Models, code, and papers for "Dinggang Shen":

Semantic-guided Encoder Feature Learning for Blurry Boundary Delineation

Jun 10, 2019
Dong Nie, Dinggang Shen

Encoder-decoder architectures are widely adopted for medical image segmentation tasks. With the lateral skip connection, the models can obtain and fuse both semantic and resolution information in deep layers to achieve more accurate segmentation performance. However, in many applications (e.g., blurry boundary images), these models often cannot precisely locate complex boundaries and segment tiny isolated parts. To solve this challenging problem, we firstly analyze why simple skip connections are not enough to help accurately locate indistinct boundaries and argue that it is due to the fuzzy information in the skip connection provided in the encoder layers. Then we propose a semantic-guided encoder feature learning strategy to learn both high resolution and rich semantic encoder features so that we can more accurately locate the blurry boundaries, which can also enhance the network by selectively learning discriminative features. Besides, we further propose a soft contour constraint mechanism to model the blurry boundary detection. Experimental results on real clinical datasets show that our proposed method can achieve state-of-the-art segmentation accuracy, especially for the blurry regions. Further analysis also indicates that our proposed network components indeed contribute to the improvement of performance. Experiments on additional datasets validate the generalization ability of our proposed method.


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Population-Guided Large Margin Classifier for High-Dimension Low -Sample-Size Problems

Jan 05, 2019
Qingbo Yin, Ehsan Adeli, Liran Shen, Dinggang Shen

Various applications in different fields, such as gene expression analysis or computer vision, suffer from data sets with high-dimensional low-sample-size (HDLSS), which has posed significant challenges for standard statistical and modern machine learning methods. In this paper, we propose a novel linear binary classifier, denoted by population-guided large margin classifier (PGLMC), which is applicable to any sorts of data, including HDLSS. PGLMC is conceived with a projecting direction w given by the comprehensive consideration of local structural information of the hyperplane and the statistics of the training samples. Our proposed model has several advantages compared to those widely used approaches. First, it is not sensitive to the intercept term b. Second, it operates well with imbalanced data. Third, it is relatively simple to be implemented based on Quadratic Programming. Fourth, it is robust to the model specification for various real applications. The theoretical properties of PGLMC are proven. We conduct a series of evaluations on two simulated and six real-world benchmark data sets, including DNA classification, digit recognition, medical image analysis, and face recognition. PGLMC outperforms the state-of-the-art classification methods in most cases, or at least obtains comparable results.

* 48 Pages 

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Dual Adversarial Learning with Attention Mechanism for Fine-grained Medical Image Synthesis

Jul 07, 2019
Dong Nie, Lei Xiang, Qian Wang, Dinggang Shen

Medical imaging plays a critical role in various clinical applications. However, due to multiple considerations such as cost and risk, the acquisition of certain image modalities could be limited. To address this issue, many cross-modality medical image synthesis methods have been proposed. However, the current methods cannot well model the hard-to-synthesis regions (e.g., tumor or lesion regions). To address this issue, we propose a simple but effective strategy, that is, we propose a dual-discriminator (dual-D) adversarial learning system, in which, a global-D is used to make an overall evaluation for the synthetic image, and a local-D is proposed to densely evaluate the local regions of the synthetic image. More importantly, we build an adversarial attention mechanism which targets at better modeling hard-to-synthesize regions (e.g., tumor or lesion regions) based on the local-D. Experimental results show the robustness and accuracy of our method in synthesizing fine-grained target images from the corresponding source images. In particular, we evaluate our method on two datasets, i.e., to address the tasks of generating T2 MRI from T1 MRI for the brain tumor images and generating MRI from CT. Our method outperforms the state-of-the-art methods under comparison in all datasets and tasks. And the proposed difficult-region-aware attention mechanism is also proved to be able to help generate more realistic images, especially for the hard-to-synthesize regions.


