arXiv subjects

Yalin Zheng

Publications and source records attributed to Yalin Zheng.

At least 37 records · Page 2Linked to original sources

arXiv2025

GLCP: Global-to-Local Connectivity Preservation for Tubular Structure Segmentation

Accurate segmentation of tubular structures, such as vascular networks, plays a critical role in various medical domains. A remaining significant challenge in this task is structural fragmentation, which can adversely impact downstream applications. Existing methods primarily focus on designing various loss functions to constrain global topological structures. However, they often overlook local discontinuity regions, leading to suboptimal segmentation results. To overcome this limitation, we propose a novel Global-to-Local Connectivity Preservation (GLCP) framework that can simultaneously perceive global and local structural characteristics of tubular networks. Specifically, we propose an Interactive Multi-head Segmentation (IMS) module to jointly learn global segmentation, skeleton maps, and local discontinuity maps, respectively. This enables our model to explicitly target local discontinuity regions while maintaining global topological integrity. In addition, we design a lightweight Dual-Attention-based Refinement (DAR) module to further improve segmentation quality by refining the resulting segmentation maps. Extensive experiments on both 2D and 3D datasets demonstrate that our GLCP achieves superior accuracy and continuity in tubular structure segmentation compared to several state-of-the-art approaches. The source codes will be available at https://github.com/FeixiangZhou/GLCP.

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arXiv2025

Parameterized Diffusion Optimization enabled Autoregressive Ordinal Regression for Diabetic Retinopathy Grading

As a long-term complication of diabetes, diabetic retinopathy (DR) progresses slowly, potentially taking years to threaten vision. An accurate and robust evaluation of its severity is vital to ensure prompt management and care. Ordinal regression leverages the underlying inherent order between categories to achieve superior performance beyond traditional classification. However, there exist challenges leading to lower DR classification performance: 1) The uneven distribution of DR severity levels, characterized by a long-tailed pattern, adds complexity to the grading process. 2)The ambiguity in defining category boundaries introduces additional challenges, making the classification process more complex and prone to inconsistencies. This work proposes a novel autoregressive ordinal regression method called AOR-DR to address the above challenges by leveraging the clinical knowledge of inherent ordinal information in DR grading dataset settings. Specifically, we decompose the DR grading task into a series of ordered steps by fusing the prediction of the previous steps with extracted image features as conditions for the current prediction step. Additionally, we exploit the diffusion process to facilitate conditional probability modeling, enabling the direct use of continuous global image features for autoregression without relearning contextual information from patch-level features. This ensures the effectiveness of the autoregressive process and leverages the capabilities of pre-trained large-scale foundation models. Extensive experiments were conducted on four large-scale publicly available color fundus datasets, demonstrating our model's effectiveness and superior performance over six recent state-of-the-art ordinal regression methods. The implementation code is available at https://github.com/Qinkaiyu/AOR-DR.

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arXiv2025

Robust Incomplete-Modality Alignment for Ophthalmic Disease Grading and Diagnosis via Labeled Optimal Transport

Multimodal ophthalmic imaging-based diagnosis integrates color fundus image with optical coherence tomography (OCT) to provide a comprehensive view of ocular pathologies. However, the uneven global distribution of healthcare resources often results in real-world clinical scenarios encountering incomplete multimodal data, which significantly compromises diagnostic accuracy. Existing commonly used pipelines, such as modality imputation and distillation methods, face notable limitations: 1)Imputation methods struggle with accurately reconstructing key lesion features, since OCT lesions are localized, while fundus images vary in style. 2)distillation methods rely heavily on fully paired multimodal training data. To address these challenges, we propose a novel multimodal alignment and fusion framework capable of robustly handling missing modalities in the task of ophthalmic diagnostics. By considering the distinctive feature characteristics of OCT and fundus images, we emphasize the alignment of semantic features within the same category and explicitly learn soft matching between modalities, allowing the missing modality to utilize existing modality information, achieving robust cross-modal feature alignment under the missing modality. Specifically, we leverage the Optimal Transport for multi-scale modality feature alignment: class-wise alignment through predicted class prototypes and feature-wise alignment via cross-modal shared feature transport. Furthermore, we propose an asymmetric fusion strategy that effectively exploits the distinct characteristics of OCT and fundus modalities. Extensive evaluations on three large ophthalmic multimodal datasets demonstrate our model's superior performance under various modality-incomplete scenarios, achieving Sota performance in both complete modality and inter-modality incompleteness conditions. Code is available at https://github.com/Qinkaiyu/RIMA

