arXiv subjects

Hongwei Li

Publications and source records attributed to Hongwei Li.

At least 127 records · Page 7Linked to original sources

arXiv2021

Micro-CT Synthesis and Inner Ear Super Resolution via Generative Adversarial Networks and Bayesian Inference

Existing medical image super-resolution methods rely on pairs of low- and high- resolution images to learn a mapping in a fully supervised manner. However, such image pairs are often not available in clinical practice. In this paper, we address super-resolution problem in a real-world scenario using unpaired data and synthesize linearly \textbf{eight times} higher resolved Micro-CT images of temporal bone structure, which is embedded in the inner ear. We explore cycle-consistency generative adversarial networks for super-resolution task and equip the translation approach with Bayesian inference. We further introduce \emph{Hu Moment distance} the evaluation metric to quantify the shape of the temporal bone. We evaluate our method on a public inner ear CT dataset and have seen both visual and quantitative improvement over state-of-the-art deep-learning-based methods. In addition, we perform a multi-rater visual evaluation experiment and find that trained experts consistently rate the proposed method the highest quality scores among all methods. Furthermore, we are able to quantify uncertainty in the unpaired translation task and the uncertainty map can provide structural information of the temporal bone.

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arXiv2021

Deep Class-Specific Affinity-Guided Convolutional Network for Multimodal Unpaired Image Segmentation

Multi-modal medical image segmentation plays an essential role in clinical diagnosis. It remains challenging as the input modalities are often not well-aligned spatially. Existing learning-based methods mainly consider sharing trainable layers across modalities and minimizing visual feature discrepancies. While the problem is often formulated as joint supervised feature learning, multiple-scale features and class-specific representation have not yet been explored. In this paper, we propose an affinity-guided fully convolutional network for multimodal image segmentation. To learn effective representations, we design class-specific affinity matrices to encode the knowledge of hierarchical feature reasoning, together with the shared convolutional layers to ensure the cross-modality generalization. Our affinity matrix does not depend on spatial alignments of the visual features and thus allows us to train with unpaired, multimodal inputs. We extensively evaluated our method on two public multimodal benchmark datasets and outperform state-of-the-art methods.

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arXiv2020

Generalisable Cardiac Structure Segmentation via Attentional and Stacked Image Adaptation

Tackling domain shifts in multi-centre and multi-vendor data sets remains challenging for cardiac image segmentation. In this paper, we propose a generalisable segmentation framework for cardiac image segmentation in which multi-centre, multi-vendor, multi-disease datasets are involved. A generative adversarial networks with an attention loss was proposed to translate the images from existing source domains to a target domain, thus to generate good-quality synthetic cardiac structure and enlarge the training set. A stack of data augmentation techniques was further used to simulate real-world transformation to boost the segmentation performance for unseen domains.We achieved an average Dice score of 90.3% for the left ventricle, 85.9% for the myocardium, and 86.5% for the right ventricle on the hidden validation set across four vendors. We show that the domain shifts in heterogeneous cardiac imaging datasets can be drastically reduced by two aspects: 1) good-quality synthetic data by learning the underlying target domain distribution, and 2) stacked classical image processing techniques for data augmentation.

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arXiv2020

Domain Adaptive Medical Image Segmentation via Adversarial Learning of Disease-Specific Spatial Patterns

In medical imaging, the heterogeneity of multi-centre data impedes the applicability of deep learning-based methods and results in significant performance degradation when applying models in an unseen data domain, e.g. a new centreor a new scanner. In this paper, we propose an unsupervised domain adaptation framework for boosting image segmentation performance across multiple domains without using any manual annotations from the new target domains, but by re-calibrating the networks on few images from the target domain. To achieve this, we enforce architectures to be adaptive to new data by rejecting improbable segmentation patterns and implicitly learning through semantic and boundary information, thus to capture disease-specific spatial patterns in an adversarial optimization. The adaptation process needs continuous monitoring, however, as we cannot assume the presence of ground-truth masks for the target domain, we propose two new metrics to monitor the adaptation process, and strategies to train the segmentation algorithm in a stable fashion. We build upon well-established 2D and 3D architectures and perform extensive experiments on three cross-centre brain lesion segmentation tasks, involving multicentre public and in-house datasets. We demonstrate that recalibrating the deep networks on a few unlabeled images from the target domain improves the segmentation accuracy significantly.

