Daily Papers

Accurate and reliable C-arm positioning is essential for fluoroscopy-guided interventions. However, clinical workflows rely on manual alignment that increases radiation exposure and procedural delays. In this work, we present a pipeline that autonomously navigates the C-arm to predefined anatomical landmarks utilizing X-ray images. Given an input X-ray image from an arbitrary starting location on the operating table, the model predicts a 3D displacement vector toward each target landmark along the body. To ensure reliable deployment, we capture both aleatoric and epistemic uncertainties in the model's predictions and further calibrate them using conformal prediction. The derived prediction regions are interpreted as 3D confidence regions around the predicted landmark locations. The training framework combines a probabilistic loss with skeletal pose regularization to encourage anatomically plausible outputs. We validate our approach on a synthetic X-ray dataset generated from DeepDRR. Results show not only strong localization accuracy across multiple architectures but also well-calibrated prediction bounds. These findings highlight the pipeline's potential as a component in safe and reliable autonomous C-arm systems. Code is available at https://github.com/AhmadArrabi/C_arm_guidance_APAH

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

Vision-grounded medical report generation aims to produce clinically accurate descriptions of medical images, anchored in explicit visual evidence to improve interpretability and facilitate integration into clinical workflows. However, existing methods often rely on separately trained detection modules that require extensive expert annotations, introducing high labeling costs and limiting generalizability due to pathology distribution bias across datasets. To address these challenges, we propose Self-Supervised Anatomical Consistency Learning (SS-ACL) -- a novel and annotation-free framework that aligns generated reports with corresponding anatomical regions using simple textual prompts. SS-ACL constructs a hierarchical anatomical graph inspired by the invariant top-down inclusion structure of human anatomy, organizing entities by spatial location. It recursively reconstructs fine-grained anatomical regions to enforce intra-sample spatial alignment, inherently guiding attention maps toward visually relevant areas prompted by text. To further enhance inter-sample semantic alignment for abnormality recognition, SS-ACL introduces a region-level contrastive learning based on anatomical consistency. These aligned embeddings serve as priors for report generation, enabling attention maps to provide interpretable visual evidence. Extensive experiments demonstrate that SS-ACL, without relying on expert annotations, (i) generates accurate and visually grounded reports -- outperforming state-of-the-art methods by 10\% in lexical accuracy and 25\% in clinical efficacy, and (ii) achieves competitive performance on various downstream visual tasks, surpassing current leading visual foundation models by 8\% in zero-shot visual grounding.

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.

In this study, we present a method for generating automated anatomy segmentation datasets using a sequential process that involves nnU-Net-based pseudo-labeling and anatomy-guided pseudo-label refinement. By combining various fragmented knowledge bases, we generate a dataset of whole-body CT scans with 142 voxel-level labels for 533 volumes providing comprehensive anatomical coverage which experts have approved. Our proposed procedure does not rely on manual annotation during the label aggregation stage. We examine its plausibility and usefulness using three complementary checks: Human expert evaluation which approved the dataset, a Deep Learning usefulness benchmark on the BTCV dataset in which we achieve 85% dice score without using its training dataset, and medical validity checks. This evaluation procedure combines scalable automated checks with labor-intensive high-quality expert checks. Besides the dataset, we release our trained unified anatomical segmentation model capable of predicting 142 anatomical structures on CT data.

Vision-language models are increasingly integrated into clinical workflows. However, existing benchmarks primarily assess performance on common anatomical presentations and fail to capture the challenges posed by rare variants. To address this gap, we introduce AdversarialAnatomyBench, the first benchmark comprising naturally occurring rare anatomical variants across diverse imaging modalities and anatomical regions. We call such variants that violate learned priors about "typical" human anatomy natural adversarial anatomy. Benchmarking 22 state-of-the-art VLMs with AdversarialAnatomyBench yielded three key insights. First, when queried with basic medical perception tasks, mean accuracy dropped from 74% on typical to 29% on atypical anatomy. Even the best-performing models, GPT-5, Gemini 2.5 Pro, and Llama 4 Maverick, showed performance drops of 41-51%. Second, model errors closely mirrored expected anatomical biases. Third, neither model scaling nor interventions, including bias-aware prompting and test-time reasoning, resolved these issues. These findings highlight a critical and previously unquantified limitation in current VLM: their poor generalization to rare anatomical presentations. AdversarialAnatomyBench provides a foundation for systematically measuring and mitigating anatomical bias in multimodal medical AI systems.

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.

Deep learning underpins a wide range of applications in MRI, including reconstruction, artifact removal, and segmentation. However, progress has been driven largely by public datasets focused on brain and knee imaging, shaping how models are trained and evaluated. As a result, careful studies of the reliability of these models across diverse anatomical settings remain limited. In this work, we introduce MosaicMRI, a large and diverse collection of fully sampled raw musculoskeletal (MSK) MR measurements designed for training and evaluating machine-learning-based methods. MosaicMRI is the largest open-source raw MSK MRI dataset to date, comprising 2,671 volumes and 80,156 slices. The dataset offers substantial diversity in volume orientation (e.g., axial, sagittal), imaging contrasts (e.g., PD, T1, T2), anatomies (e.g., spine, knee, hip, ankle, and others), and numbers of acquisition coils. Using VarNet as a baseline for accelerated reconstruction task, we perform a comprehensive set of experiments to study scaling behavior with respect to both model capacity and dataset size. Interestingly, models trained on the combined anatomies significantly outperform anatomy-specific models in low-sample regimes, highlighting the benefits of anatomical diversity and the presence of exploitable cross-anatomical correlations. We further evaluate robustness and cross-anatomy generalization by training models on one anatomy (e.g., spine) and testing them on another (e.g., knee). Notably, we identify groups of body parts (e.g., foot and elbow) that generalize well with each other, and highlight that performance under domain shifts depends on both training set size, anatomy, and protocol-specific factors.

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

We participated in the SynthRAD2025 challenge (Tasks 1 and 2) with a unified pipeline for synthetic CT (sCT) generation from MRI and CBCT, implemented using the KonfAI framework. Our model is a 2.5D U-Net++ with a ResNet-34 encoder, trained jointly across anatomical regions and fine-tuned per region. The loss function combined pixel-wise L1 loss with IMPACT-Synth, a perceptual loss derived from SAM and TotalSegmentator to enhance structural fidelity. Training was performed using AdamW (initial learning rate = 0.001, halved every 25k steps) on patch-based, normalized, body-masked inputs (320x320 for MRI, 256x256 for CBCT), with random flipping as the only augmentation. No post-processing was applied. Final predictions leveraged test-time augmentation and five-fold ensembling. The best model was selected based on validation MAE. Two registration strategies were evaluated: (i) Elastix with mutual information, consistent with the challenge pipeline, and (ii) IMPACT, a feature-based similarity metric leveraging pretrained segmentation networks. On the local test sets, IMPACT-based registration achieved more accurate and anatomically consistent alignments than mutual-information-based registration, resulting in improved sCT synthesis with lower MAE and more realistic anatomical structures. On the public validation set, however, models trained with Elastix-aligned data achieved higher scores, reflecting a registration bias favoring alignment strategies consistent with the evaluation pipeline. This highlights how registration errors can propagate into supervised learning, influencing both training and evaluation, and potentially inflating performance metrics at the expense of anatomical fidelity. By promoting anatomically consistent alignment, IMPACT helps mitigate this bias and supports the development of more robust and generalizable sCT synthesis models.

Current Vision-Language Models (VLMs) struggle to ground anatomical regions in 3D medical images and reason about them in a step-by-step manner, a key requirement of real-world diagnostic assessment. This ability is essential for aligning model outputs with the diagnostic workflows clinicians use in practice, enabling trustworthy clinician-AI collaboration. Existing 3D datasets provide localization labels, but none support this "grounded reasoning" ability. To address this gap, we introduce 3DReasonKnee, the first 3D grounded reasoning dataset for medical images, which provides 494k high-quality quintuples derived from 7,970 3D knee MRI volumes. Each quintuple includes: (1) the 3D MRI volume, (2) a diagnostic question targeting a specific anatomical region (3) a 3D bounding box localizing the relevant anatomical structures, (4) clinician-generated diagnostic reasoning steps that explicitly detail the 3D reasoning process, and (5) structured severity assessments for the relevant anatomical region. The creation and validation of 3DReasonKnee, involving over 450 hours of expert clinician time for manually segmenting MRIs and generating reasoning chains, ensures its superior quality and clinical relevance. We establish ReasonKnee-Bench to evaluate localization and diagnostic accuracy, providing insight into VLM ability to perform grounding and severity assessment across anatomical regions and diagnostic inquiries. We benchmark five state-of-the-art VLMs, providing baseline performance for ReasonKnee-Bench. By providing this unique resource of expert-annotated 3D reasoning pathways, 3DReasonKnee serves as a repository of orthopedic surgeons' diagnostic expertise and offers a vital testbed for advancing multimodal medical AI systems towards 3D, clinically aligned, localized decision-making capabilities. The dataset can be found in: https://huggingface.co/datasets/rajpurkarlab/3DReasonKnee

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/

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.

Self-supervised learning (SSL) has recently achieved promising performance for 3D medical image analysis tasks. Most current methods follow existing SSL paradigm originally designed for photographic or natural images, which cannot explicitly and thoroughly exploit the intrinsic similar anatomical structures across varying medical images. This may in fact degrade the quality of learned deep representations by maximizing the similarity among features containing spatial misalignment information and different anatomical semantics. In this work, we propose a new self-supervised learning framework, namely Alice, that explicitly fulfills Anatomical invariance modeling and semantic alignment via elaborately combining discriminative and generative objectives. Alice introduces a new contrastive learning strategy which encourages the similarity between views that are diversely mined but with consistent high-level semantics, in order to learn invariant anatomical features. Moreover, we design a conditional anatomical feature alignment module to complement corrupted embeddings with globally matched semantics and inter-patch topology information, conditioned by the distribution of local image content, which permits to create better contrastive pairs. Our extensive quantitative experiments on three 3D medical image analysis tasks demonstrate and validate the performance superiority of Alice, surpassing the previous best SSL counterpart methods and showing promising ability for united representation learning. Codes are available at https://github.com/alibaba-damo-academy/alice.

