arXiv subjects

Yanwu Xu

Publications and source records attributed to Yanwu Xu.

At least 73 records · Page 4Linked to original sources

arXiv2021

Box-Adapt: Domain-Adaptive Medical Image Segmentation using Bounding BoxSupervision

Deep learning has achieved remarkable success in medicalimage segmentation, but it usually requires a large numberof images labeled with fine-grained segmentation masks, andthe annotation of these masks can be very expensive andtime-consuming. Therefore, recent methods try to use un-supervised domain adaptation (UDA) methods to borrow in-formation from labeled data from other datasets (source do-mains) to a new dataset (target domain). However, due tothe absence of labels in the target domain, the performance ofUDA methods is much worse than that of the fully supervisedmethod. In this paper, we propose a weakly supervised do-main adaptation setting, in which we can partially label newdatasets with bounding boxes, which are easier and cheaperto obtain than segmentation masks. Accordingly, we proposea new weakly-supervised domain adaptation method calledBox-Adapt, which fully explores the fine-grained segmenta-tion mask in the source domain and the weak bounding boxin the target domain. Our Box-Adapt is a two-stage methodthat first performs joint training on the source and target do-mains, and then conducts self-training with the pseudo-labelsof the target domain. We demonstrate the effectiveness of ourmethod in the liver segmentation task. Weakly supervised do-main adaptation

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arXiv2021

DSANet: Dynamic Segment Aggregation Network for Video-Level Representation Learning

Long-range and short-range temporal modeling are two complementary and crucial aspects of video recognition. Most of the state-of-the-arts focus on short-range spatio-temporal modeling and then average multiple snippet-level predictions to yield the final video-level prediction. Thus, their video-level prediction does not consider spatio-temporal features of how video evolves along the temporal dimension. In this paper, we introduce a novel Dynamic Segment Aggregation (DSA) module to capture relationship among snippets. To be more specific, we attempt to generate a dynamic kernel for a convolutional operation to aggregate long-range temporal information among adjacent snippets adaptively. The DSA module is an efficient plug-and-play module and can be combined with the off-the-shelf clip-based models (i.e., TSM, I3D) to perform powerful long-range modeling with minimal overhead. The final video architecture, coined as DSANet. We conduct extensive experiments on several video recognition benchmarks (i.e., Mini-Kinetics-200, Kinetics-400, Something-Something V1 and ActivityNet) to show its superiority. Our proposed DSA module is shown to benefit various video recognition models significantly. For example, equipped with DSA modules, the top-1 accuracy of I3D ResNet-50 is improved from 74.9% to 78.2% on Kinetics-400. Codes are available at https://github.com/whwu95/DSANet.

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arXiv2021

Weighing Features of Lung and Heart Regions for Thoracic Disease Classification

Chest X-rays are the most commonly available and affordable radiological examination for screening thoracic diseases. According to the domain knowledge of screening chest X-rays, the pathological information usually lay on the lung and heart regions. However, it is costly to acquire region-level annotation in practice, and model training mainly relies on image-level class labels in a weakly supervised manner, which is highly challenging for computer-aided chest X-ray screening. To address this issue, some methods have been proposed recently to identify local regions containing pathological information, which is vital for thoracic disease classification. Inspired by this, we propose a novel deep learning framework to explore discriminative information from lung and heart regions. We design a feature extractor equipped with a multi-scale attention module to learn global attention maps from global images. To exploit disease-specific cues effectively, we locate lung and heart regions containing pathological information by a well-trained pixel-wise segmentation model to generate binarization masks. By introducing element-wise logical AND operator on the learned global attention maps and the binarization masks, we obtain local attention maps in which pixels are $1$ for lung and heart region and $0$ for other regions. By zeroing features of non-lung and heart regions in attention maps, we can effectively exploit their disease-specific cues in lung and heart regions. Compared to existing methods fusing global and local features, we adopt feature weighting to avoid weakening visual cues unique to lung and heart regions. Evaluated by the benchmark split on the publicly available chest X-ray14 dataset, the comprehensive experiments show that our method achieves superior performance compared to the state-of-the-art methods.

