arXiv subjects

Pujin Cheng

Publications and source records attributed to Pujin Cheng.

28 records · Page 2Linked to original sources

arXiv2023

UNO-QA: An Unsupervised Anomaly-Aware Framework with Test-Time Clustering for OCTA Image Quality Assessment

Medical image quality assessment (MIQA) is a vital prerequisite in various medical image analysis applications. Most existing MIQA algorithms are fully supervised that request a large amount of annotated data. However, annotating medical images is time-consuming and labor-intensive. In this paper, we propose an unsupervised anomaly-aware framework with test-time clustering for optical coherence tomography angiography (OCTA) image quality assessment in a setting wherein only a set of high-quality samples are accessible in the training phase. Specifically, a feature-embedding-based low-quality representation module is proposed to quantify the quality of OCTA images and then to discriminate between outstanding quality and non-outstanding quality. Within the non-outstanding quality class, to further distinguish gradable images from ungradable ones, we perform dimension reduction and clustering of multi-scale image features extracted by the trained OCTA quality representation network. Extensive experiments are conducted on one publicly accessible dataset sOCTA-3*3-10k, with superiority of our proposed framework being successfully established.

cs.CV↗

arXiv2022

Identifying the key components in ResNet-50 for diabetic retinopathy grading from fundus images: a systematic investigation

Although deep learning based diabetic retinopathy (DR) classification methods typically benefit from well-designed architectures of convolutional neural networks, the training setting also has a non-negligible impact on the prediction performance. The training setting includes various interdependent components, such as objective function, data sampling strategy and data augmentation approach. To identify the key components in a standard deep learning framework (ResNet-50) for DR grading, we systematically analyze the impact of several major components. Extensive experiments are conducted on a publicly-available dataset EyePACS. We demonstrate that (1) the DR grading framework is sensitive to input resolution, objective function, and composition of data augmentation, (2) using mean square error as the loss function can effectively improve the performance with respect to a task-specific evaluation metric, namely the quadratically-weighted Kappa, (3) utilizing eye pairs boosts the performance of DR grading and (4) using data resampling to address the problem of imbalanced data distribution in EyePACS hurts the performance. Based on these observations and an optimal combination of the investigated components, our framework, without any specialized network design, achieves the state-of-the-art result (0.8631 for Kappa) on the EyePACS test set (a total of 42670 fundus images) with only image-level labels. We also examine the proposed training practices on other fundus datasets and other network architectures to evaluate their generalizability. Our codes and pre-trained model are available at https://github.com/YijinHuang/pytorch-classification.

eess.IV↗

arXiv2022

Student Becomes Decathlon Master in Retinal Vessel Segmentation via Dual-teacher Multi-target Domain Adaptation

Unsupervised domain adaptation has been proposed recently to tackle the so-called domain shift between training data and test data with different distributions. However, most of them only focus on single-target domain adaptation and cannot be applied to the scenario with multiple target domains. In this paper, we propose RVms, a novel unsupervised multi-target domain adaptation approach to segment retinal vessels (RVs) from multimodal and multicenter retinal images. RVms mainly consists of a style augmentation and transfer (SAT) module and a dual-teacher knowledge distillation (DTKD) module. SAT augments and clusters images into source-similar domains and source-dissimilar domains via Bezier and Fourier transformations. DTKD utilizes the augmented and transformed data to train two teachers, one for source-similar domains and the other for source-dissimilar domains. Afterwards, knowledge distillation is performed to iteratively distill different domain knowledge from teachers to a generic student. The local relative intensity transformation is employed to characterize RVs in a domain invariant manner and promote the generalizability of teachers and student models. Moreover, we construct a new multimodal and multicenter vascular segmentation dataset from existing publicly-available datasets, which can be used to benchmark various domain adaptation and domain generalization methods. Through extensive experiments, RVms is found to be very close to the target-trained Oracle in terms of segmenting the RVs, largely outperforming other state-of-the-art methods.

eess.IV↗

arXiv2022

AADG: Automatic Augmentation for Domain Generalization on Retinal Image Segmentation

