Baiying Lei

Xiongri Shen, Jiaqi Wang, Zhenxi Song et al.

Mild cognitive impairment (MCI) and subjective cognitive decline (SCD) are closely associated with the early Alzheimer's disease continuum, where accurate and explainable diagnosis is important for early risk assessment and intervention. Existing connectome-based deep learning models can improve classification performance but often provide limited insight into disease-related functional and structural connectivity changes. This paper proposes an atlas-knowledge-guided Generative Counterfactual Attention-guided Network (GCAN) for explainable cognitive decline diagnosis using multimodal brain connectomes. GCAN formulates diagnosis as a source-to-target counterfactual generation problem, where target-label connectomes are generated from source-label inputs and their differences are used to construct counterfactual attention maps. To preserve connectome topology, an Atlas-aware Bidirectional Transformer (AABT) performs network-level token encoding and decoding under brain-atlas constraints. The framework is further extended from functional connectivity (FC) to joint functional and structural connectivity (SC) modeling, enabling counterfactual analysis of complementary functional reorganization and structural topology changes. Experiments on hospital-collected and ADNI datasets show that GCAN achieves competitive performance across HC vs. SCD, HC vs. MCI, and SCD vs. MCI classification tasks. Visualization, circular connectome analysis, CAM-based comparison, ablation studies, and confidence interval analysis further support the interpretability and reliability of the proposed framework. Modality-specific FC and SC pre-trained classifiers are used to provide target-state priors for counterfactual generation while being separated from the downstream diagnostic classifier to prevent data leakage.

Xuhang Chen, Baiying Lei, Chi-Man Pun et al.

Brain network analysis is essential for diagnosing and intervention for Alzheimer's disease (AD). However, previous research relied primarily on specific time-consuming and subjective toolkits. Only few tools can obtain the structural brain networks from brain diffusion tensor images (DTI). In this paper, we propose a diffusion based end-to-end brain network generative model Brain Diffuser that directly shapes the structural brain networks from DTI. Compared to existing toolkits, Brain Diffuser exploits more structural connectivity features and disease-related information by analyzing disparities in structural brain networks across subjects. For the case of Alzheimer's disease, the proposed model performs better than the results from existing toolkits on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database.

Xiongri Shen, Jiaqi Wang, Yi Zhong et al.

Functional and structural connectivity (FC/SC) are key multimodal biomarkers for brain analysis, yet their clinical utility is hindered by costly acquisition, complex preprocessing, and frequent missing modalities. Existing foundation models either process single modalities or lack explicit mechanisms for cross-modal and cross-scale consistency. We propose BrainCSD, a hierarchical mixture-of-experts (MoE) foundation model that jointly synthesizes FC/SC biomarkers and supports downstream decoding tasks (diagnosis and prediction). BrainCSD features three neuroanatomically grounded components: (1) a ROI-specific MoE that aligns regional activations from canonical networks (e.g., DMN, FPN) with a global atlas via contrastive consistency; (2) a Encoding-Activation MOE that models dynamic cross-time/gradient dependencies in fMRI/dMRI; and (3) a network-aware refinement MoE that enforces structural priors and symmetry at individual and population levels. Evaluated on the datasets under complete and missing-modality settings, BrainCSD achieves SOTA results: 95.6\% accuracy for MCI vs. CN classification without FC, low synthesis error (FC RMSE: 0.038; SC RMSE: 0.006), brain age prediction (MAE: 4.04 years), and MMSE score estimation (MAE: 1.72 points). Code is available in \href{https://github.com/SXR3015/BrainCSD}{BrainCSD}

Xiongri Shen, Jiaqi Wang, Yi Zhong et al.

