Weijian Huang

Weijian Huang, Cheng Li, Hong-Yu Zhou et al.

Recently, multi-modal vision-language foundation models have gained significant attention in the medical field. While these models offer great opportunities, they still face crucial challenges, such as the requirement for fine-grained knowledge understanding in computer-aided diagnosis and the capability of utilizing very limited or even no task-specific labeled data in real-world clinical applications. In this study, we present MaCo, a masked contrastive chest X-ray foundation model that tackles these challenges. MaCo explores masked contrastive learning to simultaneously achieve fine-grained image understanding and zero-shot learning for a variety of medical imaging tasks. It designs a correlation weighting mechanism to adjust the correlation between masked chest X-ray image patches and their corresponding reports, thereby enhancing the model's representation learning capabilities. To evaluate the performance of MaCo, we conducted extensive experiments using 6 well-known open-source X-ray datasets. The experimental results demonstrate the superiority of MaCo over 10 state-of-the-art approaches across tasks such as classification, segmentation, detection, and phrase grounding. These findings highlight the significant potential of MaCo in advancing a wide range of medical image analysis tasks.

Weijian Huang, Hao Yang, Cheng Li et al.

Multi-modal representation methods have achieved advanced performance in medical applications by extracting more robust features from multi-domain data. However, existing methods usually need to train additional branches for downstream tasks, which may increase the model complexities in clinical applications as well as introduce additional human inductive bias. Besides, very few studies exploit the rich clinical knowledge embedded in clinical daily reports. To this end, we propose a novel medical generalist agent, MGA, that can address three kinds of common clinical tasks via clinical reports knowledge transformation. Unlike the existing methods, MGA can easily adapt to different tasks without specific downstream branches when their corresponding annotations are missing. More importantly, we are the first attempt to use medical professional language guidance as a transmission medium to guide the agent's behavior. The proposed method is implemented on four well-known X-ray open-source datasets, MIMIC-CXR, CheXpert, MIMIC-CXR-JPG, and MIMIC-CXR-MS. Promising results are obtained, which validate the effectiveness of our proposed MGA. Code is available at: https://github.com/SZUHvern/MGA

Weijian Huang, Cheng Li, Wenxin Fan et al.

Recovering high-quality images from undersampled measurements is critical for accelerated MRI reconstruction. Recently, various supervised deep learning-based MRI reconstruction methods have been developed. Despite the achieved promising performances, these methods require fully sampled reference data, the acquisition of which is resource-intensive and time-consuming. Self-supervised learning has emerged as a promising solution to alleviate the reliance on fully sampled datasets. However, existing self-supervised methods suffer from reconstruction errors due to the insufficient constraint enforced on the non-sampled data points and the error accumulation happened alongside the iterative image reconstruction process for model-driven deep learning reconstrutions. To address these challenges, we propose K2Calibrate, a K-space adaptation strategy for self-supervised model-driven MR reconstruction optimization. By iteratively calibrating the learned measurements, K2Calibrate can reduce the network's reconstruction deterioration caused by statistically dependent noise. Extensive experiments have been conducted on the open-source dataset FastMRI, and K2Calibrate achieves better results than five state-of-the-art methods. The proposed K2Calibrate is plug-and-play and can be easily integrated with different model-driven deep learning reconstruction methods.

Hao Yang, Weijian Huang, Jiarun Liu et al.

The ability to incrementally learn new classes from limited samples is crucial to the development of artificial intelligence systems for real clinical application. Although existing incremental learning techniques have attempted to address this issue, they still struggle with only few labeled data, particularly when the samples are from varied domains. In this paper, we explore the cross-domain few-shot incremental learning (CDFSCIL) problem. CDFSCIL requires models to learn new classes from very few labeled samples incrementally, and the new classes may be vastly different from the target space. To counteract this difficulty, we propose a cross-domain enhancement constraint and cross-domain data augmentation method. Experiments on MedMNIST show that the classification performance of this method is better than other similar incremental learning methods.

Haoran Li, Cheng Li, Weijian Huang et al.

