Yunxiang Li

Zihan Li, Yunxiang Li, Qingde Li et al. · uw

Deep learning has been widely used in medical image segmentation and other aspects. However, the performance of existing medical image segmentation models has been limited by the challenge of obtaining sufficient high-quality labeled data due to the prohibitive data annotation cost. To alleviate this limitation, we propose a new text-augmented medical image segmentation model LViT (Language meets Vision Transformer). In our LViT model, medical text annotation is incorporated to compensate for the quality deficiency in image data. In addition, the text information can guide to generate pseudo labels of improved quality in the semi-supervised learning. We also propose an Exponential Pseudo label Iteration mechanism (EPI) to help the Pixel-Level Attention Module (PLAM) preserve local image features in semi-supervised LViT setting. In our model, LV (Language-Vision) loss is designed to supervise the training of unlabeled images using text information directly. For evaluation, we construct three multimodal medical segmentation datasets (image + text) containing X-rays and CT images. Experimental results show that our proposed LViT has superior segmentation performance in both fully-supervised and semi-supervised setting. The code and datasets are available at https://github.com/HUANGLIZI/LViT.

Kai Wang, Yunxiang Li, Michael Dohopolski et al.

For Head and Neck Cancers (HNC) patient management, automatic gross tumor volume (GTV) segmentation and accurate pre-treatment cancer recurrence prediction are of great importance to assist physicians in designing personalized management plans, which have the potential to improve the treatment outcome and quality of life for HNC patients. In this paper, we developed an automated primary tumor (GTVp) and lymph nodes (GTVn) segmentation method based on combined pre-treatment positron emission tomography/computed tomography (PET/CT) scans of HNC patients. We extracted radiomics features from the segmented tumor volume and constructed a multi-modality tumor recurrence-free survival (RFS) prediction model, which fused the prediction results from separate CT radiomics, PET radiomics, and clinical models. We performed 5-fold cross-validation to train and evaluate our methods on the MICCAI 2022 HEad and neCK TumOR segmentation and outcome prediction challenge (HECKTOR) dataset. The ensemble prediction results on the testing cohort achieved Dice scores of 0.77 and 0.73 for GTVp and GTVn segmentation, respectively, and a C-index value of 0.67 for RFS prediction. The code is publicly available (https://github.com/wangkaiwan/HECKTOR-2022-AIRT). Our team's name is AIRT.

Ruilong Dan, Yunxiang Li, Yijie Wang et al.

Precise and rapid categorization of images in the B-scan ultrasound modality is vital for diagnosing ocular diseases. Nevertheless, distinguishing various diseases in ultrasound still challenges experienced ophthalmologists. Thus a novel contrastive disentangled network (CDNet) is developed in this work, aiming to tackle the fine-grained image categorization (FGIC) challenges of ocular abnormalities in ultrasound images, including intraocular tumor (IOT), retinal detachment (RD), posterior scleral staphyloma (PSS), and vitreous hemorrhage (VH). Three essential components of CDNet are the weakly-supervised lesion localization module (WSLL), contrastive multi-zoom (CMZ) strategy, and hyperspherical contrastive disentangled loss (HCD-Loss), respectively. These components facilitate feature disentanglement for fine-grained recognition in both the input and output aspects. The proposed CDNet is validated on our ZJU Ocular Ultrasound Dataset (ZJUOUSD), consisting of 5213 samples. Furthermore, the generalization ability of CDNet is validated on two public and widely-used chest X-ray FGIC benchmarks. Quantitative and qualitative results demonstrate the efficacy of our proposed CDNet, which achieves state-of-the-art performance in the FGIC task. Code is available at: https://github.com/ZeroOneGame/CDNet-for-OUS-FGIC .