Magnetic resonance imaging (MRI), especially functional MRI (fMRI) and diffusion MRI (dMRI), is essential for studying neurodegenerative diseases. However, missing modalities pose a major barrier to their clinical use. Although GAN- and diffusion model-based approaches have shown some promise in modality completion, they remain limited in fMRI-dMRI synthesis due to (1) significant BOLD vs. diffusion-weighted signal differences between fMRI and dMRI in time/gradient axis, and (2) inadequate integration of disease-related neuroanatomical patterns during generation. To address these challenges, we propose PDS, introducing two key innovations: (1) a pattern-aware dual-modal 3D diffusion framework for cross-modality learning, and (2) a tissue refinement network integrated with a efficient microstructure refinement to maintain structural fidelity and fine details. Evaluated on OASIS-3, ADNI, and in-house datasets, our method achieves state-of-the-art results, with PSNR/SSIM scores of 29.83 dB/90.84\% for fMRI synthesis (+1.54 dB/+4.12\% over baselines) and 30.00 dB/77.55\% for dMRI synthesis (+1.02 dB/+2.2\%). In clinical validation, the synthesized data show strong diagnostic performance, achieving 67.92\%/66.02\%/64.15\% accuracy (NC vs. MCI vs. AD) in hybrid real-synthetic experiments. Code is available in \href{https://github.com/SXR3015/PDS}{PDS GitHub Repository}

Weiheng Yao, Zhihan Lyu, Mufti Mahmud et al.

Multi-modal neuroimaging analysis is crucial for a comprehensive understanding of brain function and pathology, as it allows for the integration of different imaging techniques, thus overcoming the limitations of individual modalities. However, the high costs and limited availability of certain modalities pose significant challenges. To address these issues, this paper proposes the Condition-Aligned Temporal Diffusion (CATD) framework for end-to-end cross-modal synthesis of neuroimaging, enabling the generation of functional magnetic resonance imaging (fMRI)-detected Blood Oxygen Level Dependent (BOLD) signals from more accessible Electroencephalography (EEG) signals. By constructing Conditionally Aligned Block (CAB), heterogeneous neuroimages are aligned into a latent space, achieving a unified representation that provides the foundation for cross-modal transformation in neuroimaging. The combination with the constructed Dynamic Time-Frequency Segmentation (DTFS) module also enables the use of EEG signals to improve the temporal resolution of BOLD signals, thus augmenting the capture of the dynamic details of the brain. Experimental validation demonstrates that the framework improves the accuracy of brain activity state prediction by 9.13% (reaching 69.8%), enhances the diagnostic accuracy of brain disorders by 4.10% (reaching 99.55%), effectively identifies abnormal brain regions, enhancing the temporal resolution of BOLD signals. The proposed framework establishes a new paradigm for cross-modal synthesis of neuroimaging by unifying heterogeneous neuroimaging data into a latent representation space, showing promise in medical applications such as improving Parkinson's disease prediction and identifying abnormal brain regions.

Huihui Fang, Fei Li, Junde Wu et al.

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge -- Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application.

Qiankun Zuo, Ling Chen, Yanyan Shen et al.

Effective connectivity estimation plays a crucial role in understanding the interactions and information flow between different brain regions. However, the functional time series used for estimating effective connectivity is derived from certain software, which may lead to large computing errors because of different parameter settings and degrade the ability to model complex causal relationships between brain regions. In this paper, a brain diffuser with hierarchical transformer (BDHT) is proposed to estimate effective connectivity for mild cognitive impairment (MCI) analysis. To our best knowledge, the proposed brain diffuser is the first generative model to apply diffusion models to the application of generating and analyzing multimodal brain networks. Specifically, the BDHT leverages structural connectivity to guide the reverse processes in an efficient way. It makes the denoising process more reliable and guarantees effective connectivity estimation accuracy. To improve denoising quality, the hierarchical denoising transformer is designed to learn multi-scale features in topological space. By stacking the multi-head attention and graph convolutional network, the graph convolutional transformer (GraphConformer) module is devised to enhance structure-function complementarity and improve the ability in noise estimation. Experimental evaluations of the denoising diffusion model demonstrate its effectiveness in estimating effective connectivity. The proposed model achieves superior performance in terms of accuracy and robustness compared to existing approaches. Moreover, the proposed model can identify altered directional connections and provide a comprehensive understanding of parthenogenesis for MCI treatment.