Brain tumor segmentation based on multi-modal magnetic resonance imaging (MRI) plays a pivotal role in assisting brain cancer diagnosis, treatment, and postoperative evaluations. Despite the achieved inspiring performance by existing automatic segmentation methods, multi-modal MRI data are still unavailable in real-world clinical applications due to quite a few uncontrollable factors (e.g. different imaging protocols, data corruption, and patient condition limitations), which lead to a large performance drop during practical applications. In this work, we propose a Deeply supervIsed knowledGE tranSfer neTwork (DIGEST), which achieves accurate brain tumor segmentation under different modality-missing scenarios. Specifically, a knowledge transfer learning frame is constructed, enabling a student model to learn modality-shared semantic information from a teacher model pretrained with the complete multi-modal MRI data. To simulate all the possible modality-missing conditions under the given multi-modal data, we generate incomplete multi-modal MRI samples based on Bernoulli sampling. Finally, a deeply supervised knowledge transfer loss is designed to ensure the consistency of the teacher-student structure at different decoding stages, which helps the extraction of inherent and effective modality representations. Experiments on the BraTS 2020 dataset demonstrate that our method achieves promising results for the incomplete multi-modal MR image segmentation task.

Yousuf Babiker M. Osman, Cheng Li, Weijian Huang et al.

Volumetric magnetic resonance (MR) image segmentation plays an important role in many clinical applications. Deep learning (DL) has recently achieved state-of-the-art or even human-level performance on various image segmentation tasks. Nevertheless, manually annotating volumetric MR images for DL model training is labor-exhaustive and time-consuming. In this work, we aim to train a semi-supervised and self-supervised collaborative learning framework for prostate 3D MR image segmentation while using extremely sparse annotations, for which the ground truth annotations are provided for just the central slice of each volumetric MR image. Specifically, semi-supervised learning and self-supervised learning methods are used to generate two independent sets of pseudo labels. These pseudo labels are then fused by Boolean operation to extract a more confident pseudo label set. The images with either manual or network self-generated labels are then employed to train a segmentation model for target volume extraction. Experimental results on a publicly available prostate MR image dataset demonstrate that, while requiring significantly less annotation effort, our framework generates very encouraging segmentation results. The proposed framework is very useful in clinical applications when training data with dense annotations are difficult to obtain.

Cheng Li, Yousuf Babiker M. Osman, Weijian Huang et al.

Multi-parametric magnetic resonance (MR) imaging is an indispensable tool in the clinic. Consequently, automatic volume-of-interest segmentation based on multi-parametric MR imaging is crucial for computer-aided disease diagnosis, treatment planning, and prognosis monitoring. Despite the extensive studies conducted in deep learning-based medical image analysis, further investigations are still required to effectively exploit the information provided by different imaging parameters. How to fuse the information is a key question in this field. Here, we propose an uncertainty-aware multi-parametric MR image feature fusion method to fully exploit the information for enhanced 3D image segmentation. Uncertainties in the independent predictions of individual modalities are utilized to guide the fusion of multi-modal image features. Extensive experiments on two datasets, one for brain tissue segmentation and the other for abdominal multi-organ segmentation, have been conducted, and our proposed method achieves better segmentation performance when compared to existing models.

Yeqi Wang, Weijian Huang, Cheng Li et al.

Multi-contrast magnetic resonance imaging (MRI)-based automatic auxiliary glioma diagnosis plays an important role in the clinic. Contrast-enhanced MRI sequences (e.g., contrast-enhanced T1-weighted imaging) were utilized in most of the existing relevant studies, in which remarkable diagnosis results have been reported. Nevertheless, acquiring contrast-enhanced MRI data is sometimes not feasible due to the patients physiological limitations. Furthermore, it is more time-consuming and costly to collect contrast-enhanced MRI data in the clinic. In this paper, we propose an adaptive PromptNet to address these issues. Specifically, a PromptNet for glioma grading utilizing only non-enhanced MRI data has been constructed. PromptNet receives constraints from features of contrast-enhanced MR data during training through a designed prompt loss. To further boost the performance, an adaptive strategy is designed to dynamically weight the prompt loss in a sample-based manner. As a result, PromptNet is capable of dealing with more difficult samples. The effectiveness of our method is evaluated on a widely-used BraTS2020 dataset, and competitive glioma grading performance on NE-MRI data is achieved.

Cheng Li, Weijian Huang, Jiarun Liu et al.

