Jiong Zhang

Jinkui Hao, Ting Shen, Xueli Zhu et al.

Automated detection of retinal structures, such as retinal vessels (RV), the foveal avascular zone (FAZ), and retinal vascular junctions (RVJ), are of great importance for understanding diseases of the eye and clinical decision-making. In this paper, we propose a novel Voting-based Adaptive Feature Fusion multi-task network (VAFF-Net) for joint segmentation, detection, and classification of RV, FAZ, and RVJ in optical coherence tomography angiography (OCTA). A task-specific voting gate module is proposed to adaptively extract and fuse different features for specific tasks at two levels: features at different spatial positions from a single encoder, and features from multiple encoders. In particular, since the complexity of the microvasculature in OCTA images makes simultaneous precise localization and classification of retinal vascular junctions into bifurcation/crossing a challenging task, we specifically design a task head by combining the heatmap regression and grid classification. We take advantage of three different \textit{en face} angiograms from various retinal layers, rather than following existing methods that use only a single \textit{en face}. To facilitate further research, part of these datasets with the source code and evaluation benchmark have been released for public access:https://github.com/iMED-Lab/VAFF-Net.

Qinkai Yu, Jianyang Xie, Anh Nguyen et al.

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}

Jiong Zhang, Remco Duits, Gonzalo Sanguinetti et al.

Left-invariant PDE-evolutions on the roto-translation group $SE(2)$ (and their resolvent equations) have been widely studied in the fields of cortical modeling and image analysis. They include hypo-elliptic diffusion (for contour enhancement) proposed by Citti & Sarti, and Petitot, and they include the direction process (for contour completion) proposed by Mumford. This paper presents a thorough study and comparison of the many numerical approaches, which, remarkably, is missing in the literature. Existing numerical approaches can be classified into 3 categories: Finite difference methods, Fourier based methods (equivalent to $SE(2)$-Fourier methods), and stochastic methods (Monte Carlo simulations). There are also 3 types of exact solutions to the PDE-evolutions that were derived explicitly (in the spatial Fourier domain) in previous works by Duits and van Almsick in 2005. Here we provide an overview of these 3 types of exact solutions and explain how they relate to each of the 3 numerical approaches. We compute relative errors of all numerical approaches to the exact solutions, and the Fourier based methods show us the best performance with smallest relative errors. We also provide an improvement of Mathematica algorithms for evaluating Mathieu-functions, crucial in implementations of the exact solutions. Furthermore, we include an asymptotical analysis of the singularities within the kernels and we propose a probabilistic extension of underlying stochastic processes that overcomes the singular behavior in the origin of time-integrated kernels. Finally, we show retinal imaging applications of combining left-invariant PDE-evolutions with invertible orientation scores.

Huaying Hao, Cong Xu, Dan Zhang et al.

Retinal Optical Coherence Tomography Angiography (OCTA) with high-resolution is important for the quantification and analysis of retinal vasculature. However, the resolution of OCTA images is inversely proportional to the field of view at the same sampling frequency, which is not conducive to clinicians for analyzing larger vascular areas. In this paper, we propose a novel Sparse-based domain Adaptation Super-Resolution network (SASR) for the reconstruction of realistic 6x6 mm2/low-resolution (LR) OCTA images to high-resolution (HR) representations. To be more specific, we first perform a simple degradation of the 3x3 mm2/high-resolution (HR) image to obtain the synthetic LR image. An efficient registration method is then employed to register the synthetic LR with its corresponding 3x3 mm2 image region within the 6x6 mm2 image to obtain the cropped realistic LR image. We then propose a multi-level super-resolution model for the fully-supervised reconstruction of the synthetic data, guiding the reconstruction of the realistic LR images through a generative-adversarial strategy that allows the synthetic and realistic LR images to be unified in the feature domain. Finally, a novel sparse edge-aware loss is designed to dynamically optimize the vessel edge structure. Extensive experiments on two OCTA sets have shown that our method performs better than state-of-the-art super-resolution reconstruction methods. In addition, we have investigated the performance of the reconstruction results on retina structure segmentations, which further validate the effectiveness of our approach.

Shouyue Liu, Jinkui Hao, Yanwu Xu et al.

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.

Tao Chen, Dan Zhang, Da Chen et al.