Leading vision-language models (VLMs) are trained on general Internet content, overlooking scientific journals' rich, domain-specific knowledge. Training on specialty-specific literature could yield high-performance, task-specific tools, enabling generative AI to match generalist models in specialty publishing, educational, and clinical tasks. We created NeuroPubs, a multimodal dataset of 23,000 Neurosurgery Publications articles (134M words, 78K image-caption pairs). Using NeuroPubs, VLMs generated publication-ready graphical abstracts (70% of 100 abstracts) and board-style questions indistinguishable from human-written ones (54% of 89,587 questions). We used these questions to train CNS-Obsidian, a 34B-parameter VLM. In a blinded, randomized controlled trial, our model demonstrated non-inferiority to then state-of-the-art GPT-4o in neurosurgical differential diagnosis (clinical utility, 40.62% upvotes vs. 57.89%, p=0.1150; accuracy, 59.38% vs. 65.79%, p=0.3797). Our pilot study demonstrates how training generative AI models on specialty-specific journal content - without large-scale internet data - results in high-performance academic and clinical tools, enabling domain-tailored AI across diverse fields.

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.

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.

The accelerating development of general medical artificial intelligence (GMAI), powered by multimodal large language models (MLLMs), offers transformative potential for addressing persistent healthcare challenges, including workforce deficits and escalating costs. The parallel development of systematic evaluation benchmarks emerges as a critical imperative to enable performance assessment and provide technological guidance. Meanwhile, as an invaluable knowledge source, the potential of medical textbooks for benchmark development remains underexploited. Here, we present MedBookVQA, a systematic and comprehensive multimodal benchmark derived from open-access medical textbooks. To curate this benchmark, we propose a standardized pipeline for automated extraction of medical figures while contextually aligning them with corresponding medical narratives. Based on this curated data, we generate 5,000 clinically relevant questions spanning modality recognition, disease classification, anatomical identification, symptom diagnosis, and surgical procedures. A multi-tier annotation system categorizes queries through hierarchical taxonomies encompassing medical imaging modalities (42 categories), body anatomies (125 structures), and clinical specialties (31 departments), enabling nuanced analysis across medical subdomains. We evaluate a wide array of MLLMs, including proprietary, open-sourced, medical, and reasoning models, revealing significant performance disparities across task types and model categories. Our findings highlight critical capability gaps in current GMAI systems while establishing textbook-derived multimodal benchmarks as essential evaluation tools. MedBookVQA establishes textbook-derived benchmarking as a critical paradigm for advancing clinical AI, exposing limitations in GMAI systems while providing anatomically structured performance metrics across specialties.

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

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.

Transfer learning has become a central paradigm in modern machine learning, yet it suffers from the long-standing problem of negative transfer, where leveraging source representations can harm rather than help performance on the target task. Although empirical remedies have been proposed, there remains little theoretical understanding of how to reliably avoid negative transfer. In this paper, we investigate a simple yet remarkably effective strategy: augmenting frozen, pretrained source-side features with a trainable target-side encoder that adapts target features to capture residual signals overlooked by models pretrained on the source data. We show this residual feature integration strategy is sufficient to provably prevent negative transfer, by establishing theoretical guarantees that it has no worse convergence rate than training from scratch under the informative class of target distributions up to logarithmic factors, and that the convergence rate can transition seamlessly from nonparametric to near-parametric when source representations are informative. To our knowledge, this is the first theoretical work that ensures protection against negative transfer. We carry out extensive numerical experiments across image, text and tabular benchmarks, and empirically verify that the method consistently safeguards performance under distribution shift, label noise, semantic perturbation, and class imbalance. We additionally demonstrate that this residual integration mechanism uniquely supports adapt-time multimodality extension, enabling a pretrained single-cell foundation model to incorporate spatial signals for lymph-node anatomical classification despite the source model being trained without them. Our study thus advances the theory of safe transfer learning, and provides a principled approach that is simple, robust, architecture-agnostic, and broadly applicable.

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

We develop a learning framework for building deformable templates, which play a fundamental role in many image analysis and computational anatomy tasks. Conventional methods for template creation and image alignment to the template have undergone decades of rich technical development. In these frameworks, templates are constructed using an iterative process of template estimation and alignment, which is often computationally very expensive. Due in part to this shortcoming, most methods compute a single template for the entire population of images, or a few templates for specific sub-groups of the data. In this work, we present a probabilistic model and efficient learning strategy that yields either universal or conditional templates, jointly with a neural network that provides efficient alignment of the images to these templates. We demonstrate the usefulness of this method on a variety of domains, with a special focus on neuroimaging. This is particularly useful for clinical applications where a pre-existing template does not exist, or creating a new one with traditional methods can be prohibitively expensive. Our code and atlases are available online as part of the VoxelMorph library at http://voxelmorph.csail.mit.edu.

Do machines and humans process language in similar ways? A recent line of research has hinted in the affirmative, demonstrating that human brain signals can be effectively predicted using the internal representations of language models (LMs). This is thought to reflect shared computational principles between LMs and human language processing. However, there are also clear differences in how LMs and humans acquire and use language, even if the final task they are performing is the same. Despite this, there is little work exploring systematic differences between human and machine language processing using brain data. To address this question, we examine the differences between LM representations and the human brain's responses to language, specifically by examining a dataset of Magnetoencephalography (MEG) responses to a written narrative. In doing so we identify three phenomena that, in prior work, LMs have been found to not capture well: emotional understanding, figurative language processing, and physical commonsense. By fine-tuning LMs on datasets related to these phenomena, we observe that fine-tuned LMs show improved alignment with human brain responses across these tasks. Our study implies that the observed divergences between LMs and human brains may stem from LMs' inadequate representation of these specific types of knowledge.

High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal physiology - specifically, the parameters (e.g., synaptic efficacies, local conductances) that govern neural dynamics. We propose to translate molecularly annotated ultrastructure into physiology, introducing the concept of an ultrastructure-to-dynamics compiler: a learned mapping from molecularly annotated ultrastructure to simulator-ready, uncertainty-aware physiological parameters. The requirement is paired training data, with jointly acquired ultrastructure from imaging, and dynamical responses to perturbations from physiological experiments. With this data we can train models that predict local physiology directly from structure. Such a compiler would support biophysical simulations by turning anatomical maps into models of circuit dynamics, shifting structure-to-function from a descriptive program to a predictive one and opening routes to understanding neural computation and forecasting intervention effects.

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.

Recent progress in Large Vision-Language Models (LVLMs) has enabled promising applications in medical tasks, such as report generation and visual question answering. However, existing benchmarks focus mainly on the final diagnostic answer, offering limited insight into whether models engage in clinically meaningful reasoning. To address this, we present CheXStruct and CXReasonBench, a structured pipeline and benchmark built on the publicly available MIMIC-CXR-JPG dataset. CheXStruct automatically derives a sequence of intermediate reasoning steps directly from chest X-rays, such as segmenting anatomical regions, deriving anatomical landmarks and diagnostic measurements, computing diagnostic indices, and applying clinical thresholds. CXReasonBench leverages this pipeline to evaluate whether models can perform clinically valid reasoning steps and to what extent they can learn from structured guidance, enabling fine-grained and transparent assessment of diagnostic reasoning. The benchmark comprises 18,988 QA pairs across 12 diagnostic tasks and 1,200 cases, each paired with up to 4 visual inputs, and supports multi-path, multi-stage evaluation including visual grounding via anatomical region selection and diagnostic measurements. Even the strongest of 10 evaluated LVLMs struggle with structured reasoning and generalization, often failing to link abstract knowledge with anatomically grounded visual interpretation. The code is available at https://github.com/ttumyche/CXReasonBench

Partially inspired by features of computation in visual cortex, deep neural networks compute hierarchical representations of their inputs. While these networks have been highly successful in machine learning, it remains unclear to what extent they can aid our understanding of cortical function. Several groups have developed metrics that provide a quantitative comparison between representations computed by networks and representations measured in cortex. At the same time, neuroscience is well into an unprecedented phase of large-scale data collection, as evidenced by projects such as the Allen Brain Observatory. Despite the magnitude of these efforts, in a given experiment only a fraction of units are recorded, limiting the information available about the cortical representation. Moreover, only a finite number of stimuli can be shown to an animal over the course of a realistic experiment. These limitations raise the question of how and whether metrics that compare representations of deep networks are meaningful on these datasets. Here, we empirically quantify the capabilities and limitations of these metrics due to limited image presentations and neuron samples. We find that the comparison procedure is robust to different choices of stimuli set and the level of subsampling that one might expect in a large-scale brain survey with thousands of neurons. Using these results, we compare the representations measured in the Allen Brain Observatory in response to natural image presentations to deep neural network. We show that the visual cortical areas are relatively high order representations (in that they map to deeper layers of convolutional neural networks). Furthermore, we see evidence of a broad, more parallel organization rather than a sequential hierarchy, with the primary area VISp(V1) being lower order relative to the other areas.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Humans effortlessly interpret images by parsing them into part-whole hierarchies; deep learning excels in learning multi-level feature spaces, but they often lack explicit coding of part-whole relations, a prominent property of medical imaging. To overcome this limitation, we introduce Adam-v2, a new self-supervised learning framework extending Adam [79] by explicitly incorporating part-whole hierarchies into its learning objectives through three key branches: (1) Localizability, acquiring discriminative representations to distinguish different anatomical patterns; (2) Composability, learning each anatomical structure in a parts-to-whole manner; and (3) Decomposability, comprehending each anatomical structure in a whole-to-parts manner. Experimental results across 10 tasks, compared to 11 baselines in zero-shot, few-shot transfer, and full fine-tuning settings, showcase Adam-v2's superior performance over large-scale medical models and existing SSL methods across diverse downstream tasks. The higher generality and robustness of Adam-v2's representations originate from its explicit construction of hierarchies for distinct anatomical structures from unlabeled medical images. Adam-v2 preserves a semantic balance of anatomical diversity and harmony in its embedding, yielding representations that are both generic and semantically meaningful, yet overlooked in existing SSL methods. All code and pretrained models are available at https://github.com/JLiangLab/Eden.