The integration of medical imaging and clinical text has enabled the emergence of generalist artificial intelligence (AI) systems for healthcare. However, pervasive biases, such as imbalanced disease prevalence, skewed anatomical region distributions, heterogeneous imaging protocols, and demographic disparities, pose significant challenges to the fairness and reliability of vision-language systems in real-world clinical settings. Here we present BiasCareVL, a bias-aware multimodal learning framework that introduces bias control directly into model design, rather than treating it as a post hoc correction. BiasCareVL incorporates adaptive uncertainty modeling with optional human-in-the-loop refinement to regulate the influence of dominant data patterns and to promote equitable reasoning under distributional imbalance. Trained on 3.44 million samples spanning over 15 imaging modalities, the framework supports diverse clinical tasks, including visual question answering, disease classification, segmentation, and report generation within a unified representation space. Across eight public benchmarks covering dermatology, oncology, radiology, and pathology, BiasCareVL consistently outperforms 20 state-of-the-art methods, with pronounced gains in clinically challenging scenarios, including over 10% accuracy improvement in multi-class skin lesion diagnosis and more than 20% Dice improvement in small tumor segmentation. Furthermore, BiasCareVL achieves diagnostic performance exceeding human accuracy with substantially reduced time requirements when evaluated with board-certified radiologists. By open-sourcing BiasCareVL, we aim to promote a transparent, reproducible, and equitable future for AI in healthcare, paving the way for general-purpose, trustworthy, and clinically reliable AI systems.

Weijian Huang, Cheng Li, Hong-Yu Zhou et al.

The development of medical vision-language foundation models has attracted significant attention in the field of medicine and healthcare due to their promising prospect in various clinical applications. While previous studies have commonly focused on feature learning at a single learning scale, investigation on integrating multi-scale information is lacking, which may hinder the potential for mutual reinforcement among these features. This paper aims to bridge this gap by proposing a method that effectively exploits multi-scale information to enhance the performance of medical foundation models. The proposed method simultaneously exploits features at the local, instance, modality and global aspects, facilitating comprehensive representation learning within the models. We evaluate the effectiveness of the proposed method on six open-source datasets across different clinical tasks, demonstrating its ability to enhance the performance of medical foundation models.

Hao Yang, Weijian Huang, Kehan Qi et al.

Segmenting stroke lesions from T1-weighted MR images is of great value for large-scale stroke rehabilitation neuroimaging analyses. Nevertheless, there are great challenges with this task, such as large range of stroke lesion scales and the tissue intensity similarity. The famous encoder-decoder convolutional neural network, which although has made great achievements in medical image segmentation areas, may fail to address these challenges due to the insufficient uses of multi-scale features and context information. To address these challenges, this paper proposes a Cross-Level fusion and Context Inference Network (CLCI-Net) for the chronic stroke lesion segmentation from T1-weighted MR images. Specifically, a Cross-Level feature Fusion (CLF) strategy was developed to make full use of different scale features across different levels; Extending Atrous Spatial Pyramid Pooling (ASPP) with CLF, we have enriched multi-scale features to handle the different lesion sizes; In addition, convolutional long short-term memory (ConvLSTM) is employed to infer context information and thus capture fine structures to address the intensity similarity issue. The proposed approach was evaluated on an open-source dataset, the Anatomical Tracings of Lesions After Stroke (ATLAS) with the results showing that our network outperforms five state-of-the-art methods. We make our code and models available at https://github.com/YH0517/CLCI_Net.

Jiarun Liu, Hong-Yu Zhou, Cheng Li et al.

Existing contrastive language-image pre-training aims to learn a joint representation by matching abundant image-text pairs. However, the number of image-text pairs in medical datasets is usually orders of magnitude smaller than that in natural datasets. Besides, medical image-text pairs often involve numerous complex fine-grained correspondences. This paper aims to enhance the data efficiency by introducing multiple-to-multiple local relationship modeling to capture denser supervisions. More specifically, we propose a Medical Language-Image Pre-training (MLIP) framework, which exploits the limited image-text medical data more efficiently through patch-sentence matching. Furthermore, we introduce a masked contrastive learning strategy with semantic integrity estimation to reduce redundancy in images while preserving the underlying semantics. Our evaluation results show that MLIP outperforms previous work in zero/few-shot classification and few-shot segmentation tasks by a large margin.

Hao Yang, Hong-Yu Zhou, Cheng Li et al.

