arXiv subjects

Yitian Zhao

Publications and source records attributed to Yitian Zhao.

At least 37 records · Page 2Linked to original sources

arXiv2022

Sparse-based Domain Adaptation Network for OCTA Image Super-Resolution Reconstruction

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.

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arXiv2022

OCTAve: 2D en face Optical Coherence Tomography Angiography Vessel Segmentation in Weakly-Supervised Learning with Locality Augmentation

While there have been increased researches using deep learning techniques for the extraction of vascular structure from the 2D en face OCTA, for such approach, it is known that the data annotation process on the curvilinear structure like the retinal vasculature is very costly and time consuming, albeit few tried to address the annotation problem. In this work, we propose the application of the scribble-base weakly-supervised learning method to automate the pixel-level annotation. The proposed method, called OCTAve, combines the weakly-supervised learning using scribble-annotated ground truth augmented with an adversarial and a novel self-supervised deep supervision. Our novel mechanism is designed to utilize the discriminative outputs from the discrimination layer of a UNet-like architecture where the Kullback-Liebler Divergence between the aggregate discriminative outputs and the segmentation map predicate is minimized during the training. This combined method leads to the better localization of the vascular structure as shown in our experiments. We validate our proposed method on the large public datasets i.e., ROSE, OCTA-500. The segmentation performance is compared against both state-of-the-art fully-supervised and scribble-based weakly-supervised approaches. The implementation of our work used in the experiments is located at [LINK].

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arXiv2022

Structure-consistent Restoration Network for Cataract Fundus Image Enhancement

Fundus photography is a routine examination in clinics to diagnose and monitor ocular diseases. However, for cataract patients, the fundus image always suffers quality degradation caused by the clouding lens. The degradation prevents reliable diagnosis by ophthalmologists or computer-aided systems. To improve the certainty in clinical diagnosis, restoration algorithms have been proposed to enhance the quality of fundus images. Unfortunately, challenges remain in the deployment of these algorithms, such as collecting sufficient training data and preserving retinal structures. In this paper, to circumvent the strict deployment requirement, a structure-consistent restoration network (SCR-Net) for cataract fundus images is developed from synthesized data that shares an identical structure. A cataract simulation model is firstly designed to collect synthesized cataract sets (SCS) formed by cataract fundus images sharing identical structures. Then high-frequency components (HFCs) are extracted from the SCS to constrain structure consistency such that the structure preservation in SCR-Net is enforced. The experiments demonstrate the effectiveness of SCR-Net in the comparison with state-of-the-art methods and the follow-up clinical applications. The code is available at https://github.com/liamheng/ArcNet-Medical-Image-Enhancement.

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arXiv2022

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

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

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arXiv2022

An Annotation-free Restoration Network for Cataractous Fundus Images

Cataracts are the leading cause of vision loss worldwide. Restoration algorithms are developed to improve the readability of cataract fundus images in order to increase the certainty in diagnosis and treatment for cataract patients. Unfortunately, the requirement of annotation limits the application of these algorithms in clinics. This paper proposes a network to annotation-freely restore cataractous fundus images (ArcNet) so as to boost the clinical practicability of restoration. Annotations are unnecessary in ArcNet, where the high-frequency component is extracted from fundus images to replace segmentation in the preservation of retinal structures. The restoration model is learned from the synthesized images and adapted to real cataract images. Extensive experiments are implemented to verify the performance and effectiveness of ArcNet. Favorable performance is achieved using ArcNet against state-of-the-art algorithms, and the diagnosis of ocular fundus diseases in cataract patients is promoted by ArcNet. The capability of properly restoring cataractous images in the absence of annotated data promises the proposed algorithm outstanding clinical practicability.

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arXiv2022

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

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

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arXiv2022

Counting with Adaptive Auxiliary Learning

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

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arXiv2022

Spatial-context-aware deep neural network for multi-class image classification

Multi-label image classification is a fundamental but challenging task in computer vision. Over the past few decades, solutions exploring relationships between semantic labels have made great progress. However, the underlying spatial-contextual information of labels is under-exploited. To tackle this problem, a spatial-context-aware deep neural network is proposed to predict labels taking into account both semantic and spatial information. This proposed framework is evaluated on Microsoft COCO and PASCAL VOC, two widely used benchmark datasets for image multi-labelling. The results show that the proposed approach is superior to the state-of-the-art solutions on dealing with the multi-label image classification problem.

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arXiv2021

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

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

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arXiv2021

Spatial Uncertainty-Aware Semi-Supervised Crowd Counting

Semi-supervised approaches for crowd counting attract attention, as the fully supervised paradigm is expensive and laborious due to its request for a large number of images of dense crowd scenarios and their annotations. This paper proposes a spatial uncertainty-aware semi-supervised approach via regularized surrogate task (binary segmentation) for crowd counting problems. Different from existing semi-supervised learning-based crowd counting methods, to exploit the unlabeled data, our proposed spatial uncertainty-aware teacher-student framework focuses on high confident regions' information while addressing the noisy supervision from the unlabeled data in an end-to-end manner. Specifically, we estimate the spatial uncertainty maps from the teacher model's surrogate task to guide the feature learning of the main task (density regression) and the surrogate task of the student model at the same time. Besides, we introduce a simple yet effective differential transformation layer to enforce the inherent spatial consistency regularization between the main task and the surrogate task in the student model, which helps the surrogate task to yield more reliable predictions and generates high-quality uncertainty maps. Thus, our model can also address the task-level perturbation problems that occur spatial inconsistency between the primary and surrogate tasks in the student model. Experimental results on four challenging crowd counting datasets demonstrate that our method achieves superior performance to the state-of-the-art semi-supervised methods.