Yunxiang Li, Bowen Jing, Zihan Li et al. · uw

Automatic segmentation of medical images is crucial in modern clinical workflows. The Segment Anything Model (SAM) has emerged as a versatile tool for image segmentation without specific domain training, but it requires human prompts and may have limitations in specific domains. Traditional models like nnUNet perform automatic segmentation during inference and are effective in specific domains but need extensive domain-specific training. To combine the strengths of foundational and domain-specific models, we propose nnSAM, integrating SAM's robust feature extraction with nnUNet's automatic configuration to enhance segmentation accuracy on small datasets. Our nnSAM model optimizes two main approaches: leveraging SAM's feature extraction and nnUNet's domain-specific adaptation, and incorporating a boundary shape supervision loss function based on level set functions and curvature calculations to learn anatomical shape priors from limited data. We evaluated nnSAM on four segmentation tasks: brain white matter, liver, lung, and heart segmentation. Our method outperformed others, achieving the highest DICE score of 82.77% and the lowest ASD of 1.14 mm in brain white matter segmentation with 20 training samples, compared to nnUNet's DICE score of 79.25% and ASD of 1.36 mm. A sample size study highlighted nnSAM's advantage with fewer training samples. Our results demonstrate significant improvements in segmentation performance with nnSAM, showcasing its potential for small-sample learning in medical image segmentation.

Yunxiang Li, Hua-Chieh Shao, Xiao Liang et al.

Recently, the diffusion model has emerged as a superior generative model that can produce high quality and realistic images. However, for medical image translation, the existing diffusion models are deficient in accurately retaining structural information since the structure details of source domain images are lost during the forward diffusion process and cannot be fully recovered through learned reverse diffusion, while the integrity of anatomical structures is extremely important in medical images. For instance, errors in image translation may distort, shift, or even remove structures and tumors, leading to incorrect diagnosis and inadequate treatments. Training and conditioning diffusion models using paired source and target images with matching anatomy can help. However, such paired data are very difficult and costly to obtain, and may also reduce the robustness of the developed model to out-of-distribution testing data. We propose a frequency-guided diffusion model (FGDM) that employs frequency-domain filters to guide the diffusion model for structure-preserving image translation. Based on its design, FGDM allows zero-shot learning, as it can be trained solely on the data from the target domain, and used directly for source-to-target domain translation without any exposure to the source-domain data during training. We evaluated it on three cone-beam CT (CBCT)-to-CT translation tasks for different anatomical sites, and a cross-institutional MR imaging translation task. FGDM outperformed the state-of-the-art methods (GAN-based, VAE-based, and diffusion-based) in metrics of Frechet Inception Distance (FID), Peak Signal-to-Noise Ratio (PSNR), and Structural Similarity Index Measure (SSIM), showing its significant advantages in zero-shot medical image translation.

Yunxiang Li, Ruilong Dan, Shuai Wang et al.

Skull stripping is a crucial prerequisite step in the analysis of brain magnetic resonance images (MRI). Although many excellent works or tools have been proposed, they suffer from low generalization capability. For instance, the model trained on a dataset with specific imaging parameters cannot be well applied to other datasets with different imaging parameters. Especially, for the lifespan datasets, the model trained on an adult dataset is not applicable to an infant dataset due to the large domain difference. To address this issue, numerous methods have been proposed, where domain adaptation based on feature alignment is the most common. Unfortunately, this method has some inherent shortcomings, which need to be retrained for each new domain and requires concurrent access to the input images of both domains. In this paper, we design a plug-and-play shape refinement (PSR) framework for multi-site and lifespan skull stripping. To deal with the domain shift between multi-site lifespan datasets, we take advantage of the brain shape prior, which is invariant to imaging parameters and ages. Experiments demonstrate that our framework can outperform the state-of-the-art methods on multi-site lifespan datasets.

Tengjin Weng, Yang Shen, Kai Jin et al.