Multimodal deep learning utilizing imaging and diagnostic reports has made impressive progress in the field of medical imaging diagnostics, demonstrating a particularly strong capability for auxiliary diagnosis in cases where sufficient annotation information is lacking. Nonetheless, localizing diseases accurately without detailed positional annotations remains a challenge. Although existing methods have attempted to utilize local information to achieve fine-grained semantic alignment, their capability in extracting the fine-grained semantics of the comprehensive context within reports is limited. To address this problem, a new method is introduced that takes full sentences from textual reports as the basic units for local semantic alignment. This approach combines chest X-ray images with their corresponding textual reports, performing contrastive learning at both global and local levels. The leading results obtained by this method on multiple datasets confirm its efficacy in the task of lesion localization.

Yousuf Babiker M. Osman, Cheng Li, Weijian Huang et al.

Background: Deep learning has presented great potential in accurate MR image segmentation when enough labeled data are provided for network optimization. However, manually annotating 3D MR images is tedious and time-consuming, requiring experts with rich domain knowledge and experience. Purpose: To build a deep learning method exploring sparse annotations, namely only a single 2D slice label for each 3D training MR image. Population: 3D MR images of 150 subjects from two publicly available datasets were included. Among them, 50 (1,377 image slices) are for prostate segmentation. The other 100 (8,800 image slices) are for left atrium segmentation. Five-fold cross-validation experiments were carried out utilizing the first dataset. For the second dataset, 80 subjects were used for training and 20 were used for testing. Assessment: A collaborative learning method by integrating the strengths of semi-supervised and self-supervised learning schemes was developed. The method was trained using labeled central slices and unlabeled non-central slices. Segmentation performance on testing set was reported quantitatively and qualitatively. Results: Compared to FS-LCS, MT, UA-MT, DCT-Seg, ICT, and AC-MT, the proposed method achieved a substantial improvement in segmentation accuracy, increasing the mean B-IoU significantly by more than 10.0% for prostate segmentation (proposed method B-IoU: 70.3% vs. ICT B-IoU: 60.3%) and by more than 6.0% for left atrium segmentation (proposed method B-IoU: 66.1% vs. ICT B-IoU: 60.1%).

Dongning Song, Weijian Huang, Jiarun Liu et al.

Accurate segmentation of blood vessels is essential for various clinical assessments and postoperative analyses. However, the inherent challenges of vascular imaging, such as sparsity, fine granularity, low contrast, data distribution variability, and the critical need for preserving topological structure, making generalized vessel segmentation particularly complex. While specialized segmentation methods have been developed for specific anatomical regions, their over-reliance on tailored models hinders broader applicability and generalization. General-purpose segmentation models introduced in medical imaging often fail to address critical vascular characteristics, including the connectivity of segmentation results. To overcome these limitations, we propose an optimized vessel segmentation framework: a structure-agnostic approach incorporating small vessel enhancement and morphological correction for multi-modality vessel segmentation. To train and validate this framework, we compiled a comprehensive multi-modality dataset spanning 17 datasets and benchmarked our model against six SAM-based methods and 17 expert models. The results demonstrate that our approach achieves superior segmentation accuracy, generalization, and a 34.6% improvement in connectivity, underscoring its clinical potential. An ablation study further validates the effectiveness of the proposed improvements. We will release the code and dataset at github following the publication of this work.

Hao Yang, Hong-Yu Zhou, Jiarun Liu et al.

Existing deep learning models for defining pathology from clinical imaging data rely on expert annotations and lack generalization capabilities in open clinical environments. Here, we present a generalizable vision-language model for Annotation-Free pathology Localization (AFLoc). The core strength of AFLoc is extensive multi-level semantic structure-based contrastive learning, which comprehensively aligns multi-granularity medical concepts with abundant image features to adapt to the diverse expressions of pathologies without the reliance on expert image annotations. We conduct primary experiments on a dataset of 220K pairs of image-report chest X-ray images and perform validation across eight external datasets encompassing 34 types of chest pathologies. The results demonstrate that AFLoc outperforms state-of-the-art methods in both annotation-free localization and classification tasks. Additionally, we assess the generalizability of AFLoc on other modalities, including histopathology and retinal fundus images. We show that AFLoc exhibits robust generalization capabilities, even surpassing human benchmarks in localizing five different types of pathological images. These results highlight the potential of AFLoc in reducing annotation requirements and its applicability in complex clinical environments.

Jiarun Liu, Hong-Yu Zhou, Weijian Huang et al.