Choroidal neovascularization (CNV), a primary characteristic of wet age-related macular degeneration (wet AMD), represents a leading cause of blindness worldwide. In clinical practice, optical coherence tomography angiography (OCTA) is commonly used for studying CNV-related pathological changes, due to its micron-level resolution and non-invasive nature. Thus, accurate segmentation of CNV regions and vessels in OCTA images is crucial for clinical assessment of wet AMD. However, challenges existed due to irregular CNV shapes and imaging limitations like projection artifacts, noises and boundary blurring. Moreover, the lack of publicly available datasets constraints the CNV analysis. To address these challenges, this paper constructs the first publicly accessible CNV dataset (CNVSeg), and proposes a novel multilateral graph convolutional interaction-enhanced CNV segmentation network (MTG-Net). This network integrates both region and vessel morphological information, exploring semantic and geometric duality constraints within the graph domain. Specifically, MTG-Net consists of a multi-task framework and two graph-based cross-task modules: Multilateral Interaction Graph Reasoning (MIGR) and Multilateral Reinforcement Graph Reasoning (MRGR). The multi-task framework encodes rich geometric features of lesion shapes and surfaces, decoupling the image into three task-specific feature maps. MIGR and MRGR iteratively reason about higher-order relationships across tasks through a graph mechanism, enabling complementary optimization for task-specific objectives. Additionally, an uncertainty-weighted loss is proposed to mitigate the impact of artifacts and noise on segmentation accuracy. Experimental results demonstrate that MTG-Net outperforms existing methods, achieving a Dice socre of 87.21\% for region segmentation and 88.12\% for vessel segmentation.

Zhuoshuo Li, Jiong Zhang, Youbing Zeng et al.

Current brain surface-based prediction models often overlook the variability of regional attributes at the cortical feature level. While graph neural networks (GNNs) excel at capturing regional differences, they encounter challenges when dealing with complex, high-density graph structures. In this work, we consider the cortical surface mesh as a sparse graph and propose an interpretable prediction model-Surface Graph Neural Network (SurfGNN). SurfGNN employs topology-sampling learning (TSL) and region-specific learning (RSL) structures to manage individual cortical features at both lower and higher scales of the surface mesh, effectively tackling the challenges posed by the overly abundant mesh nodes and addressing the issue of heterogeneity in cortical regions. Building on this, a novel score-weighted fusion (SWF) method is implemented to merge nodal representations associated with each cortical feature for prediction. We apply our model to a neonatal brain age prediction task using a dataset of harmonized MR images from 481 subjects (503 scans). SurfGNN outperforms all existing state-of-the-art methods, demonstrating an improvement of at least 9.0% and achieving a mean absolute error (MAE) of 0.827+0.056 in postmenstrual weeks. Furthermore, it generates feature-level activation maps, indicating its capability to identify robust regional variations in different morphometric contributions for prediction.

Lin Zhang, Chenggang Lu, Xin-yang Shi et al.

Atherosclerosis is a chronic, progressive disease that primarily affects the arterial walls. It is one of the major causes of cardiovascular disease. Magnetic Resonance (MR) black-blood vessel wall imaging (BB-VWI) offers crucial insights into vascular disease diagnosis by clearly visualizing vascular structures. However, the complex anatomy of the neck poses challenges in distinguishing the carotid artery (CA) from surrounding structures, especially with changes like atherosclerosis. In order to address these issues, we propose GAPNet, which is a consisting of a novel geometric prior deduced from.

Jiong Zhang, Qihang Xie, Lei Mou et al.

Cerebrovascular diseases (CVDs) remain a leading cause of global disability and mortality. Digital Subtraction Angiography (DSA) sequences, recognized as the gold standard for diagnosing CVDs, can clearly visualize the dynamic flow and reveal pathological conditions within the cerebrovasculature. Therefore, precise segmentation of cerebral arteries (CAs) and classification between their main trunks and branches are crucial for physicians to accurately quantify diseases. However, achieving accurate CA segmentation in DSA sequences remains a challenging task due to small vessels with low contrast, and ambiguity between vessels and residual skull structures. Moreover, the lack of publicly available datasets limits exploration in the field. In this paper, we introduce a DSA Sequence-based Cerebral Artery segmentation dataset (DSCA), the publicly accessible dataset designed specifically for pixel-level semantic segmentation of CAs. Additionally, we propose DSANet, a spatio-temporal network for CA segmentation in DSA sequences. Unlike existing DSA segmentation methods that focus only on a single frame, the proposed DSANet introduces a separate temporal encoding branch to capture dynamic vessel details across multiple frames. To enhance small vessel segmentation and improve vessel connectivity, we design a novel TemporalFormer module to capture global context and correlations among sequential frames. Furthermore, we develop a Spatio-Temporal Fusion (STF) module to effectively integrate spatial and temporal features from the encoder. Extensive experiments demonstrate that DSANet outperforms other state-of-the-art methods in CA segmentation, achieving a Dice of 0.9033.