Automatic segmentation of fluid in Optical Coherence Tomography (OCT) images is beneficial for ophthalmologists to make an accurate diagnosis. Although semi-supervised OCT fluid segmentation networks enhance their performance by introducing additional unlabeled data, the performance enhancement is limited. To address this, we propose Superpixel and Confident Learning Guide Point Annotations Network (SCLGPA-Net) based on the teacher-student architecture, which can learn OCT fluid segmentation from limited fully-annotated data and abundant point-annotated data. Specifically, we use points to annotate fluid regions in unlabeled OCT images and the Superpixel-Guided Pseudo-Label Generation (SGPLG) module generates pseudo-labels and pixel-level label trust maps from the point annotations. The label trust maps provide an indication of the reliability of the pseudo-labels. Furthermore, we propose the Confident Learning Guided Label Refinement (CLGLR) module identifies error information in the pseudo-labels and leads to further refinement. Experiments on the RETOUCH dataset show that we are able to reduce the need for fully-annotated data by 94.22\%, closing the gap with the best fully supervised baselines to a mean IoU of only 2\%. Furthermore, We constructed a private 2D OCT fluid segmentation dataset for evaluation. Compared with other methods, comprehensive experimental results demonstrate that the proposed method can achieve excellent performance in OCT fluid segmentation.

Yaqi Wang, Yifan Zhang, Xiaodiao Chen et al.

Computer-aided design (CAD) tools are increasingly popular in modern dental practice, particularly for treatment planning or comprehensive prognosis evaluation. In particular, the 2D panoramic X-ray image efficiently detects invisible caries, impacted teeth and supernumerary teeth in children, while the 3D dental cone beam computed tomography (CBCT) is widely used in orthodontics and endodontics due to its low radiation dose. However, there is no open-access 2D public dataset for children's teeth and no open 3D dental CBCT dataset, which limits the development of automatic algorithms for segmenting teeth and analyzing diseases. The Semi-supervised Teeth Segmentation (STS) Challenge, a pioneering event in tooth segmentation, was held as a part of the MICCAI 2023 ToothFairy Workshop on the Alibaba Tianchi platform. This challenge aims to investigate effective semi-supervised tooth segmentation algorithms to advance the field of dentistry. In this challenge, we provide two modalities including the 2D panoramic X-ray images and the 3D CBCT tooth volumes. In Task 1, the goal was to segment tooth regions in panoramic X-ray images of both adult and pediatric teeth. Task 2 involved segmenting tooth sections using CBCT volumes. Limited labelled images with mostly unlabelled ones were provided in this challenge prompt using semi-supervised algorithms for training. In the preliminary round, the challenge received registration and result submission by 434 teams, with 64 advancing to the final round. This paper summarizes the diverse methods employed by the top-ranking teams in the STS MICCAI 2023 Challenge.

Yunxiang Li, Hua-Chieh Shao, Xiaoxue Qian et al.

Diffusion models have demonstrated significant potential in producing high-quality images in medical image translation to aid disease diagnosis, localization, and treatment. Nevertheless, current diffusion models have limited success in achieving faithful image translations that can accurately preserve the anatomical structures of medical images, especially for unpaired datasets. The preservation of structural and anatomical details is essential to reliable medical diagnosis and treatment planning, as structural mismatches can lead to disease misidentification and treatment errors. In this study, we introduce the Frequency Decoupled Diffusion Model (FDDM) for MR-to-CT conversion. FDDM first obtains the anatomical information of the CT image from the MR image through an initial conversion module. This anatomical information then guides a subsequent diffusion model to generate high-quality CT images. Our diffusion model uses a dual-path reverse diffusion process for low-frequency and high-frequency information, achieving a better balance between image quality and anatomical accuracy. We extensively evaluated FDDM using public datasets for brain MR-to-CT and pelvis MR-to-CT translations, demonstrating its superior performance to other GAN-based, VAE-based, and diffusion-based models. The evaluation metrics included Frechet Inception Distance (FID), Peak Signal-to-Noise Ratio (PSNR), and Structural Similarity Index Measure (SSIM). FDDM achieved the best scores on all metrics for both datasets, particularly excelling in FID, with scores of 25.9 for brain data and 29.2 for pelvis data, significantly outperforming other methods. These results demonstrate that FDDM can generate high-quality target domain images while maintaining the accuracy of translated anatomical structures.

Yunxiang Li, Wenbin Zou, Qiaomu Wei et al.

