training efficiency. Existing data selection methods for VIT either require costly training or gradient computation. Training-free alternatives often depend on proxy models or datasets, instruction-agnostic representations, and pairwise similarity with quadratic complexity, limiting scalability and representation fidelity. In this work, we propose ScalSelect, a scalable training-free multimodal data selection method with linear-time complexity with respect to the number of samples, eliminating the need for external models or auxiliary datasets. ScalSelect first constructs sample representations by extracting visual features most attended by instruction tokens in the target VLM, capturing instruction-relevant information. It then identifies samples whose representations best approximate the dominant subspace of the full dataset representations, enabling scalable importance scoring without pairwise comparisons. Extensive experiments across multiple VLMs, datasets, and selection budgets demonstrate that ScalSelect achieves over 97.5% of the performance of training on the full dataset using only 16% of the data, and even outperforms full-data training in some settings. The code is available at https://github.com/ChangtiWu/ScalSelect{ScalSelect}.

In this work, we present LesionLocator, a framework for zero-shot longitudinal lesion tracking and segmentation in 3D medical imaging, establishing the first end-to-end model capable of 4D tracking with dense spatial prompts. Our model leverages an extensive dataset of 23,262 annotated medical scans, as well as synthesized longitudinal data across diverse lesion types. The diversity and scale of our dataset significantly enhances model generalizability to real-world medical imaging challenges and addresses key limitations in longitudinal data availability. LesionLocator outperforms all existing promptable models in lesion segmentation by nearly 10 dice points, reaching human-level performance, and achieves state-of-the-art results in lesion tracking, with superior lesion retrieval and segmentation accuracy. LesionLocator not only sets a new benchmark in universal promptable lesion segmentation and automated longitudinal lesion tracking but also provides the first open-access solution of its kind, releasing our synthetic 4D dataset and model to the community, empowering future advancements in medical imaging. Code is available at: www.github.com/MIC-DKFZ/LesionLocator

Conventional few-shot medical image segmentation (FSMIS) approaches face performance bottlenecks that hinder broader clinical applicability. Although the Segment Anything Model (SAM) exhibits strong category-agnostic segmentation capabilities, its direct application to medical images often leads to over-segmentation due to ambiguous anatomical boundaries. In this paper, we reformulate SAM-based FSMIS as a prompt localization task and propose FoB (Focus on Background), a background-centric prompt generator that provides accurate background prompts to constrain SAM's over-segmentation. Specifically, FoB bridges the gap between segmentation and prompt localization by category-agnostic generation of support background prompts and localizing them directly in the query image. To address the challenge of prompt localization for novel categories, FoB models rich contextual information to capture foreground-background spatial dependencies. Moreover, inspired by the inherent structural patterns of background prompts in medical images, FoB models this structure as a constraint to progressively refine background prompt predictions. Experiments on three diverse medical image datasets demonstrate that FoB outperforms other baselines by large margins, achieving state-of-the-art performance on FSMIS, and exhibiting strong cross-domain generalization. Our code is available at https://github.com/primebo1/FoB_SAM.

While accelerated computing has transformed many domains of computing, its impact on logical reasoning, specifically Boolean satisfiability (SAT), remains limited. State-of-the-art SAT solvers rely heavily on inherently sequential conflict-driven search algorithms that offer powerful heuristics but limit the amount of parallelism that could otherwise enable significantly more scalable SAT solving. Inspired by neural network training, we formulate the SAT problem as a binarized matrix-matrix multiplication layer that could be optimized using a differentiable objective function. Enabled by this encoding, we combine the strengths of parallel differentiable optimization and sequential search to accelerate SAT on a hybrid GPU-CPU system. In this system, the GPUs leverage parallel differentiable solving to rapidly evaluate SAT clauses and use gradients to stochastically explore the solution space and optimize variable assignments. Promising partial assignments generated by the GPUs are post-processed on many CPU threads which exploit conflict-driven sequential search to further traverse the solution subspaces and identify complete assignments. Prototyping the hybrid solver on an NVIDIA DGX GB200 node, our solver achieves runtime speedups up to over 200x when compared to a state-of-the-art CPU-based solver on public satisfiable benchmark problems from the SAT Competition.

