arXiv subjects

Zhongying Deng

Publications and source records attributed to Zhongying Deng.

At least 19 recordsLinked to original sources

arXiv2026

MMBU: A Massive Multi-modal Biomedical Understanding Benchmark to Probe the Perception Capabilities of Vision-Language Models

Vision and language models (VLMs) hold immense promise to transform biomedical imaging workflows, from detecting lesions in chest X-rays to profiling cellular features in microscopy. Realizing this potential, however, requires robust and fine-grained visual perception. Models need to correctly interpret subtle features in images, and they must do so across diverse biomedical modalities, scales, and contexts. Nevertheless, current benchmarks remain limited. To address these gaps, we introduce the Massive Multimodal Biomedical Understanding (MMBU) benchmark. It is the largest biomedical vision and language benchmark to date, covering 35 submodalities with rich structured metadata. It includes both open and closed versions of ungrounded classification, grounded classification, and object detection, enabling systematic evaluation of model performance across biological scales, clinical settings, and imaging modalities. Evaluating 15 open-weight and 2 frontier VLMs, we find that while medical adaptation provides measurable gains for some models, the high accuracy often reported on established benchmarks can mask deficiencies in visual perception and domain generalization.

cs.CV↗

arXiv2026

UniMedVL: Unifying Medical Multimodal Understanding and Generation through Observation-Knowledge-Analysis

Medical workflows routinely combine reading images with producing visual and textual outputs, making both image understanding and generation central to medical AI. Most existing systems, however, address these abilities in isolated models, losing the shared knowledge that a unified architecture could exploit. To bridge this gap, we present UniMedVL, the first unified medical model that seamlessly integrates multimodal understanding and generation capabilities within a single model without switching weights. We achieve this via a tailored progressive training pipeline where understanding and generation mutually reinforce each other. To effectively train UniMedVL, we curate UniMedVL-5M, the first large-scale medical dataset comprising over 5.6M instances across 8 medical imaging modalities, tailored for multimodal input-output tasks in unified medical understanding and generation. Experimental results demonstrate that UniMedVL achieves competitive performance on five medical understanding benchmarks. Crucially, UniMedVL natively supports diverse interleaved generation tasks, e.g., virtual staining, super-resolution, cross-modal synthesis, essential for complex medical workflows. Our code and dataset are publicly available.

cs.CV↗

arXiv2026

Adaptive Coordinate Transforms for Neural Operators

Neural operators have achieved promising performance on partial differential equations (PDEs), but most existing models are built on fixed Eulerian coordinates. This mismatch between evolving physical structures and static coordinates creates spatial misalignment, leading to unnecessarily non-local operator mappings and reinforcing a smoothness preference near sharp transitions. Inspired by adaptive coordinate transformations in classical PDE analysis, we propose the Adaptive Coordinate Transform (ACT) block, a plug-and-play module for data-driven geometric adaptation in neural operators. ACT blocks resolve this structural limitation by learning adaptive coordinate systems within the operator learning pipeline. Specifically, given an input feature, the ACT block learns a coordinate transformation and represents the same feature under the transformed coordinates via differentiable sampling. This operation preserves the underlying signal while changing its spatial representation, equivalent to expressing the same physical quantity in different coordinate systems. By adapting the coordinate system to the data, ACT allows the network to better track evolving structures, reduce operator complexity, and dynamically focus on critical features to improve learning. We evaluate the proposed approach across diverse PDE benchmarks and multiple neural operator architectures. Experimental results demonstrate consistent and significant improvements in predictive accuracy, indicating that learning coordinate systems provides a powerful mechanism for enhancing operator learning.

cs.CE↗

arXiv2026

Project Imaging-X: A Survey of 1000+ Open-Access Medical Imaging Datasets for Foundation Model Development