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Brain MR Image Segmentation in Small Dataset with Adversarial Defense and Task Reorganization

Jun 25, 2019
Xuhua Ren, Lichi Zhang, Qian Wang, Dinggang Shen

Medical image segmentation is challenging especially in dealing with small dataset of 3D MR images. Encoding the variation of brain anatomical struc-tures from individual subjects cannot be easily achieved, which is further chal-lenged by only a limited number of well labeled subjects for training. In this study, we aim to address the issue of brain MR image segmentation in small da-taset. First, concerning the limited number of training images, we adopt adver-sarial defense to augment the training data and therefore increase the robustness of the network. Second, inspired by the prior knowledge of neural anatomies, we reorganize the segmentation tasks of different regions into several groups in a hierarchical way. Third, the task reorganization extends to the semantic level, as we incorporate an additional object-level classification task to contribute high-order visual features toward the pixel-level segmentation task. In experiments we validate our method by segmenting gray matter, white matter, and several major regions on a challenge dataset. The proposed method with only seven subjects for training can achieve 84.46% of Dice score in the onsite test set.


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Global Deep Learning Methods for Multimodality Isointense Infant Brain Image Segmentation

Dec 10, 2018
Zhengyang Wang, Na Zou, Dinggang Shen, Shuiwang Ji

An important step in early brain development study is to perform automatic segmentation of infant brain magnetic resonance (MR) images into cerebrospinal fluid (CSF), gray matter (GM) and white matter (WM) regions. This task is especially challenging in the isointense stage (approximately 6-8 months of age) when GM and WM exhibit similar levels of intensities in MR images. Deep learning has shown its great promise in various image segmentation tasks. However, existing models do not have an efficient and effective way to aggregate global information. They also suffer from information loss during up-sampling operations. In this work, we address these problems by proposing a global aggregation block, which can be flexibly used for global information fusion. We build a novel model based on 3D U-Net to make fast and accurate voxel-wise dense prediction. We perform thorough experiments, and results indicate that our model outperforms previous best models significantly on 3D multimodality isointense infant brain MR image segmentation.

* 10 pages, 9 figures, 8 tables 

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Deep Chronnectome Learning via Full Bidirectional Long Short-Term Memory Networks for MCI Diagnosis

Aug 30, 2018
Weizheng Yan, Han Zhang, Jing Sui, Dinggang Shen

Brain functional connectivity (FC) extracted from resting-state fMRI (RS-fMRI) has become a popular approach for disease diagnosis, where discriminating subjects with mild cognitive impairment (MCI) from normal controls (NC) is still one of the most challenging problems. Dynamic functional connectivity (dFC), consisting of time-varying spatiotemporal dynamics, may characterize "chronnectome" diagnostic information for improving MCI classification. However, most of the current dFC studies are based on detecting discrete major brain status via spatial clustering, which ignores rich spatiotemporal dynamics contained in such chronnectome. We propose Deep Chronnectome Learning for exhaustively mining the comprehensive information, especially the hidden higher-level features, i.e., the dFC time series that may add critical diagnostic power for MCI classification. To this end, we devise a new Fully-connected Bidirectional Long Short-Term Memory Network (Full-BiLSTM) to effectively learn the periodic brain status changes using both past and future information for each brief time segment and then fuse them to form the final output. We have applied our method to a rigorously built large-scale multi-site database (i.e., with 164 data from NCs and 330 from MCIs, which can be further augmented by 25 folds). Our method outperforms other state-of-the-art approaches with an accuracy of 73.6% under solid cross-validations. We also made extensive comparisons among multiple variants of LSTM models. The results suggest high feasibility of our method with promising value also for other brain disorder diagnoses.