Medical image retrieval is essential for clinical decision-making and translational research, relying on discriminative visual representations. Yet, current methods remain fragmented, relying on separate architectures and training strategies for 2D, 3D, and video-based medical data. This modality-specific design hampers scalability and inhibits the development of unified representations. To enable unified learning, we curate a large-scale hybrid-modality dataset comprising 867,653 medical imaging samples, including 2D X-rays and ultrasounds, RGB endoscopy videos, and 3D CT scans. Leveraging this dataset, we train M3Ret, a unified visual encoder without any modality-specific customization. It successfully learns transferable representations using both generative (MAE) and contrastive (SimDINO) self-supervised learning (SSL) paradigms. Our approach sets a new state-of-the-art in zero-shot image-to-image retrieval across all individual modalities, surpassing strong baselines such as DINOv3 and the text-supervised BMC-CLIP. More remarkably, strong cross-modal alignment emerges without paired data, and the model generalizes to unseen MRI tasks, despite never observing MRI during pretraining, demonstrating the generalizability of purely visual self-supervision to unseen modalities. Comprehensive analyses further validate the scalability of our framework across model and data sizes. These findings deliver a promising signal to the medical imaging community, positioning M3Ret as a step toward foundation models for visual SSL in multimodal medical image understanding.

Medical imaging is crucial for diagnosing a patient's health condition, and accurate segmentation of these images is essential for isolating regions of interest to ensure precise diagnosis and treatment planning. Existing methods primarily rely on bounding boxes or point-based prompts, while few have explored text-related prompts, despite clinicians often describing their observations and instructions in natural language. To address this gap, we first propose a RAG-based free-form text prompt generator, that leverages the domain corpus to generate diverse and realistic descriptions. Then, we introduce FLanS, a novel medical image segmentation model that handles various free-form text prompts, including professional anatomy-informed queries, anatomy-agnostic position-driven queries, and anatomy-agnostic size-driven queries. Additionally, our model also incorporates a symmetry-aware canonicalization module to ensure consistent, accurate segmentations across varying scan orientations and reduce confusion between the anatomical position of an organ and its appearance in the scan. FLanS is trained on a large-scale dataset of over 100k medical images from 7 public datasets. Comprehensive experiments demonstrate the model's superior language understanding and segmentation precision, along with a deep comprehension of the relationship between them, outperforming SOTA baselines on both in-domain and out-of-domain datasets.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

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

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

Motivated by the need to efficiently identify multiple candidates in high trial-and-error cost tasks such as drug discovery, we propose a near-optimal algorithm to identify all ε-best arms (i.e., those at most ε worse than the optimum). Specifically, we introduce LinFACT, an algorithm designed to optimize the identification of all ε-best arms in linear bandits. We establish a novel information-theoretic lower bound on the sample complexity of this problem and demonstrate that LinFACT achieves instance optimality by matching this lower bound up to a logarithmic factor. A key ingredient of our proof is to integrate the lower bound directly into the scaling process for upper bound derivation, determining the termination round and thus the sample complexity. We also extend our analysis to settings with model misspecification and generalized linear models. Numerical experiments, including synthetic and real drug discovery data, demonstrate that LinFACT identifies more promising candidates with reduced sample complexity, offering significant computational efficiency and accelerating early-stage exploratory experiments.

Mammography, an X-ray-based imaging technique, remains central to the early detection of breast cancer. Recent advances in artificial intelligence have enabled increasingly sophisticated computer-aided diagnostic methods, evolving from patch-based classifiers to whole-image approaches and then to multi-view architectures that jointly analyze complementary projections. Despite this progress, several critical questions remain unanswered. In this study, we systematically investigate these issues by addressing five key research questions: (1) the role of patch classifiers in performance, (2) the transferability of natural-image-trained backbones, (3) the advantages of learn-to-resize over conventional downscaling, (4) the contribution of multi-view integration, and (5) the robustness of findings across varying image quality. Beyond benchmarking, our experiments demonstrate clear performance gains over prior work. For the CBIS-DDSM dataset, we improved single-view AUC from 0.8153 to 0.8343, and multiple-view AUC from 0.8483 to 0.8658. Using a new comparative method, we also observed a 0.0217 AUC increase when extending from single to multiple-view analysis. On the complete VinDr-Mammo dataset, the multiple-view approach further improved results, achieving a 0.0492 AUC increase over single view and reaching 0.8511 AUC overall. These results establish new state-of-the-art benchmarks, providing clear evidence of the advantages of multi-view architectures for mammogram interpretation. Beyond performance, our analysis offers principled insights into model design and transfer learning strategies, contributing to the development of more accurate and reliable breast cancer screening tools. The inference code and trained models are publicly available at https://github.com/dpetrini/multiple-view.