Stereo image super-resolution utilizes the cross-view complementary information brought by the disparity effect of left and right perspective images to reconstruct higher-quality images. Cascading feature extraction modules and cross-view feature interaction modules to make use of the information from stereo images is the focus of numerous methods. However, this adds a great deal of network parameters and structural redundancy. To facilitate the application of stereo image super-resolution in downstream tasks, we propose an efficient Multi-Level Feature Fusion Network for Lightweight Stereo Image Super-Resolution (MFFSSR). Specifically, MFFSSR utilizes the Hybrid Attention Feature Extraction Block (HAFEB) to extract multi-level intra-view features. Using the channel separation strategy, HAFEB can efficiently interact with the embedded cross-view interaction module. This structural configuration can efficiently mine features inside the view while improving the efficiency of cross-view information sharing. Hence, reconstruct image details and textures more accurately. Abundant experiments demonstrate the effectiveness of MFFSSR. We achieve superior performance with fewer parameters. The source code is available at https://github.com/KarosLYX/MFFSSR.

Yunxiang Li, Meixu Chen, Kai Wang et al.

Image translation has wide applications, such as style transfer and modality conversion, usually aiming to generate images having both high degrees of realism and faithfulness. These problems remain difficult, especially when it is important to preserve content structures. Traditional image-level similarity metrics are of limited use, since the content structures of an image are high-level, and not strongly governed by pixel-wise faithfulness to an original image. To fill this gap, we introduce SAMScore, a generic content structural similarity metric for evaluating the faithfulness of image translation models. SAMScore is based on the recent high-performance Segment Anything Model (SAM), which allows content similarity comparisons with standout accuracy. We applied SAMScore on 19 image translation tasks, and found that it is able to outperform all other competitive metrics on all tasks. We envision that SAMScore will prove to be a valuable tool that will help to drive the vibrant field of image translation, by allowing for more precise evaluations of new and evolving translation models. The code is available at https://github.com/Kent0n-Li/SAMScore.

Xiaoning Liu, Zongwei Wu, Ao Li et al.

This paper reviews the NTIRE 2024 low light image enhancement challenge, highlighting the proposed solutions and results. The aim of this challenge is to discover an effective network design or solution capable of generating brighter, clearer, and visually appealing results when dealing with a variety of conditions, including ultra-high resolution (4K and beyond), non-uniform illumination, backlighting, extreme darkness, and night scenes. A notable total of 428 participants registered for the challenge, with 22 teams ultimately making valid submissions. This paper meticulously evaluates the state-of-the-art advancements in enhancing low-light images, reflecting the significant progress and creativity in this field.

Kun Li, Tianhua Zhang, Yunxiang Li et al.

Improving context faithfulness in large language models is essential for developing trustworthy retrieval augmented generation systems and mitigating hallucinations, especially in long-form question answering (LFQA) tasks or scenarios involving knowledge conflicts. Existing methods either intervene LLMs only at inference without addressing their inherent limitations or overlook the potential for self-improvement. In this paper, we introduce GenDiE (Generate, Discriminate, Evolve), a novel self-evolving framework that enhances context faithfulness through fine-grained sentence-level optimization. GenDiE combines both generative and discriminative training, equipping LLMs with self-generation and self-scoring capabilities to facilitate iterative self-evolution. This supports both data construction for model alignment and score-guided search during inference. Furthermore, by treating each sentence in a response as an independent optimization unit, GenDiE effectively addresses the limitations of previous approaches that optimize at the holistic answer level, which may miss unfaithful details. Experiments on ASQA (in-domain LFQA) and ConFiQA (out-of-domain counterfactual QA) datasets demonstrate that GenDiE surpasses various baselines in both faithfulness and correctness, and exhibits robust performance for domain adaptation.

Kun Li, Yunxiang Li, Tianhua Zhang et al.