Qiankun Zuo, Baiying Lei, Ning Zhong et al.

Integrating the brain structural and functional connectivity features is of great significance in both exploring brain science and analyzing cognitive impairment clinically. However, it remains a challenge to effectively fuse structural and functional features in exploring the brain network. In this paper, a novel brain structure-function fusing-representation learning (BSFL) model is proposed to effectively learn fused representation from diffusion tensor imaging (DTI) and resting-state functional magnetic resonance imaging (fMRI) for mild cognitive impairment (MCI) analysis. Specifically, the decomposition-fusion framework is developed to first decompose the feature space into the union of the uniform and the unique spaces for each modality, and then adaptively fuse the decomposed features to learn MCI-related representation. Moreover, a knowledge-aware transformer module is designed to automatically capture local and global connectivity features throughout the brain. Also, a uniform-unique contrastive loss is further devised to make the decomposition more effective and enhance the complementarity of structural and functional features. The extensive experiments demonstrate that the proposed model achieves better performance than other competitive methods in predicting and analyzing MCI. More importantly, the proposed model could be a potential tool for reconstructing unified brain networks and predicting abnormal connections during the degenerative processes in MCI.

Huihui Fang, Fei Li, Huazhu Fu et al.

Age-related macular degeneration (AMD) is the leading cause of visual impairment among elderly in the world. Early detection of AMD is of great importance, as the vision loss caused by this disease is irreversible and permanent. Color fundus photography is the most cost-effective imaging modality to screen for retinal disorders. Cutting edge deep learning based algorithms have been recently developed for automatically detecting AMD from fundus images. However, there are still lack of a comprehensive annotated dataset and standard evaluation benchmarks. To deal with this issue, we set up the Automatic Detection challenge on Age-related Macular degeneration (ADAM), which was held as a satellite event of the ISBI 2020 conference. The ADAM challenge consisted of four tasks which cover the main aspects of detecting and characterizing AMD from fundus images, including detection of AMD, detection and segmentation of optic disc, localization of fovea, and detection and segmentation of lesions. As part of the challenge, we have released a comprehensive dataset of 1200 fundus images with AMD diagnostic labels, pixel-wise segmentation masks for both optic disc and AMD-related lesions (drusen, exudates, hemorrhages and scars, among others), as well as the coordinates corresponding to the location of the macular fovea. A uniform evaluation framework has been built to make a fair comparison of different models using this dataset. During the challenge, 610 results were submitted for online evaluation, with 11 teams finally participating in the onsite challenge. This paper introduces the challenge, the dataset and the evaluation methods, as well as summarizes the participating methods and analyzes their results for each task. In particular, we observed that the ensembling strategy and the incorporation of clinical domain knowledge were the key to improve the performance of the deep learning models.

Wen Yu, Baiying Lei, Yanyan Shen et al.

The diagnosis of early stages of Alzheimer's disease (AD) is essential for timely treatment to slow further deterioration. Visualizing the morphological features for the early stages of AD is of great clinical value. In this work, a novel Multidirectional Perception Generative Adversarial Network (MP-GAN) is proposed to visualize the morphological features indicating the severity of AD for patients of different stages. Specifically, by introducing a novel multidirectional mapping mechanism into the model, the proposed MP-GAN can capture the salient global features efficiently. Thus, by utilizing the class-discriminative map from the generator, the proposed model can clearly delineate the subtle lesions via MR image transformations between the source domain and the pre-defined target domain. Besides, by integrating the adversarial loss, classification loss, cycle consistency loss and \emph{L}1 penalty, a single generator in MP-GAN can learn the class-discriminative maps for multiple-classes. Extensive experimental results on Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate that MP-GAN achieves superior performance compared with the existing methods. The lesions visualized by MP-GAN are also consistent with what clinicians observe.

Qiankun Zuo, Baiying Lei, Shuqiang Wang et al.