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arXiv2021

A Multi-Branch Hybrid Transformer Networkfor Corneal Endothelial Cell Segmentation

Corneal endothelial cell segmentation plays a vital role inquantifying clinical indicators such as cell density, coefficient of variation,and hexagonality. However, the corneal endothelium's uneven reflectionand the subject's tremor and movement cause blurred cell edges in theimage, which is difficult to segment, and need more details and contextinformation to release this problem. Due to the limited receptive field oflocal convolution and continuous downsampling, the existing deep learn-ing segmentation methods cannot make full use of global context andmiss many details. This paper proposes a Multi-Branch hybrid Trans-former Network (MBT-Net) based on the transformer and body-edgebranch. Firstly, We use the convolutional block to focus on local tex-ture feature extraction and establish long-range dependencies over space,channel, and layer by the transformer and residual connection. Besides,We use the body-edge branch to promote local consistency and to provideedge position information. On the self-collected dataset TM-EM3000 andpublic Alisarine dataset, compared with other State-Of-The-Art (SOTA)methods, the proposed method achieves an improvement.

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arXiv2021

Robust Collaborative Learning of Patch-level and Image-level Annotations for Diabetic Retinopathy Grading from Fundus Image

Diabetic retinopathy (DR) grading from fundus images has attracted increasing interest in both academic and industrial communities. Most convolutional neural network (CNN) based algorithms treat DR grading as a classification task via image-level annotations. However, these algorithms have not fully explored the valuable information in the DR-related lesions. In this paper, we present a robust framework, which collaboratively utilizes patch-level and image-level annotations, for DR severity grading. By an end-to-end optimization, this framework can bi-directionally exchange the fine-grained lesion and image-level grade information. As a result, it exploits more discriminative features for DR grading. The proposed framework shows better performance than the recent state-of-the-art algorithms and three clinical ophthalmologists with over nine years of experience. By testing on datasets of different distributions (such as label and camera), we prove that our algorithm is robust when facing image quality and distribution variations that commonly exist in real-world practice. We inspect the proposed framework through extensive ablation studies to indicate the effectiveness and necessity of each motivation. The code and some valuable annotations are now publicly available.

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arXiv2020

Attention-based Saliency Hashing for Ophthalmic Image Retrieval

Deep hashing methods have been proved to be effective for the large-scale medical image search assisting reference-based diagnosis for clinicians. However, when the salient region plays a maximal discriminative role in ophthalmic image, existing deep hashing methods do not fully exploit the learning ability of the deep network to capture the features of salient regions pointedly. The different grades or classes of ophthalmic images may be share similar overall performance but have subtle differences that can be differentiated by mining salient regions. To address this issue, we propose a novel end-to-end network, named Attention-based Saliency Hashing (ASH), for learning compact hash-code to represent ophthalmic images. ASH embeds a spatial-attention module to focus more on the representation of salient regions and highlights their essential role in differentiating ophthalmic images. Benefiting from the spatial-attention module, the information of salient regions can be mapped into the hash-code for similarity calculation. In the training stage, we input the image pairs to share the weights of the network, and a pairwise loss is designed to maximize the discriminability of the hash-code. In the retrieval stage, ASH obtains the hash-code by inputting an image with an end-to-end manner, then the hash-code is used to similarity calculation to return the most similar images. Extensive experiments on two different modalities of ophthalmic image datasets demonstrate that the proposed ASH can further improve the retrieval performance compared to the state-of-the-art deep hashing methods due to the huge contributions of the spatial-attention module.

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arXiv2020

Probabilistic Latent Factor Model for Collaborative Filtering with Bayesian Inference

Latent Factor Model (LFM) is one of the most successful methods for Collaborative filtering (CF) in the recommendation system, in which both users and items are projected into a joint latent factor space. Base on matrix factorization applied usually in pattern recognition, LFM models user-item interactions as inner products of factor vectors of user and item in that space and can be efficiently solved by least square methods with optimal estimation. However, such optimal estimation methods are prone to overfitting due to the extreme sparsity of user-item interactions. In this paper, we propose a Bayesian treatment for LFM, named Bayesian Latent Factor Model (BLFM). Based on observed user-item interactions, we build a probabilistic factor model in which the regularization is introduced via placing prior constraint on latent factors, and the likelihood function is established over observations and parameters. Then we draw samples of latent factors from the posterior distribution with Variational Inference (VI) to predict expected value. We further make an extension to BLFM, called BLFMBias, incorporating user-dependent and item-dependent biases into the model for enhancing performance. Extensive experiments on the movie rating dataset show the effectiveness of our proposed models by compared with several strong baselines.