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

cs.CV↗

arXiv2026

Adaptive Correction for Ensuring Conservation Laws in Neural Operators

Physical laws, such as the conversation of mass and momentum, are fundamental principles in many physical systems. Neural operators have achieved promising performance in learning the solutions to those systems, but often fail to ensure conservation. Existing methods typically enforce strict conservation via hand-crafted post-processing or architectural constraints, leading to limited model flexibility and adaptability. In this work, we propose a novel plug-and-play adaptive correction approach to ensure the conservation of fundamental linear and quadratic quantities for neural operator outputs. Our method introduces a lightweight learnable operator to adaptively enforce the target conservation law during training. This method allows the model to flexibly and adaptively correct its output to guarantee strict conservation. We provide a theoretical result showing that our correction method does not hamper the expression ability of neural operators and can potentially achieve lower reconstruction loss than their conservation-constrained counterparts. Our method is evaluated across multiple neural operator architectures and representative PDEs. Extensive experiments show that incorporating our correction method into baseline models significantly improves both accuracy and stability. In addition, the experimental results demonstrate that our approach consistently achieves superior performance over widely used conservation-enforcement techniques on various PDE benchmarks.

cs.LG↗

arXiv2025

HIBMatch: Hypergraph Information Bottleneck for Semi-supervised Alzheimer's Progression

Alzheimer's disease progression prediction is critical for patients with early Mild Cognitive Impairment (MCI) to enable timely intervention and improve their quality of life. While existing progression prediction techniques demonstrate potential with multimodal data, they are highly limited by their reliance on labelled data and fail to account for a key element of future progression prediction: not all features extracted at the current moment may be relevant for predicting progression several years later. To address these limitations in the literature, we design a novel semi-supervised multimodal learning hypergraph architecture, termed HIBMatch, by harnessing hypergraph knowledge based on information bottleneck and consistency regularisation strategies. Firstly, our framework utilises hypergraphs to represent multimodal data, encompassing both imaging and non-imaging modalities. Secondly, to harmonise relevant information from the currently captured data for future MCI conversion prediction, we propose a Hypergraph Information Bottleneck (HIB) that discriminates against irrelevant information, thereby focusing exclusively on harmonising relevant information for future MCI conversion prediction. Thirdly, our method enforces consistency regularisation between the HIB and a discriminative classifier to enhance the robustness and generalisation capabilities of HIBMatch under both topological and feature perturbations. Finally, to fully exploit the unlabeled data, HIBMatch incorporates a cross-modal contrastive loss for data efficiency. Extensive experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate that our proposed HIBMatch framework surpasses existing state-of-the-art methods in Alzheimer's disease prognosis.

cs.CV↗

arXiv2025

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

cs.CL↗

arXiv2025

MedQ-Bench: Evaluating and Exploring Medical Image Quality Assessment Abilities in MLLMs

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

cs.CV↗

arXiv2025

D2SA: Dual-Stage Distribution and Slice Adaptation for Efficient Test-Time Adaptation in MRI Reconstruction

Variations in Magnetic resonance imaging (MRI) scanners and acquisition protocols cause distribution shifts that degrade reconstruction performance on unseen data. Test-time adaptation (TTA) offers a promising solution to address this discrepancies. However, previous single-shot TTA approaches are inefficient due to repeated training and suboptimal distributional models. Self-supervised learning methods may risk over-smoothing in scarce data scenarios. To address these challenges, we propose a novel Dual-Stage Distribution and Slice Adaptation (D2SA) via MRI implicit neural representation (MR-INR) to improve MRI reconstruction performance and efficiency, which features two stages. In the first stage, an MR-INR branch performs patient-wise distribution adaptation by learning shared representations across slices and modelling patient-specific shifts with mean and variance adjustments. In the second stage, single-slice adaptation refines the output from frozen convolutional layers with a learnable anisotropic diffusion module, preventing over-smoothing and reducing computation. Experiments across five MRI distribution shifts demonstrate that our method can integrate well with various self-supervised learning (SSL) framework, improving performance and accelerating convergence under diverse conditions.

eess.IV↗

arXiv2025

Brain Foundation Models with Hypergraph Dynamic Adapter for Brain Disease Analysis