* The paper has been accepted by MICCAI2018 

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Multi-Kernel Filtering: An Extension of Bilateral Filtering Using Image Context

Aug 27, 2019
Feihong Liu, Jun Feng, Pew-Thian Yap, Dinggang Shen

Bilateral filtering is one of the most classical denoising filters. However, the parameter of its range kernel needs to be initialized manually, which hampers its adaptivity across images with different characteristics. For coping with image variation (e.g., changeable signal-to-noise ratio and spatially-varying noise), it is necessary to adapt the kernel to specific image characteristics automatically. In this paper, we propose multi-kernel filter (MKF) inspired by adaptive mechanisms of human vision. We first design a hierarchically clustering algorithm to generate a hierarchy of large to small coherent image patches, organized as a cluster tree, so that obtain multi-scale image representation. The leaf cluster and corresponding predecessor clusters are used to generate one of multiple range kernels that are capable of catering to image variation. We evaluate MKF on two public datasets, BSD$300$ and BrainWeb. Extensive experimental results show that MKF outperforms state-of-the-art filters on both mean absolute error and structural similarity.

* 11 pages, 9 figures 

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BIRNet: Brain Image Registration Using Dual-Supervised Fully Convolutional Networks

Feb 13, 2018
Jingfan Fan, Xiaohuan Cao, Pew-Thian Yap, Dinggang Shen

In this paper, we propose a deep learning approach for image registration by predicting deformation from image appearance. Since obtaining ground-truth deformation fields for training can be challenging, we design a fully convolutional network that is subject to dual-guidance: (1) Coarse guidance using deformation fields obtained by an existing registration method; and (2) Fine guidance using image similarity. The latter guidance helps avoid overly relying on the supervision from the training deformation fields, which could be inaccurate. For effective training, we further improve the deep convolutional network with gap filling, hierarchical loss, and multi-source strategies. Experiments on a variety of datasets show promising registration accuracy and efficiency compared with state-of-the-art methods.


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Medical Image Synthesis with Context-Aware Generative Adversarial Networks

Dec 16, 2016
Dong Nie, Roger Trullo, Caroline Petitjean, Su Ruan, Dinggang Shen

Computed tomography (CT) is critical for various clinical applications, e.g., radiotherapy treatment planning and also PET attenuation correction. However, CT exposes radiation during acquisition, which may cause side effects to patients. Compared to CT, magnetic resonance imaging (MRI) is much safer and does not involve any radiations. Therefore, recently, researchers are greatly motivated to estimate CT image from its corresponding MR image of the same subject for the case of radiotherapy planning. In this paper, we propose a data-driven approach to address this challenging problem. Specifically, we train a fully convolutional network to generate CT given an MR image. To better model the nonlinear relationship from MRI to CT and to produce more realistic images, we propose to use the adversarial training strategy and an image gradient difference loss function. We further apply AutoContext Model to implement a context-aware generative adversarial network. Experimental results show that our method is accurate and robust for predicting CT images from MRI images, and also outperforms three state-of-the-art methods under comparison.


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Learning Discriminative Bayesian Networks from High-dimensional Continuous Neuroimaging Data

Jun 23, 2015
Luping Zhou, Lei Wang, Lingqiao Liu, Philip Ogunbona, Dinggang Shen

Due to its causal semantics, Bayesian networks (BN) have been widely employed to discover the underlying data relationship in exploratory studies, such as brain research. Despite its success in modeling the probability distribution of variables, BN is naturally a generative model, which is not necessarily discriminative. This may cause the ignorance of subtle but critical network changes that are of investigation values across populations. In this paper, we propose to improve the discriminative power of BN models for continuous variables from two different perspectives. This brings two general discriminative learning frameworks for Gaussian Bayesian networks (GBN). In the first framework, we employ Fisher kernel to bridge the generative models of GBN and the discriminative classifiers of SVMs, and convert the GBN parameter learning to Fisher kernel learning via minimizing a generalization error bound of SVMs. In the second framework, we employ the max-margin criterion and build it directly upon GBN models to explicitly optimize the classification performance of the GBNs. The advantages and disadvantages of the two frameworks are discussed and experimentally compared. Both of them demonstrate strong power in learning discriminative parameters of GBNs for neuroimaging based brain network analysis, as well as maintaining reasonable representation capacity. The contributions of this paper also include a new Directed Acyclic Graph (DAG) constraint with theoretical guarantee to ensure the graph validity of GBN.