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arXiv2020

Fast non-convex low-rank matrix decomposition for separation of potential field data using minimal memory

A fast non-convex low-rank matrix decomposition method for potential field data separation is proposed. The singular value decomposition of the large size trajectory matrix, which is also a block Hankel matrix, is obtained using a fast randomized singular value decomposition algorithm in which fast block Hankel matrix-vector multiplications are implemented with minimal memory storage. This fast block Hankel matrix randomized singular value decomposition algorithm is integrated into the \texttt{Altproj} algorithm, which is a standard non-convex method for solving the robust principal component analysis optimization problem. The improved algorithm avoids the construction of the trajectory matrix. Hence, gravity and magnetic data matrices of large size can be computed. Moreover, it is more efficient than the traditional low-rank matrix decomposition method, which is based on the use of an inexact augmented Lagrange multiplier algorithm. The presented algorithm is also robust and, hence, algorithm-dependent parameters are easily determined. The improved and traditional algorithms are contrasted for the separation of synthetic gravity and magnetic data matrices of different sizes. The presented results demonstrate that the improved algorithm is not only computationally more efficient but it is also more accurate. Moreover, it is possible to solve far larger problems. As an example, for the adopted computational environment, matrices of sizes larger than $205 \times 205$ generate "out of memory" exceptions with the traditional method, but a matrix of size $2001\times 2001$ can be calculated in $1062.29$s with the new algorithm. Finally, the improved method is applied to separate real gravity and magnetic data in the Tongling area, Anhui province, China. Areas which may exhibit mineralizations are inferred based on the separated anomalies.

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arXiv2019

Quantum algorithms for the Goldreich-Levin learning problem

The Goldreich-Levin algorithm was originally proposed for a cryptographic purpose and then applied to learning. The algorithm is to find some larger Walsh coefficients of an $n$ variable Boolean function. Roughly speaking, it takes a $poly(n,\frac{1}ε\log\frac{1}δ)$ time to output the vectors $w$ with Walsh coefficients $S(w)\geqε$ with probability at least $1-δ$. However, in this paper, a quantum algorithm for this problem is given with query complexity $O(\frac{\log\frac{1}δ}{ε^4})$, which is independent of $n$. Furthermore, the quantum algorithm is generalized to apply for an $n$ variable $m$ output Boolean function $F$ with query complexity $O(2^m\frac{\log\frac{1}δ}{ε^4})$.

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arXiv2019

Invasiveness Prediction of Pulmonary Adenocarcinomas Using Deep Feature Fusion Networks

Early diagnosis of pathological invasiveness of pulmonary adenocarcinomas using computed tomography (CT) imaging would alter the course of treatment of adenocarcinomas and subsequently improve the prognosis. Most of the existing systems use either conventional radiomics features or deep-learning features alone to predict the invasiveness. In this study, we explore the fusion of the two kinds of features and claim that radiomics features can be complementary to deep-learning features. An effective deep feature fusion network is proposed to exploit the complementarity between the two kinds of features, which improves the invasiveness prediction results. We collected a private dataset that contains lung CT scans of 676 patients categorized into four invasiveness types from a collaborating hospital. Evaluations on this dataset demonstrate the effectiveness of our proposal.

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arXiv2019

Adversarial Convolutional Networks with Weak Domain-Transfer for Multi-Sequence Cardiac MR Images Segmentation

Analysis and modeling of the ventricles and myocardium are important in the diagnostic and treatment of heart diseases. Manual delineation of those tissues in cardiac MR (CMR) scans is laborious and time-consuming. The ambiguity of the boundaries makes the segmentation task rather challenging. Furthermore, the annotations on some modalities such as Late Gadolinium Enhancement (LGE) MRI, are often not available. We propose an end-to-end segmentation framework based on convolutional neural network (CNN) and adversarial learning. A dilated residual U-shape network is used as a segmentor to generate the prediction mask; meanwhile, a CNN is utilized as a discriminator model to judge the segmentation quality. To leverage the available annotations across modalities per patient, a new loss function named weak domain-transfer loss is introduced to the pipeline. The proposed model is evaluated on the public dataset released by the challenge organizer in MICCAI 2019, which consists of 45 sets of multi-sequence CMR images. We demonstrate that the proposed adversarial pipeline outperforms baseline deep-learning methods.

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arXiv2019

Restricted Linearized Augmented Lagrangian Method for Euler's Elastica Model

Euler's elastica model has been extensively studied and applied to image processing tasks. However, due to the high nonlinearity and nonconvexity of the involved curvature term, conventional algorithms suffer from slow convergence and high computational cost. Various fast algorithms have been proposed, among which, the augmented Lagrangian based ones are very popular in the community. However, parameter tuning might be very challenging for these methods. In this paper, a simple cutting-off strategy is introduced into the augmented Lagrangian based algorithms for minimizing the Euler's elastica energy, which leads to easy parameter tuning and fast convergence. The cutting-off strategy is based on an observation of inconsistency inside the augmented Lagrangian based algorithms. When the weighting parameter of the curvature term goes to zero, the energy functional boils down to the ROF model. So, a natural requirement is that its augmented Lagrangian based algorithms should also approach the augmented Lagrangian based algorithms formulated directly for solving the ROF model from the very beginning. Unfortunately, this is not the case for certain existing augmented Lagrangian based algorithms. The proposed cutting-off strategy helps to decouple the tricky dependence between the auxiliary splitting variables, so as to remove the observed inconsistency. Numerical experiments suggest that the proposed algorithm enjoys easier parameter-tuning, faster convergence and even higher quality of image restorations.

