arXiv subjects

Wenjia Bai

Publications and source records attributed to Wenjia Bai.

At least 19 recordsLinked to original sources

arXiv2026

LongAgent: History-Guided Agentic Search for Longitudinal Outcome Prediction

Extracting informative representations from longitudinal data that can predict future outcomes remains a critical challenge in medicine. Medical datasets are inherently heterogeneous, consisting of a large number of variables collected from different sources, sampled with different temporal spacings, and representing different aspects of human health status. This requires identifying those variables with predictive value, processing longitudinal information, and integrating multiple variables for outcome prediction. Here, we propose a novel agent-based approach, LongAgent, that can autonomously search over combinations of variable sets, temporal windows and longitudinal aggregation functions, and identify candidates with promising predictive performance. LongAgent utilises a history memory of previous searches and numerical evidence to guide subsequent exploration. On synthetic data, LongAgent achieves a mean prediction RMSE of 1.7376 and improves over the strongest non-agent baseline by 0.0151 (95% CI: [0.0045,0.0260]; p=0.0273). On a real clinical dataset, it performs comparably to the best baseline.

cs.AI↗

arXiv2026

CPAgents: Agentic Composite Phenotype Generation for Cardiac Disease Association

Identifying robust associations between cardiac imaging phenotypes and clinical diseases is fundamental to population-scale cardiovascular research and reliable risk stratification. However, current phenome-wide association studies rely on pre-defined, single-variable phenotypes or expert-crafted features, which limits their ability to capture clinically meaningful non-linear effects and cross-phenotype interactions. To address this, we propose CPAgents, an iterative phenotype-Composition framework for cardiovascular Phenome-wide association study (PheWAS) that automatically constructs and validates interpretable composite phenotypes (e.g., polynomial, ratio, and interaction forms) from base imaging features. Specifically, our system coordinates three agents: (i) an Analyst that identifies statistical pathologies and nominates candidate transformations; (ii) a Proposer that generates constrained, medically and statistically motivated expressions under numerical safety rules; and (iii) a Verifier that evaluates candidates using multi-stage criteria and produces transparent evidence trails for accepted phenotypes. Evaluated on a population-scale cardiac imaging cohort, the discovered composite phenotypes markedly improve disease discrimination: across 72 classifier-disease-metric combinations, our variants achieve the top rank in 56 cases versus 18 for baselines, with gains observed across all nine clinical disease categories. Our framework yields compact, clinically interpretable phenotype formulas with transparent evidence trails, enabling scalable discovery of stronger phenotype-disease associations beyond expert-driven feature selection.

cs.LG↗

arXiv2026

Unified Multimodal Model for Brain MRI Imputation and Understanding

Multimodal large language models (MLLMs) hold great potential for medicine, as they inherit knowledge from LLM and allow multiple data modalities to be integrated, analysed and interpreted in natural language. However, the field of medical MLLMs is constrained by non-trivial challenges, notably the scarcity of high-quality training data and the frequent occurrence of missing data in the real-world clinical setting. Here, we propose a novel unified multimodal model, UniBrain, for brain magnetic resonance image (MRI) analysis. To address potential missing brain MRI modalities, we employ a unified training strategy to perform joint imaging modality imputation and brain image understanding. During training, an interleaved and description-enriched data flow is constructed to train the model in an autoregressive manner, enabling medical reasoning with generated multimodal data. A self-alignment strategy is introduced to leverage dense image embeddings to learn fine-grained anatomical features without requiring detailed image captions. Furthermore, we propose a dynamic hidden state mechanism to alleviate the exposure bias during long-context multimodal inference. Extensive experiments on multi-disease brain MRI dataset demonstrate that UniBrain achieves high performance for brain image imputation, understanding, and disease diagnosis under various extents of modality incompleteness.

cs.CV↗

arXiv2026

Cardiac Mesh Flow: One-Step Generation of 3D+t Cardiac Four-Chamber Meshes via Flow Matching