Scaling up model and data size have demonstrated impressive performance improvement over a wide range of tasks. Despite extensive studies on scaling behaviors for general-purpose tasks, medical images exhibit substantial differences from natural data. It remains unclear the key factors in developing medical vision foundation models at scale due to the absence of an extensive understanding of scaling behavior in the medical domain. In this paper, we explored the scaling behavior across model sizes, training algorithms, data sizes, and imaging modalities in developing scalable medical vision foundation models by self-supervised learning. To support scalable pretraining, we introduce BioVFM-21M, a large-scale biomedical image dataset encompassing a wide range of biomedical image modalities and anatomies. We observed that scaling up does provide benefits but varies across tasks. Additional analysis reveals several factors correlated with scaling benefits. Finally, we propose BioVFM, a large-scale medical vision foundation model pretrained on 21 million biomedical images, which outperforms the previous state-of-the-art foundation models across 12 medical benchmarks. Our results highlight that while scaling up is beneficial for pursuing better performance, task characteristics, data diversity, pretraining methods, and computational efficiency remain critical considerations for developing scalable medical foundation models.

Weijian Huang, Cheng Li, Hao Yang et al.

Recently, vision-language representation learning has made remarkable advancements in building up medical foundation models, holding immense potential for transforming the landscape of clinical research and medical care. The underlying hypothesis is that the rich knowledge embedded in radiology reports can effectively assist and guide the learning process, reducing the need for additional labels. However, these reports tend to be complex and sometimes even consist of redundant descriptions that make the representation learning too challenging to capture the key semantic information. This paper develops a novel iterative vision-language representation learning framework by proposing a key semantic knowledge-emphasized report refinement method. Particularly, raw radiology reports are refined to highlight the key information according to a constructed clinical dictionary and two model-optimized knowledge-enhancement metrics. The iterative framework is designed to progressively learn, starting from gaining a general understanding of the patient's condition based on raw reports and gradually refines and extracts critical information essential to the fine-grained analysis tasks. The effectiveness of the proposed framework is validated on various downstream medical image analysis tasks, including disease classification, region-of-interest segmentation, and phrase grounding. Our framework surpasses seven state-of-the-art methods in both fine-tuning and zero-shot settings, demonstrating its encouraging potential for different clinical applications.

Weijian Huang, Hao Yang, Xinfeng Liu et al.

Multi-contrast magnetic resonance (MR) image registration is useful in the clinic to achieve fast and accurate imaging-based disease diagnosis and treatment planning. Nevertheless, the efficiency and performance of the existing registration algorithms can still be improved. In this paper, we propose a novel unsupervised learning-based framework to achieve accurate and efficient multi-contrast MR image registrations. Specifically, an end-to-end coarse-to-fine network architecture consisting of affine and deformable transformations is designed to improve the robustness and achieve end-to-end registration. Furthermore, a dual consistency constraint and a new prior knowledge-based loss function are developed to enhance the registration performances. The proposed method has been evaluated on a clinical dataset containing 555 cases, and encouraging performances have been achieved. Compared to the commonly utilized registration methods, including VoxelMorph, SyN, and LT-Net, the proposed method achieves better registration performance with a Dice score of 0.8397 in identifying stroke lesions. With regards to the registration speed, our method is about 10 times faster than the most competitive method of SyN (Affine) when testing on a CPU. Moreover, we prove that our method can still perform well on more challenging tasks with lacking scanning information data, showing high robustness for the clinical application.

Yongjin Zhou, Weijian Huang, Pei Dong et al.

Assessing the location and extent of lesions caused by chronic stroke is critical for medical diagnosis, surgical planning, and prognosis. In recent years, with the rapid development of 2D and 3D convolutional neural networks (CNN), the encoder-decoder structure has shown great potential in the field of medical image segmentation. However, the 2D CNN ignores the 3D information of medical images, while the 3D CNN suffers from high computational resource demands. This paper proposes a new architecture called dimension-fusion-UNet (D-UNet), which combines 2D and 3D convolution innovatively in the encoding stage. The proposed architecture achieves a better segmentation performance than 2D networks, while requiring significantly less computation time in comparison to 3D networks. Furthermore, to alleviate the data imbalance issue between positive and negative samples for the network training, we propose a new loss function called Enhance Mixing Loss (EML). This function adds a weighted focal coefficient and combines two traditional loss functions. The proposed method has been tested on the ATLAS dataset and compared to three state-of-the-art methods. The results demonstrate that the proposed method achieves the best quality performance in terms of DSC = 0.5349+0.2763 and precision = 0.6331+0.295).