Alzheimer's disease is characterized by alterations of the brain's structural and functional connectivity during its progressive degenerative processes. Existing auxiliary diagnostic methods have accomplished the classification task, but few of them can accurately evaluate the changing characteristics of brain connectivity. In this work, a prior guided adversarial representation learning and hypergraph perceptual network (PGARL-HPN) is proposed to predict abnormal brain connections using triple-modality medical images. Concretely, a prior distribution from the anatomical knowledge is estimated to guide multimodal representation learning using an adversarial strategy. Also, the pairwise collaborative discriminator structure is further utilized to narrow the difference of representation distribution. Moreover, the hypergraph perceptual network is developed to effectively fuse the learned representations while establishing high-order relations within and between multimodal images. Experimental results demonstrate that the proposed model outperforms other related methods in analyzing and predicting Alzheimer's disease progression. More importantly, the identified abnormal connections are partly consistent with the previous neuroscience discoveries. The proposed model can evaluate characteristics of abnormal brain connections at different stages of Alzheimer's disease, which is helpful for cognitive disease study and early treatment.

Junren Pan, Baiying Lei, Shuqiang Wang et al.

One of the main reasons for Alzheimer's disease (AD) is the disorder of some neural circuits. Existing methods for AD prediction have achieved great success, however, detecting abnormal neural circuits from the perspective of brain networks is still a big challenge. In this work, a novel decoupling generative adversarial network (DecGAN) is proposed to detect abnormal neural circuits for AD. Concretely, a decoupling module is designed to decompose a brain network into two parts: one part is composed of a few sparse graphs which represent the neural circuits largely determining the development of AD; the other part is a supplement graph, whose influence on AD can be ignored. Furthermore, the adversarial strategy is utilized to guide the decoupling module to extract the feature more related to AD. Meanwhile, by encoding the detected neural circuits to hypergraph data, an analytic module associated with the hyperedge neurons algorithm is designed to identify the neural circuits. More importantly, a novel sparse capacity loss based on the spatial-spectral hypergraph similarity is developed to minimize the intrinsic topological distribution of neural circuits, which can significantly improve the accuracy and robustness of the proposed model. Experimental results demonstrate that the proposed model can effectively detect the abnormal neural circuits at different stages of AD, which is helpful for pathological study and early treatment.

Bowen Hu, Baiying Lei, Shuqiang Wang et al.

3D shape reconstruction is essential in the navigation of minimally-invasive and auto robot-guided surgeries whose operating environments are indirect and narrow, and there have been some works that focused on reconstructing the 3D shape of the surgical organ through limited 2D information available. However, the lack and incompleteness of such information caused by intraoperative emergencies (such as bleeding) and risk control conditions have not been considered. In this paper, a novel hierarchical shape-perception network (HSPN) is proposed to reconstruct the 3D point clouds (PCs) of specific brains from one single incomplete image with low latency. A branching predictor and several hierarchical attention pipelines are constructed to generate point clouds that accurately describe the incomplete images and then complete these point clouds with high quality. Meanwhile, attention gate blocks (AGBs) are designed to efficiently aggregate geometric local features of incomplete PCs transmitted by hierarchical attention pipelines and internal features of reconstructing point clouds. With the proposed HSPN, 3D shape perception and completion can be achieved spontaneously. Comprehensive results measured by Chamfer distance and PC-to-PC error demonstrate that the performance of the proposed HSPN outperforms other competitive methods in terms of qualitative displays, quantitative experiment, and classification evaluation.

Junren Pan, Baiying Lei, Yanyan Shen et al.

