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.

Wei-Cheng Chang, Jyun-Yu Jiang, Jiong Zhang et al.

Embedding-based Retrieval Models (ERMs) have emerged as a promising framework for large-scale text retrieval problems due to powerful large language models. Nevertheless, fine-tuning ERMs to reach state-of-the-art results can be expensive due to the extreme scale of data as well as the complexity of multi-stages pipelines (e.g., pre-training, fine-tuning, distillation). In this work, we propose the PEFA framework, namely ParamEter-Free Adapters, for fast tuning of ERMs without any backward pass in the optimization. At index building stage, PEFA equips the ERM with a non-parametric k-nearest neighbor (kNN) component. At inference stage, PEFA performs a convex combination of two scoring functions, one from the ERM and the other from the kNN. Based on the neighborhood definition, PEFA framework induces two realizations, namely PEFA-XL (i.e., extra large) using double ANN indices and PEFA-XS (i.e., extra small) using a single ANN index. Empirically, PEFA achieves significant improvement on two retrieval applications. For document retrieval, regarding Recall@100 metric, PEFA improves not only pre-trained ERMs on Trivia-QA by an average of 13.2%, but also fine-tuned ERMs on NQ-320K by an average of 5.5%, respectively. For product search, PEFA improves the Recall@100 of the fine-tuned ERMs by an average of 5.3% and 14.5%, for PEFA-XS and PEFA-XL, respectively. Our code is available at https://github.com/amzn/pecos/tree/mainline/examples/pefa-wsdm24.

Shuo Jiang, Zhuwen Chen, Liaoman Xu et al.

Survival analysis plays a vital role in making clinical decisions. However, the models currently in use are often difficult to interpret, which reduces their usefulness in clinical settings. Prototype learning presents a potential solution, yet traditional methods focus on local similarities and static matching, neglecting the broader tumor context and lacking strong semantic alignment with genomic data. To overcome these issues, we introduce an innovative prototype-based multimodal framework, FeatProto, aimed at enhancing cancer survival prediction by addressing significant limitations in current prototype learning methodologies within pathology. Our framework establishes a unified feature prototype space that integrates both global and local features of whole slide images (WSI) with genomic profiles. This integration facilitates traceable and interpretable decision-making processes. Our approach includes three main innovations: (1) A robust phenotype representation that merges critical patches with global context, harmonized with genomic data to minimize local bias. (2) An Exponential Prototype Update Strategy (EMA ProtoUp) that sustains stable cross-modal associations and employs a wandering mechanism to adapt prototypes flexibly to tumor heterogeneity. (3) A hierarchical prototype matching scheme designed to capture global centrality, local typicality, and cohort-level trends, thereby refining prototype inference. Comprehensive evaluations on four publicly available cancer datasets indicate that our method surpasses current leading unimodal and multimodal survival prediction techniques in both accuracy and interoperability, providing a new perspective on prototype learning for critical medical applications. Our source code is available at https://github.com/JSLiam94/FeatProto.

Hao Yang, Xinlong Liang, Zhang Li et al.

Deep learning offers transformative potential in medical imaging, yet its clinical adoption is frequently hampered by challenges such as data scarcity, distribution shifts, and the need for robust task generalization. Prompt-based methodologies have emerged as a pivotal strategy to guide deep learning models, providing flexible, domain-specific adaptations that significantly enhance model performance and adaptability without extensive retraining. This systematic review critically examines the burgeoning landscape of prompt engineering in medical imaging. We dissect diverse prompt modalities, including textual instructions, visual prompts, and learnable embeddings, and analyze their integration for core tasks such as image generation, segmentation, and classification. Our synthesis reveals how these mechanisms improve task-specific outcomes by enhancing accuracy, robustness, and data efficiency and reducing reliance on manual feature engineering while fostering greater model interpretability by making the model's guidance explicit. Despite substantial advancements, we identify persistent challenges, particularly in prompt design optimization, data heterogeneity, and ensuring scalability for clinical deployment. Finally, this review outlines promising future trajectories, including advanced multimodal prompting and robust clinical integration, underscoring the critical role of prompt-driven AI in accelerating the revolution of diagnostics and personalized treatment planning in medicine.