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arXiv2020

AGE Challenge: Angle Closure Glaucoma Evaluation in Anterior Segment Optical Coherence Tomography

Angle closure glaucoma (ACG) is a more aggressive disease than open-angle glaucoma, where the abnormal anatomical structures of the anterior chamber angle (ACA) may cause an elevated intraocular pressure and gradually lead to glaucomatous optic neuropathy and eventually to visual impairment and blindness. Anterior Segment Optical Coherence Tomography (AS-OCT) imaging provides a fast and contactless way to discriminate angle closure from open angle. Although many medical image analysis algorithms have been developed for glaucoma diagnosis, only a few studies have focused on AS-OCT imaging. In particular, there is no public AS-OCT dataset available for evaluating the existing methods in a uniform way, which limits progress in the development of automated techniques for angle closure detection and assessment. To address this, we organized the Angle closure Glaucoma Evaluation challenge (AGE), held in conjunction with MICCAI 2019. The AGE challenge consisted of two tasks: scleral spur localization and angle closure classification. For this challenge, we released a large dataset of 4800 annotated AS-OCT images from 199 patients, and also proposed an evaluation framework to benchmark and compare different models. During the AGE challenge, over 200 teams registered online, and more than 1100 results were submitted for online evaluation. Finally, eight teams participated in the onsite challenge. In this paper, we summarize these eight onsite challenge methods and analyze their corresponding results for the two tasks. We further discuss limitations and future directions. In the AGE challenge, the top-performing approach had an average Euclidean Distance of 10 pixels (10um) in scleral spur localization, while in the task of angle closure classification, all the algorithms achieved satisfactory performances, with two best obtaining an accuracy rate of 100%.

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arXiv2020

Residual-CycleGAN based Camera Adaptation for Robust Diabetic Retinopathy Screening

There are extensive researches focusing on automated diabetic reti-nopathy (DR) detection from fundus images. However, the accuracy drop is ob-served when applying these models in real-world DR screening, where the fun-dus camera brands are different from the ones used to capture the training im-ages. How can we train a classification model on labeled fundus images ac-quired from only one camera brand, yet still achieves good performance on im-ages taken by other brands of cameras? In this paper, we quantitatively verify the impact of fundus camera brands related domain shift on the performance of DR classification models, from an experimental perspective. Further, we pro-pose camera-oriented residual-CycleGAN to mitigate the camera brand differ-ence by domain adaptation and achieve increased classification performance on target camera images. Extensive ablation experiments on both the EyePACS da-taset and a private dataset show that the camera brand difference can signifi-cantly impact the classification performance and prove that our proposed meth-od can effectively improve the model performance on the target domain. We have inferred and labeled the camera brand for each image in the EyePACS da-taset and will publicize the camera brand labels for further research on domain adaptation.

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arXiv2020

Retinal Image Segmentation with a Structure-Texture Demixing Network

Retinal image segmentation plays an important role in automatic disease diagnosis. This task is very challenging because the complex structure and texture information are mixed in a retinal image, and distinguishing the information is difficult. Existing methods handle texture and structure jointly, which may lead biased models toward recognizing textures and thus results in inferior segmentation performance. To address it, we propose a segmentation strategy that seeks to separate structure and texture components and significantly improve the performance. To this end, we design a structure-texture demixing network (STD-Net) that can process structures and textures differently and better. Extensive experiments on two retinal image segmentation tasks (i.e., blood vessel segmentation, optic disc and cup segmentation) demonstrate the effectiveness of the proposed method.

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arXiv2020

Reconstruction and Quantification of 3D Iris Surface for Angle-Closure Glaucoma Detection in Anterior Segment OCT

Precise characterization and analysis of iris shape from Anterior Segment OCT (AS-OCT) are of great importance in facilitating diagnosis of angle-closure-related diseases. Existing methods focus solely on analyzing structural properties identified from the 2D slice, while accurate characterization of morphological changes of iris shape in 3D AS-OCT may be able to reveal in addition the risk of disease progression. In this paper, we propose a novel framework for reconstruction and quantification of 3D iris surface from AS-OCT imagery. We consider it to be the first work to detect angle-closure glaucoma by means of 3D representation. An iris segmentation network with wavelet refinement block (WRB) is first proposed to generate the initial shape of the iris from single AS-OCT slice. The 3D iris surface is then reconstructed using a guided optimization method with Poisson-disk sampling. Finally, a set of surface-based features are extracted, which are used in detecting of angle-closure glaucoma. Experimental results demonstrate that our method is highly effective in iris segmentation and surface reconstruction. Moreover, we show that 3D-based representation achieves better performance in angle-closure glaucoma detection than does 2D-based feature.