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arXiv2025

Benchmarking Large Multimodal Models for Ophthalmic Visual Question Answering with OphthalWeChat

Purpose: To develop a bilingual multimodal visual question answering (VQA) benchmark for evaluating VLMs in ophthalmology. Methods: Ophthalmic image posts and associated captions published between January 1, 2016, and December 31, 2024, were collected from WeChat Official Accounts. Based on these captions, bilingual question-answer (QA) pairs in Chinese and English were generated using GPT-4o-mini. QA pairs were categorized into six subsets by question type and language: binary (Binary_CN, Binary_EN), single-choice (Single-choice_CN, Single-choice_EN), and open-ended (Open-ended_CN, Open-ended_EN). The benchmark was used to evaluate the performance of three VLMs: GPT-4o, Gemini 2.0 Flash, and Qwen2.5-VL-72B-Instruct. Results: The final OphthalWeChat dataset included 3,469 images and 30,120 QA pairs across 9 ophthalmic subspecialties, 548 conditions, 29 imaging modalities, and 68 modality combinations. Gemini 2.0 Flash achieved the highest overall accuracy (0.548), outperforming GPT-4o (0.522, P < 0.001) and Qwen2.5-VL-72B-Instruct (0.514, P < 0.001). It also led in both Chinese (0.546) and English subsets (0.550). Subset-specific performance showed Gemini 2.0 Flash excelled in Binary_CN (0.687), Single-choice_CN (0.666), and Single-choice_EN (0.646), while GPT-4o ranked highest in Binary_EN (0.717), Open-ended_CN (BLEU-1: 0.301; BERTScore: 0.382), and Open-ended_EN (BLEU-1: 0.183; BERTScore: 0.240). Conclusions: This study presents the first bilingual VQA benchmark for ophthalmology, distinguished by its real-world context and inclusion of multiple examinations per patient. The dataset reflects authentic clinical decision-making scenarios and enables quantitative evaluation of VLMs, supporting the development of accurate, specialized, and trustworthy AI systems for eye care.

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arXiv2025

Are Spatial-Temporal Graph Convolution Networks for Human Action Recognition Over-Parameterized?

Spatial-temporal graph convolutional networks (ST-GCNs) showcase impressive performance in skeleton-based human action recognition (HAR). However, despite the development of numerous models, their recognition performance does not differ significantly after aligning the input settings. With this observation, we hypothesize that ST-GCNs are over-parameterized for HAR, a conjecture subsequently confirmed through experiments employing the lottery ticket hypothesis. Additionally, a novel sparse ST-GCNs generator is proposed, which trains a sparse architecture from a randomly initialized dense network while maintaining comparable performance levels to the dense components. Moreover, we generate multi-level sparsity ST-GCNs by integrating sparse structures at various sparsity levels and demonstrate that the assembled model yields a significant enhancement in HAR performance. Thorough experiments on four datasets, including NTU-RGB+D 60(120), Kinetics-400, and FineGYM, demonstrate that the proposed sparse ST-GCNs can achieve comparable performance to their dense components. Even with 95% fewer parameters, the sparse ST-GCNs exhibit a degradation of <1% in top-1 accuracy. Meanwhile, the multi-level sparsity ST-GCNs, which require only 66% of the parameters of the dense ST-GCNs, demonstrate an improvement of >1% in top-1 accuracy. The code is available at https://github.com/davelailai/Sparse-ST-GCN.

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arXiv2025

Predicting Diabetic Macular Edema Treatment Responses Using OCT: Dataset and Methods of APTOS Competition

Diabetic macular edema (DME) significantly contributes to visual impairment in diabetic patients. Treatment responses to intravitreal therapies vary, highlighting the need for patient stratification to predict therapeutic benefits and enable personalized strategies. To our knowledge, this study is the first to explore pre-treatment stratification for predicting DME treatment responses. To advance this research, we organized the 2nd Asia-Pacific Tele-Ophthalmology Society (APTOS) Big Data Competition in 2021. The competition focused on improving predictive accuracy for anti-VEGF therapy responses using ophthalmic OCT images. We provided a dataset containing tens of thousands of OCT images from 2,000 patients with labels across four sub-tasks. This paper details the competition's structure, dataset, leading methods, and evaluation metrics. The competition attracted strong scientific community participation, with 170 teams initially registering and 41 reaching the final round. The top-performing team achieved an AUC of 80.06%, highlighting the potential of AI in personalized DME treatment and clinical decision-making.