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.

Yau-Shian Wang, Wei-Cheng Chang, Jyun-Yu Jiang et al.

Extreme multi-label classification (XMC) seeks to find relevant labels from an extremely large label collection for a given text input. To tackle such a vast label space, current state-of-the-art methods fall into two categories. The one-versus-all (OVA) method uses learnable label embeddings for each label, excelling at memorization (i.e., capturing detailed training signals for accurate head label prediction). In contrast, the dual-encoder (DE) model maps input and label text into a shared embedding space for better generalization (i.e., the capability of predicting tail labels with limited training data), but may fall short at memorization. To achieve generalization and memorization, existing XMC methods often combine DE and OVA models, which involves complex training pipelines. Inspired by the success of retrieval-augmented language models, we propose the Retrieval-augmented Encoders for XMC (RAEXMC), a novel framework that equips a DE model with retrieval-augmented capability for efficient memorization without additional trainable parameter. During training, RAEXMC is optimized by the contrastive loss over a knowledge memory that consists of both input instances and labels. During inference, given a test input, RAEXMC retrieves the top-$K$ keys from the knowledge memory, and aggregates the corresponding values as the prediction scores. We showcase the effectiveness and efficiency of RAEXMC on four public LF-XMC benchmarks. RAEXMC not only advances the state-of-the-art (SOTA) DE method DEXML, but also achieves more than 10x speedup on the largest LF-AmazonTitles-1.3M dataset under the same 8 A100 GPUs training environments.

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.

Che-Ping Tsai, Jiong Zhang, Eli Chien et al.

We introduce a novel class of sample-based explanations we term high-dimensional representers, that can be used to explain the predictions of a regularized high-dimensional model in terms of importance weights for each of the training samples. Our workhorse is a novel representer theorem for general regularized high-dimensional models, which decomposes the model prediction in terms of contributions from each of the training samples: with positive (negative) values corresponding to positive (negative) impact training samples to the model's prediction. We derive consequences for the canonical instances of $\ell_1$ regularized sparse models, and nuclear norm regularized low-rank models. As a case study, we further investigate the application of low-rank models in the context of collaborative filtering, where we instantiate high-dimensional representers for specific popular classes of models. Finally, we study the empirical performance of our proposed methods on three real-world binary classification datasets and two recommender system datasets. We also showcase the utility of high-dimensional representers in explaining model recommendations.

Eli Chien, Jiong Zhang, Cho-Jui Hsieh et al.

The eXtreme Multi-label Classification~(XMC) problem seeks to find relevant labels from an exceptionally large label space. Most of the existing XMC learners focus on the extraction of semantic features from input query text. However, conventional XMC studies usually neglect the side information of instances and labels, which can be of use in many real-world applications such as recommendation systems and e-commerce product search. We propose Predicted Instance Neighborhood Aggregation (PINA), a data enhancement method for the general XMC problem that leverages beneficial side information. Unlike most existing XMC frameworks that treat labels and input instances as featureless indicators and independent entries, PINA extracts information from the label metadata and the correlations among training instances. Extensive experimental results demonstrate the consistent gain of PINA on various XMC tasks compared to the state-of-the-art methods: PINA offers a gain in accuracy compared to standard XR-Transformers on five public benchmark datasets. Moreover, PINA achieves a $\sim 5\%$ gain in accuracy on the largest dataset LF-AmazonTitles-1.3M. Our implementation is publicly available.

Eli Chien, Wei-Cheng Chang, Cho-Jui Hsieh et al.