Using multimodal neuroimaging data to characterize brain network is currently an advanced technique for Alzheimer's disease(AD) Analysis. Over recent years the neuroimaging community has made tremendous progress in the study of resting-state functional magnetic resonance imaging (rs-fMRI) derived from blood-oxygen-level-dependent (BOLD) signals and Diffusion Tensor Imaging (DTI) derived from white matter fiber tractography. However, Due to the heterogeneity and complexity between BOLD signals and fiber tractography, Most existing multimodal data fusion algorithms can not sufficiently take advantage of the complementary information between rs-fMRI and DTI. To overcome this problem, a novel Hypergraph Generative Adversarial Networks(HGGAN) is proposed in this paper, which utilizes Interactive Hyperedge Neurons module (IHEN) and Optimal Hypergraph Homomorphism algorithm(OHGH) to generate multimodal connectivity of Brain Network from rs-fMRI combination with DTI. To evaluate the performance of this model, We use publicly available data from the ADNI database to demonstrate that the proposed model not only can identify discriminative brain regions of AD but also can effectively improve classification performance.

Qiankun Zuo, Baiying Lei, Yanyan Shen et al.

Multimodal neuroimage can provide complementary information about the dementia, but small size of complete multimodal data limits the ability in representation learning. Moreover, the data distribution inconsistency from different modalities may lead to ineffective fusion, which fails to sufficiently explore the intra-modal and inter-modal interactions and compromises the disease diagnosis performance. To solve these problems, we proposed a novel multimodal representation learning and adversarial hypergraph fusion (MRL-AHF) framework for Alzheimer's disease diagnosis using complete trimodal images. First, adversarial strategy and pre-trained model are incorporated into the MRL to extract latent representations from multimodal data. Then two hypergraphs are constructed from the latent representations and the adversarial network based on graph convolution is employed to narrow the distribution difference of hyperedge features. Finally, the hyperedge-invariant features are fused for disease prediction by hyperedge convolution. Experiments on the public Alzheimer's Disease Neuroimaging Initiative(ADNI) database demonstrate that our model achieves superior performance on Alzheimer's disease detection compared with other related models and provides a possible way to understand the underlying mechanisms of disorder's progression by analyzing the abnormal brain connections.

Bowen Hu, Baiying Lei, Yanyan Shen et al.

Fusing medical images and the corresponding 3D shape representation can provide complementary information and microstructure details to improve the operational performance and accuracy in brain surgery. However, compared to the substantial image data, it is almost impossible to obtain the intraoperative 3D shape information by using physical methods such as sensor scanning, especially in minimally invasive surgery and robot-guided surgery. In this paper, a general generative adversarial network (GAN) architecture based on graph convolutional networks is proposed to reconstruct the 3D point clouds (PCs) of brains by using one single 2D image, thus relieving the limitation of acquiring 3D shape data during surgery. Specifically, a tree-structured generative mechanism is constructed to use the latent vector effectively and transfer features between hidden layers accurately. With the proposed generative model, a spontaneous image-to-PC conversion is finished in real-time. Competitive qualitative and quantitative experimental results have been achieved on our model. In multiple evaluation methods, the proposed model outperforms another common point cloud generative model PointOutNet.

Mohammad Hamghalam, Alejandro F. Frangi, Baiying Lei et al.

In large studies involving multi protocol Magnetic Resonance Imaging (MRI), it can occur to miss one or more sub-modalities for a given patient owing to poor quality (e.g. imaging artifacts), failed acquisitions, or hallway interrupted imaging examinations. In some cases, certain protocols are unavailable due to limited scan time or to retrospectively harmonise the imaging protocols of two independent studies. Missing image modalities pose a challenge to segmentation frameworks as complementary information contributed by the missing scans is then lost. In this paper, we propose a novel model, Multi-modal Gaussian Process Prior Variational Autoencoder (MGP-VAE), to impute one or more missing sub-modalities for a patient scan. MGP-VAE can leverage the Gaussian Process (GP) prior on the Variational Autoencoder (VAE) to utilize the subjects/patients and sub-modalities correlations. Instead of designing one network for each possible subset of present sub-modalities or using frameworks to mix feature maps, missing data can be generated from a single model based on all the available samples. We show the applicability of MGP-VAE on brain tumor segmentation where either, two, or three of four sub-modalities may be missing. Our experiments against competitive segmentation baselines with missing sub-modality on BraTS'19 dataset indicate the effectiveness of the MGP-VAE model for segmentation tasks.