Shuai Yu, Jianyang Xie, Jinkui Hao et al.

Optical Coherence Tomography Angiography (OCTA) has been increasingly used in the management of eye and systemic diseases in recent years. Manual or automatic analysis of blood vessel in 2D OCTA images (en face angiograms) is commonly used in clinical practice, however it may lose rich 3D spatial distribution information of blood vessels or capillaries that are useful for clinical decision-making. In this paper, we introduce a novel 3D vessel reconstruction framework based on the estimation of vessel depth maps from OCTA images. First, we design a network with structural constraints to predict the depth of blood vessels in OCTA images. In order to promote the accuracy of the predicted depth map at both the overall structure- and pixel- level, we combine MSE and SSIM loss as the training loss function. Finally, the 3D vessel reconstruction is achieved by utilizing the estimated depth map and 2D vessel segmentation results. Experimental results demonstrate that our method is effective in the depth prediction and 3D vessel reconstruction for OCTA images.% results may be used to guide subsequent vascular analysis

Yuhui Ma, Huaying Hao, Huazhu Fu et al.

Optical Coherence Tomography Angiography (OCT-A) is a non-invasive imaging technique, and has been increasingly used to image the retinal vasculature at capillary level resolution. However, automated segmentation of retinal vessels in OCT-A has been under-studied due to various challenges such as low capillary visibility and high vessel complexity, despite its significance in understanding many eye-related diseases. In addition, there is no publicly available OCT-A dataset with manually graded vessels for training and validation. To address these issues, for the first time in the field of retinal image analysis we construct a dedicated Retinal OCT-A SEgmentation dataset (ROSE), which consists of 229 OCT-A images with vessel annotations at either centerline-level or pixel level. This dataset has been released for public access to assist researchers in the community in undertaking research in related topics. Secondly, we propose a novel Split-based Coarse-to-Fine vessel segmentation network (SCF-Net), with the ability to detect thick and thin vessels separately. In the SCF-Net, a split-based coarse segmentation (SCS) module is first introduced to produce a preliminary confidence map of vessels, and a split-based refinement (SRN) module is then used to optimize the shape/contour of the retinal microvasculature. Thirdly, we perform a thorough evaluation of the state-of-the-art vessel segmentation models and our SCF-Net on the proposed ROSE dataset. The experimental results demonstrate that our SCF-Net yields better vessel segmentation performance in OCT-A than both traditional methods and other deep learning methods.

Jiong Zhang, Hsiang-fu Yu, Inderjit S. Dhillon

Deep neural networks have yielded superior performance in many applications; however, the gradient computation in a deep model with millions of instances lead to a lengthy training process even with modern GPU/TPU hardware acceleration. In this paper, we propose AutoAssist, a simple framework to accelerate training of a deep neural network. Typically, as the training procedure evolves, the amount of improvement in the current model by a stochastic gradient update on each instance varies dynamically. In AutoAssist, we utilize this fact and design a simple instance shrinking operation, which is used to filter out instances with relatively low marginal improvement to the current model; thus the computationally intensive gradient computations are performed on informative instances as much as possible. We prove that the proposed technique outperforms vanilla SGD with existing importance sampling approaches for linear SVM problems, and establish an O(1/k) convergence for strongly convex problems. In order to apply the proposed techniques to accelerate training of deep models, we propose to jointly train a very lightweight Assistant network in addition to the original deep network referred to as Boss. The Assistant network is designed to gauge the importance of a given instance with respect to the current Boss such that a shrinking operation can be applied in the batch generator. With careful design, we train the Boss and Assistant in a nonblocking and asynchronous fashion such that overhead is minimal. We demonstrate that AutoAssist reduces the number of epochs by 40% for training a ResNet to reach the same test accuracy on an image classification data set and saves 30% training time needed for a transformer model to yield the same BLEU scores on a translation dataset.