Spatio-temporal (3D+t) generative modelling of cardiac shape and motion is crucial for understanding heart structure and function at population scale. Existing generative models for cardiac shape synthesis either adopt volumetric shape representations that lack anatomical correspondence across different time points and subjects, or rely on VAE-based frameworks that suffer from a trade-off between reconstruction fidelity and generative diversity. In this work, we propose Cardiac Mesh Flow, a novel generative flow model for 3D+t cardiac four-chamber mesh generation with anatomical correspondence, temporal coherence, and periodic consistency. Leveraging the flow matching technique, Cardiac Mesh Flow performs efficient one-step generation of multi-scale free-form deformation fields, which warp a template mesh to generate cardiac four-chamber meshes across a cardiac cycle. Furthermore, Cardiac Mesh Flow enables controllable generation conditioned on cardiac chamber volumes, allowing precise control of the synthetic heart. Experimental results demonstrate that Cardiac Mesh Flow achieves high fidelity and diversity on both unconditional and conditional generation, compared to state-of-the-art 3D+t cardiac mesh generation methods.

eess.IV↗

arXiv2026

Dynamic Decision Learning: Test-Time Evolution for Abnormality Grounding in Rare Diseases

Clinical abnormality grounding for rare diseases is often hindered by data scarcity, making supervised fine-tuning impractical and single-pass inference highly unstable. We propose Dynamic Decision Learning (DDL), a framework that enables frozen large vision-language models (LVLMs) to refine their decisions across both language and visual spaces by optimizing instructions and consolidating predictions under visual perturbations. This process improves localization quality and produces a consensus-based reliability score that quantifies model confidence. Results on brain imaging benchmarks, including a rare-disease dataset with 281 pathology types across models ranging from 3B to 72B parameters, show that DDL improves mAP@75 by up to 105% on rare-disease cases and outperforms adaptation baselines and supervised fine-tuning. Furthermore, DDL demonstrates stronger calibration between reliability scores and localization accuracy under severe distribution shifts and increasing task difficulty. Code is available at: https://lijunrio.github.io/DDL/

cs.CL↗

arXiv2026

Enabling Ultra-Fast Cardiovascular Imaging Across Heterogeneous Clinical Environments with A Generalist Foundation Model and Multimodal Database

Multimodal cardiovascular magnetic resonance (CMR) imaging provides comprehensive and non-invasive insights into cardiovascular disease (CVD) diagnosis and underlying mechanisms. Despite decades of advancements, its widespread clinical adoption remains constrained by prolonged scan times, inconsistent image quality, and heterogeneity across medical environments. This underscores the urgent need for a generalist reconstruction foundation model for ultra-fast CMR imaging, one formulated for physics-constrained inverse problems in the sensor (k-space) domain, capable of adapting across diverse imaging scenarios and serving as the essential substrate for all downstream analyses. To enable this goal, we curate MMCMR-427K, the largest and most comprehensive multimodal CMR k-space database to date, comprising 427,465 multi-coil k-space data paired with structured metadata across 13 international centers, 12 CMR modalities, 15 scanners spanning four field strengths, and 17 CVD categories in populations across three continents. Building on this unprecedented resource, we introduce CardioMM, a generalist reconstruction foundation model capable of dynamically adapting to heterogeneous fast CMR imaging scenarios. CardioMM unifies semantic contextual understanding with physics-informed data consistency to deliver robust reconstructions across varied scanners, protocols, and patient presentations. Comprehensive evaluations demonstrate that CardioMM achieves state-of-the-art performance across internal centers and exhibits strong zero-shot generalization to unseen external settings. Importantly, CardioMM supports acceleration up to 24x, providing the first evidence that such extreme acquisition speed can preserve key cardiac phenotypes, quantitative myocardial biomarkers, and diagnostic image quality without compromising clinical integrity.

eess.IV↗

arXiv2026

AdamFlow: Adam-based Wasserstein Gradient Flows for Surface Registration in Medical Imaging