Learning on graphs has attracted significant attention in the learning community due to numerous real-world applications. In particular, graph neural networks (GNNs), which take numerical node features and graph structure as inputs, have been shown to achieve state-of-the-art performance on various graph-related learning tasks. Recent works exploring the correlation between numerical node features and graph structure via self-supervised learning have paved the way for further performance improvements of GNNs. However, methods used for extracting numerical node features from raw data are still graph-agnostic within standard GNN pipelines. This practice is sub-optimal as it prevents one from fully utilizing potential correlations between graph topology and node attributes. To mitigate this issue, we propose a new self-supervised learning framework, Graph Information Aided Node feature exTraction (GIANT). GIANT makes use of the eXtreme Multi-label Classification (XMC) formalism, which is crucial for fine-tuning the language model based on graph information, and scales to large datasets. We also provide a theoretical analysis that justifies the use of XMC over link prediction and motivates integrating XR-Transformers, a powerful method for solving XMC problems, into the GIANT framework. We demonstrate the superior performance of GIANT over the standard GNN pipeline on Open Graph Benchmark datasets: For example, we improve the accuracy of the top-ranked method GAMLP from $68.25\%$ to $69.67\%$, SGC from $63.29\%$ to $66.10\%$ and MLP from $47.24\%$ to $61.10\%$ on the ogbn-papers100M dataset by leveraging GIANT.

Jiong Zhang, Wei-cheng Chang, Hsiang-fu Yu et al.

Extreme multi-label text classification (XMC) seeks to find relevant labels from an extreme large label collection for a given text input. Many real-world applications can be formulated as XMC problems, such as recommendation systems, document tagging and semantic search. Recently, transformer based XMC methods, such as X-Transformer and LightXML, have shown significant improvement over other XMC methods. Despite leveraging pre-trained transformer models for text representation, the fine-tuning procedure of transformer models on large label space still has lengthy computational time even with powerful GPUs. In this paper, we propose a novel recursive approach, XR-Transformer to accelerate the procedure through recursively fine-tuning transformer models on a series of multi-resolution objectives related to the original XMC objective function. Empirical results show that XR-Transformer takes significantly less training time compared to other transformer-based XMC models while yielding better state-of-the-art results. In particular, on the public Amazon-3M dataset with 3 million labels, XR-Transformer is not only 20x faster than X-Transformer but also improves the Precision@1 from 51% to 54%.

Wei-Cheng Chang, Daniel Jiang, Hsiang-Fu Yu et al.

We consider the problem of semantic matching in product search: given a customer query, retrieve all semantically related products from a huge catalog of size 100 million, or more. Because of large catalog spaces and real-time latency constraints, semantic matching algorithms not only desire high recall but also need to have low latency. Conventional lexical matching approaches (e.g., Okapi-BM25) exploit inverted indices to achieve fast inference time, but fail to capture behavioral signals between queries and products. In contrast, embedding-based models learn semantic representations from customer behavior data, but the performance is often limited by shallow neural encoders due to latency constraints. Semantic product search can be viewed as an eXtreme Multi-label Classification (XMC) problem, where customer queries are input instances and products are output labels. In this paper, we aim to improve semantic product search by using tree-based XMC models where inference time complexity is logarithmic in the number of products. We consider hierarchical linear models with n-gram features for fast real-time inference. Quantitatively, our method maintains a low latency of 1.25 milliseconds per query and achieves a 65% improvement of Recall@100 (60.9% v.s. 36.8%) over a competing embedding-based DSSM model. Our model is robust to weight pruning with varying thresholds, which can flexibly meet different system requirements for online deployments. Qualitatively, our method can retrieve products that are complementary to existing product search system and add diversity to the match set.

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

Hsiang-Fu Yu, Kai Zhong, Jiong Zhang et al.

