Wu Yuan

Jianing Qiu, Lin Li, Jiankai Sun et al.

Large AI models, or foundation models, are models recently emerging with massive scales both parameter-wise and data-wise, the magnitudes of which can reach beyond billions. Once pretrained, large AI models demonstrate impressive performance in various downstream tasks. A prime example is ChatGPT, whose capability has compelled people's imagination about the far-reaching influence that large AI models can have and their potential to transform different domains of our lives. In health informatics, the advent of large AI models has brought new paradigms for the design of methodologies. The scale of multi-modal data in the biomedical and health domain has been ever-expanding especially since the community embraced the era of deep learning, which provides the ground to develop, validate, and advance large AI models for breakthroughs in health-related areas. This article presents a comprehensive review of large AI models, from background to their applications. We identify seven key sectors in which large AI models are applicable and might have substantial influence, including 1) bioinformatics; 2) medical diagnosis; 3) medical imaging; 4) medical informatics; 5) medical education; 6) public health; and 7) medical robotics. We examine their challenges, followed by a critical discussion about potential future directions and pitfalls of large AI models in transforming the field of health informatics.

Beilei Cui, Minqing Zhang, Mengya Xu et al.

Noisy label problems are inevitably in existence within medical image segmentation causing severe performance degradation. Previous segmentation methods for noisy label problems only utilize a single image while the potential of leveraging the correlation between images has been overlooked. Especially for video segmentation, adjacent frames contain rich contextual information beneficial in cognizing noisy labels. Based on two insights, we propose a Multi-Scale Temporal Feature Affinity Learning (MS-TFAL) framework to resolve noisy-labeled medical video segmentation issues. First, we argue the sequential prior of videos is an effective reference, i.e., pixel-level features from adjacent frames are close in distance for the same class and far in distance otherwise. Therefore, Temporal Feature Affinity Learning (TFAL) is devised to indicate possible noisy labels by evaluating the affinity between pixels in two adjacent frames. We also notice that the noise distribution exhibits considerable variations across video, image, and pixel levels. In this way, we introduce Multi-Scale Supervision (MSS) to supervise the network from three different perspectives by re-weighting and refining the samples. This design enables the network to concentrate on clean samples in a coarse-to-fine manner. Experiments with both synthetic and real-world label noise demonstrate that our method outperforms recent state-of-the-art robust segmentation approaches. Code is available at https://github.com/BeileiCui/MS-TFAL.

Jianing Qiu, Jian Wu, Hao Wei et al.

We present VisionFM, a foundation model pre-trained with 3.4 million ophthalmic images from 560,457 individuals, covering a broad range of ophthalmic diseases, modalities, imaging devices, and demography. After pre-training, VisionFM provides a foundation to foster multiple ophthalmic artificial intelligence (AI) applications, such as disease screening and diagnosis, disease prognosis, subclassification of disease phenotype, and systemic biomarker and disease prediction, with each application enhanced with expert-level intelligence and accuracy. The generalist intelligence of VisionFM outperformed ophthalmologists with basic and intermediate levels in jointly diagnosing 12 common ophthalmic diseases. Evaluated on a new large-scale ophthalmic disease diagnosis benchmark database, as well as a new large-scale segmentation and detection benchmark database, VisionFM outperformed strong baseline deep neural networks. The ophthalmic image representations learned by VisionFM exhibited noteworthy explainability, and demonstrated strong generalizability to new ophthalmic modalities, disease spectrum, and imaging devices. As a foundation model, VisionFM has a large capacity to learn from diverse ophthalmic imaging data and disparate datasets. To be commensurate with this capacity, in addition to the real data used for pre-training, we also generated and leveraged synthetic ophthalmic imaging data. Experimental results revealed that synthetic data that passed visual Turing tests, can also enhance the representation learning capability of VisionFM, leading to substantial performance gains on downstream ophthalmic AI tasks. Beyond the ophthalmic AI applications developed, validated, and demonstrated in this work, substantial further applications can be achieved in an efficient and cost-effective manner using VisionFM as the foundation.

Peilun Shi, Jianing Qiu, Sai Mu Dalike Abaxi et al.

In this paper, we examine the recent Segment Anything Model (SAM) on medical images, and report both quantitative and qualitative zero-shot segmentation results on nine medical image segmentation benchmarks, covering various imaging modalities, such as optical coherence tomography (OCT), magnetic resonance imaging (MRI), and computed tomography (CT), as well as different applications including dermatology, ophthalmology, and radiology. Those benchmarks are representative and commonly used in model development. Our experimental results indicate that while SAM presents remarkable segmentation performance on images from the general domain, its zero-shot segmentation ability remains restricted for out-of-distribution images, e.g., medical images. In addition, SAM exhibits inconsistent zero-shot segmentation performance across different unseen medical domains. For certain structured targets, e.g., blood vessels, the zero-shot segmentation of SAM completely failed. In contrast, a simple fine-tuning of it with a small amount of data could lead to remarkable improvement of the segmentation quality, showing the great potential and feasibility of using fine-tuned SAM to achieve accurate medical image segmentation for a precision diagnostics. Our study indicates the versatility of generalist vision foundation models on medical imaging, and their great potential to achieve desired performance through fine-turning and eventually address the challenges associated with accessing large and diverse medical datasets in support of clinical diagnostics.