Surface registration plays an important role for anatomical shape analysis in medical imaging. Existing surface registration methods often face a trade-off between efficiency and robustness. Local point matching methods are computationally efficient, but vulnerable to noise and initialisation. Methods designed for global point set alignment tend to incur a high computational cost. To address the challenge, here we present a fast surface registration method, which formulates surface meshes as probability measures and surface registration as a distributional optimisation problem. The discrepancy between two meshes is measured using an efficient sliced Wasserstein distance with log-linear computational complexity. We propose a novel optimisation method, AdamFlow, which generalises the well-known Adam optimisation method from the Euclidean space to the probability space for minimising the sliced Wasserstein distance. We theoretically analyse the asymptotic convergence of AdamFlow and empirically demonstrate its superior performance in both affine and non-rigid surface registration across various anatomical structures.

cs.CV↗

arXiv2026

Learning a dynamic four-chamber shape model of the human heart for 95,695 UK Biobank participants

The human heart is a sophisticated system composed of four cardiac chambers with distinct shapes, which function in a coordinated manner. Existing shape models of the heart mainly focus on the ventricular chambers and they are derived from relatively small datasets. Here, we present a spatio-temporal (3D+t) statistical shape model of all four cardiac chambers, learnt from a large population of nearly 100,000 participants from the UK Biobank. A deep learning-based pipeline is developed to reconstruct 3D+t four-chamber meshes from the cardiac magnetic resonance images of the UK Biobank imaging population. Based on the reconstructed meshes, a 3D+t statistical shape model is learnt to characterise the shape variations and motion patterns of the four cardiac chambers. We reveal the associations of the four-chamber shape model with demographics, anthropometrics, cardiovascular risk factors, and cardiac diseases. Compared to conventional image-derived phenotypes, we validate that the four-chamber shape-derived phenotypes significantly enhance the performance in downstream tasks, including cardiovascular disease classification and heart age prediction. Furthermore, we demonstrate the effectiveness of shape-derived phenotypes in novel applications such as heart shape retrieval and heart re-identification from longitudinal data. To facilitate future research, we will release the learning-based mesh reconstruction pipeline, the four-chamber cardiac shape model, and return all derived four-chamber meshes to the UK Biobank.

eess.IV↗

arXiv2026

Virtual Full-stack Scanning of Brain MRI via Imputing Any Quantised Code

Magnetic resonance imaging (MRI) is a powerful and versatile imaging technique, offering a wide spectrum of information about the anatomy by employing different acquisition modalities. However, in the clinical workflow, it is impractical to collect all relevant modalities due to the scan time and cost constraints. Virtual full-stack scanning aims to impute missing MRI modalities from available but incomplete acquisitions, offering a cost-efficient solution to enhance data completeness and clinical usability. Existing imputation methods often depend on global conditioning or modality-specific designs, which limit their generalisability across patient cohorts and imaging protocols. To address these limitations, we propose CodeBrain, a unified framework that reformulates various ``any-to-any'' imputation tasks as a region-level full-stack code prediction problem. CodeBrain adopts a two-stage pipeline: (1) it learns the compact representation of a complete MRI modality set by encoding it into scalar-quantised codes at the region level, enabling high-fidelity image reconstruction after decoding these codes along with modality-agnostic common features; (2) it trains a projection encoder to predict the full-stack code map from incomplete modalities via a grading-based design for diverse imputation scenarios. Extensive experiments on two public brain MRI datasets, i.e., IXI and BraTS 2023, demonstrate that CodeBrain consistently outperforms state-of-the-art methods, establishing a new benchmark for unified brain MRI imputation and enabling virtual full-stack scanning. Our code will be released at https://github.com/ycwu1997/CodeBrain.

cs.CV↗

arXiv2026

Flow Matching-enabled Test-Time Refinement for Unsupervised Cardiac MR Registration