Convolutional neural networks have been widely applied to medical image segmentation and have achieved considerable performance. However, the performance may be significantly affected by the domain gap between training data (source domain) and testing data (target domain). To address this issue, we propose a data manipulation based domain generalization method, called Automated Augmentation for Domain Generalization (AADG). Our AADG framework can effectively sample data augmentation policies that generate novel domains and diversify the training set from an appropriate search space. Specifically, we introduce a novel proxy task maximizing the diversity among multiple augmented novel domains as measured by the Sinkhorn distance in a unit sphere space, making automated augmentation tractable. Adversarial training and deep reinforcement learning are employed to efficiently search the objectives. Quantitative and qualitative experiments on 11 publicly-accessible fundus image datasets (four for retinal vessel segmentation, four for optic disc and cup (OD/OC) segmentation and three for retinal lesion segmentation) are comprehensively performed. Two OCTA datasets for retinal vasculature segmentation are further involved to validate cross-modality generalization. Our proposed AADG exhibits state-of-the-art generalization performance and outperforms existing approaches by considerable margins on retinal vessel, OD/OC and lesion segmentation tasks. The learned policies are empirically validated to be model-agnostic and can transfer well to other models. The source code is available at https://github.com/CRazorback/AADG.

eess.IV↗

arXiv2022

DS3-Net: Difficulty-perceived Common-to-T1ce Semi-Supervised Multimodal MRI Synthesis Network

Contrast-enhanced T1 (T1ce) is one of the most essential magnetic resonance imaging (MRI) modalities for diagnosing and analyzing brain tumors, especially gliomas. In clinical practice, common MRI modalities such as T1, T2, and fluid attenuation inversion recovery are relatively easy to access while T1ce is more challenging considering the additional cost and potential risk of allergies to the contrast agent. Therefore, it is of great clinical necessity to develop a method to synthesize T1ce from other common modalities. Current paired image translation methods typically have the issue of requiring a large amount of paired data and do not focus on specific regions of interest, e.g., the tumor region, in the synthesization process. To address these issues, we propose a Difficulty-perceived common-to-T1ce Semi-Supervised multimodal MRI Synthesis network (DS3-Net), involving both paired and unpaired data together with dual-level knowledge distillation. DS3-Net predicts a difficulty map to progressively promote the synthesis task. Specifically, a pixelwise constraint and a patchwise contrastive constraint are guided by the predicted difficulty map. Through extensive experiments on the publiclyavailable BraTS2020 dataset, DS3-Net outperforms its supervised counterpart in each respect. Furthermore, with only 5% paired data, the proposed DS3-Net achieves competitive performance with state-of-theart image translation methods utilizing 100% paired data, delivering an average SSIM of 0.8947 and an average PSNR of 23.60.

eess.IV↗

arXiv2022

Multi-modal Brain Tumor Segmentation via Missing Modality Synthesis and Modality-level Attention Fusion

Multi-modal magnetic resonance (MR) imaging provides great potential for diagnosing and analyzing brain gliomas. In clinical scenarios, common MR sequences such as T1, T2 and FLAIR can be obtained simultaneously in a single scanning process. However, acquiring contrast enhanced modalities such as T1ce requires additional time, cost, and injection of contrast agent. As such, it is clinically meaningful to develop a method to synthesize unavailable modalities which can also be used as additional inputs to downstream tasks (e.g., brain tumor segmentation) for performance enhancing. In this work, we propose an end-to-end framework named Modality-Level Attention Fusion Network (MAF-Net), wherein we innovatively conduct patchwise contrastive learning for extracting multi-modal latent features and dynamically assigning attention weights to fuse different modalities. Through extensive experiments on BraTS2020, our proposed MAF-Net is found to yield superior T1ce synthesis performance (SSIM of 0.8879 and PSNR of 22.78) and accurate brain tumor segmentation (mean Dice scores of 67.9%, 41.8% and 88.0% on segmenting the tumor core, enhancing tumor and whole tumor).

eess.IV↗

arXiv2022

Unsupervised Domain Adaptation for Cross-Modality Retinal Vessel Segmentation via Disentangling Representation Style Transfer and Collaborative Consistency Learning