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arXiv2019

DiamondGAN: Unified Multi-Modal Generative Adversarial Networks for MRI Sequences Synthesis

Synthesizing MR imaging sequences is highly relevant in clinical practice, as single sequences are often missing or are of poor quality (e.g. due to motion). Naturally, the idea arises that a target modality would benefit from multi-modal input, as proprietary information of individual modalities can be synergistic. However, existing methods fail to scale up to multiple non-aligned imaging modalities, facing common drawbacks of complex imaging sequences. We propose a novel, scalable and multi-modal approach called DiamondGAN. Our model is capable of performing exible non-aligned cross-modality synthesis and data infill, when given multiple modalities or any of their arbitrary subsets, learning structured information in an end-to-end fashion. We synthesize two MRI sequences with clinical relevance (i.e., double inversion recovery (DIR) and contrast-enhanced T1 (T1-c)), reconstructed from three common sequences. In addition, we perform a multi-rater visual evaluation experiment and find that trained radiologists are unable to distinguish synthetic DIR images from real ones.

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arXiv2019

Cross-view Relation Networks for Mammogram Mass Detection

Mammogram is the most effective imaging modality for the mass lesion detection of breast cancer at the early stage. The information from the two paired views (i.e., medio-lateral oblique and cranio-caudal) are highly relational and complementary, and this is crucial for doctors' decisions in clinical practice. However, existing mass detection methods do not consider jointly learning effective features from the two relational views. To address this issue, this paper proposes a novel mammogram mass detection framework, termed Cross-View Relation Region-based Convolutional Neural Networks (CVR-RCNN). The proposed CVR-RCNN is expected to capture the latent relation information between the corresponding mass region of interests (ROIs) from the two paired views. Evaluations on a new large-scale private dataset and a public mammogram dataset show that the proposed CVR-RCNN outperforms existing state-of-the-art mass detection methods. Meanwhile, our experimental results suggest that incorporating the relation information across two views helps to train a superior detection model, which is a promising avenue for mammogram mass detection.

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arXiv2019

Group-Attention Single-Shot Detector (GA-SSD): Finding Pulmonary Nodules in Large-Scale CT Images

Early diagnosis of pulmonary nodules (PNs) can improve the survival rate of patients and yet is a challenging task for radiologists due to the image noise and artifacts in computed tomography (CT) images. In this paper, we propose a novel and effective abnormality detector implementing the attention mechanism and group convolution on 3D single-shot detector (SSD) called group-attention SSD (GA-SSD). We find that group convolution is effective in extracting rich context information between continuous slices, and attention network can learn the target features automatically. We collected a large-scale dataset that contained 4146 CT scans with annotations of varying types and sizes of PNs (even PNs smaller than 3mm were annotated). To the best of our knowledge, this dataset is the largest cohort with relatively complete annotations for PNs detection. Our experimental results show that the proposed group-attention SSD outperforms the classic SSD framework as well as the state-of-the-art 3DCNN, especially on some challenging lesion types.

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arXiv2019

Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. Automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their method on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge (https://wmh.isi.uu.nl/). Sixty T1+FLAIR images from three MR scanners were released with manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. Segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: (1) Dice similarity coefficient, (2) modified Hausdorff distance (95th percentile), (3) absolute log-transformed volume difference, (4) sensitivity for detecting individual lesions, and (5) F1-score for individual lesions. Additionally, methods were ranked on their inter-scanner robustness. Twenty participants submitted their method for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation.

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arXiv2019

Multi-Scale Convolutional-Stack Aggregation for Robust White Matter Hyperintensities Segmentation

Segmentation of both large and small white matter hyperintensities/lesions in brain MR images is a challenging task which has drawn much attention in recent years. We propose a multi-scale aggregation model framework to deal with volume-varied lesions. Firstly, we present a specifically-designed network for small lesion segmentation called Stack-Net, in which multiple convolutional layers are connected, aiming to preserve rich local spatial information of small lesions before the sub-sampling layer. Secondly, we aggregate multi-scale Stack-Nets with different receptive fields to learn multi-scale contextual information of both large and small lesions. Our model is evaluated on recent MICCAI WMH Challenge Dataset and outperforms the state-of-the-art on lesion recall and lesion F1-score under 5-fold cross validation. In addition, we further test our pre-trained models on a Multiple Sclerosis lesion dataset with 30 subjects under cross-center evaluation. Results show that the aggregation model is effective in learning multi-scale spatial information.It claimed the first place on the hidden test set after independent evaluation by the challenge organizer. In addition, we further test our pre-trained models on a Multiple Sclerosis lesion dataset with 30 subjects under cross-center evaluation. Results show that the aggregation model is effective in learning multi-scale spatial information.