Diffusion-based unsupervised image registration has been explored for cardiac cine MR, but expensive multi-step inference limits practical use. We propose FlowReg, a flow-matching framework in displacement field space that achieves strong registration in as few as two steps and supports further refinement with more steps. FlowReg uses warmup-reflow training: a single-step network first acts as a teacher, then a student learns to refine from arbitrary intermediate states, removing the need for a pre-trained model as in existing methods. An Initial Guess strategy feeds back the model prediction as the next starting point, improving refinement from step two onward. On ACDC and MM2 across six tasks (including cross-dataset generalization), FlowReg outperforms the state of the art on five tasks (+0.6% mean Dice score on average), with the largest gain in the left ventricle (+1.09%), and reduces LVEF estimation error on all six tasks (-2.58 percentage points), using only 0.7% extra parameters and no segmentation labels. Code is available at https://github.com/mathpluscode/FlowReg.

cs.CV↗

arXiv2026

Does DINOv3 Set a New Medical Vision Standard? Benchmarking 2D and 3D Classification, Segmentation, and Registration

The advent of large-scale vision foundation models, pre-trained on diverse natural images, has marked a paradigm shift in computer vision. However, how the frontier vision foundation models' efficacies transfer to specialised domains such as medical imaging remains an open question. This report investigates whether DINOv3, a state-of-the-art self-supervised vision transformer (ViT) pre-trained on natural images, can directly serve as a powerful, unified encoder for medical vision tasks without domain-specific fine-tuning. To answer this, we benchmark DINOv3 across common medical vision tasks, including 2D and 3D classification, segmentation, and registration on a wide range of medical imaging modalities. We systematically analyse its scalability by varying model sizes and input image resolutions. Our findings reveal that DINOv3 shows impressive performance and establishes a formidable new baseline. Remarkably, it can even outperform medical-specific foundation models like BiomedCLIP and CT-Net on several tasks, despite being trained solely on natural images. However, we identify clear limitations: The model's features degrade in scenarios requiring deep domain specialisation, such as in whole-slide images (WSIs), electron microscopy (EM), and positron emission tomography (PET). Furthermore, we observe that DINOv3 does not consistently follow the scaling law in the medical domain. Its performance does not reliably increase with larger models or finer feature resolutions, showing diverse scaling behaviours across tasks. Overall, our work establishes DINOv3 as a strong baseline, whose powerful visual features can serve as a robust prior for multiple medical tasks. This opens promising future directions, such as leveraging its features to enforce multiview consistency in 3D reconstruction.

cs.CV↗

arXiv2026

SAM-aware Test-time Adaptation for Universal Medical Image Segmentation

Leveraging the Segment Anything Model (SAM) for medical image segmentation remains challenging due to its limited adaptability across diverse medical domains. Although fine-tuned variants, such as MedSAM, improve performance in scenarios similar to the training modalities or organs, they may lack generalizability to unseen data. To overcome this limitation, we propose SAM-aware Test-time Adaptation (SAM-TTA), a lightweight and flexible framework that preserves SAM's inherent generalization ability while enhancing segmentation accuracy for medical images. SAM-TTA tackles two major challenges: (1) input-level discrepancy caused by channel mismatches between natural and medical images, and (2) semantic-level discrepancy due to different object characteristics in natural versus medical images (e.g., with clear boundaries vs. ambiguous structures). To this end, we introduce two complementary components: a self-adaptive Bezier Curve-based Transformation (SBCT), which maps single-channel medical images into SAM-compatible three-channel images via a few learnable parameters to be optimized at test time; and IoU-guided Multi-scale Adaptation (IMA), which leverages SAM's intrinsic IoU scores to enforce high output confidence, dual-scale prediction consistency, and intermediate feature consistency, to improve semantic-level alignments. Extensive experiments on eight public medical image segmentation tasks, covering six grayscale and two color (endoscopic) tasks, demonstrate that SAM-TTA consistently outperforms state-of-the-art test-time adaptation methods. Notably, on six grayscale datasets, SAM-TTA even surpasses fully fine-tuned models, achieving significant Dice improvements (i.e., average 4.8% and 7.4% gains over MedSAM and SAM-Med2D) and establishing a new paradigm for universal medical image segmentation. Code is available at https://github.com/JianghaoWu/SAM-TTA.

cs.CV↗

arXiv2025

Towards Modality- and Sampling-Universal Learning Strategies for Accelerating Cardiovascular Imaging: Summary of the CMRxRecon2024 Challenge