Recent advances in multimodal large language models enable new possibilities for image-based decision support. However, their reliability and operational trade-offs in neuroimaging remain insufficiently understood. We present a comprehensive benchmarking study of vision-enabled large language models for 2D neuroimaging using curated MRI and CT datasets covering multiple sclerosis, stroke, brain tumors, other abnormalities, and normal controls. Models are required to generate multiple outputs simultaneously, including diagnosis, diagnosis subtype, imaging modality, specialized sequence, and anatomical plane. Performance is evaluated across four directions: discriminative classification with abstention, calibration, structured-output validity, and computational efficiency. A multi-phase framework ensures fair comparison while controlling for selection bias. Across twenty frontier multimodal models, the results show that technical imaging attributes such as modality and plane are nearly solved, whereas diagnostic reasoning, especially subtype prediction, remains challenging. Tumor classification emerges as the most reliable task, stroke is moderately solvable, while multiple sclerosis and rare abnormalities remain difficult. Few-shot prompting improves performance for several models but increases token usage, latency, and cost. Gemini-2.5-Pro and GPT-5-Chat achieve the strongest overall diagnostic performance, while Gemini-2.5-Flash offers the best efficiency-performance trade-off. Among open-weight architectures, MedGemma-1.5-4B demonstrates the most promising results, as under few-shot prompting, it approaches the zero-shot performance of several proprietary models, while maintaining perfect structured output. These findings provide practical insights into performance, reliability, and efficiency trade-offs, supporting standardized evaluation of multimodal LLMs in neuroimaging.

Diffusion models have found widespread adoption in various areas. However, their sampling process is slow because it requires hundreds to thousands of network evaluations to emulate a continuous process defined by differential equations. In this work, we use neural operators, an efficient method to solve the probability flow differential equations, to accelerate the sampling process of diffusion models. Compared to other fast sampling methods that have a sequential nature, we are the first to propose parallel decoding method that generates images with only one model forward pass. We propose diffusion model sampling with neural operator (DSNO) that maps the initial condition, i.e., Gaussian distribution, to the continuous-time solution trajectory of the reverse diffusion process. To model the temporal correlations along the trajectory, we introduce temporal convolution layers that are parameterized in the Fourier space into the given diffusion model backbone. We show our method achieves state-of-the-art FID of 4.12 for CIFAR-10 and 8.35 for ImageNet-64 in the one-model-evaluation setting.

Language promptable X-ray image segmentation would enable greater flexibility for human-in-the-loop workflows in diagnostic and interventional precision medicine. Prior efforts have contributed task-specific models capable of solving problems within a narrow scope, but expanding to broader use requires additional data, annotations, and training time. Recently, language-aligned foundation models (LFMs) -- machine learning models trained on large amounts of highly variable image and text data thus enabling broad applicability -- have emerged as promising tools for automated image analysis. Existing foundation models for medical image analysis focus on scenarios and modalities where large, richly annotated datasets are available. However, the X-ray imaging modality features highly variable image appearance and applications, from diagnostic chest X-rays to interventional fluoroscopy, with varying availability of data. To pave the way toward an LFM for comprehensive and language-aligned analysis of arbitrary medical X-ray images, we introduce FluoroSAM, a language-promptable variant of the Segment Anything Model, trained from scratch on 3M synthetic X-ray images from a wide variety of human anatomies, imaging geometries, and viewing angles. These include pseudo-ground truth masks for 128 organ types and 464 tools with associated text descriptions. FluoroSAM is capable of segmenting myriad anatomical structures and tools based on natural language prompts, thanks to the novel incorporation of vector quantization (VQ) of text embeddings in the training process. We demonstrate FluoroSAM's performance quantitatively on real X-ray images and showcase on several applications how FluoroSAM is a key enabler for rich human-machine interaction in the X-ray image acquisition and analysis context. Code is available at https://github.com/arcadelab/fluorosam.