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arXiv2025

Advancing Cross-Organ Domain Generalization with Test-Time Style Transfer and Diversity Enhancement

Deep learning has made significant progress in addressing challenges in various fields including computational pathology (CPath). However, due to the complexity of the domain shift problem, the performance of existing models will degrade, especially when it comes to multi-domain or cross-domain tasks. In this paper, we propose a Test-time style transfer (T3s) that uses a bidirectional mapping mechanism to project the features of the source and target domains into a unified feature space, enhancing the generalization ability of the model. To further increase the style expression space, we introduce a Cross-domain style diversification module (CSDM) to ensure the orthogonality between style bases. In addition, data augmentation and low-rank adaptation techniques are used to improve feature alignment and sensitivity, enabling the model to adapt to multi-domain inputs effectively. Our method has demonstrated effectiveness on three unseen datasets.

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arXiv2025

Incomplete Modality Disentangled Representation for Ophthalmic Disease Grading and Diagnosis

Ophthalmologists typically require multimodal data sources to improve diagnostic accuracy in clinical decisions. However, due to medical device shortages, low-quality data and data privacy concerns, missing data modalities are common in real-world scenarios. Existing deep learning methods tend to address it by learning an implicit latent subspace representation for different modality combinations. We identify two significant limitations of these methods: (1) implicit representation constraints that hinder the model's ability to capture modality-specific information and (2) modality heterogeneity, causing distribution gaps and redundancy in feature representations. To address these, we propose an Incomplete Modality Disentangled Representation (IMDR) strategy, which disentangles features into explicit independent modal-common and modal-specific features by guidance of mutual information, distilling informative knowledge and enabling it to reconstruct valuable missing semantics and produce robust multimodal representations. Furthermore, we introduce a joint proxy learning module that assists IMDR in eliminating intra-modality redundancy by exploiting the extracted proxies from each class. Experiments on four ophthalmology multimodal datasets demonstrate that the proposed IMDR outperforms the state-of-the-art methods significantly.

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arXiv2024

CathAction: A Benchmark for Endovascular Intervention Understanding

Real-time visual feedback from catheterization analysis is crucial for enhancing surgical safety and efficiency during endovascular interventions. However, existing datasets are often limited to specific tasks, small scale, and lack the comprehensive annotations necessary for broader endovascular intervention understanding. To tackle these limitations, we introduce CathAction, a large-scale dataset for catheterization understanding. Our CathAction dataset encompasses approximately 500,000 annotated frames for catheterization action understanding and collision detection, and 25,000 ground truth masks for catheter and guidewire segmentation. For each task, we benchmark recent related works in the field. We further discuss the challenges of endovascular intentions compared to traditional computer vision tasks and point out open research questions. We hope that CathAction will facilitate the development of endovascular intervention understanding methods that can be applied to real-world applications. The dataset is available at https://airvlab.github.io/cathaction/.

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arXiv2024

CLIP-DR: Textual Knowledge-Guided Diabetic Retinopathy Grading with Ranking-aware Prompting

Diabetic retinopathy (DR) is a complication of diabetes and usually takes decades to reach sight-threatening levels. Accurate and robust detection of DR severity is critical for the timely management and treatment of diabetes. However, most current DR grading methods suffer from insufficient robustness to data variability (\textit{e.g.} colour fundus images), posing a significant difficulty for accurate and robust grading. In this work, we propose a novel DR grading framework CLIP-DR based on three observations: 1) Recent pre-trained visual language models, such as CLIP, showcase a notable capacity for generalisation across various downstream tasks, serving as effective baseline models. 2) The grading of image-text pairs for DR often adheres to a discernible natural sequence, yet most existing DR grading methods have primarily overlooked this aspect. 3) A long-tailed distribution among DR severity levels complicates the grading process. This work proposes a novel ranking-aware prompting strategy to help the CLIP model exploit the ordinal information. Specifically, we sequentially design learnable prompts between neighbouring text-image pairs in two different ranking directions. Additionally, we introduce a Similarity Matrix Smooth module into the structure of CLIP to balance the class distribution. Finally, we perform extensive comparisons with several state-of-the-art methods on the GDRBench benchmark, demonstrating our CLIP-DR's robustness and superior performance. The implementation code is available \footnote{\url{https://github.com/Qinkaiyu/CLIP-DR}