Various deep learning models have been developed to segment anatomical structures from medical images, but they typically have poor performance when tested on another target domain with different data distribution. Recently, unsupervised domain adaptation methods have been proposed to alleviate this so-called domain shift issue, but most of them are designed for scenarios with relatively small domain shifts and are likely to fail when encountering a large domain gap. In this paper, we propose DCDA, a novel cross-modality unsupervised domain adaptation framework for tasks with large domain shifts, e.g., segmenting retinal vessels from OCTA and OCT images. DCDA mainly consists of a disentangling representation style transfer (DRST) module and a collaborative consistency learning (CCL) module. DRST decomposes images into content components and style codes and performs style transfer and image reconstruction. CCL contains two segmentation models, one for source domain and the other for target domain. The two models use labeled data (together with the corresponding transferred images) for supervised learning and perform collaborative consistency learning on unlabeled data. Each model focuses on the corresponding single domain and aims to yield an expertized domain-specific segmentation model. Through extensive experiments on retinal vessel segmentation, our framework achieves Dice scores close to target-trained oracle both from OCTA to OCT and from OCT to OCTA, significantly outperforming other state-of-the-art methods.

eess.IV↗

arXiv2021

LDDMM-Face: Large Deformation Diffeomorphic Metric Learning for Flexible and Consistent Face Alignment

We innovatively propose a flexible and consistent face alignment framework, LDDMM-Face, the key contribution of which is a deformation layer that naturally embeds facial geometry in a diffeomorphic way. Instead of predicting facial landmarks via heatmap or coordinate regression, we formulate this task in a diffeomorphic registration manner and predict momenta that uniquely parameterize the deformation between initial boundary and true boundary, and then perform large deformation diffeomorphic metric mapping (LDDMM) simultaneously for curve and landmark to localize the facial landmarks. Due to the embedding of LDDMM into a deep network, LDDMM-Face can consistently annotate facial landmarks without ambiguity and flexibly handle various annotation schemes, and can even predict dense annotations from sparse ones. Our method can be easily integrated into various face alignment networks. We extensively evaluate LDDMM-Face on four benchmark datasets: 300W, WFLW, HELEN and COFW-68. LDDMM-Face is comparable or superior to state-of-the-art methods for traditional within-dataset and same-annotation settings, but truly distinguishes itself with outstanding performance when dealing with weakly-supervised learning (partial-to-full), challenging cases (e.g., occluded faces), and different training and prediction datasets. In addition, LDDMM-Face shows promising results on the most challenging task of predicting across datasets with different annotation schemes.

cs.CV↗

arXiv2021

Lesion-based Contrastive Learning for Diabetic Retinopathy Grading from Fundus Images

Manually annotating medical images is extremely expensive, especially for large-scale datasets. Self-supervised contrastive learning has been explored to learn feature representations from unlabeled images. However, unlike natural images, the application of contrastive learning to medical images is relatively limited. In this work, we propose a self-supervised framework, namely lesion-based contrastive learning for automated diabetic retinopathy (DR) grading. Instead of taking entire images as the input in the common contrastive learning scheme, lesion patches are employed to encourage the feature extractor to learn representations that are highly discriminative for DR grading. We also investigate different data augmentation operations in defining our contrastive prediction task. Extensive experiments are conducted on the publicly-accessible dataset EyePACS, demonstrating that our proposed framework performs outstandingly on DR grading in terms of both linear evaluation and transfer capacity evaluation.

cs.CV↗

arXiv2021

BSDA-Net: A Boundary Shape and Distance Aware Joint Learning Framework for Segmenting and Classifying OCTA Images

Optical coherence tomography angiography (OCTA) is a novel non-invasive imaging technique that allows visualizations of vasculature and foveal avascular zone (FAZ) across retinal layers. Clinical researches suggest that the morphology and contour irregularity of FAZ are important biomarkers of various ocular pathologies. Therefore, precise segmentation of FAZ has great clinical interest. Also, there is no existing research reporting that FAZ features can improve the performance of deep diagnostic classification networks. In this paper, we propose a novel multi-level boundary shape and distance aware joint learning framework, named BSDA-Net, for FAZ segmentation and diagnostic classification from OCTA images. Two auxiliary branches, namely boundary heatmap regression and signed distance map reconstruction branches, are constructed in addition to the segmentation branch to improve the segmentation performance, resulting in more accurate FAZ contours and fewer outliers. Moreover, both low-level and high-level features from the aforementioned three branches, including shape, size, boundary, and signed directional distance map of FAZ, are fused hierarchically with features from the diagnostic classifier. Through extensive experiments, the proposed BSDA-Net is found to yield state-of-the-art segmentation and classification results on the OCTA-500, OCTAGON, and FAZID datasets.

eess.IV↗