* 16 pages and 5 figures for the article (excluding appendix) 

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FRNET: Flattened Residual Network for Infant MRI Skull Stripping

Apr 11, 2019
Qian Zhang, Li Wang, Xiaopeng Zong, Weili Lin, Gang Li, Dinggang Shen

Skull stripping for brain MR images is a basic segmentation task. Although many methods have been proposed, most of them focused mainly on the adult MR images. Skull stripping for infant MR images is more challenging due to the small size and dynamic intensity changes of brain tissues during the early ages. In this paper, we propose a novel CNN based framework to robustly extract brain region from infant MR image without any human assistance. Specifically, we propose a simplified but more robust flattened residual network architecture (FRnet). We also introduce a new boundary loss function to highlight ambiguous and low contrast regions between brain and non-brain regions. To make the whole framework more robust to MR images with different imaging quality, we further introduce an artifact simulator for data augmentation. We have trained and tested our proposed framework on a large dataset (N=343), covering newborns to 48-month-olds, and obtained performance better than the state-of-the-art methods in all age groups.

* 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI) 

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Deep Learning based Inter-Modality Image Registration Supervised by Intra-Modality Similarity

Apr 28, 2018
Xiaohuan Cao, Jianhua Yang, Li Wang, Zhong Xue, Qian Wang, Dinggang Shen

Non-rigid inter-modality registration can facilitate accurate information fusion from different modalities, but it is challenging due to the very different image appearances across modalities. In this paper, we propose to train a non-rigid inter-modality image registration network, which can directly predict the transformation field from the input multimodal images, such as CT and MR images. In particular, the training of our inter-modality registration network is supervised by intra-modality similarity metric based on the available paired data, which is derived from a pre-aligned CT and MR dataset. Specifically, in the training stage, to register the input CT and MR images, their similarity is evaluated on the warped MR image and the MR image that is paired with the input CT. So that, the intra-modality similarity metric can be directly applied to measure whether the input CT and MR images are well registered. Moreover, we use the idea of dual-modality fashion, in which we measure the similarity on both CT modality and MR modality. In this way, the complementary anatomies in both modalities can be jointly considered to more accurately train the inter-modality registration network. In the testing stage, the trained inter-modality registration network can be directly applied to register the new multimodal images without any paired data. Experimental results have shown that, the proposed method can achieve promising accuracy and efficiency for the challenging non-rigid inter-modality registration task and also outperforms the state-of-the-art approaches.

* 8 pages, 4 figures 

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Regularized Spherical Polar Fourier Diffusion MRI with Optimal Dictionary Learning

Jul 02, 2013
Jian Cheng, Tianzi Jiang, Rachid Deriche, Dinggang Shen, Pew-Thian Yap