Robust evaluation is critical for deploying trustworthy retrieval-augmented generation (RAG) systems. However, current LLM-based evaluation frameworks predominantly rely on directly prompting resource-intensive models with complex multi-stage prompts, underutilizing models' reasoning capabilities and introducing significant computational cost. In this paper, we present RAG-Zeval (RAG-Zero Evaluator), a novel end-to-end framework that formulates faithfulness and correctness evaluation as a rule-guided reasoning task. Our approach trains evaluators with reinforcement learning, facilitating compact models to generate comprehensive and sound assessments with detailed explanation in one-pass. We introduce a ranking-based outcome reward mechanism, using preference judgments rather than absolute scores, to address the challenge of obtaining precise pointwise reward signals. To this end, we synthesize the ranking references by generating quality-controlled responses with zero human annotation. Experiments demonstrate RAG-Zeval's superior performance, achieving the strongest correlation with human judgments and outperforming baselines that rely on LLMs with 10-100 times more parameters. Our approach also exhibits superior interpretability in response evaluation.

Jiacheng Xie, Hua-Chieh Shao, Yunxiang Li et al.

Cone-beam computed tomography (CBCT) is widely used in image-guided radiotherapy. Reconstructing CBCTs from limited-angle acquisitions (LA-CBCT) is highly desired for improved imaging efficiency, dose reduction, and better mechanical clearance. LA-CBCT reconstruction, however, suffers from severe under-sampling artifacts, making it a highly ill-posed inverse problem. Diffusion models can generate data/images by reversing a data-noising process through learned data distributions; and can be incorporated as a denoiser/regularizer in LA-CBCT reconstruction. In this study, we developed a diffusion model-based framework, prior frequency-guided diffusion model (PFGDM), for robust and structure-preserving LA-CBCT reconstruction. PFGDM uses a conditioned diffusion model as a regularizer for LA-CBCT reconstruction, and the condition is based on high-frequency information extracted from patient-specific prior CT scans which provides a strong anatomical prior for LA-CBCT reconstruction. Specifically, we developed two variants of PFGDM (PFGDM-A and PFGDM-B) with different conditioning schemes. PFGDM-A applies the high-frequency CT information condition until a pre-optimized iteration step, and drops it afterwards to enable both similar and differing CT/CBCT anatomies to be reconstructed. PFGDM-B, on the other hand, continuously applies the prior CT information condition in every reconstruction step, while with a decaying mechanism, to gradually phase out the reconstruction guidance from the prior CT scans. The two variants of PFGDM were tested and compared with current available LA-CBCT reconstruction solutions, via metrics including PSNR and SSIM. PFGDM outperformed all traditional and diffusion model-based methods. PFGDM reconstructs high-quality LA-CBCTs under very-limited gantry angles, allowing faster and more flexible CBCT scans with dose reductions.

Yunxiang Li, Jingxiong Li, Ruilong Dan et al.

Accurate segmentation is a crucial step in medical image analysis and applying supervised machine learning to segment the organs or lesions has been substantiated effective. However, it is costly to perform data annotation that provides ground truth labels for training the supervised algorithms, and the high variance of data that comes from different domains tends to severely degrade system performance over cross-site or cross-modality datasets. To mitigate this problem, a novel unsupervised domain adaptation (UDA) method named dispensed Transformer network (DTNet) is introduced in this paper. Our novel DTNet contains three modules. First, a dispensed residual transformer block is designed, which realizes global attention by dispensed interleaving operation and deals with the excessive computational cost and GPU memory usage of the Transformer. Second, a multi-scale consistency regularization is proposed to alleviate the loss of details in the low-resolution output for better feature alignment. Finally, a feature ranking discriminator is introduced to automatically assign different weights to domain-gap features to lessen the feature distribution distance, reducing the performance shift of two domains. The proposed method is evaluated on large fluorescein angiography (FA) retinal nonperfusion (RNP) cross-site dataset with 676 images and a wide used cross-modality dataset from the MM-WHS challenge. Extensive results demonstrate that our proposed network achieves the best performance in comparison with several state-of-the-art techniques.

Yunxiang Li, Guodong Zeng, Yifan Zhang et al.