Large language models (LLMs) have demonstrated remarkable prediction performance for a growing array of tasks. However, their rapid proliferation and increasing opaqueness have created a growing need for interpretability. Here, we ask whether we can automatically obtain natural language explanations for black box text modules. A "text module" is any function that maps text to a scalar continuous value, such as a submodule within an LLM or a fitted model of a brain region. "Black box" indicates that we only have access to the module's inputs/outputs. We introduce Summarize and Score (SASC), a method that takes in a text module and returns a natural language explanation of the module's selectivity along with a score for how reliable the explanation is. We study SASC in 3 contexts. First, we evaluate SASC on synthetic modules and find that it often recovers ground truth explanations. Second, we use SASC to explain modules found within a pre-trained BERT model, enabling inspection of the model's internals. Finally, we show that SASC can generate explanations for the response of individual fMRI voxels to language stimuli, with potential applications to fine-grained brain mapping. All code for using SASC and reproducing results is made available on Github.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Medical imaging is widely used in clinical practice for diagnosis and treatment. Report-writing can be error-prone for unexperienced physicians, and time- consuming and tedious for experienced physicians. To address these issues, we study the automatic generation of medical imaging reports. This task presents several challenges. First, a complete report contains multiple heterogeneous forms of information, including findings and tags. Second, abnormal regions in medical images are difficult to identify. Third, the re- ports are typically long, containing multiple sentences. To cope with these challenges, we (1) build a multi-task learning framework which jointly performs the pre- diction of tags and the generation of para- graphs, (2) propose a co-attention mechanism to localize regions containing abnormalities and generate narrations for them, (3) develop a hierarchical LSTM model to generate long paragraphs. We demonstrate the effectiveness of the proposed methods on two publicly available datasets.

The process of reconstructing experiences from human brain activity offers a unique lens into how the brain interprets and represents the world. In this paper, we introduce a method for reconstructing music from brain activity, captured using functional magnetic resonance imaging (fMRI). Our approach uses either music retrieval or the MusicLM music generation model conditioned on embeddings derived from fMRI data. The generated music resembles the musical stimuli that human subjects experienced, with respect to semantic properties like genre, instrumentation, and mood. We investigate the relationship between different components of MusicLM and brain activity through a voxel-wise encoding modeling analysis. Furthermore, we discuss which brain regions represent information derived from purely textual descriptions of music stimuli. We provide supplementary material including examples of the reconstructed music at https://google-research.github.io/seanet/brain2music

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Emerging tissue profiling technologies enable the construction of a comprehensive atlas of the mammalian brain with sub-cellular resolution and spatially resolved gene expression data. However, such tera-scale volumetric datasets present significant computational challenges in understanding complex brain functions within their native 3D spatial context. Here, we propose the novel generative approach Tera-MIND, which can simulate Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial transcriptomic data as the conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D gene-gene self-attention, we identify spatial molecular interactions for key transcriptomic pathways in the murine brain, exemplified by glutamatergic and dopaminergic neuronal systems. Importantly, these in-silico biological findings are consistent and reproducible across three tera-scale virtual mouse brains. Therefore, Tera-MIND showcases a promising path toward efficient and generative simulations of whole organ systems for biomedical research. Project website: http://musikisomorphie.github.io/Tera-MIND.html{https}

Current medical vision-language models (VLMs) process volumetric brain MRI using 2D slice-based approximations, fragmenting the spatial context required for accurate neuroradiological interpretation. We developed Brain3D, a staged vision-language framework for automated radiology report generation from 3D brain tumor MRI. Our approach inflates a pretrained 2D medical encoder into a native 3D architecture and progressively aligns it with a causal language model through three stages: contrastive grounding, supervised projector warmup, and LoRA-based linguistic specialization. Unlike generalist 3D medical VLMs, Brain3D is tailored to neuroradiology, where hemispheric laterality, tumor infiltration patterns, and anatomical localization are critical. Evaluated on 468 subjects (BraTS pathological cases plus healthy controls), our model achieves a Clinical Pathology F1 of 0.951 versus 0.413 for a strong 2D baseline while maintaining perfect specificity on healthy scans. The staged alignment proves essential: contrastive grounding establishes visual-textual correspondence, projector warmup stabilizes conditioning, and LoRA adaptation shifts output from verbose captions to structured clinical reports\footnote{Our code is publicly available for transparency and reproducibility

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

We address prevailing challenges of the brain-powered research, departing from the observation that the literature hardly recover accurate spatial information and require subject-specific models. To address these challenges, we propose UMBRAE, a unified multimodal decoding of brain signals. First, to extract instance-level conceptual and spatial details from neural signals, we introduce an efficient universal brain encoder for multimodal-brain alignment and recover object descriptions at multiple levels of granularity from subsequent multimodal large language model (MLLM). Second, we introduce a cross-subject training strategy mapping subject-specific features to a common feature space. This allows a model to be trained on multiple subjects without extra resources, even yielding superior results compared to subject-specific models. Further, we demonstrate this supports weakly-supervised adaptation to new subjects, with only a fraction of the total training data. Experiments demonstrate that UMBRAE not only achieves superior results in the newly introduced tasks but also outperforms methods in well established tasks. To assess our method, we construct and share with the community a comprehensive brain understanding benchmark BrainHub. Our code and benchmark are available at https://weihaox.github.io/UMBRAE.

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.

Endoscopic procedures are essential for diagnosing and treating internal diseases, and multi-modal large language models (MLLMs) are increasingly applied to assist in endoscopy analysis. However, current benchmarks are limited, as they typically cover specific endoscopic scenarios and a small set of clinical tasks, failing to capture the real-world diversity of endoscopic scenarios and the full range of skills needed in clinical workflows. To address these issues, we introduce EndoBench, the first comprehensive benchmark specifically designed to assess MLLMs across the full spectrum of endoscopic practice with multi-dimensional capacities. EndoBench encompasses 4 distinct endoscopic scenarios, 12 specialized clinical tasks with 12 secondary subtasks, and 5 levels of visual prompting granularities, resulting in 6,832 rigorously validated VQA pairs from 21 diverse datasets. Our multi-dimensional evaluation framework mirrors the clinical workflow--spanning anatomical recognition, lesion analysis, spatial localization, and surgical operations--to holistically gauge the perceptual and diagnostic abilities of MLLMs in realistic scenarios. We benchmark 23 state-of-the-art models, including general-purpose, medical-specialized, and proprietary MLLMs, and establish human clinician performance as a reference standard. Our extensive experiments reveal: (1) proprietary MLLMs outperform open-source and medical-specialized models overall, but still trail human experts; (2) medical-domain supervised fine-tuning substantially boosts task-specific accuracy; and (3) model performance remains sensitive to prompt format and clinical task complexity. EndoBench establishes a new standard for evaluating and advancing MLLMs in endoscopy, highlighting both progress and persistent gaps between current models and expert clinical reasoning. We publicly release our benchmark and code.

A key requirement for the development of effective learning representations is their evaluation and comparison to representations we know to be effective. In natural sensory domains, the community has viewed the brain as a source of inspiration and as an implicit benchmark for success. However, it has not been possible to directly test representational learning algorithms directly against the representations contained in neural systems. Here, we propose a new benchmark for visual representations on which we have directly tested the neural representation in multiple visual cortical areas in macaque (utilizing data from [Majaj et al., 2012]), and on which any computer vision algorithm that produces a feature space can be tested. The benchmark measures the effectiveness of the neural or machine representation by computing the classification loss on the ordered eigendecomposition of a kernel matrix [Montavon et al., 2011]. In our analysis we find that the neural representation in visual area IT is superior to visual area V4. In our analysis of representational learning algorithms, we find that three-layer models approach the representational performance of V4 and the algorithm in [Le et al., 2012] surpasses the performance of V4. Impressively, we find that a recent supervised algorithm [Krizhevsky et al., 2012] achieves performance comparable to that of IT for an intermediate level of image variation difficulty, and surpasses IT at a higher difficulty level. We believe this result represents a major milestone: it is the first learning algorithm we have found that exceeds our current estimate of IT representation performance. We hope that this benchmark will assist the community in matching the representational performance of visual cortex and will serve as an initial rallying point for further correspondence between representations derived in brains and machines.

Recent Artificial Intelligence (AI) models have matched or exceeded human experts in several benchmarks of biomedical task performance, but have lagged behind on surgical image-analysis benchmarks. Since surgery requires integrating disparate tasks -- including multimodal data integration, human interaction, and physical effects -- generally-capable AI models could be particularly attractive as a collaborative tool if performance could be improved. On the one hand, the canonical approach of scaling architecture size and training data is attractive, especially since there are millions of hours of surgical video data generated per year. On the other hand, preparing surgical data for AI training requires significantly higher levels of professional expertise, and training on that data requires expensive computational resources. These trade-offs paint an uncertain picture of whether and to-what-extent modern AI could aid surgical practice. In this paper, we explore this question through a case study of surgical tool detection using state-of-the-art AI methods available in 2026. We demonstrate that even with multi-billion parameter models and extensive training, current Vision Language Models fall short in the seemingly simple task of tool detection in neurosurgery. Additionally, we show scaling experiments indicating that increasing model size and training time only leads to diminishing improvements in relevant performance metrics. Thus, our experiments suggest that current models could still face significant obstacles in surgical use cases. Moreover, some obstacles cannot be simply ``scaled away'' with additional compute and persist across diverse model architectures, raising the question of whether data and label availability are the only limiting factors. We discuss the main contributors to these constraints and advance potential solutions.

Over the past decade, predictive modeling of neural responses in the primate visual system has advanced significantly, largely driven by various DNN approaches. These include models optimized directly for visual recognition, cross-modal alignment through contrastive objectives, neural response prediction from scratch, and large language model embeddings.Likewise, different readout mechanisms, ranging from fully linear to spatial-feature factorized methods have been explored for mapping network activations to neural responses. Despite the diversity of these approaches, it remains unclear which method performs best across different visual regions. In this study, we systematically compare these approaches for modeling the human visual system and investigate alternative strategies to improve response predictions. Our findings reveal that for early to mid-level visual areas, response-optimized models with visual inputs offer superior prediction accuracy, while for higher visual regions, embeddings from LLMs based on detailed contextual descriptions of images and task-optimized models pretrained on large vision datasets provide the best fit. Through comparative analysis of these modeling approaches, we identified three distinct regions in the visual cortex: one sensitive primarily to perceptual features of the input that are not captured by linguistic descriptions, another attuned to fine-grained visual details representing semantic information, and a third responsive to abstract, global meanings aligned with linguistic content. We also highlight the critical role of readout mechanisms, proposing a novel scheme that modulates receptive fields and feature maps based on semantic content, resulting in an accuracy boost of 3-23% over existing SOTAs for all models and brain regions. Together, these findings offer key insights into building more precise models of the visual system.