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arXiv2020

Open-Narrow-Synechiae Anterior Chamber Angle Classification in AS-OCT Sequences

Anterior chamber angle (ACA) classification is a key step in the diagnosis of angle-closure glaucoma in Anterior Segment Optical Coherence Tomography (AS-OCT). Existing automated analysis methods focus on a binary classification system (i.e., open angle or angle-closure) in a 2D AS-OCT slice. However, clinical diagnosis requires a more discriminating ACA three-class system (i.e., open, narrow, or synechiae angles) for the benefit of clinicians who seek better to understand the progression of the spectrum of angle-closure glaucoma types. To address this, we propose a novel sequence multi-scale aggregation deep network (SMA-Net) for open-narrow-synechiae ACA classification based on an AS-OCT sequence. In our method, a Multi-Scale Discriminative Aggregation (MSDA) block is utilized to learn the multi-scale representations at slice level, while a ConvLSTM is introduced to study the temporal dynamics of these representations at sequence level. Finally, a multi-level loss function is used to combine the slice-based and sequence-based losses. The proposed method is evaluated across two AS-OCT datasets. The experimental results show that the proposed method outperforms existing state-of-the-art methods in applicability, effectiveness, and accuracy. We believe this work to be the first attempt to classify ACAs into open, narrow, or synechia types grading using AS-OCT sequences.

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arXiv2020

Closed-loop Matters: Dual Regression Networks for Single Image Super-Resolution

Deep neural networks have exhibited promising performance in image super-resolution (SR) by learning a nonlinear mapping function from low-resolution (LR) images to high-resolution (HR) images. However, there are two underlying limitations to existing SR methods. First, learning the mapping function from LR to HR images is typically an ill-posed problem, because there exist infinite HR images that can be downsampled to the same LR image. As a result, the space of the possible functions can be extremely large, which makes it hard to find a good solution. Second, the paired LR-HR data may be unavailable in real-world applications and the underlying degradation method is often unknown. For such a more general case, existing SR models often incur the adaptation problem and yield poor performance. To address the above issues, we propose a dual regression scheme by introducing an additional constraint on LR data to reduce the space of the possible functions. Specifically, besides the mapping from LR to HR images, we learn an additional dual regression mapping estimates the down-sampling kernel and reconstruct LR images, which forms a closed-loop to provide additional supervision. More critically, since the dual regression process does not depend on HR images, we can directly learn from LR images. In this sense, we can easily adapt SR models to real-world data, e.g., raw video frames from YouTube. Extensive experiments with paired training data and unpaired real-world data demonstrate our superiority over existing methods.

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arXiv2020

A Thorough Comparison Study on Adversarial Attacks and Defenses for Common Thorax Disease Classification in Chest X-rays

Recently, deep neural networks (DNNs) have made great progress on automated diagnosis with chest X-rays images. However, DNNs are vulnerable to adversarial examples, which may cause misdiagnoses to patients when applying the DNN based methods in disease detection. Recently, there is few comprehensive studies exploring the influence of attack and defense methods on disease detection, especially for the multi-label classification problem. In this paper, we aim to review various adversarial attack and defense methods on chest X-rays. First, the motivations and the mathematical representations of attack and defense methods are introduced in details. Second, we evaluate the influence of several state-of-the-art attack and defense methods for common thorax disease classification in chest X-rays. We found that the attack and defense methods have poor performance with excessive iterations and large perturbations. To address this, we propose a new defense method that is robust to different degrees of perturbations. This study could provide new insights into methodological development for the community.