Compressed Sensing (CS) takes advantage of signal sparsity or compressibility and allows superb signal reconstruction from relatively few measurements. Based on CS theory, a suitable dictionary for sparse representation of the signal is required. In diffusion MRI (dMRI), CS methods were proposed to reconstruct diffusion-weighted signal and the Ensemble Average Propagator (EAP), and there are two kinds of Dictionary Learning (DL) methods: 1) Discrete Representation DL (DR-DL), and 2) Continuous Representation DL (CR-DL). DR-DL is susceptible to numerical inaccuracy owing to interpolation and regridding errors in a discretized q-space. In this paper, we propose a novel CR-DL approach, called Dictionary Learning - Spherical Polar Fourier Imaging (DL-SPFI) for effective compressed-sensing reconstruction of the q-space diffusion-weighted signal and the EAP. In DL-SPFI, an dictionary that sparsifies the signal is learned from the space of continuous Gaussian diffusion signals. The learned dictionary is then adaptively applied to different voxels using a weighted LASSO framework for robust signal reconstruction. The adaptive dictionary is proved to be optimal. Compared with the start-of-the-art CR-DL and DR-DL methods proposed by Merlet et al. and Bilgic et al., espectively, our work offers the following advantages. First, the learned dictionary is proved to be optimal for Gaussian diffusion signals. Second, to our knowledge, this is the first work to learn a voxel-adaptive dictionary. The importance of the adaptive dictionary in EAP reconstruction will be demonstrated theoretically and empirically. Third, optimization in DL-SPFI is only performed in a small subspace resided by the SPF coefficients, as opposed to the q-space approach utilized by Merlet et al. The experiment results demonstrate the advantages of DL-SPFI over the original SPF basis and Bilgic et al.'s method.

* Accepted by MICCAI 2013. Abstract shortened to respect the arXiv limit of 1920 characters 

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Automatic Data Augmentation by Learning the Deterministic Policy

Oct 22, 2019
Yinghuan Shi, Tiexin Qin, Yong Liu, Jiwen Lu, Yang Gao, Dinggang Shen

Aiming to produce sufficient and diverse training samples, data augmentation has been demonstrated for its effectiveness in training deep models. Regarding that the criterion of the best augmentation is challenging to define, we in this paper present a novel learning-based augmentation method termed as DeepAugNet, which formulates the final augmented data as a collection of several sequentially augmented subsets. Specifically, the current augmented subset is required to maximize the performance improvement compared with the last augmented subset by learning the deterministic augmentation policy using deep reinforcement learning. By introducing an unified optimization goal, DeepAugNet intends to combine the data augmentation and the deep model training in an end-to-end training manner which is realized by simultaneously training a hybrid architecture of dueling deep Q-learning algorithm and a surrogate deep model. We extensively evaluated our proposed DeepAugNet on various benchmark datasets including Fashion MNIST, CUB, CIFAR-100 and WebCaricature. Compared with the current state-of-the-arts, our method can achieve a significant improvement in small-scale datasets, and a comparable performance in large-scale datasets. Code will be available soon.

* Sorry for withdrawing our paper, there exists a mistake in the experiment, and we will reupload once we have fixed it 

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Real-Time Quality Assessment of Pediatric MRI via Semi-Supervised Deep Nonlocal Residual Neural Networks

Apr 07, 2019
Siyuan Liu, Kim-Han Thung, Weili Lin, Pew-Thian Yap, Dinggang~Shen

In this paper, we introduce an image quality assessment (IQA) method for pediatric T1- and T2-weighted MR images. IQA is first performed slice-wise using a nonlocal residual neural network (NR-Net) and then volume-wise by agglomerating the slice QA results using random forest. Our method requires only a small amount of quality-annotated images for training and is designed to be robust to annotation noise that might occur due to rater errors and the inevitable mix of good and bad slices in an image volume. Using a small set of quality-assessed images, we pre-train NR-Net to annotate each image slice with an initial quality rating (i.e., pass, questionable, fail), which we then refine by semi-supervised learning and iterative self-training. Experimental results demonstrate that our method, trained using only samples of modest size, exhibit great generalizability, capable of real-time (milliseconds per volume) large-scale IQA with near-perfect accuracy.