Hongyang Jiang, Mengdi Gao, Zirong Liu et al.

Early-stage diabetic retinopathy (DR) presents challenges in clinical diagnosis due to inconspicuous and minute microangioma lesions, resulting in limited research in this area. Additionally, the potential of emerging foundation models, such as the segment anything model (SAM), in medical scenarios remains rarely explored. In this work, we propose a human-in-the-loop, label-free early DR diagnosis framework called GlanceSeg, based on SAM. GlanceSeg enables real-time segmentation of microangioma lesions as ophthalmologists review fundus images. Our human-in-the-loop framework integrates the ophthalmologist's gaze map, allowing for rough localization of minute lesions in fundus images. Subsequently, a saliency map is generated based on the located region of interest, which provides prompt points to assist the foundation model in efficiently segmenting microangioma lesions. Finally, a domain knowledge filter refines the segmentation of minute lesions. We conducted experiments on two newly-built public datasets, i.e., IDRiD and Retinal-Lesions, and validated the feasibility and superiority of GlanceSeg through visualized illustrations and quantitative measures. Additionally, we demonstrated that GlanceSeg improves annotation efficiency for clinicians and enhances segmentation performance through fine-tuning using annotations. This study highlights the potential of GlanceSeg-based annotations for self-model optimization, leading to enduring performance advancements through continual learning.

Hao Wei, Jianing Qiu, Haibao Yu et al.

Large language models (LLMs) have had a significant impact on diverse research domains, including medicine and healthcare. However, the potential of LLMs as copilots in medical education remains underexplored. Current AI-assisted educational tools are limited by their solitary learning approach and inability to simulate the multi-disciplinary and interactive nature of actual medical training. To address these limitations, we propose MEDCO (Medical EDucation COpilots), a novel multi-agent-based copilot system specially developed to emulate real-world medical training environments. MEDCO incorporates three primary agents: an agentic patient, an expert doctor, and a radiologist, facilitating a multi-modal and interactive learning environment. Our framework emphasizes the learning of proficient question-asking skills, multi-disciplinary collaboration, and peer discussions between students. Our experiments show that simulated virtual students who underwent training with MEDCO not only achieved substantial performance enhancements comparable to those of advanced models, but also demonstrated human-like learning behaviors and improvements, coupled with an increase in the number of learning samples. This work contributes to medical education by introducing a copilot that implements an interactive and collaborative learning approach. It also provides valuable insights into the effectiveness of AI-integrated training paradigms.

Hao Wei, Peilun Shi, Juzheng Miao et al.

Diabetic retinopathy (DR) is the most common diabetic complication, which usually leads to retinal damage, vision loss, and even blindness. A computer-aided DR grading system has a significant impact on helping ophthalmologists with rapid screening and diagnosis. Recent advances in fundus photography have precipitated the development of novel retinal imaging cameras and their subsequent implementation in clinical practice. However, most deep learning-based algorithms for DR grading demonstrate limited generalization across domains. This inferior performance stems from variance in imaging protocols and devices inducing domain shifts. We posit that declining model performance between domains arises from learning spurious correlations in the data. Incorporating do-operations from causality analysis into model architectures may mitigate this issue and improve generalizability. Specifically, a novel universal structural causal model (SCM) was proposed to analyze spurious correlations in fundus imaging. Building on this, a causality-inspired diabetic retinopathy grading framework named CauDR was developed to eliminate spurious correlations and achieve more generalizable DR diagnostics. Furthermore, existing datasets were reorganized into 4DR benchmark for DG scenario. Results demonstrate the effectiveness and the state-of-the-art (SOTA) performance of CauDR.

Hulingxiao He, Wu Yuan, Yidian Huang et al.

In this work, we propose Branch-to-Trunk network (BTNet), a representation learning method for multi-resolution face recognition. It consists of a trunk network (TNet), namely a unified encoder, and multiple branch networks (BNets), namely resolution adapters. As per the input, a resolution-specific BNet is used and the output are implanted as feature maps in the feature pyramid of TNet, at a layer with the same resolution. The discriminability of tiny faces is significantly improved, as the interpolation error introduced by rescaling, especially up-sampling, is mitigated on the inputs. With branch distillation and backward-compatible training, BTNet transfers discriminative high-resolution information to multiple branches while guaranteeing representation compatibility. Our experiments demonstrate strong performance on face recognition benchmarks, both for multi-resolution identity matching and feature aggregation, with much less computation amount and parameter storage. We establish new state-of-the-art on the challenging QMUL-SurvFace 1: N face identification task. Our code is available at https://github.com/StevenSmith2000/BTNet.