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arXiv2018

Automatic Brain Structures Segmentation Using Deep Residual Dilated U-Net

Brain image segmentation is used for visualizing and quantifying anatomical structures of the brain. We present an automated ap-proach using 2D deep residual dilated networks which captures rich context information of different tissues for the segmentation of eight brain structures. The proposed system was evaluated in the MICCAI Brain Segmentation Challenge and ranked 9th out of 22 teams. We further compared the method with traditional U-Net using leave-one-subject-out cross-validation setting on the public dataset. Experimental results shows that the proposed method outperforms traditional U-Net (i.e. 80.9% vs 78.3% in averaged Dice score, 4.35mm vs 11.59mm in averaged robust Hausdorff distance) and is computationally efficient.

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arXiv2018

Hierarchical multi-class segmentation of glioma images using networks with multi-level activation function

For many segmentation tasks, especially for the biomedical image, the topological prior is vital information which is useful to exploit. The containment/nesting is a typical inter-class geometric relationship. In the MICCAI Brain tumor segmentation challenge, with its three hierarchically nested classes 'whole tumor', 'tumor core', 'active tumor', the nested classes relationship is introduced into the 3D-residual-Unet architecture. The network comprises a context aggregation pathway and a localization pathway, which encodes increasingly abstract representation of the input as going deeper into the network, and then recombines these representations with shallower features to precisely localize the interest domain via a localization path. The nested-class-prior is combined by proposing the multi-class activation function and its corresponding loss function. The model is trained on the training dataset of Brats2018, and 20% of the dataset is regarded as the validation dataset to determine parameters. When the parameters are fixed, we retrain the model on the whole training dataset. The performance achieved on the validation leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing tumor and tumor core classes without relying on ensembles or complicated post-processing steps. Based on the same start-of-the-art network architecture, the accuracy of nested-class (enhancing tumor) is reasonably improved from 69% to 72% compared with the traditional Softmax-based method which blind to topological prior.

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arXiv2018

Fully Convolutional Network Ensembles for White Matter Hyperintensities Segmentation in MR Images

White matter hyperintensities (WMH) are commonly found in the brains of healthy elderly individuals and have been associated with various neurological and geriatric disorders. In this paper, we present a study using deep fully convolutional network and ensemble models to automatically detect such WMH using fluid attenuation inversion recovery (FLAIR) and T1 magnetic resonance (MR) scans. The algorithm was evaluated and ranked 1 st in the WMH Segmentation Challenge at MICCAI 2017. In the evaluation stage, the implementation of the algorithm was submitted to the challenge organizers, who then independently tested it on a hidden set of 110 cases from 5 scanners. Averaged dice score, precision and robust Hausdorff distance obtained on held-out test datasets were 80%, 84% and 6.30mm respectively. These were the highest achieved in the challenge, suggesting the proposed method is the state-of-the-art. In this paper, we provide detailed descriptions and quantitative analysis on key components of the system. Furthermore, a study of cross-scanner evaluation is presented to discuss how the combination of modalities and data augmentation affect the generalization capability of the system. The adaptability of the system to different scanners and protocols is also investigated. A quantitative study is further presented to test the effect of ensemble size. Additionally, software and models of our method are made publicly available. The effectiveness and generalization capability of the proposed system show its potential for real-world clinical practice.

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arXiv2018

Differential Diagnosis for Pancreatic Cysts in CT Scans Using Densely-Connected Convolutional Networks

The lethal nature of pancreatic ductal adenocarcinoma (PDAC) calls for early differential diagnosis of pancreatic cysts, which are identified in up to 16% of normal subjects, and some of which may develop into PDAC. Previous computer-aided developments have achieved certain accuracy for classification on segmented cystic lesions in CT. However, pancreatic cysts have a large variation in size and shape, and the precise segmentation of them remains rather challenging, which restricts the computer-aided interpretation of CT images acquired for differential diagnosis. We propose a computer-aided framework for early differential diagnosis of pancreatic cysts without pre-segmenting the lesions using densely-connected convolutional networks (Dense-Net). The Dense-Net learns high-level features from whole abnormal pancreas and builds mappings between medical imaging appearance to different pathological types of pancreatic cysts. To enhance the clinical applicability, we integrate saliency maps in the framework to assist the physicians to understand the decision of the deep learning method. The test on a cohort of 206 patients with 4 pathologically confirmed subtypes of pancreatic cysts has achieved an overall accuracy of 72.8%, which is significantly higher than the baseline accuracy of 48.1%, which strongly supports the clinical potential of our developed method.

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