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arXiv2023

SenseAI: Real-Time Inpainting for Electron Microscopy

Despite their proven success and broad applicability to Electron Microscopy (EM) data, joint dictionary-learning and sparse-coding based inpainting algorithms have so far remained impractical for real-time usage with an Electron Microscope. For many EM applications, the reconstruction time for a single frame is orders of magnitude longer than the data acquisition time, making it impossible to perform exclusively subsampled acquisition. This limitation has led to the development of SenseAI, a C++/CUDA library capable of extremely efficient dictionary-based inpainting. SenseAI provides N-dimensional dictionary learning, live reconstructions, dictionary transfer and visualization, as well as real-time plotting of statistics, parameters, and image quality metrics.

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arXiv2023

Polar-Net: A Clinical-Friendly Model for Alzheimer's Disease Detection in OCTA Images

Optical Coherence Tomography Angiography (OCTA) is a promising tool for detecting Alzheimer's disease (AD) by imaging the retinal microvasculature. Ophthalmologists commonly use region-based analysis, such as the ETDRS grid, to study OCTA image biomarkers and understand the correlation with AD. However, existing studies have used general deep computer vision methods, which present challenges in providing interpretable results and leveraging clinical prior knowledge. To address these challenges, we propose a novel deep-learning framework called Polar-Net. Our approach involves mapping OCTA images from Cartesian coordinates to polar coordinates, which allows for the use of approximate sector convolution and enables the implementation of the ETDRS grid-based regional analysis method commonly used in clinical practice. Furthermore, Polar-Net incorporates clinical prior information of each sector region into the training process, which further enhances its performance. Additionally, our framework adapts to acquire the importance of the corresponding retinal region, which helps researchers and clinicians understand the model's decision-making process in detecting AD and assess its conformity to clinical observations. Through evaluations on private and public datasets, we have demonstrated that Polar-Net outperforms existing state-of-the-art methods and provides more valuable pathological evidence for the association between retinal vascular changes and AD. In addition, we also show that the two innovative modules introduced in our framework have a significant impact on improving overall performance.

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arXiv2023

Automatically Segment the Left Atrium and Scars from LGE-MRIs Using a Boundary-focused nnU-Net

Atrial fibrillation (AF) is the most common cardiac arrhythmia. Accurate segmentation of the left atrial (LA) and LA scars can provide valuable information to predict treatment outcomes in AF. In this paper, we proposed to automatically segment LA cavity and quantify LA scars with late gadolinium enhancement Magnetic Resonance Imagings (LGE-MRIs). We adopted nnU-Net as the baseline model and exploited the importance of LA boundary characteristics with the TopK loss as the loss function. Specifically, a focus on LA boundary pixels is achieved during training, which provides a more accurate boundary prediction. On the other hand, a distance map transformation of the predicted LA boundary is regarded as an additional input for the LA scar prediction, which provides marginal constraint on scar locations. We further designed a novel uncertainty-aware module (UAM) to produce better results for predictions with high uncertainty. Experiments on the LAScarQS 2022 dataset demonstrated our model's superior performance on the LA cavity and LA scar segmentation. Specifically, we achieved 88.98\% and 64.08\% Dice coefficient for LA cavity and scar segmentation, respectively. We will make our implementation code public available at https://github.com/level6626/Boundary-focused-nnU-Net.

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arXiv2023

Weakly supervised segmentation with point annotations for histopathology images via contrast-based variational model

Image segmentation is a fundamental task in the field of imaging and vision. Supervised deep learning for segmentation has achieved unparalleled success when sufficient training data with annotated labels are available. However, annotation is known to be expensive to obtain, especially for histopathology images where the target regions are usually with high morphology variations and irregular shapes. Thus, weakly supervised learning with sparse annotations of points is promising to reduce the annotation workload. In this work, we propose a contrast-based variational model to generate segmentation results, which serve as reliable complementary supervision to train a deep segmentation model for histopathology images. The proposed method considers the common characteristics of target regions in histopathology images and can be trained in an end-to-end manner. It can generate more regionally consistent and smoother boundary segmentation, and is more robust to unlabeled `novel' regions. Experiments on two different histology datasets demonstrate its effectiveness and efficiency in comparison to previous models.