Brain diseases, such as Alzheimer's disease and brain tumors, present profound challenges due to their complexity and societal impact. Recent advancements in brain foundation models have shown significant promise in addressing a range of brain-related tasks. However, current brain foundation models are limited by task and data homogeneity, restricted generalization beyond segmentation or classification, and inefficient adaptation to diverse clinical tasks. In this work, we propose SAM-Brain3D, a brain-specific foundation model trained on over 66,000 brain image-label pairs across 14 MRI sub-modalities, and Hypergraph Dynamic Adapter (HyDA), a lightweight adapter for efficient and effective downstream adaptation. SAM-Brain3D captures detailed brain-specific anatomical and modality priors for segmenting diverse brain targets and broader downstream tasks. HyDA leverages hypergraphs to fuse complementary multi-modal data and dynamically generate patient-specific convolutional kernels for multi-scale feature fusion and personalized patient-wise adaptation. Together, our framework excels across a broad spectrum of brain disease segmentation and classification tasks. Extensive experiments demonstrate that our method consistently outperforms existing state-of-the-art approaches, offering a new paradigm for brain disease analysis through multi-modal, multi-scale, and dynamic foundation modeling.

cs.CV↗

arXiv2025

GMAI-VL & GMAI-VL-5.5M: A Large Vision-Language Model and A Comprehensive Multimodal Dataset Towards General Medical AI

Despite significant advancements in general AI, its effectiveness in the medical domain is limited by the lack of specialized medical knowledge. To address this, we formulate GMAI-VL-5.5M, a multimodal medical dataset created by converting hundreds of specialized medical datasets with various annotations into high-quality image-text pairs. This dataset offers comprehensive task coverage, diverse modalities, and rich image-text data. Building upon this dataset, we develop GMAI-VL, a general medical vision-language model, with a three-stage training strategy that enhances the integration of visual and textual information. This approach significantly improves the model's ability to process multimodal data, supporting accurate diagnoses and clinical decision-making. Experiments show that GMAI-VL achieves state-of-the-art performance across various multimodal medical tasks, including visual question answering and medical image diagnosis.

cs.CV↗

arXiv2025

Where Do We Stand with Implicit Neural Representations? A Technical and Performance Survey

Implicit Neural Representations (INRs) have emerged as a paradigm in knowledge representation, offering exceptional flexibility and performance across a diverse range of applications. INRs leverage multilayer perceptrons (MLPs) to model data as continuous implicit functions, providing critical advantages such as resolution independence, memory efficiency, and generalisation beyond discretised data structures. Their ability to solve complex inverse problems makes them particularly effective for tasks including audio reconstruction, image representation, 3D object reconstruction, and high-dimensional data synthesis. This survey provides a comprehensive review of state-of-the-art INR methods, introducing a clear taxonomy that categorises them into four key areas: activation functions, position encoding, combined strategies, and network structure optimisation. We rigorously analyse their critical properties, such as full differentiability, smoothness, compactness, and adaptability to varying resolutions while also examining their strengths and limitations in addressing locality biases and capturing fine details. Our experimental comparison offers new insights into the trade-offs between different approaches, showcasing the capabilities and challenges of the latest INR techniques across various tasks. In addition to identifying areas where current methods excel, we highlight key limitations and potential avenues for improvement, such as developing more expressive activation functions, enhancing positional encoding mechanisms, and improving scalability for complex, high-dimensional data. This survey serves as a roadmap for researchers, offering practical guidance for future exploration in the field of INRs. We aim to foster new methodologies by outlining promising research directions for INRs and applications.