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Deep Morphological Simplification Network (MS-Net) for Guided Registration of Brain Magnetic Resonance Images

Feb 06, 2019
Dongming Wei, Zhengwang Wu, Gang Li, Xiaohuan Cao, Dinggang Shen, Qian Wang

Objective: Deformable brain MR image registration is challenging due to large inter-subject anatomical variation. For example, the highly complex cortical folding pattern makes it hard to accurately align corresponding cortical structures of individual images. In this paper, we propose a novel deep learning way to simplify the difficult registration problem of brain MR images. Methods: We train a morphological simplification network (MS-Net), which can generate a "simple" image with less anatomical details based on the "complex" input. With MS-Net, the complexity of the fixed image or the moving image under registration can be reduced gradually, thus building an individual (simplification) trajectory represented by MS-Net outputs. Since the generated images at the ends of the two trajectories (of the fixed and moving images) are so simple and very similar in appearance, they are easy to register. Thus, the two trajectories can act as a bridge to link the fixed and the moving images, and guide their registration. Results: Our experiments show that the proposed method can achieve highly accurate registration performance on different datasets (i.e., NIREP, LPBA, IBSR, CUMC, and MGH). Moreover, the method can be also easily transferred across diverse image datasets and obtain superior accuracy on surface alignment. Conclusion and Significance: We propose MS-Net as a powerful and flexible tool to simplify brain MR images and their registration. To our knowledge, this is the first work to simplify brain MR image registration by deep learning, instead of estimating deformation field directly.


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Deep Embedding Convolutional Neural Network for Synthesizing CT Image from T1-Weighted MR Image

Nov 09, 2017
Lei Xiang, Qian Wang, Xiyao Jin, Dong Nie, Yu Qiao, Dinggang Shen

Recently, more and more attention is drawn to the field of medical image synthesis across modalities. Among them, the synthesis of computed tomography (CT) image from T1-weighted magnetic resonance (MR) image is of great importance, although the mapping between them is highly complex due to large gaps of appearances of the two modalities. In this work, we aim to tackle this MR-to-CT synthesis by a novel deep embedding convolutional neural network (DECNN). Specifically, we generate the feature maps from MR images, and then transform these feature maps forward through convolutional layers in the network. We can further compute a tentative CT synthesis from the midway of the flow of feature maps, and then embed this tentative CT synthesis back to the feature maps. This embedding operation results in better feature maps, which are further transformed forward in DECNN. After repeat-ing this embedding procedure for several times in the network, we can eventually synthesize a final CT image in the end of the DECNN. We have validated our proposed method on both brain and prostate datasets, by also compar-ing with the state-of-the-art methods. Experimental results suggest that our DECNN (with repeated embedding op-erations) demonstrates its superior performances, in terms of both the perceptive quality of the synthesized CT image and the run-time cost for synthesizing a CT image.


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Interactive Medical Image Segmentation via Point-Based Interaction and Sequential Patch Learning

May 09, 2018
Jinquan Sun, Yinghuan Shi, Yang Gao, Lei Wang, Luping Zhou, Wanqi Yang, Dinggang Shen

Due to low tissue contrast, irregular object appearance, and unpredictable location variation, segmenting the objects from different medical imaging modalities (e.g., CT, MR) is considered as an important yet challenging task. In this paper, we present a novel method for interactive medical image segmentation with the following merits. (1) Our design is fundamentally different from previous pure patch-based and image-based segmentation methods. We observe that during delineation, the physician repeatedly check the inside-outside intensity changing to determine the boundary, which indicates that comparison in an inside-outside manner is extremely important. Thus, we innovatively model our segmentation task as learning the representation of the bi-directional sequential patches, starting from (or ending in) the given central point of the object. This can be realized by our proposed ConvRNN network embedded with a gated memory propagation unit. (2) Unlike previous interactive methods (requiring bounding box or seed points), we only ask the physician to merely click on the rough central point of the object before segmentation, which could simultaneously enhance the performance and reduce the segmentation time. (3) We utilize our method in a multi-level framework for better performance. We systematically evaluate our method in three different segmentation tasks including CT kidney tumor, MR prostate, and PROMISE12 challenge, showing promising results compared with state-of-the-art methods. The code is available here: \href{https://github.com/sunalbert/Sequential-patch-based-segmentation}{Sequential-patch-based-segmentation}.


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