Humans can develop internal world models that encode common sense knowledge, telling them how the world works and predicting the consequences of their actions. This concept has emerged as a promising direction for establishing general-purpose machine-learning models in recent preliminary works, e.g., for visual representation learning. In this paper, we present CheXWorld, the first effort towards a self-supervised world model for radiographic images. Specifically, our work develops a unified framework that simultaneously models three aspects of medical knowledge essential for qualified radiologists, including 1) local anatomical structures describing the fine-grained characteristics of local tissues (e.g., architectures, shapes, and textures); 2) global anatomical layouts describing the global organization of the human body (e.g., layouts of organs and skeletons); and 3) domain variations that encourage CheXWorld to model the transitions across different appearance domains of radiographs (e.g., varying clarity, contrast, and exposure caused by collecting radiographs from different hospitals, devices, or patients). Empirically, we design tailored qualitative and quantitative analyses, revealing that CheXWorld successfully captures these three dimensions of medical knowledge. Furthermore, transfer learning experiments across eight medical image classification and segmentation benchmarks showcase that CheXWorld significantly outperforms existing SSL methods and large-scale medical foundation models. Code & pre-trained models are available at https://github.com/LeapLabTHU/CheXWorld.

Self-supervised learning (SSL) approaches have recently shown substantial success in learning visual representations from unannotated images. Compared with photographic images, medical images acquired with the same imaging protocol exhibit high consistency in anatomy. To exploit this anatomical consistency, this paper introduces a novel SSL approach, called PEAC (patch embedding of anatomical consistency), for medical image analysis. Specifically, in this paper, we propose to learn global and local consistencies via stable grid-based matching, transfer pre-trained PEAC models to diverse downstream tasks, and extensively demonstrate that (1) PEAC achieves significantly better performance than the existing state-of-the-art fully/self-supervised methods, and (2) PEAC captures the anatomical structure consistency across views of the same patient and across patients of different genders, weights, and healthy statuses, which enhances the interpretability of our method for medical image analysis.

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.

Deep generative models have emerged as a transformative tool in medical imaging, offering substantial potential for synthetic data generation. However, recent empirical studies highlight a critical vulnerability: these models can memorize sensitive training data, posing significant risks of unauthorized patient information disclosure. Detecting memorization in generative models remains particularly challenging, necessitating scalable methods capable of identifying training data leakage across large sets of generated samples. In this work, we propose DeepSSIM, a novel self-supervised metric for quantifying memorization in generative models. DeepSSIM is trained to: i) project images into a learned embedding space and ii) force the cosine similarity between embeddings to match the ground-truth SSIM (Structural Similarity Index) scores computed in the image space. To capture domain-specific anatomical features, training incorporates structure-preserving augmentations, allowing DeepSSIM to estimate similarity reliably without requiring precise spatial alignment. We evaluate DeepSSIM in a case study involving synthetic brain MRI data generated by a Latent Diffusion Model (LDM) trained under memorization-prone conditions, using 2,195 MRI scans from two publicly available datasets (IXI and CoRR). Compared to state-of-the-art memorization metrics, DeepSSIM achieves superior performance, improving F1 scores by an average of +52.03% over the best existing method. Code and data of our approach are publicly available at the following link: https://github.com/brAIn-science/DeepSSIM.

Despite the recent successes of deep learning, such models are still far from some human abilities like learning from few examples, reasoning and explaining decisions. In this paper, we focus on organ annotation in medical images and we introduce a reasoning framework that is based on learning fuzzy relations on a small dataset for generating explanations. Given a catalogue of relations, it efficiently induces the most relevant relations and combines them for building constraints in order to both solve the organ annotation task and generate explanations. We test our approach on a publicly available dataset of medical images where several organs are already segmented. A demonstration of our model is proposed with an example of explained annotations. It was trained on a small training set containing as few as a couple of examples.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

An increasing number of public datasets have shown a marked impact on automated organ segmentation and tumor detection. However, due to the small size and partially labeled problem of each dataset, as well as a limited investigation of diverse types of tumors, the resulting models are often limited to segmenting specific organs/tumors and ignore the semantics of anatomical structures, nor can they be extended to novel domains. To address these issues, we propose the CLIP-Driven Universal Model, which incorporates text embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models. This CLIP-based label encoding captures anatomical relationships, enabling the model to learn a structured feature embedding and segment 25 organs and 6 types of tumors. The proposed model is developed from an assembly of 14 datasets, using a total of 3,410 CT scans for training and then evaluated on 6,162 external CT scans from 3 additional datasets. We rank first on the Medical Segmentation Decathlon (MSD) public leaderboard and achieve state-of-the-art results on Beyond The Cranial Vault (BTCV). Additionally, the Universal Model is computationally more efficient (6x faster) compared with dataset-specific models, generalized better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks.

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 um^3 EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large-scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/AxonEM/index.html to foster the development of advanced methods.

Multimodal large language models (MLLMs) hold significant potential in the medical field, but their capabilities are often limited by insufficient data in certain medical domains, highlighting the need for understanding what kinds of images can be used by MLLMs for generalization. Current research suggests that multi-task training outperforms single-task as different tasks can benefit each other, but they often overlook the internal relationships within these tasks, providing limited guidance on selecting datasets to enhance specific tasks. To analyze this phenomenon, we attempted to employ compositional generalization (CG)-the ability of models to understand novel combinations by recombining learned elements-as a guiding framework. Since medical images can be precisely defined by Modality, Anatomical area, and Task, naturally providing an environment for exploring CG. Therefore, we assembled 106 medical datasets to create Med-MAT for comprehensive experiments. The experiments confirmed that MLLMs can use CG to understand unseen medical images and identified CG as one of the main drivers of the generalization observed in multi-task training. Additionally, further studies demonstrated that CG effectively supports datasets with limited data and delivers consistent performance across different backbones, highlighting its versatility and broad applicability. Med-MAT is publicly available at https://github.com/FreedomIntelligence/Med-MAT.

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.

Recently, large language models (LLMs) have outperformed human experts in predicting the results of neuroscience experiments (Luo et al., 2024). What is the basis for this performance? One possibility is that statistical patterns in that specific scientific literature, as opposed to emergent reasoning abilities arising from broader training, underlie LLMs' performance. To evaluate this possibility, we trained (next word prediction) a relatively small 124M-parameter GPT-2 model on 1.3 billion tokens of domain-specific knowledge. Despite being orders of magnitude smaller than larger LLMs trained on trillions of tokens, small models achieved expert-level performance in predicting neuroscience results. Small models trained on the neuroscience literature succeeded when they were trained from scratch using a tokenizer specifically trained on neuroscience text or when the neuroscience literature was used to finetune a pretrained GPT-2. Our results indicate that expert-level performance may be attained by even small LLMs through domain-specific, auto-regressive training approaches.

Frontier artificial intelligence (AI) models, such as OpenAI's GPT-5 and Meta's DINOv3, have advanced rapidly through training on internet-scale public data, yet such systems lack access to private clinical data. Neuroimaging, in particular, is underrepresented in the public domain due to identifiable facial features within MRI and CT scans, fundamentally restricting model performance in clinical medicine. Here, we show that frontier models underperform on neuroimaging tasks and that learning directly from uncurated data generated during routine clinical care at health systems, a paradigm we call health system learning, yields high-performance, generalist neuroimaging models. We introduce NeuroVFM, a visual foundation model trained on 5.24 million clinical MRI and CT volumes using a scalable volumetric joint-embedding predictive architecture. NeuroVFM learns comprehensive representations of brain anatomy and pathology, achieving state-of-the-art performance across multiple clinical tasks, including radiologic diagnosis and report generation. The model exhibits emergent neuroanatomic understanding and interpretable visual grounding of diagnostic findings. When paired with open-source language models through lightweight visual instruction tuning, NeuroVFM generates radiology reports that surpass frontier models in accuracy, clinical triage, and expert preference. Through clinically grounded visual understanding, NeuroVFM reduces hallucinated findings and critical errors, offering safer clinical decision support. These results establish health system learning as a paradigm for building generalist medical AI and provide a scalable framework for clinical foundation models.

We create a reusable Transformer, BrainBERT, for intracranial recordings bringing modern representation learning approaches to neuroscience. Much like in NLP and speech recognition, this Transformer enables classifying complex concepts, i.e., decoding neural data, with higher accuracy and with much less data by being pretrained in an unsupervised manner on a large corpus of unannotated neural recordings. Our approach generalizes to new subjects with electrodes in new positions and to unrelated tasks showing that the representations robustly disentangle the neural signal. Just like in NLP where one can study language by investigating what a language model learns, this approach opens the door to investigating the brain by what a model of the brain learns. As a first step along this path, we demonstrate a new analysis of the intrinsic dimensionality of the computations in different areas of the brain. To construct these representations, we combine a technique for producing super-resolution spectrograms of neural data with an approach designed for generating contextual representations of audio by masking. In the future, far more concepts will be decodable from neural recordings by using representation learning, potentially unlocking the brain like language models unlocked language.

Accurate disease interpretation from radiology remains challenging due to imaging heterogeneity. Achieving expert-level diagnostic decisions requires integration of subtle image features with clinical knowledge. Yet major vision-language models (VLMs) treat images as holistic entities and overlook fine-grained image details that are vital for disease diagnosis. Clinicians analyze images by utilizing their prior medical knowledge and identify anatomical structures as important region of interests (ROIs). Inspired from this human-centric workflow, we introduce Anatomy-VLM, a fine-grained, vision-language model that incorporates multi-scale information. First, we design a model encoder to localize key anatomical features from entire medical images. Second, these regions are enriched with structured knowledge for contextually-aware interpretation. Finally, the model encoder aligns multi-scale medical information to generate clinically-interpretable disease prediction. Anatomy-VLM achieves outstanding performance on both in- and out-of-distribution datasets. We also validate the performance of Anatomy-VLM on downstream image segmentation tasks, suggesting that its fine-grained alignment captures anatomical and pathology-related knowledge. Furthermore, the Anatomy-VLM's encoder facilitates zero-shot anatomy-wise interpretation, providing its strong expert-level clinical interpretation capabilities.