Many large-scale applications amount to finding relevant results from an enormous output space of potential candidates. For example, finding the best matching product from a large catalog or suggesting related search phrases on a search engine. The size of the output space for these problems can range from millions to billions, and can even be infinite in some applications. Moreover, training data is often limited for the long-tail items in the output space. Fortunately, items in the output space are often correlated thereby presenting an opportunity to alleviate the data sparsity issue. In this paper, we propose the Prediction for Enormous and Correlated Output Spaces (PECOS) framework, a versatile and modular machine learning framework for solving prediction problems for very large output spaces, and apply it to the eXtreme Multilabel Ranking (XMR) problem: given an input instance, find and rank the most relevant items from an enormous but fixed and finite output space. We propose a three phase framework for PECOS: (i) in the first phase, PECOS organizes the output space using a semantic indexing scheme, (ii) in the second phase, PECOS uses the indexing to narrow down the output space by orders of magnitude using a machine learned matching scheme, and (iii) in the third phase, PECOS ranks the matched items using a final ranking scheme. The versatility and modularity of PECOS allows for easy plug-and-play of various choices for the indexing, matching, and ranking phases. We also develop very fast inference procedures which allow us to perform XMR predictions in real time; for example, inference takes less than 1 millisecond per input on the dataset with 2.8 million labels. The PECOS software is available at https://libpecos.org.

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.

Da Chen, Jiong Zhang, Laurent D. Cohen

The minimal path method has proven to be particularly useful and efficient in tubular structure segmentation applications. In this paper, we propose a new minimal path model associated with a dynamic Riemannian metric embedded with an appearance feature coherence penalty and an adaptive anisotropy enhancement term. The features that characterize the appearance and anisotropy properties of a tubular structure are extracted through the associated orientation score. The proposed dynamic Riemannian metric is updated in the course of the geodesic distance computation carried out by the efficient single-pass fast marching method. Compared to state-of-the-art minimal path models, the proposed minimal path model is able to extract the desired tubular structures from a complicated vessel tree structure. In addition, we propose an efficient prior path-based method to search for vessel radius value at each centerline position of the target. Finally, we perform the numerical experiments on both synthetic and real images. The quantitive validation is carried out on retinal vessel images. The results indicate that the proposed model indeed achieves a promising performance.

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.

Samaneh Abbasi-Sureshjani, Jiong Zhang, Remco Duits et al.

Natural images contain often curvilinear structures, which might be disconnected, or partly occluded. Recovering the missing connection of disconnected structures is an open issue and needs appropriate geometric reasoning. We propose to find line co-occurrence statistics from the centerlines of blood vessels in retinal images and show its remarkable similarity to a well-known probabilistic model for the connectivity pattern in the primary visual cortex. Furthermore, the probabilistic model is trained from the data via statistics and used for automated grouping of interrupted vessels in a spectral clustering based approach. Several challenging image patches are investigated around junction points, where successful results indicate the perfect match of the trained model to the profiles of blood vessels in retinal images. Also, comparisons among several statistical models obtained from different datasets reveals their high similarity i.e., they are independent of the dataset. On top of that, the best approximation of the statistical model with the symmetrized extension of the probabilistic model on the projective line bundle is found with a least square error smaller than 2%. Apparently, the direction process on the projective line bundle is a good continuation model for vessels in retinal images.

Jiong Zhang, Parameswaran Raman, Shihao Ji et al.

Stochastic variational inference (SVI), the state-of-the-art algorithm for scaling variational inference to large-datasets, is inherently serial. Moreover, it requires the parameters to fit in the memory of a single processor; this is problematic when the number of parameters is in billions. In this paper, we propose extreme stochastic variational inference (ESVI), an asynchronous and lock-free algorithm to perform variational inference for mixture models on massive real world datasets. ESVI overcomes the limitations of SVI by requiring that each processor only access a subset of the data and a subset of the parameters, thus providing data and model parallelism simultaneously. We demonstrate the effectiveness of ESVI by running Latent Dirichlet Allocation (LDA) on UMBC-3B, a dataset that has a vocabulary of 3 million and a token size of 3 billion. In our experiments, we found that ESVI not only outperforms VI and SVI in wallclock-time, but also achieves a better quality solution. In addition, we propose a strategy to speed up computation and save memory when fitting large number of topics.

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.