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arXiv2021

Explainable Diabetic Retinopathy Detection and Retinal Image Generation

Though deep learning has shown successful performance in classifying the label and severity stage of certain diseases, most of them give few explanations on how to make predictions. Inspired by Koch's Postulates, the foundation in evidence-based medicine (EBM) to identify the pathogen, we propose to exploit the interpretability of deep learning application in medical diagnosis. By determining and isolating the neuron activation patterns on which diabetic retinopathy (DR) detector relies to make decisions, we demonstrate the direct relation between the isolated neuron activation and lesions for a pathological explanation. To be specific, we first define novel pathological descriptors using activated neurons of the DR detector to encode both spatial and appearance information of lesions. Then, to visualize the symptom encoded in the descriptor, we propose Patho-GAN, a new network to synthesize medically plausible retinal images. By manipulating these descriptors, we could even arbitrarily control the position, quantity, and categories of generated lesions. We also show that our synthesized images carry the symptoms directly related to diabetic retinopathy diagnosis. Our generated images are both qualitatively and quantitatively superior to the ones by previous methods. Besides, compared to existing methods that take hours to generate an image, our second level speed endows the potential to be an effective solution for data augmentation.

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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

3D Vessel Reconstruction in OCT-Angiography via Depth Map Estimation

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

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arXiv2020

ROSE: A Retinal OCT-Angiography Vessel Segmentation Dataset and New Model

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.

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arXiv2020

Learning Euler's Elastica Model for Medical Image Segmentation

Image segmentation is a fundamental topic in image processing and has been studied for many decades. Deep learning-based supervised segmentation models have achieved state-of-the-art performance but most of them are limited by using pixel-wise loss functions for training without geometrical constraints. Inspired by Euler's Elastica model and recent active contour models introduced into the field of deep learning, we propose a novel active contour with elastica (ACE) loss function incorporating Elastica (curvature and length) and region information as geometrically-natural constraints for the image segmentation tasks. We introduce the mean curvature i.e. the average of all principal curvatures, as a more effective image prior to representing curvature in our ACE loss function. Furthermore, based on the definition of the mean curvature, we propose a fast solution to approximate the ACE loss in three-dimensional (3D) by using Laplace operators for 3D image segmentation. We evaluate our ACE loss function on four 2D and 3D natural and biomedical image datasets. Our results show that the proposed loss function outperforms other mainstream loss functions on different segmentation networks. Our source code is available at https://github.com/HiLab-git/ACELoss.

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arXiv2020

CS2-Net: Deep Learning Segmentation of Curvilinear Structures in Medical Imaging

Automated detection of curvilinear structures, e.g., blood vessels or nerve fibres, from medical and biomedical images is a crucial early step in automatic image interpretation associated to the management of many diseases. Precise measurement of the morphological changes of these curvilinear organ structures informs clinicians for understanding the mechanism, diagnosis, and treatment of e.g. cardiovascular, kidney, eye, lung, and neurological conditions. In this work, we propose a generic and unified convolution neural network for the segmentation of curvilinear structures and illustrate in several 2D/3D medical imaging modalities. We introduce a new curvilinear structure segmentation network (CS2-Net), which includes a self-attention mechanism in the encoder and decoder to learn rich hierarchical representations of curvilinear structures. Two types of attention modules - spatial attention and channel attention - are utilized to enhance the inter-class discrimination and intra-class responsiveness, to further integrate local features with their global dependencies and normalization, adaptively. Furthermore, to facilitate the segmentation of curvilinear structures in medical images, we employ a 1x3 and a 3x1 convolutional kernel to capture boundary features. ...

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arXiv2020

Automatic Segmentation and Visualization of Choroid in OCT with Knowledge Infused Deep Learning

The choroid provides oxygen and nourishment to the outer retina thus is related to the pathology of various ocular diseases. Optical coherence tomography (OCT) is advantageous in visualizing and quantifying the choroid in vivo. (1) The lower boundary of the choroid (choroid-sclera interface) in OCT is fuzzy, which makes the automatic segmentation difficult and inaccurate. (2) The visualization of the choroid is hindered by the vessel shadows from the superficial layers of the inner retina. In this paper, we propose to incorporate medical and imaging prior knowledge with deep learning to address these two problems. We propose a biomarker infused global-to-local network for the choroid segmentation. It leverages the choroidal thickness, a primary biomarker in clinic, as a constraint to improve the segmentation accuracy. We also design a global-to-local strategy in the choroid segmentation: a global module is used to segment all the retinal and choroidal layers simultaneously for suppressing overfitting and providing global structure information, then a local module is used to refine the segmentation with the biomarker infusion. To eliminate the retinal vessel shadows, we propose a pipeline that firstly use anatomical and OCT imaging knowledge to locate the shadows using their projection on the retinal pigment epithelium layer, then the contents of the choroidal vasculature at the shadow locations are predicted with an edge-to-texture generative adversarial inpainting network. The experiments show our method outperforms the existing methods on both the segmentation and shadow elimination tasks. We further apply the proposed method in a clinical prospective study for understanding the pathology of glaucoma by detecting the structure and vascular changes of the choroid related to the elevation of intra-ocular pressure.

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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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