Understanding the property of neural populations (or voxels) in the human brain can advance our comprehension of human perceptual and cognitive processing capabilities and contribute to developing brain-inspired computer models. Recent encoding models using deep neural networks (DNNs) have successfully predicted voxel-wise activity. However, interpreting the properties that explain voxel responses remains challenging because of the black-box nature of DNNs. As a solution, we propose LLM-assisted Visual Cortex Captioning (LaVCa), a data-driven approach that uses large language models (LLMs) to generate natural-language captions for images to which voxels are selective. By applying LaVCa for image-evoked brain activity, we demonstrate that LaVCa generates captions that describe voxel selectivity more accurately than the previously proposed method. Furthermore, the captions generated by LaVCa quantitatively capture more detailed properties than the existing method at both the inter-voxel and intra-voxel levels. Furthermore, a more detailed analysis of the voxel-specific properties generated by LaVCa reveals fine-grained functional differentiation within regions of interest (ROIs) in the visual cortex and voxels that simultaneously represent multiple distinct concepts. These findings offer profound insights into human visual representations by assigning detailed captions throughout the visual cortex while highlighting the potential of LLM-based methods in understanding brain representations. Please check out our webpage at https://sites.google.com/view/lavca-llm/

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

Modern language models can process inputs across diverse languages and modalities. We hypothesize that models acquire this capability through learning a shared representation space across heterogeneous data types (e.g., different languages and modalities), which places semantically similar inputs near one another, even if they are from different modalities/languages. We term this the semantic hub hypothesis, following the hub-and-spoke model from neuroscience (Patterson et al., 2007) which posits that semantic knowledge in the human brain is organized through a transmodal semantic "hub" which integrates information from various modality-specific "spokes" regions. We first show that model representations for semantically equivalent inputs in different languages are similar in the intermediate layers, and that this space can be interpreted using the model's dominant pretraining language via the logit lens. This tendency extends to other data types, including arithmetic expressions, code, and visual/audio inputs. Interventions in the shared representation space in one data type also predictably affect model outputs in other data types, suggesting that this shared representations space is not simply a vestigial byproduct of large-scale training on broad data, but something that is actively utilized by the model during input processing.

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, dataset-agnostic initialization for finetuning on new datasets. As a result, we set new standards across both multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.

Although the preservation of shape continuity and physiological anatomy is a natural assumption in the segmentation of medical images, it is often neglected by deep learning methods that mostly aim for the statistical modeling of input data as pixels rather than interconnected structures. In biological structures, however, organs are not separate entities; for example, in reality, a severed vessel is an indication of an underlying problem, but traditional segmentation models are not designed to strictly enforce the continuity of anatomy, potentially leading to inaccurate medical diagnoses. To address this issue, we propose a graph-based approach that enforces the continuity and connectivity of anatomical topology in medical images. Our method encodes the continuity of shapes as a graph constraint, ensuring that the network's predictions maintain this continuity. We evaluate our method on two public benchmarks on retinal vessel segmentation, showing significant improvements in connectivity metrics compared to traditional methods while getting better or on-par performance on segmentation metrics.

Trustworthy interpretation of deep learning models is critical for neuroimaging applications, yet commonly used Explainable AI (XAI) methods lack rigorous validation, risking misinterpretation. We performed the first large-scale, systematic comparison of XAI methods on ~45,000 structural brain MRIs using a novel XAI validation framework. This framework establishes verifiable ground truth by constructing prediction tasks with known signal sources - from localized anatomical features to subject-specific clinical lesions - without artificially altering input images. Our analysis reveals systematic failures in two of the most widely used methods: GradCAM consistently failed to localize predictive features, while Layer-wise Relevance Propagation generated extensive, artifactual explanations that suggest incompatibility with neuroimaging data characteristics. Our results indicate that these failures stem from a domain mismatch, where methods with design principles tailored to natural images require substantial adaptation for neuroimaging data. In contrast, the simpler, gradient-based method SmoothGrad, which makes fewer assumptions about data structure, proved consistently accurate, suggesting its conceptual simplicity makes it more robust to this domain shift. These findings highlight the need for domain-specific adaptation and validation of XAI methods, suggest that interpretations from prior neuroimaging studies using standard XAI methodology warrant re-evaluation, and provide urgent guidance for practical application of XAI in neuroimaging.

Medical report generation has achieved remarkable advancements yet has still been faced with several challenges. First, the inherent imbalance in the distribution of normal and abnormal cases may lead models to exhibit a biased focus on normal samples, resulting in unreliable diagnoses. Second, the frequent occurrence of common template sentences in the reports may overwhelm the critical abnormal information. Moreover, existing works focus on 2D chest X-rays, leaving CT report generation underexplored due to the high-dimensional nature of CT images and the limited availability of CT-report pairs. Recently, LLM has shown a great ability to generate reliable answers with appropriate prompts, which shed light on addressing the aforementioned challenges. In this paper, we propose Dia-LLaMA, a framework to adapt the LLaMA2-7B for CT report generation by incorporating diagnostic information as guidance prompts. Considering the high dimension of CT, we leverage a pre-trained ViT3D with perceiver to extract the visual information. To tailor the LLM for report generation and emphasize abnormality, we extract additional diagnostic information by referring to a disease prototype memory bank, which is updated during training to capture common disease representations. Furthermore, we introduce disease-aware attention to enable the model to adjust attention for different diseases. Experiments on the chest CT dataset demonstrated that our proposed method outperformed previous methods and achieved state-of-the-art on both clinical efficacy performance and natural language generation metrics. The code will be made publically available.

Rationale and Objectives: To develop and validate PARROT (Polyglottal Annotated Radiology Reports for Open Testing), a large, multicentric, open-access dataset of fictional radiology reports spanning multiple languages for testing natural language processing applications in radiology. Materials and Methods: From May to September 2024, radiologists were invited to contribute fictional radiology reports following their standard reporting practices. Contributors provided at least 20 reports with associated metadata including anatomical region, imaging modality, clinical context, and for non-English reports, English translations. All reports were assigned ICD-10 codes. A human vs. AI report differentiation study was conducted with 154 participants (radiologists, healthcare professionals, and non-healthcare professionals) assessing whether reports were human-authored or AI-generated. Results: The dataset comprises 2,658 radiology reports from 76 authors across 21 countries and 13 languages. Reports cover multiple imaging modalities (CT: 36.1%, MRI: 22.8%, radiography: 19.0%, ultrasound: 16.8%) and anatomical regions, with chest (19.9%), abdomen (18.6%), head (17.3%), and pelvis (14.1%) being most prevalent. In the differentiation study, participants achieved 53.9% accuracy (95% CI: 50.7%-57.1%) in distinguishing between human and AI-generated reports, with radiologists performing significantly better (56.9%, 95% CI: 53.3%-60.6%, p<0.05) than other groups. Conclusion: PARROT represents the largest open multilingual radiology report dataset, enabling development and validation of natural language processing applications across linguistic, geographic, and clinical boundaries without privacy constraints.

3D medical image generation is essential for data augmentation and patient privacy, calling for reliable and efficient models suited for clinical practice. However, current methods suffer from limited anatomical fidelity, restricted axial length, and substantial computational cost, placing them beyond reach for regions with limited resources and infrastructure. We introduce TRACE, a framework that generates 3D medical images with spatiotemporal alignment using a 2D multimodal-conditioned diffusion approach. TRACE models sequential 2D slices as video frame pairs, combining segmentation priors and radiology reports for anatomical alignment, incorporating optical flow to sustain temporal coherence. During inference, an overlapping-frame strategy links frame pairs into a flexible length sequence, reconstructed into a spatiotemporally and anatomically aligned 3D volume. Experimental results demonstrate that TRACE effectively balances computational efficiency with preserving anatomical fidelity and spatiotemporal consistency. Code is available at: https://github.com/VinyehShaw/TRACE.

Recent advances in context optimization (CoOp) guided by large language model (LLM)-distilled medical semantic priors offer a scalable alternative to manual prompt engineering and full fine-tuning for adapting biomedical CLIP-based vision-language models (VLMs). However, prompt learning in this context is challenged by semantic misalignment between LLMs and CLIP variants due to divergent training corpora and model architectures; it further lacks scalability across continuously evolving families of foundation models. More critically, pairwise multimodal alignment via conventional Euclidean-space optimization lacks the capacity to model unified representations or apply localized geometric constraints, which tends to amplify modality gaps in complex biomedical imaging and destabilize few-shot adaptation. In this work, we propose vMFCoOp, a framework that inversely estimates von Mises-Fisher (vMF) distributions on a shared Hyperspherical Manifold, aligning semantic biases between arbitrary LLMs and CLIP backbones via Unified Semantic Anchors to achieve robust biomedical prompting and superior few-shot classification. Grounded in three complementary constraints, vMFCoOp demonstrates consistent improvements across 14 medical datasets, 12 medical imaging modalities, and 13 anatomical regions, outperforming state-of-the-art methods in accuracy, generalization, and clinical applicability. This work aims to continuously expand to encompass more downstream applications, and the corresponding resources are intended to be shared through https://github.com/VinyehShaw/UniEqui.

We present the Brain Treebank, a large-scale dataset of electrophysiological neural responses, recorded from intracranial probes while 10 subjects watched one or more Hollywood movies. Subjects watched on average 2.6 Hollywood movies, for an average viewing time of 4.3 hours, and a total of 43 hours. The audio track for each movie was transcribed with manual corrections. Word onsets were manually annotated on spectrograms of the audio track for each movie. Each transcript was automatically parsed and manually corrected into the universal dependencies (UD) formalism, assigning a part of speech to every word and a dependency parse to every sentence. In total, subjects heard over 38,000 sentences (223,000 words), while they had on average 168 electrodes implanted. This is the largest dataset of intracranial recordings featuring grounded naturalistic language, one of the largest English UD treebanks in general, and one of only a few UD treebanks aligned to multimodal features. We hope that this dataset serves as a bridge between linguistic concepts, perception, and their neural representations. To that end, we present an analysis of which electrodes are sensitive to language features while also mapping out a rough time course of language processing across these electrodes. The Brain Treebank is available at https://BrainTreebank.dev/

The article explores an encoding and structural information processing approach using sparse bit vectors and fixed-length linear vectors. The following are presented: a discrete method of speculative stochastic dimensionality reduction of multidimensional code and linear spaces with linear asymptotic complexity; a geometric method for obtaining discrete embeddings of an organised code space that reflect the internal structure of a given modality. The structure and properties of a code space are investigated using three modalities as examples: morphology of Russian and English languages, and immunohistochemical markers. Parallels are drawn between the resulting map of the code space layout and so-called pinwheels appearing on the mammalian neocortex. A cautious assumption is made about similarities between neocortex organisation and processes happening in our models.