Jiong Zhang, Qi Lei, Inderjit S. Dhillon

Vanishing and exploding gradients are two of the main obstacles in training deep neural networks, especially in capturing long range dependencies in recurrent neural networks~(RNNs). In this paper, we present an efficient parametrization of the transition matrix of an RNN that allows us to stabilize the gradients that arise in its training. Specifically, we parameterize the transition matrix by its singular value decomposition(SVD), which allows us to explicitly track and control its singular values. We attain efficiency by using tools that are common in numerical linear algebra, namely Householder reflectors for representing the orthogonal matrices that arise in the SVD. By explicitly controlling the singular values, our proposed Spectral-RNN method allows us to easily solve the exploding gradient problem and we observe that it empirically solves the vanishing gradient issue to a large extent. We note that the SVD parameterization can be used for any rectangular weight matrix, hence it can be easily extended to any deep neural network, such as a multi-layer perceptron. Theoretically, we demonstrate that our parameterization does not lose any expressive power, and show how it controls generalization of RNN for the classification task. %, and show how it potentially makes the optimization process easier. Our extensive experimental results also demonstrate that the proposed framework converges faster, and has good generalization, especially in capturing long range dependencies, as shown on the synthetic addition and copy tasks, as well as on MNIST and Penn Tree Bank data sets.

Jiong Zhang, Yibo Lin, Zhao Song et al.

It is a known fact that training recurrent neural networks for tasks that have long term dependencies is challenging. One of the main reasons is the vanishing or exploding gradient problem, which prevents gradient information from propagating to early layers. In this paper we propose a simple recurrent architecture, the Fourier Recurrent Unit (FRU), that stabilizes the gradients that arise in its training while giving us stronger expressive power. Specifically, FRU summarizes the hidden states $h^{(t)}$ along the temporal dimension with Fourier basis functions. This allows gradients to easily reach any layer due to FRU's residual learning structure and the global support of trigonometric functions. We show that FRU has gradient lower and upper bounds independent of temporal dimension. We also show the strong expressivity of sparse Fourier basis, from which FRU obtains its strong expressive power. Our experimental study also demonstrates that with fewer parameters the proposed architecture outperforms other recurrent architectures on many tasks.

Behdad Dashtbozorg, Jiong Zhang, Bart M. ter Haar Romeny

Retinal microaneurysms are the earliest clinical sign of diabetic retinopathy disease. Detection of microaneurysms is crucial for the early diagnosis of diabetic retinopathy and prevention of blindness. In this paper, a novel and reliable method for automatic detection of microaneurysms in retinal images is proposed. In the first stage of the proposed method, several preliminary microaneurysm candidates are extracted using a gradient weighting technique and an iterative thresholding approach. In the next stage, in addition to intensity and shape descriptors, a new set of features based on local convergence index filters is extracted for each candidate. Finally, the collective set of features is fed to a hybrid sampling/boosting classifier to discriminate the MAs from non-MAs candidates. The method is evaluated on images with different resolutions and modalities (RGB and SLO) using five publicly available datasets including the Retinopathy Online Challenge's dataset. The proposed method achieves an average sensitivity score of 0.471 on the ROC dataset outperforming state-of-the-art approaches in an extensive comparison. The experimental results on the other four datasets demonstrate the effectiveness and robustness of the proposed microaneurysms detection method regardless of different image resolutions and modalities.

Jiong Zhang, Remco Duits, Gonzalo Sanguinetti et al.

Left-invariant PDE-evolutions on the roto-translation group $SE(2)$ (and their resolvent equations) have been widely studied in the fields of cortical modeling and image analysis. They include hypo-elliptic diffusion (for contour enhancement) proposed by Citti & Sarti, and Petitot, and they include the direction process (for contour completion) proposed by Mumford. This paper presents a thorough study and comparison of the many numerical approaches, which, remarkably, is missing in the literature. Existing numerical approaches can be classified into 3 categories: Finite difference methods, Fourier based methods (equivalent to $SE(2)$-Fourier methods), and stochastic methods (Monte Carlo simulations). There are also 3 types of exact solutions to the PDE-evolutions that were derived explicitly (in the spatial Fourier domain) in previous works by Duits and van Almsick in 2005. Here we provide an overview of these 3 types of exact solutions and explain how they relate to each of the 3 numerical approaches. We compute relative errors of all numerical approaches to the exact solutions, and the Fourier based methods show us the best performance with smallest relative errors. We also provide an improvement of Mathematica algorithms for evaluating Mathieu-functions, crucial in implementations of the exact solutions. Furthermore, we include an asymptotical analysis of the singularities within the kernels and we propose a probabilistic extension of underlying stochastic processes that overcomes the singular behavior in the origin of time-integrated kernels. Finally, we show retinal imaging applications of combining left-invariant PDE-evolutions with invertible orientation scores.