Xiaofeng Deng, Defu Chen, Bowen Liu et al.

Accurate classification of port wine stains (PWS, vascular malformations present at birth), is critical for subsequent treatment planning. However, the current method of classifying PWS based on the external skin appearance rarely reflects the underlying angiopathological heterogeneity of PWS lesions, resulting in inconsistent outcomes with the common vascular-targeted photodynamic therapy (V-PDT) treatments. Conversely, optical coherence tomography angiography (OCTA) is an ideal tool for visualizing the vascular malformations of PWS. Previous studies have shown no significant correlation between OCTA quantitative metrics and the PWS subtypes determined by the current classification approach. This study proposes a new classification approach for PWS using both OCT and OCTA. By examining the hypodermic histopathology and vascular structure of PWS, we have devised a fine-grained classification method that subdivides PWS into five distinct types. To assess the angiopathological differences of various PWS subtypes, we have analyzed six metrics related to vascular morphology and depth information of PWS lesions. The five PWS types present significant differences across all metrics compared to the conventional subtypes. Our findings suggest that an angiopathology-based classification accurately reflects the heterogeneity in PWS lesions. This research marks the first attempt to classify PWS based on angiopathology, potentially guiding more effective subtyping and treatment strategies for PWS.

Jun Ma, Feifei Li, Sumin Kim et al.

Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.

Hao Wei, Bowen Liu, Minqing Zhang et al.

Generalist foundation model has ushered in newfound capabilities in medical domain. However, the contradiction between the growing demand for high-quality annotated data with patient privacy continues to intensify. The utilization of medical artificial intelligence generated content (Med-AIGC) as an inexhaustible resource repository arises as a potential solution to address the aforementioned challenge. Here we harness 1 million open-source synthetic fundus images paired with natural language descriptions, to curate an ethical language-image foundation model for retina image analysis named VisionCLIP. VisionCLIP achieves competitive performance on three external datasets compared with the existing method pre-trained on real-world data in a zero-shot fashion. The employment of artificially synthetic images alongside corresponding textual data for training enables the medical foundation model to successfully assimilate knowledge of disease symptomatology, thereby circumventing potential breaches of patient confidentiality.

Hao Wei, Peilun Shi, Guitao Bai et al.

Ultra-wide optical coherence tomography angiography (UW-OCTA) is an emerging imaging technique that offers significant advantages over traditional OCTA by providing an exceptionally wide scanning range of up to 24 x 20 $mm^{2}$, covering both the anterior and posterior regions of the retina. However, the currently accessible UW-OCTA datasets suffer from limited comprehensive hierarchical information and corresponding disease annotations. To address this limitation, we have curated the pioneering M3OCTA dataset, which is the first multimodal (i.e., multilayer), multi-disease, and widest field-of-view UW-OCTA dataset. Furthermore, the effective utilization of multi-layer ultra-wide ocular vasculature information from UW-OCTA remains underdeveloped. To tackle this challenge, we propose the first cross-modal fusion framework that leverages multi-modal information for diagnosing multiple diseases. Through extensive experiments conducted on our openly available M3OCTA dataset, we demonstrate the effectiveness and superior performance of our method, both in fixed and varying modalities settings. The construction of the M3OCTA dataset, the first multimodal OCTA dataset encompassing multiple diseases, aims to advance research in the ophthalmic image analysis community.

Linyuan Li, Jianing Qiu, Anujit Saha et al.

As a prominent subfield of Artificial Intelligence Generated Content (AIGC), video generation has achieved notable advancements in recent years. The introduction of Sora-alike models represents a pivotal breakthrough in video generation technologies, significantly enhancing the quality of synthesized videos. Particularly in the realm of biomedicine, video generation technology has shown immense potential such as medical concept explanation, disease simulation, and biomedical data augmentation. In this article, we thoroughly examine the latest developments in video generation models and explore their applications, challenges, and future opportunities in the biomedical sector. We have conducted an extensive review and compiled a comprehensive list of datasets from various sources to facilitate the development and evaluation of video generative models in biomedicine. Given the rapid progress in this field, we have also created a github repository to regularly update the advances of biomedical video generation at: https://github.com/Lee728243228/Biomedical-Video-Generation

Jiankai Sun, Chuanyang Zheng, Enze Xie et al.