Enabling effective brain-computer interfaces requires understanding how the human brain encodes stimuli across modalities such as visual, language (or text), etc. Brain encoding aims at constructing fMRI brain activity given a stimulus. There exists a plethora of neural encoding models which study brain encoding for single mode stimuli: visual (pretrained CNNs) or text (pretrained language models). Few recent papers have also obtained separate visual and text representation models and performed late-fusion using simple heuristics. However, previous work has failed to explore: (a) the effectiveness of image Transformer models for encoding visual stimuli, and (b) co-attentive multi-modal modeling for visual and text reasoning. In this paper, we systematically explore the efficacy of image Transformers (ViT, DEiT, and BEiT) and multi-modal Transformers (VisualBERT, LXMERT, and CLIP) for brain encoding. Extensive experiments on two popular datasets, BOLD5000 and Pereira, provide the following insights. (1) To the best of our knowledge, we are the first to investigate the effectiveness of image and multi-modal Transformers for brain encoding. (2) We find that VisualBERT, a multi-modal Transformer, significantly outperforms previously proposed single-mode CNNs, image Transformers as well as other previously proposed multi-modal models, thereby establishing new state-of-the-art. The supremacy of visio-linguistic models raises the question of whether the responses elicited in the visual regions are affected implicitly by linguistic processing even when passively viewing images. Future fMRI tasks can verify this computational insight in an appropriate experimental setting.

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

Expert interpretation of anatomical images of the human brain is the central part of neuro-radiology. Several machine learning-based techniques have been proposed to assist in the analysis process. However, the ML models typically need to be trained to perform a specific task, e.g., brain tumour segmentation or classification. Not only do the corresponding training data require laborious manual annotations, but a wide variety of abnormalities can be present in a human brain MRI - even more than one simultaneously, which renders representation of all possible anomalies very challenging. Hence, a possible solution is an unsupervised anomaly detection (UAD) system that can learn a data distribution from an unlabelled dataset of healthy subjects and then be applied to detect out of distribution samples. Such a technique can then be used to detect anomalies - lesions or abnormalities, for example, brain tumours, without explicitly training the model for that specific pathology. Several Variational Autoencoder (VAE) based techniques have been proposed in the past for this task. Even though they perform very well on controlled artificially simulated anomalies, many of them perform poorly while detecting anomalies in clinical data. This research proposes a compact version of the "context-encoding" VAE (ceVAE) model, combined with pre and post-processing steps, creating a UAD pipeline (StRegA), which is more robust on clinical data, and shows its applicability in detecting anomalies such as tumours in brain MRIs. The proposed pipeline achieved a Dice score of 0.642pm0.101 while detecting tumours in T2w images of the BraTS dataset and 0.859pm0.112 while detecting artificially induced anomalies, while the best performing baseline achieved 0.522pm0.135 and 0.783pm0.111, respectively.

With the rise of Large Language Models (LLMs), the novel metric "Brainscore" emerged as a means to evaluate the functional similarity between LLMs and human brain/neural systems. Our efforts were dedicated to mining the meaning of the novel score by constructing topological features derived from both human fMRI data involving 190 subjects, and 39 LLMs plus their untrained counterparts. Subsequently, we trained 36 Linear Regression Models and conducted thorough statistical analyses to discern reliable and valid features from our constructed ones. Our findings reveal distinctive feature combinations conducive to interpreting existing brainscores across various brain regions of interest (ROIs) and hemispheres, thereby significantly contributing to advancing interpretable machine learning (iML) studies. The study is enriched by our further discussions and analyses concerning existing brainscores. To our knowledge, this study represents the first attempt to comprehend the novel metric brainscore within this interdisciplinary domain.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

Self-supervised learning has emerged as a powerful paradigm for training deep neural networks, particularly in medical imaging where labeled data is scarce. While current approaches typically rely on synthetic augmentations of single images, we propose VET-DINO, a framework that leverages a unique characteristic of medical imaging: the availability of multiple standardized views from the same study. Using a series of clinical veterinary radiographs from the same patient study, we enable models to learn view-invariant anatomical structures and develop an implied 3D understanding from 2D projections. We demonstrate our approach on a dataset of 5 million veterinary radiographs from 668,000 canine studies. Through extensive experimentation, including view synthesis and downstream task performance, we show that learning from real multi-view pairs leads to superior anatomical understanding compared to purely synthetic augmentations. VET-DINO achieves state-of-the-art performance on various veterinary imaging tasks. Our work establishes a new paradigm for self-supervised learning in medical imaging that leverages domain-specific properties rather than merely adapting natural image techniques.

PanTS is a large-scale, multi-institutional dataset curated to advance research in pancreatic CT analysis. It contains 36,390 CT scans from 145 medical centers, with expert-validated, voxel-wise annotations of over 993,000 anatomical structures, covering pancreatic tumors, pancreas head, body, and tail, and 24 surrounding anatomical structures such as vascular/skeletal structures and abdominal/thoracic organs. Each scan includes metadata such as patient age, sex, diagnosis, contrast phase, in-plane spacing, slice thickness, etc. AI models trained on PanTS achieve significantly better performance in pancreatic tumor detection, localization, and segmentation compared to those trained on existing public datasets. Our analysis indicates that these gains are directly attributable to the 16x larger-scale tumor annotations and indirectly supported by the 24 additional surrounding anatomical structures. As the largest and most comprehensive resource of its kind, PanTS offers a new benchmark for developing and evaluating AI models in pancreatic CT analysis.

Decoding non-invasive brain recordings is pivotal for advancing our understanding of human cognition but faces challenges due to individual differences and complex neural signal representations. Traditional methods often require customized models and extensive trials, lacking interpretability in visual reconstruction tasks. Our framework integrates 3D brain structures with visual semantics using a Vision Transformer 3D. This unified feature extractor efficiently aligns fMRI features with multiple levels of visual embeddings, eliminating the need for subject-specific models and allowing extraction from single-trial data. The extractor consolidates multi-level visual features into one network, simplifying integration with Large Language Models (LLMs). Additionally, we have enhanced the fMRI dataset with diverse fMRI-image-related textual data to support multimodal large model development. Integrating with LLMs enhances decoding capabilities, enabling tasks such as brain captioning, complex reasoning, concept localization, and visual reconstruction. Our approach demonstrates superior performance across these tasks, precisely identifying language-based concepts within brain signals, enhancing interpretability, and providing deeper insights into neural processes. These advances significantly broaden the applicability of non-invasive brain decoding in neuroscience and human-computer interaction, setting the stage for advanced brain-computer interfaces and cognitive models.

Rich and accurate medical image segmentation is poised to underpin the next generation of AI-defined clinical practice by delineating critical anatomy for pre-operative planning, guiding real-time intra-operative navigation, and supporting precise post-operative assessment. However, commonly used learning methods for medical and surgical imaging segmentation tasks penalise all errors equivalently and thus fail to exploit any inter-class semantics in the labels space. This becomes particularly problematic as the cardinality and richness of labels increases to include subtly different classes. In this work, we propose two tree-based semantic loss functions which take advantage of a hierarchical organisation of the labels. We further incorporate our losses in a recently proposed approach for training with sparse, background-free annotations to extend the applicability of our proposed losses. Extensive experiments are reported on two medical and surgical image segmentation tasks, namely head MRI for whole brain parcellation (WBP) with full supervision and neurosurgical hyperspectral imaging (HSI) for scene understanding with sparse annotations. Results demonstrate that our proposed method reaches state-of-the-art performance in both cases.

Reconstructing 3D shapes from planar cross-sections is a challenge inspired by downstream applications like medical imaging and geographic informatics. The input is an in/out indicator function fully defined on a sparse collection of planes in space, and the output is an interpolation of the indicator function to the entire volume. Previous works addressing this sparse and ill-posed problem either produce low quality results, or rely on additional priors such as target topology, appearance information, or input normal directions. In this paper, we present OReX, a method for 3D shape reconstruction from slices alone, featuring a Neural Field as the interpolation prior. A modest neural network is trained on the input planes to return an inside/outside estimate for a given 3D coordinate, yielding a powerful prior that induces smoothness and self-similarities. The main challenge for this approach is high-frequency details, as the neural prior is overly smoothing. To alleviate this, we offer an iterative estimation architecture and a hierarchical input sampling scheme that encourage coarse-to-fine training, allowing the training process to focus on high frequencies at later stages. In addition, we identify and analyze a ripple-like effect stemming from the mesh extraction step. We mitigate it by regularizing the spatial gradients of the indicator function around input in/out boundaries during network training, tackling the problem at the root. Through extensive qualitative and quantitative experimentation, we demonstrate our method is robust, accurate, and scales well with the size of the input. We report state-of-the-art results compared to previous approaches and recent potential solutions, and demonstrate the benefit of our individual contributions through analysis and ablation studies.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

Vision-language models hold considerable promise for ophthalmology, but their development depends on large-scale, high-quality image-text datasets that remain scarce. We present PubMed-Ophtha, a hierarchical dataset of 102,023 ophthalmological image-caption pairs extracted from 15,842 open-access articles in PubMed Central. Unlike existing datasets, figures are extracted directly from article PDFs at full resolution and decomposed into their constituent panels, panel identifiers, and individual images. Each image is annotated with its imaging modality -- color fundus photography, optical coherence tomography, retinal imaging, or other -- and a mark status indicating the presence of annotation marks such as arrows. Figure captions are split into panel-level subcaptions using a two-step LLM approach, achieving a mean average sentence BLEU score of 0.913 on human-annotated data. Panel and image detection models reach a mAP@0.50 of 0.909 and 0.892, respectively, and figure extraction achieves a median IoU of 0.997. To support reproducibility, we additionally release the human-annotated ground-truth data, all trained models, and the full dataset generation pipeline.

Vision-Language Models (VLM) can support clinicians by analyzing medical images and engaging in natural language interactions to assist in diagnostic and treatment tasks. However, VLMs often exhibit "hallucinogenic" behavior, generating textual outputs not grounded in contextual multimodal information. This challenge is particularly pronounced in the medical domain, where we do not only require VLM outputs to be accurate in single interactions but also to be consistent with clinical reasoning and diagnostic pathways throughout multi-turn conversations. For this purpose, we propose a new alignment algorithm that uses symbolic representations of clinical reasoning to ground VLMs in medical knowledge. These representations are utilized to (i) generate GPT-4-guided visual instruction tuning data at scale, simulating clinician-VLM conversations with demonstrations of clinical reasoning, and (ii) create an automatic reward function that evaluates the clinical validity of VLM generations throughout clinician-VLM interactions. Our algorithm eliminates the need for human involvement in training data generation or reward model construction, reducing costs compared to standard reinforcement learning with human feedback (RLHF). We apply our alignment algorithm to develop Dr-LLaVA, a conversational VLM finetuned for analyzing bone marrow pathology slides, demonstrating strong performance in multi-turn medical conversations.