The applicability of current lesion segmentation models for chest X-rays (CXRs) has been limited both by a small number of target labels and the reliance on long, detailed expert-level text inputs, creating a barrier to practical use. To address these limitations, we introduce a new paradigm: instruction-guided lesion segmentation (ILS), which is designed to segment diverse lesion types based on simple, user-friendly instructions. Under this paradigm, we construct MIMIC-ILS, the first large-scale instruction-answer dataset for CXR lesion segmentation, using our fully automated multimodal pipeline that generates annotations from chest X-ray images and their corresponding reports. MIMIC-ILS contains 1.1M instruction-answer pairs derived from 192K images and 91K unique segmentation masks, covering seven major lesion types. To empirically demonstrate its utility, we introduce ROSALIA, a vision-language model fine-tuned on MIMIC-ILS. ROSALIA can segment diverse lesions and provide textual explanations in response to user instructions. The model achieves high segmentation and textual accuracy in our newly proposed task, highlighting the effectiveness of our pipeline and the value of MIMIC-ILS as a foundational resource for pixel-level CXR lesion grounding.

Brain imaging analysis is vital for diagnosing and treating brain disorders, and multimodal large language models (MLLMs) are increasingly assisting in that analysis. However, current brain-oriented visual question-answering (VQA) benchmarks either cover a few imaging modalities or are limited to coarse-grained pathological descriptions, hindering a comprehensive assessment of MLLMs throughout the full clinical continuum. To address these, we introduce OmniBrainBench, the first comprehensive multimodal VQA benchmark specifically designed to assess the multimodal comprehension capabilities of MLLMs in brain imaging analysis.OmniBrainBench consists of 15 distinct brain imaging modalities collected from 30 verified medical sources, yielding 9,527 validated VQA pairs and 31,706 images. It simulates clinical workflows and encompasses 15 multi-stage clinical tasks rigorously validated by a professional radiologist. Evaluation of 24 state-of-the-art models, including open-source, medical, and proprietary MLLMs, highlights the substantial challenges posed by OmniBrainBench. Our experiments reveal: (1) proprietary MLLMs (e.g., GPT-5) beat open-source and medical models but lag physicians; (2) medical MLLMs vary widely in performance; (3) open-source MLLMs trail overall but excel in specific tasks; (4) MLLMs underperform sharply in complex preoperative tasks, revealing a visual-to-clinical reasoning gap. OmniBrainBench sets a new standard for evaluating and advancing MLLMs in brain imaging analysis, highlighting gaps compared to expert clinical reasoning. We release it at benchmark \& code.

Vision-language pre-training, i.e., aligning images with paired text, is a powerful paradigm to create encoders that can be directly used for tasks such as classification and retrieval, and for downstream tasks such as segmentation and report generation. In the 3D medical image domain, these capabilities allow vision-language encoders (VLEs) to support radiologists by retrieving patients with similar abnormalities or predicting likelihoods of abnormality. While the methodology holds promise, data availability limits the capabilities of current 3D VLEs. In this paper, we alleviate the lack of data by injecting additional inductive biases: introducing a report generation objective and pairing vision-language pre-training with vision-only pre-training. This allows us to leverage both image-only and paired image-text 3D datasets, increasing the total amount of data to which our model is exposed. Through these additional inductive biases, paired with best practices of the 3D medical imaging domain, we develop the Comprehensive Language-image Pre-training (COLIPRI) encoder family. Our COLIPRI encoders achieve state-of-the-art performance in report generation, classification probing, and zero-shot classification, and remain competitive for semantic segmentation.

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

High-resolution (HR) magnetic resonance imaging (MRI) is crucial for many clinical and research applications. However, achieving it remains costly and constrained by technical trade-offs and experimental limitations. Super-resolution (SR) presents a promising computational approach to overcome these challenges by generating HR images from more affordable low-resolution (LR) scans, potentially improving diagnostic accuracy and efficiency without requiring additional hardware. This survey reviews recent advances in MRI SR techniques, with a focus on deep learning (DL) approaches. It examines DL-based MRI SR methods from the perspectives of computer vision, computational imaging, inverse problems, and MR physics, covering theoretical foundations, architectural designs, learning strategies, benchmark datasets, and performance metrics. We propose a systematic taxonomy to categorize these methods and present an in-depth study of both established and emerging SR techniques applicable to MRI, considering unique challenges in clinical and research contexts. We also highlight open challenges and directions that the community needs to address. Additionally, we provide a collection of essential open-access resources, tools, and tutorials, available on our GitHub: https://github.com/mkhateri/Awesome-MRI-Super-Resolution. IEEE keywords: MRI, Super-Resolution, Deep Learning, Computational Imaging, Inverse Problem, Survey.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.