Cardiovascular health is vital to human well-being, and cardiac magnetic resonance (CMR) imaging is considered the {clinical reference standard} for diagnosing cardiovascular disease. However, its adoption is hindered by long scan times, complex contrasts, and inconsistent quality. While deep learning methods perform well on specific CMR imaging {sequences}, they often fail to generalize across modalities and sampling schemes. The lack of benchmarks for high-quality, fast CMR image reconstruction further limits technology comparison and adoption. The CMRxRecon2024 challenge, attracting over 200 teams from 18 countries, addressed these issues with two tasks: generalization to unseen {modalities} and robustness to diverse undersampling patterns. We introduced the largest public multi-{modality} CMR raw dataset, an open benchmarking platform, and shared code. Analysis of the best-performing solutions revealed that prompt-based adaptation and enhanced physics-driven consistency enabled strong cross-scenario performance. These findings establish principles for generalizable reconstruction models and advance clinically translatable AI in cardiovascular imaging.

eess.IV↗

arXiv2025

Multi-Agent Reasoning for Cardiovascular Imaging Phenotype Analysis

Identifying associations between imaging phenotypes, disease risk factors, and clinical outcomes is essential for understanding disease mechanisms. However, traditional approaches rely on human-driven hypothesis testing and selection of association factors, often overlooking complex, non-linear dependencies among imaging phenotypes and other multi-modal data. To address this, we introduce Multi-agent Exploratory Synergy for the Heart (MESHAgents): a framework that leverages large language models as agents to dynamically elicit, surface, and decide confounders and phenotypes in association studies. Specifically, we orchestrate a multi-disciplinary team of AI agents, which spontaneously generate and converge on insights through iterative, self-organizing reasoning. The framework dynamically synthesizes statistical correlations with multi-expert consensus, providing an automated pipeline for phenome-wide association studies (PheWAS). We demonstrate the system's capabilities through a population-based study of imaging phenotypes of the heart and aorta. MESHAgents autonomously uncovered correlations between imaging phenotypes and a wide range of non-imaging factors, identifying additional confounder variables beyond standard demographic factors. Validation on diagnosis tasks reveals that MESHAgents-discovered phenotypes achieve performance comparable to expert-selected phenotypes, with mean AUC differences as small as $-0.004_{\pm0.010}$ on disease classification tasks. Notably, the recall score improves for 6 out of 9 disease types. Our framework provides clinically relevant imaging phenotypes with transparent reasoning, offering a scalable alternative to expert-driven methods.

cs.AI↗

arXiv2025

CardiacFlow: 3D+t Four-Chamber Cardiac Shape Completion and Generation via Flow Matching

Learning 3D+t shape completion and generation from multi-view cardiac magnetic resonance (CMR) images requires a large amount of high-resolution 3D whole-heart segmentations (WHS) to capture shape priors. In this work, we leverage flow matching techniques to learn deep generative flows for augmentation, completion, and generation of 3D+t shapes of four cardiac chambers represented implicitly by segmentations. Firstly, we introduce a latent rectified flow to generate 3D cardiac shapes for data augmentation, learnt from a limited number of 3D WHS data. Then, a label completion network is trained on both real and synthetic data to reconstruct 3D+t shapes from sparse multi-view CMR segmentations. Lastly, we propose CardiacFlow, a novel one-step generative flow model for efficient 3D+t four-chamber cardiac shape generation, conditioned on the periodic Gaussian kernel encoding of time frames. The experiments on the WHS datasets demonstrate that flow-based data augmentation reduces geometric errors by 16% in 3D shape completion. The evaluation on the UK Biobank dataset validates that CardiacFlow achieves superior generation quality and periodic consistency compared to existing baselines.

eess.IV↗

arXiv2025

A versatile foundation model for cine cardiac magnetic resonance image analysis tasks