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

Self-Supervised Learning (SSL) has demonstrated promising results in 3D medical image analysis. However, the lack of high-level semantics in pre-training still heavily hinders the performance of downstream tasks. We observe that 3D medical images contain relatively consistent contextual position information, i.e., consistent geometric relations between different organs, which leads to a potential way for us to learn consistent semantic representations in pre-training. In this paper, we propose a simple-yet-effective Volume Contrast (VoCo) framework to leverage the contextual position priors for pre-training. Specifically, we first generate a group of base crops from different regions while enforcing feature discrepancy among them, where we employ them as class assignments of different regions. Then, we randomly crop sub-volumes and predict them belonging to which class (located at which region) by contrasting their similarity to different base crops, which can be seen as predicting contextual positions of different sub-volumes. Through this pretext task, VoCo implicitly encodes the contextual position priors into model representations without the guidance of annotations, enabling us to effectively improve the performance of downstream tasks that require high-level semantics. Extensive experimental results on six downstream tasks demonstrate the superior effectiveness of VoCo. Code will be available at https://github.com/Luffy03/VoCo.

Do brains and language models converge toward the same internal representations of the world? Recent years have seen a rise in studies of neural activations and model alignment. In this work, we review 25 fMRI-based studies published between 2023 and 2025 and explicitly confront their findings with two key hypotheses: (i) the Platonic Representation Hypothesis -- that as models scale and improve, they converge to a representation of the real world, and (ii) the Intermediate-Layer Advantage -- that intermediate (mid-depth) layers often encode richer, more generalizable features. Our findings provide converging evidence that models and brains may share abstract representational structures, supporting both hypotheses and motivating further research on brain-model alignment.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Cognitive neuroscience is enjoying rapid increase in extensive public brain-imaging datasets. It opens the door to large-scale statistical models. Finding a unified perspective for all available data calls for scalable and automated solutions to an old challenge: how to aggregate heterogeneous information on brain function into a universal cognitive system that relates mental operations/cognitive processes/psychological tasks to brain networks? We cast this challenge in a machine-learning approach to predict conditions from statistical brain maps across different studies. For this, we leverage multi-task learning and multi-scale dimension reduction to learn low-dimensional representations of brain images that carry cognitive information and can be robustly associated with psychological stimuli. Our multi-dataset classification model achieves the best prediction performance on several large reference datasets, compared to models without cognitive-aware low-dimension representations, it brings a substantial performance boost to the analysis of small datasets, and can be introspected to identify universal template cognitive concepts.

Medical diagnostic applications require models that can process multimodal medical inputs (images, patient histories, lab results) and generate diverse outputs including both textual reports and visual content (annotations, segmentation masks, and images). Despite this need, existing medical AI systems disrupt this unified process: medical image understanding models interpret images but cannot generate visual outputs, while medical image generation models synthesize images but cannot provide textual explanations. This leads to gaps in data representation, feature integration, and task-level multimodal capabilities. To this end, we propose a multi-level framework that draws inspiration from diagnostic workflows through the Observation-Knowledge-Analysis (OKA) paradigm. Specifically, at the observation level, we construct UniMed-5M, a dataset comprising over 5.6M samples that reformat diverse unimodal data into multimodal pairs for foundational observation. At the knowledge level, we propose Progressive Curriculum Learning that systematically introduces medical multimodal knowledge. At the analysis level, we introduce UniMedVL, the first medical unified multimodal model for the simultaneous analysis of image understanding and generation tasks within a single architecture. UniMedVL achieves superior performance on five medical image understanding benchmarks, while matching specialized models in generation quality across eight medical imaging modalities. Crucially, our unified architecture enables bidirectional knowledge sharing: generation tasks enhance visual understanding features, demonstrating that integrating traditionally separate capabilities within a single medical framework unlocks improvements across diverse medical vision-language tasks. Code is available at https://github.com/uni-medical/UniMedVL.

The differential diagnosis of neurodegenerative dementias is a challenging clinical task, mainly because of the overlap in symptom presentation and the similarity of patterns observed in structural neuroimaging. To improve diagnostic efficiency and accuracy, deep learning-based methods such as Convolutional Neural Networks and Vision Transformers have been proposed for the automatic classification of brain MRIs. However, despite their strong predictive performance, these models find limited clinical utility due to their opaque decision making. In this work, we propose a framework that integrates two core components to enhance diagnostic transparency. First, we introduce a modular pipeline for converting 3D T1-weighted brain MRIs into textual radiology reports. Second, we explore the potential of modern Large Language Models (LLMs) to assist clinicians in the differential diagnosis between Frontotemporal dementia subtypes, Alzheimer's disease, and normal aging based on the generated reports. To bridge the gap between predictive accuracy and explainability, we employ reinforcement learning to incentivize diagnostic reasoning in LLMs. Without requiring supervised reasoning traces or distillation from larger models, our approach enables the emergence of structured diagnostic rationales grounded in neuroimaging findings. Unlike post-hoc explainability methods that retrospectively justify model decisions, our framework generates diagnostic rationales as part of the inference process-producing causally grounded explanations that inform and guide the model's decision-making process. In doing so, our framework matches the diagnostic performance of existing deep learning methods while offering rationales that support its diagnostic conclusions.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

Medicine is inherently multimodal, with rich data modalities spanning text, imaging, genomics, and more. Generalist biomedical artificial intelligence (AI) systems that flexibly encode, integrate, and interpret this data at scale can potentially enable impactful applications ranging from scientific discovery to care delivery. To enable the development of these models, we first curate MultiMedBench, a new multimodal biomedical benchmark. MultiMedBench encompasses 14 diverse tasks such as medical question answering, mammography and dermatology image interpretation, radiology report generation and summarization, and genomic variant calling. We then introduce Med-PaLM Multimodal (Med-PaLM M), our proof of concept for a generalist biomedical AI system. Med-PaLM M is a large multimodal generative model that flexibly encodes and interprets biomedical data including clinical language, imaging, and genomics with the same set of model weights. Med-PaLM M reaches performance competitive with or exceeding the state of the art on all MultiMedBench tasks, often surpassing specialist models by a wide margin. We also report examples of zero-shot generalization to novel medical concepts and tasks, positive transfer learning across tasks, and emergent zero-shot medical reasoning. To further probe the capabilities and limitations of Med-PaLM M, we conduct a radiologist evaluation of model-generated (and human) chest X-ray reports and observe encouraging performance across model scales. In a side-by-side ranking on 246 retrospective chest X-rays, clinicians express a pairwise preference for Med-PaLM M reports over those produced by radiologists in up to 40.50% of cases, suggesting potential clinical utility. While considerable work is needed to validate these models in real-world use cases, our results represent a milestone towards the development of generalist biomedical AI systems.

Although large language models (LLMs) are increasingly capable, these capabilities are unevenly distributed: they excel at formal linguistic tasks, such as producing fluent, grammatical text, but struggle more with functional linguistic tasks like reasoning and consistent fact retrieval. Inspired by neuroscience, recent work suggests that to succeed on both formal and functional linguistic tasks, LLMs should use different mechanisms for each; such localization could either be built-in or emerge spontaneously through training. In this paper, we ask: do current models, with fast-improving functional linguistic abilities, exhibit distinct localization of formal and functional linguistic mechanisms? We answer this by finding and comparing the "circuits", or minimal computational subgraphs, responsible for various formal and functional tasks. Comparing 5 LLMs across 10 distinct tasks, we find that while there is indeed little overlap between circuits for formal and functional tasks, there is also little overlap between formal linguistic tasks, as exists in the human brain. Thus, a single formal linguistic network, unified and distinct from functional task circuits, remains elusive. However, in terms of cross-task faithfulness - the ability of one circuit to solve another's task - we observe a separation between formal and functional mechanisms, suggesting that shared mechanisms between formal tasks may exist.

Vision-and-language models (VLMs) have been increasingly explored in the medical domain, particularly following the success of CLIP in general domain. However, unlike the relatively straightforward pairing of 2D images and text, curating large-scale paired data in the medical field for volumetric modalities such as CT scans remains a challenging and time-intensive process. This difficulty often limits the performance on downstream tasks. To address these challenges, we propose a novel vision-language pre-training (VLP) framework, termed as VELVET-Med, specifically designed for limited volumetric data such as 3D CT and associated radiology reports. Instead of relying on large-scale data collection, our method focuses on the development of effective pre-training objectives and model architectures. The key contributions are: 1) We incorporate uni-modal self-supervised learning into VLP framework, which are often underexplored in the existing literature. 2) We propose a novel language encoder, termed as TriBERT, for learning multi-level textual semantics. 3) We devise the hierarchical contrastive learning to capture multi-level vision-language correspondence. Using only 38,875 scan-report pairs, our approach seeks to uncover rich spatial and semantic relationships embedded in volumetric medical images and corresponding clinical narratives, thereby enhancing the generalization ability of the learned encoders. The resulting encoders exhibit strong transferability, achieving state-of-the-art performance across a wide range of downstream tasks, including 3D segmentation, cross-modal retrieval, visual question answering, and report generation.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

Quantification of real-time informal feedback delivered by an experienced surgeon to a trainee during surgery is important for skill improvements in surgical training. Such feedback in the live operating room is inherently multimodal, consisting of verbal conversations (e.g., questions and answers) as well as non-verbal elements (e.g., through visual cues like pointing to anatomic elements). In this work, we leverage a clinically-validated five-category classification of surgical feedback: "Anatomic", "Technical", "Procedural", "Praise" and "Visual Aid". We then develop a multi-label machine learning model to classify these five categories of surgical feedback from inputs of text, audio, and video modalities. The ultimate goal of our work is to help automate the annotation of real-time contextual surgical feedback at scale. Our automated classification of surgical feedback achieves AUCs ranging from 71.5 to 77.6 with the fusion improving performance by 3.1%. We also show that high-quality manual transcriptions of feedback audio from experts improve AUCs to between 76.5 and 96.2, which demonstrates a clear path toward future improvements. Empirically, we find that the Staged training strategy, with first pre-training each modality separately and then training them jointly, is more effective than training different modalities altogether. We also present intuitive findings on the importance of modalities for different feedback categories. This work offers an important first look at the feasibility of automated classification of real-world live surgical feedback based on text, audio, and video modalities.