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arXiv2022

DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification

Multiple instance learning (MIL) has been increasingly used in the classification of histopathology whole slide images (WSIs). However, MIL approaches for this specific classification problem still face unique challenges, particularly those related to small sample cohorts. In these, there are limited number of WSI slides (bags), while the resolution of a single WSI is huge, which leads to a large number of patches (instances) cropped from this slide. To address this issue, we propose to virtually enlarge the number of bags by introducing the concept of pseudo-bags, on which a double-tier MIL framework is built to effectively use the intrinsic features. Besides, we also contribute to deriving the instance probability under the framework of attention-based MIL, and utilize the derivation to help construct and analyze the proposed framework. The proposed method outperforms other latest methods on the CAMELYON-16 by substantially large margins, and is also better in performance on the TCGA lung cancer dataset. The proposed framework is ready to be extended for wider MIL applications. The code is available at: https://github.com/hrzhang1123/DTFD-MIL

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arXiv2022

3D Dense Face Alignment with Fused Features by Aggregating CNNs and GCNs

In this paper, we propose a novel multi-level aggregation network to regress the coordinates of the vertices of a 3D face from a single 2D image in an end-to-end manner. This is achieved by seamlessly combining standard convolutional neural networks (CNNs) with Graph Convolution Networks (GCNs). By iteratively and hierarchically fusing the features across different layers and stages of the CNNs and GCNs, our approach can provide a dense face alignment and 3D face reconstruction simultaneously for the benefit of direct feature learning of 3D face mesh. Experiments on several challenging datasets demonstrate that our method outperforms state-of-the-art approaches on both 2D and 3D face alignment tasks.

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arXiv2022

Counting with Adaptive Auxiliary Learning

This paper proposes an adaptive auxiliary task learning based approach for object counting problems. Unlike existing auxiliary task learning based methods, we develop an attention-enhanced adaptively shared backbone network to enable both task-shared and task-tailored features learning in an end-to-end manner. The network seamlessly combines standard Convolution Neural Network (CNN) and Graph Convolution Network (GCN) for feature extraction and feature reasoning among different domains of tasks. Our approach gains enriched contextual information by iteratively and hierarchically fusing the features across different task branches of the adaptive CNN backbone. The whole framework pays special attention to the objects' spatial locations and varied density levels, informed by object (or crowd) segmentation and density level segmentation auxiliary tasks. In particular, thanks to the proposed dilated contrastive density loss function, our network benefits from individual and regional context supervision in terms of pixel-independent and pixel-dependent feature learning mechanisms, along with strengthened robustness. Experiments on seven challenging multi-domain datasets demonstrate that our method achieves superior performance to the state-of-the-art auxiliary task learning based counting methods. Our code is made publicly available at: https://github.com/smallmax00/Counting_With_Adaptive_Auxiliary

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arXiv2021

BI-GCN: Boundary-Aware Input-Dependent Graph Convolution Network for Biomedical Image Segmentation

Segmentation is an essential operation of image processing. The convolution operation suffers from a limited receptive field, while global modelling is fundamental to segmentation tasks. In this paper, we apply graph convolution into the segmentation task and propose an improved \textit{Laplacian}. Different from existing methods, our \textit{Laplacian} is data-dependent, and we introduce two attention diagonal matrices to learn a better vertex relationship. In addition, it takes advantage of both region and boundary information when performing graph-based information propagation. Specifically, we model and reason about the boundary-aware region-wise correlations of different classes through learning graph representations, which is capable of manipulating long range semantic reasoning across various regions with the spatial enhancement along the object's boundary. Our model is well-suited to obtain global semantic region information while also accommodates local spatial boundary characteristics simultaneously. Experiments on two types of challenging datasets demonstrate that our method outperforms the state-of-the-art approaches on the segmentation of polyps in colonoscopy images and of the optic disc and optic cup in colour fundus images.

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