Here we present a versatile foundation model that can perform a range of clinically-relevant image analysis tasks, including segmentation, landmark localisation, diagnosis, and prognostication. A multi-view convolution-transformer masked autoencoder, named as CineMA, was trained on 15 million cine images from 74,916 subjects. The model was validated on multiple image analysis tasks and compared to existing models on >4,500 images from eight independent datasets with diverse population characteristics, representing the largest benchmark study for cine CMR so far. CineMA consistently outperformed conventional convolutional neural networks (CNNs) in delineating ventricular boundaries and estimating ejection fraction, a key measure of cardiac function. The improved performance was preserved, even when the model only used half of fine-tuning data. CineMA also surpassed CNNs in disease detection and matched their performance in long-axis function measurement. Interestingly, we found that CineMA can also detect cardiac changes in systemic diseases, such as diabetes, hypertension and cancer, and can also predict mortality. Finally, we assessed model fairness and demonstrated consistent model performance across demographic subgroups. These findings highlight CineMA's accuracy, learning efficiency, adaptability, and fairness, underscoring its potential as a foundation model for automated cardiac image analysis to support clinical workflow and cardiovascular research. All training and inference code and models are made publicly available at https://github.com/mathpluscode/CineMA.

eess.IV↗

arXiv2025

Multimodal Conditional MeshGAN for Personalized Aneurysm Growth Prediction

Personalized, accurate prediction of aortic aneurysm progression is essential for timely intervention but remains challenging due to the need to model both subtle local deformations and global anatomical changes within complex 3D geometries. We propose MCMeshGAN, the first multimodal conditional mesh-to-mesh generative adversarial network for 3D aneurysm growth prediction. MCMeshGAN introduces a dual-branch architecture combining a novel local KNN-based convolutional network (KCN) to preserve fine-grained geometric details and a global graph convolutional network (GCN) to capture long-range structural context, overcoming the over-smoothing limitations of deep GCNs. A dedicated condition branch encodes clinical attributes (age, sex) and the target time interval to generate anatomically plausible, temporally controlled predictions, enabling retrospective and prospective modeling. We curated TAAMesh, a new longitudinal thoracic aortic aneurysm mesh dataset consisting of 590 multimodal records (CT scans, 3D meshes, and clinical data) from 208 patients. Extensive experiments demonstrate that MCMeshGAN consistently outperforms state-of-the-art baselines in both geometric accuracy and clinically important diameter estimation. This framework offers a robust step toward clinically deployable, personalized 3D disease trajectory modeling. The source code for MCMeshGAN and the baseline methods is publicly available at https://github.com/ImperialCollegeLondon/MCMeshGAN.

cs.CV↗

arXiv2025

Towards Effective MLLM Jailbreaking Through Balanced On-Topicness and OOD-Intensity

Multimodal large language models (MLLMs) are widely used in vision-language reasoning tasks. However, their vulnerability to adversarial prompts remains a serious concern, as safety mechanisms often fail to prevent the generation of harmful outputs. Although recent jailbreak strategies report high success rates, many responses classified as "successful" are actually benign, vague, or unrelated to the intended malicious goal. This mismatch suggests that current evaluation standards may overestimate the effectiveness of such attacks. To address this issue, we introduce a four-axis evaluation framework that considers input on-topicness, input out-of-distribution (OOD) intensity, output harmfulness, and output refusal rate. This framework identifies truly effective jailbreaks. In a substantial empirical study, we reveal a structural trade-off: highly on-topic prompts are frequently blocked by safety filters, whereas those that are too OOD often evade detection but fail to produce harmful content. However, prompts that balance relevance and novelty are more likely to evade filters and trigger dangerous output. Building on this insight, we develop a recursive rewriting strategy called Balanced Structural Decomposition (BSD). The approach restructures malicious prompts into semantically aligned sub-tasks, while introducing subtle OOD signals and visual cues that make the inputs harder to detect. BSD was tested across 13 commercial and open-source MLLMs, where it consistently led to higher attack success rates, more harmful outputs, and fewer refusals. Compared to previous methods, it improves success rates by $67\%$ and harmfulness by $21\%$, revealing a previously underappreciated weakness in current multimodal safety systems.

cs.CV↗