Transcranial focused ultrasound (tFUS) is an emerging modality for non-invasive brain stimulation and therapeutic intervention, offering millimeter-scale spatial precision and the ability to target deep brain structures. However, the heterogeneous and anisotropic nature of the human skull introduces significant distortions to the propagating ultrasound wavefront, which require time-consuming patient-specific planning and corrections using numerical solvers for accurate targeting. To enable data-driven approaches in this domain, we introduce TFUScapes, the first large-scale, high-resolution dataset of tFUS simulations through anatomically realistic human skulls derived from T1-weighted MRI images. We have developed a scalable simulation engine pipeline using the k-Wave pseudo-spectral solver, where each simulation returns a steady-state pressure field generated by a focused ultrasound transducer placed at realistic scalp locations. In addition to the dataset, we present DeepTFUS, a deep learning model that estimates normalized pressure fields directly from input 3D CT volumes and transducer position. The model extends a U-Net backbone with transducer-aware conditioning, incorporating Fourier-encoded position embeddings and MLP layers to create global transducer embeddings. These embeddings are fused with U-Net encoder features via feature-wise modulation, dynamic convolutions, and cross-attention mechanisms. The model is trained using a combination of spatially weighted and gradient-sensitive loss functions, enabling it to approximate high-fidelity wavefields. The TFUScapes dataset is publicly released to accelerate research at the intersection of computational acoustics, neurotechnology, and deep learning. The project page is available at https://github.com/CAMMA-public/TFUScapes.

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.

Attending to what is relevant is fundamental to both the mammalian brain and modern machine learning models such as Transformers. Yet, determining relevance remains a core challenge, traditionally offloaded to learning algorithms like backpropagation. Inspired by recent cellular neurobiological evidence linking neocortical pyramidal cells to distinct mental states, this work shows how models (e.g., Transformers) can emulate high-level perceptual processing and awake thought (imagination) states to pre-select relevant information before applying attention. Triadic neuronal-level modulation loops among questions (Q), clues (keys, K), and hypotheses (values, V) enable diverse, deep, parallel reasoning chains at the representation level and allow a rapid shift from initial biases to refined understanding. This leads to orders-of-magnitude faster learning with significantly reduced computational demand (e.g., fewer heads, layers, and tokens), at an approximate cost of O(N), where N is the number of input tokens. Results span reinforcement learning (e.g., CarRacing in a high-dimensional visual setup), computer vision, and natural language question answering.

The rapid development of text-to-image (T2I) generation approaches has attracted extensive interest in evaluating the quality of generated images, leading to the development of various quality assessment methods for general-purpose T2I outputs. However, existing image quality assessment (IQA) methods are limited to providing global quality scores, failing to deliver fine-grained perceptual evaluations for structurally complex subjects like humans, which is a critical challenge considering the frequent anatomical and textural distortions in AI-generated human images (AGHIs). To address this gap, we introduce AGHI-QA, the first large-scale benchmark specifically designed for quality assessment of AGHIs. The dataset comprises 4,000 images generated from 400 carefully crafted text prompts using 10 state of-the-art T2I models. We conduct a systematic subjective study to collect multidimensional annotations, including perceptual quality scores, text-image correspondence scores, visible and distorted body part labels. Based on AGHI-QA, we evaluate the strengths and weaknesses of current T2I methods in generating human images from multiple dimensions. Furthermore, we propose AGHI-Assessor, a novel quality metric that integrates the large multimodal model (LMM) with domain-specific human features for precise quality prediction and identification of visible and distorted body parts in AGHIs. Extensive experimental results demonstrate that AGHI-Assessor showcases state-of-the-art performance, significantly outperforming existing IQA methods in multidimensional quality assessment and surpassing leading LMMs in detecting structural distortions in AGHIs.

We investigate the internal representations of vision-and-language models (VLMs) and how they encode task representations. We consider tasks specified through examples or instructions, using either text or image inputs. Surprisingly, we find that conceptually similar tasks are mapped to similar task vector representations, regardless of how they are specified. Our findings suggest that to output answers, tokens in VLMs undergo three distinct phases: input, task, and answer, a process which is consistent across different modalities and specifications. The task vectors we identify in VLMs are general enough to be derived in one modality (e.g., text) and transferred to another (e.g., image). Additionally, we find that ensembling exemplar and instruction based task vectors produce better task representations. Taken together, these insights shed light on the underlying mechanisms of VLMs, particularly their ability to represent tasks in a shared manner across different modalities and task specifications. Project page: https://task-vectors-are-cross-modal.github.io.

In recent years, the potential applications of machine learning to Minimally Invasive Surgery (MIS) have spurred interest in data sets that can be used to develop data-driven tools. This paper introduces a novel dataset recorded during ex vivo pseudo-cholecystectomy procedures on pig livers, utilizing the da Vinci Research Kit (dVRK). Unlike current datasets, ours bridges a critical gap by offering not only full kinematic data but also capturing all pedal inputs used during the procedure and providing a time-stamped record of the endoscope's movements. Contributed by seven surgeons, this data set introduces a new dimension to surgical robotics research, allowing the creation of advanced models for automating console functionalities. Our work addresses the existing limitation of incomplete recordings and imprecise kinematic data, common in other datasets. By introducing two models, dedicated to predicting clutch usage and camera activation, we highlight the dataset's potential for advancing automation in surgical robotics. The comparison of methodologies and time windows provides insights into the models' boundaries and limitations.

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.

Multimodal language models (MLMs) show promise for clinical decision support and diagnostic reasoning, raising the prospect of end-to-end automated medical image interpretation. However, clinicians are highly selective in adopting AI tools; a model that makes errors on seemingly simple perception tasks such as determining image orientation or identifying whether a CT scan is contrast-enhance are unlikely to be adopted for clinical tasks. We introduce Medblink, a benchmark designed to probe these models for such perceptual abilities. Medblink spans eight clinically meaningful tasks across multiple imaging modalities and anatomical regions, totaling 1,429 multiple-choice questions over 1,605 images. We evaluate 19 state-of-the-art MLMs, including general purpose (GPT4o, Claude 3.5 Sonnet) and domain specific (Med Flamingo, LLaVA Med, RadFM) models. While human annotators achieve 96.4% accuracy, the best-performing model reaches only 65%. These results show that current MLMs frequently fail at routine perceptual checks, suggesting the need to strengthen their visual grounding to support clinical adoption. Data is available on our project page.

Not yet. We present SPACE, a benchmark that systematically evaluates spatial cognition in frontier models. Our benchmark builds on decades of research in cognitive science. It evaluates large-scale mapping abilities that are brought to bear when an organism traverses physical environments, smaller-scale reasoning about object shapes and layouts, and cognitive infrastructure such as spatial attention and memory. For many tasks, we instantiate parallel presentations via text and images, allowing us to benchmark both large language models and large multimodal models. Results suggest that contemporary frontier models fall short of the spatial intelligence of animals, performing near chance level on a number of classic tests of animal cognition.

Background: Recent advances in large language models highlight the need for high-quality multilingual medical datasets. While Japan leads globally in CT scanner deployment and utilization, the lack of large-scale Japanese radiology datasets has hindered the development of specialized language models for medical imaging analysis. Objective: To develop a comprehensive Japanese CT report dataset through machine translation and establish a specialized language model for structured finding classification. Additionally, to create a rigorously validated evaluation dataset through expert radiologist review. Methods: We translated the CT-RATE dataset (24,283 CT reports from 21,304 patients) into Japanese using GPT-4o mini. The training dataset consisted of 22,778 machine-translated reports, while the validation dataset included 150 radiologist-revised reports. We developed CT-BERT-JPN based on "tohoku-nlp/bert-base-japanese-v3" architecture for extracting 18 structured findings from Japanese radiology reports. Results: Translation metrics showed strong performance with BLEU scores of 0.731 and 0.690, and ROUGE scores ranging from 0.770 to 0.876 for Findings and from 0.748 to 0.857 for Impression sections. CT-BERT-JPN demonstrated superior performance compared to GPT-4o in 11 out of 18 conditions, including lymphadenopathy (+14.2%), interlobular septal thickening (+10.9%), and atelectasis (+7.4%). The model maintained F1 scores exceeding 0.95 in 14 out of 18 conditions and achieved perfect scores in four conditions. Conclusions: Our study establishes a robust Japanese CT report dataset and demonstrates the effectiveness of a specialized language model for structured finding classification. The hybrid approach of machine translation and expert validation enables the creation of large-scale medical datasets while maintaining high quality.

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.

Generative models hold promise for revolutionizing medical education, robot-assisted surgery, and data augmentation for medical AI development. Diffusion models can now generate realistic images from text prompts, while recent advancements have demonstrated their ability to create diverse, high-quality videos. However, these models often struggle with generating accurate representations of medical procedures and detailed anatomical structures. This paper introduces Bora, the first spatio-temporal diffusion probabilistic model designed for text-guided biomedical video generation. Bora leverages Transformer architecture and is pre-trained on general-purpose video generation tasks. It is fine-tuned through model alignment and instruction tuning using a newly established medical video corpus, which includes paired text-video data from various biomedical fields. To the best of our knowledge, this is the first attempt to establish such a comprehensive annotated biomedical video dataset. Bora is capable of generating high-quality video data across four distinct biomedical domains, adhering to medical expert standards and demonstrating consistency and diversity. This generalist video generative model holds significant potential for enhancing medical consultation and decision-making, particularly in resource-limited settings. Additionally, Bora could pave the way for immersive medical training and procedure planning. Extensive experiments on distinct medical modalities such as endoscopy, ultrasound, MRI, and cell tracking validate the effectiveness of our model in understanding biomedical instructions and its superior performance across subjects compared to state-of-the-art generation models.

Since radiology reports needed for clinical practice and research are written and stored in free-text narrations, extraction of relative information for further analysis is difficult. In these circumstances, natural language processing (NLP) techniques can facilitate automatic information extraction and transformation of free-text formats to structured data. In recent years, deep learning (DL)-based models have been adapted for NLP experiments with promising results. Despite the significant potential of DL models based on artificial neural networks (ANN) and convolutional neural networks (CNN), the models face some limitations to implement in clinical practice. Transformers, another new DL architecture, have been increasingly applied to improve the process. Therefore, in this study, we propose a transformer-based fine-grained named entity recognition (NER) architecture for clinical information extraction. We collected 88 abdominopelvic sonography reports in free-text formats and annotated them based on our developed information schema. The text-to-text transfer transformer model (T5) and Scifive, a pre-trained domain-specific adaptation of the T5 model, were applied for fine-tuning to extract entities and relations and transform the input into a structured format. Our transformer-based model in this study outperformed previously applied approaches such as ANN and CNN models based on ROUGE-1, ROUGE-2, ROUGE-L, and BLEU scores of 0.816, 0.668, 0.528, and 0.743, respectively, while providing an interpretable structured report.

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.