cs.CV↗

arXiv2025

FCN+: Global Receptive Convolution Makes FCN Great Again

Fully convolutional network (FCN) is a seminal work for semantic segmentation. However, due to its limited receptive field, FCN cannot effectively capture global context information which is vital for semantic segmentation. As a result, it is beaten by state-of-the-art methods that leverage different filter sizes for larger receptive fields. However, such a strategy usually introduces more parameters and increases the computational cost. In this paper, we propose a novel global receptive convolution (GRC) to effectively increase the receptive field of FCN for context information extraction, which results in an improved FCN termed FCN+. The GRC provides the global receptive field for convolution without introducing any extra learnable parameters. The motivation of GRC is that different channels of a convolutional filter can have different grid sampling locations across the whole input feature map. Specifically, the GRC first divides the channels of the filter into two groups. The grid sampling locations of the first group are shifted to different spatial coordinates across the whole feature map, according to their channel indexes. This can help the convolutional filter capture the global context information. The grid sampling location of the second group remains unchanged to keep the original location information. By convolving using these two groups, the GRC can integrate the global context into the original location information of each pixel for better dense prediction results. With the GRC built in, FCN+ can achieve comparable performance to state-of-the-art methods for semantic segmentation tasks, as verified on PASCAL VOC 2012, Cityscapes, and ADE20K. Our code will be released at https://github.com/Zhongying-Deng/FCN_Plus.

cs.CV↗

arXiv2024

SegBook: A Simple Baseline and Cookbook for Volumetric Medical Image Segmentation

Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.

eess.IV↗

arXiv2024

GMAI-MMBench: A Comprehensive Multimodal Evaluation Benchmark Towards General Medical AI

Large Vision-Language Models (LVLMs) are capable of handling diverse data types such as imaging, text, and physiological signals, and can be applied in various fields. In the medical field, LVLMs have a high potential to offer substantial assistance for diagnosis and treatment. Before that, it is crucial to develop benchmarks to evaluate LVLMs' effectiveness in various medical applications. Current benchmarks are often built upon specific academic literature, mainly focusing on a single domain, and lacking varying perceptual granularities. Thus, they face specific challenges, including limited clinical relevance, incomplete evaluations, and insufficient guidance for interactive LVLMs. To address these limitations, we developed the GMAI-MMBench, the most comprehensive general medical AI benchmark with well-categorized data structure and multi-perceptual granularity to date. It is constructed from 284 datasets across 38 medical image modalities, 18 clinical-related tasks, 18 departments, and 4 perceptual granularities in a Visual Question Answering (VQA) format. Additionally, we implemented a lexical tree structure that allows users to customize evaluation tasks, accommodating various assessment needs and substantially supporting medical AI research and applications. We evaluated 50 LVLMs, and the results show that even the advanced GPT-4o only achieves an accuracy of 53.96%, indicating significant room for improvement. Moreover, we identified five key insufficiencies in current cutting-edge LVLMs that need to be addressed to advance the development of better medical applications. We believe that GMAI-MMBench will stimulate the community to build the next generation of LVLMs toward GMAI.

eess.IV↗

arXiv2024

HAMLET: Graph Transformer Neural Operator for Partial Differential Equations

We present a novel graph transformer framework, HAMLET, designed to address the challenges in solving partial differential equations (PDEs) using neural networks. The framework uses graph transformers with modular input encoders to directly incorporate differential equation information into the solution process. This modularity enhances parameter correspondence control, making HAMLET adaptable to PDEs of arbitrary geometries and varied input formats. Notably, HAMLET scales effectively with increasing data complexity and noise, showcasing its robustness. HAMLET is not just tailored to a single type of physical simulation, but can be applied across various domains. Moreover, it boosts model resilience and performance, especially in scenarios with limited data. We demonstrate, through extensive experiments, that our framework is capable of outperforming current techniques for PDEs.

cs.LG↗

arXiv2024

SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

cs.CV↗

arXiv2024

Bilevel Hypergraph Networks for Multi-Modal Alzheimer's Diagnosis

Early detection of Alzheimer's disease's precursor stages is imperative for significantly enhancing patient outcomes and quality of life. This challenge is tackled through a semi-supervised multi-modal diagnosis framework. In particular, we introduce a new hypergraph framework that enables higher-order relations between multi-modal data, while utilising minimal labels. We first introduce a bilevel hypergraph optimisation framework that jointly learns a graph augmentation policy and a semi-supervised classifier. This dual learning strategy is hypothesised to enhance the robustness and generalisation capabilities of the model by fostering new pathways for information propagation. Secondly, we introduce a novel strategy for generating pseudo-labels more effectively via a gradient-driven flow. Our experimental results demonstrate the superior performance of our framework over current techniques in diagnosing Alzheimer's disease.

cs.LG↗