Reasoning, a crucial ability for complex problem-solving, plays a pivotal role in various real-world settings such as negotiation, medical diagnosis, and criminal investigation. It serves as a fundamental methodology in the field of Artificial General Intelligence (AGI). With the ongoing development of foundation models, e.g., Large Language Models (LLMs), there is a growing interest in exploring their abilities in reasoning tasks. In this paper, we introduce seminal foundation models proposed or adaptable for reasoning, highlighting the latest advancements in various reasoning tasks, methods, and benchmarks. We then delve into the potential future directions behind the emergence of reasoning abilities within foundation models. We also discuss the relevance of multimodal learning, autonomous agents, and super alignment in the context of reasoning. By discussing these future research directions, we hope to inspire researchers in their exploration of this field, stimulate further advancements in reasoning with foundation models, and contribute to the development of AGI.

Frank P. -W. Lo, Jianing Qiu, Zeyu Wang et al.

Conventional approaches to dietary assessment are primarily grounded in self-reporting methods or structured interviews conducted under the supervision of dietitians. These methods, however, are often subjective, potentially inaccurate, and time-intensive. Although artificial intelligence (AI)-based solutions have been devised to automate the dietary assessment process, these prior AI methodologies encounter challenges in their ability to generalize across a diverse range of food types, dietary behaviors, and cultural contexts. This results in AI applications in the dietary field that possess a narrow specialization and limited accuracy. Recently, the emergence of multimodal foundation models such as GPT-4V powering the latest ChatGPT has exhibited transformative potential across a wide range of tasks (e.g., Scene understanding and image captioning) in numerous research domains. These models have demonstrated remarkable generalist intelligence and accuracy, capable of processing various data modalities. In this study, we explore the application of multimodal ChatGPT within the realm of dietary assessment. Our findings reveal that GPT-4V excels in food detection under challenging conditions with accuracy up to 87.5% without any fine-tuning or adaptation using food-specific datasets. By guiding the model with specific language prompts (e.g., African cuisine), it shifts from recognizing common staples like rice and bread to accurately identifying regional dishes like banku and ugali. Another GPT-4V's standout feature is its contextual awareness. GPT-4V can leverage surrounding objects as scale references to deduce the portion sizes of food items, further enhancing its accuracy in translating food weight into nutritional content. This alignment with the USDA National Nutrient Database underscores GPT-4V's potential to advance nutritional science and dietary assessment techniques.

Jianing Qiu, Lin Li, Jiankai Sun et al.

Large language models (LLMs)-powered AI agents exhibit a high level of autonomy in addressing medical and healthcare challenges. With the ability to access various tools, they can operate within an open-ended action space. However, with the increase in autonomy and ability, unforeseen risks also arise. In this work, we investigated one particular risk, i.e., cyber attack vulnerability of medical AI agents, as agents have access to the Internet through web browsing tools. We revealed that through adversarial prompts embedded on webpages, cyberattackers can: i) inject false information into the agent's response; ii) they can force the agent to manipulate recommendation (e.g., healthcare products and services); iii) the attacker can also steal historical conversations between the user and agent, resulting in the leak of sensitive/private medical information; iv) furthermore, the targeted agent can also cause a computer system hijack by returning a malicious URL in its response. Different backbone LLMs were examined, and we found such cyber attacks can succeed in agents powered by most mainstream LLMs, with the reasoning models such as DeepSeek-R1 being the most vulnerable.

Yuanyuan Wei, Yucheng Wu, Fuyang Qu et al.

Accurate molecular quantification is essential for advancing research and diagnostics in fields such as infectious diseases, cancer biology, and genetic disorders. Droplet digital PCR (ddPCR) has emerged as a gold standard for achieving absolute quantification. While computational ddPCR technologies have advanced significantly, achieving automatic interpretation and consistent adaptability across diverse operational environments remains a challenge. To address these limitations, we introduce the intelligent interpretable droplet digital PCR (I2ddPCR) assay, a comprehensive framework integrating front-end predictive models (for droplet segmentation and classification) with GPT-4o multimodal large language model (MLLM, for context-aware explanations and recommendations) to automate and enhance ddPCR image analysis. This approach surpasses the state-of-the-art models, affording 99.05% accuracy in processing complex ddPCR images containing over 300 droplets per image with varying signal-to-noise ratios (SNRs). By combining specialized neural networks and large language models, the I2ddPCR assay offers a robust and adaptable solution for absolute molecular quantification, achieving a sensitivity capable of detecting low-abundance targets as low as 90.32 copies/μL. Furthermore, it improves model's transparency through detailed explanation and troubleshooting guidance, empowering users to make informed decisions. This innovative framework has the potential to benefit molecular diagnostics, disease research, and clinical applications, especially in resource-constrained settings.