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arXiv2020

Evaluation of Retinal Image Quality Assessment Networks in Different Color-spaces

Retinal image quality assessment (RIQA) is essential for controlling the quality of retinal imaging and guaranteeing the reliability of diagnoses by ophthalmologists or automated analysis systems. Existing RIQA methods focus on the RGB color-space and are developed based on small datasets with binary quality labels (i.e., `Accept' and `Reject'). In this paper, we first re-annotate an Eye-Quality (EyeQ) dataset with 28,792 retinal images from the EyePACS dataset, based on a three-level quality grading system (i.e., `Good', `Usable' and `Reject') for evaluating RIQA methods. Our RIQA dataset is characterized by its large-scale size, multi-level grading, and multi-modality. Then, we analyze the influences on RIQA of different color-spaces, and propose a simple yet efficient deep network, named Multiple Color-space Fusion Network (MCF-Net), which integrates the different color-space representations at both a feature-level and prediction-level to predict image quality grades. Experiments on our EyeQ dataset show that our MCF-Net obtains a state-of-the-art performance, outperforming the other deep learning methods. Furthermore, we also evaluate diabetic retinopathy (DR) detection methods on images of different quality, and demonstrate that the performances of automated diagnostic systems are highly dependent on image quality.

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arXiv2019

Twin Auxiliary Classifiers GAN

Conditional generative models enjoy remarkable progress over the past few years. One of the popular conditional models is Auxiliary Classifier GAN (AC-GAN), which generates highly discriminative images by extending the loss function of GAN with an auxiliary classifier. However, the diversity of the generated samples by AC-GAN tends to decrease as the number of classes increases, hence limiting its power on large-scale data. In this paper, we identify the source of the low diversity issue theoretically and propose a practical solution to solve the problem. We show that the auxiliary classifier in AC-GAN imposes perfect separability, which is disadvantageous when the supports of the class distributions have significant overlap. To address the issue, we propose Twin Auxiliary Classifiers Generative Adversarial Net (TAC-GAN) that further benefits from a new player that interacts with other players (the generator and the discriminator) in GAN. Theoretically, we demonstrate that TAC-GAN can effectively minimize the divergence between the generated and real-data distributions. Extensive experimental results show that our TAC-GAN can successfully replicate the true data distributions on simulated data, and significantly improves the diversity of class-conditional image generation on real datasets.

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arXiv2019

Attention Guided Network for Retinal Image Segmentation

Learning structural information is critical for producing an ideal result in retinal image segmentation. Recently, convolutional neural networks have shown a powerful ability to extract effective representations. However, convolutional and pooling operations filter out some useful structural information. In this paper, we propose an Attention Guided Network (AG-Net) to preserve the structural information and guide the expanding operation. In our AG-Net, the guided filter is exploited as a structure sensitive expanding path to transfer structural information from previous feature maps, and an attention block is introduced to exclude the noise and reduce the negative influence of background further. The extensive experiments on two retinal image segmentation tasks (i.e., blood vessel segmentation, optic disc and cup segmentation) demonstrate the effectiveness of our proposed method.

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arXiv2019

REFUGE Challenge: A Unified Framework for Evaluating Automated Methods for Glaucoma Assessment from Fundus Photographs

Glaucoma is one of the leading causes of irreversible but preventable blindness in working age populations. Color fundus photography (CFP) is the most cost-effective imaging modality to screen for retinal disorders. However, its application to glaucoma has been limited to the computation of a few related biomarkers such as the vertical cup-to-disc ratio. Deep learning approaches, although widely applied for medical image analysis, have not been extensively used for glaucoma assessment due to the limited size of the available data sets. Furthermore, the lack of a standardize benchmark strategy makes difficult to compare existing methods in a uniform way. In order to overcome these issues we set up the Retinal Fundus Glaucoma Challenge, REFUGE (\url{https://refuge.grand-challenge.org}), held in conjunction with MICCAI 2018. The challenge consisted of two primary tasks, namely optic disc/cup segmentation and glaucoma classification. As part of REFUGE, we have publicly released a data set of 1200 fundus images with ground truth segmentations and clinical glaucoma labels, currently the largest existing one. We have also built an evaluation framework to ease and ensure fairness in the comparison of different models, encouraging the development of novel techniques in the field. 12 teams qualified and participated in the online challenge. This paper summarizes their methods and analyzes their corresponding results. In particular, we observed that two of the top-ranked teams outperformed two human experts in the glaucoma classification task. Furthermore, the segmentation results were in general consistent with the ground truth annotations, with complementary outcomes that can be further exploited by ensembling the results.

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