Accurate evaluation of the treatment result on X-ray images is a significant and challenging step in root canal therapy since the incorrect interpretation of the therapy results will hamper timely follow-up which is crucial to the patients' treatment outcome. Nowadays, the evaluation is performed in a manual manner, which is time-consuming, subjective, and error-prone. In this paper, we aim to automate this process by leveraging the advances in computer vision and artificial intelligence, to provide an objective and accurate method for root canal therapy result assessment. A novel anatomy-guided multi-branch Transformer (AGMB-Transformer) network is proposed, which first extracts a set of anatomy features and then uses them to guide a multi-branch Transformer network for evaluation. Specifically, we design a polynomial curve fitting segmentation strategy with the help of landmark detection to extract the anatomy features. Moreover, a branch fusion module and a multi-branch structure including our progressive Transformer and Group Multi-Head Self-Attention (GMHSA) are designed to focus on both global and local features for an accurate diagnosis. To facilitate the research, we have collected a large-scale root canal therapy evaluation dataset with 245 root canal therapy X-ray images, and the experiment results show that our AGMB-Transformer can improve the diagnosis accuracy from 57.96% to 90.20% compared with the baseline network. The proposed AGMB-Transformer can achieve a highly accurate evaluation of root canal therapy. To our best knowledge, our work is the first to perform automatic root canal therapy evaluation and has important clinical value to reduce the workload of endodontists.

Yunxiang Li, Yifan Zhang, Yaqi Wang et al.

As the most economical and routine auxiliary examination in the diagnosis of root canal treatment, oral X-ray has been widely used by stomatologists. It is still challenging to segment the tooth root with a blurry boundary for the traditional image segmentation method. To this end, we propose a model for high-resolution segmentation based on polynomial curve fitting with landmark detection (HS-PCL). It is based on detecting multiple landmarks evenly distributed on the edge of the tooth root to fit a smooth polynomial curve as the segmentation of the tooth root, thereby solving the problem of fuzzy edge. In our model, a maximum number of the shortest distances algorithm (MNSDA) is proposed to automatically reduce the negative influence of the wrong landmarks which are detected incorrectly and deviate from the tooth root on the fitting result. Our numerical experiments demonstrate that the proposed approach not only reduces Hausdorff95 (HD95) by 33.9% and Average Surface Distance (ASD) by 42.1% compared with the state-of-the-art method, but it also achieves excellent results on the minute quantity of datasets, which greatly improves the feasibility of automatic root canal therapy evaluation by medical image computing.

Dailin Lv, Wuteng Qi, Yunxiang Li et al.

The worldwide spread of pneumonia caused by a novel coronavirus poses an unprecedented challenge to the world's medical resources and prevention and control measures. Covid-19 attacks not only the lungs, making it difficult to breathe and life-threatening, but also the heart, kidneys, brain and other vital organs of the body, with possible sequela. At present, the detection of COVID-19 needs to be realized by the reverse transcription-polymerase Chain Reaction (RT-PCR). However, many countries are in the outbreak period of the epidemic, and the medical resources are very limited. They cannot provide sufficient numbers of gene sequence detection, and many patients may not be isolated and treated in time. Given this situation, we researched the analytical and diagnostic capabilities of deep learning on chest radiographs and proposed Cascade-SEMEnet which is cascaded with SEME-ResNet50 and SEME-DenseNet169. The two cascade networks of Cascade - SEMEnet both adopt large input sizes and SE-Structure and use MoEx and histogram equalization to enhance the data. We first used SEME-ResNet50 to screen chest X-ray and diagnosed three classes: normal, bacterial, and viral pneumonia. Then we used SEME-DenseNet169 for fine-grained classification of viral pneumonia and determined if it is caused by COVID-19. To exclude the influence of non-pathological features on the network, we preprocessed the data with U-Net during the training of SEME-DenseNet169. The results showed that our network achieved an accuracy of 85.6\% in determining the type of pneumonia infection and 97.1\% in the fine-grained classification of COVID-19. We used Grad-CAM to visualize the judgment based on the model and help doctors understand the chest radiograph while verifying the effectivene.