Wei Wang, Xiang-Gen Xia, Chuanjiang He et al.

In this paper, we first present an arc based algorithm for fan-beam computed tomography (CT) reconstruction via applying Katsevich's helical CT formula to 2D fan-beam CT reconstruction. Then, we propose a new weighting function to deal with the redundant projection data. By extending the weighted arc based fan-beam algorithm to circle cone-beam geometry, we also obtain a new FDK-similar algorithm for circle cone-beam CT reconstruction. Experiments show that our methods can obtain higher PSNR and SSIM compared to the Parker-weighted conventional fan-beam algorithm and the FDK algorithm for super-short-scan trajectories.

Senrong You, Yong Liu, Baiying Lei et al.

Magnetic resonance imaging plays an important role in computer-aided diagnosis and brain exploration. However, limited by hardware, scanning time and cost, it's challenging to acquire high-resolution (HR) magnetic resonance (MR) image clinically. In this paper, fine perceptive generative adversarial networks (FP-GANs) is proposed to produce HR MR images from low-resolution counterparts. It can cope with the detail insensitive problem of the existing super-resolution model in a divide-and-conquer manner. Specifically, FP-GANs firstly divides an MR image into low-frequency global approximation and high-frequency anatomical texture in wavelet domain. Then each sub-band generative adversarial network (sub-band GAN) conquers the super-resolution procedure of each single sub-band image. Meanwhile, sub-band attention is deployed to tune focus between global and texture information. It can focus on sub-band images instead of feature maps to further enhance the anatomical reconstruction ability of FP-GANs. In addition, inverse discrete wavelet transformation (IDWT) is integrated into model for taking the reconstruction of whole image into account. Experiments on MultiRes_7T dataset demonstrate that FP-GANs outperforms the competing methods quantitatively and qualitatively.

Mohammad Hamghalam, Baiying Lei, Tianfu Wang

Structural magnetic resonance imaging (MRI) has been widely utilized for analysis and diagnosis of brain diseases. Automatic segmentation of brain tumors is a challenging task for computer-aided diagnosis due to low-tissue contrast in the tumor subregions. To overcome this, we devise a novel pixel-wise segmentation framework through a convolutional 3D to 2D MR patch conversion model to predict class labels of the central pixel in the input sliding patches. Precisely, we first extract 3D patches from each modality to calibrate slices through the squeeze and excitation (SE) block. Then, the output of the SE block is fed directly into subsequent bottleneck layers to reduce the number of channels. Finally, the calibrated 2D slices are concatenated to obtain multimodal features through a 2D convolutional neural network (CNN) for prediction of the central pixel. In our architecture, both local inter-slice and global intra-slice features are jointly exploited to predict class label of the central voxel in a given patch through the 2D CNN classifier. We implicitly apply all modalities through trainable parameters to assign weights to the contributions of each sequence for segmentation. Experimental results on the segmentation of brain tumors in multimodal MRI scans (BraTS'19) demonstrate that our proposed method can efficiently segment the tumor regions.

Shuqiang Wang, Zhuo Chen, Wen Yu et al.

The state-of-the-art deep learning methods have demonstrated impressive performance in segmentation tasks. However, the success of these methods depends on a large amount of manually labeled masks, which are expensive and time-consuming to be collected. In this work, a novel Consistent PerceptionGenerative Adversarial Network (CPGAN) is proposed for semi-supervised stroke lesion segmentation. The proposed CPGAN can reduce the reliance on fully labeled samples. Specifically, A similarity connection module (SCM) is designed to capture the information of multi-scale features. The proposed SCM can selectively aggregate the features at each position by a weighted sum. Moreover, a consistent perception strategy is introduced into the proposed model to enhance the effect of brain stroke lesion prediction for the unlabeled data. Furthermore, an assistant network is constructed to encourage the discriminator to learn meaningful feature representations which are often forgotten during training stage. The assistant network and the discriminator are employed to jointly decide whether the segmentation results are real or fake. The CPGAN was evaluated on the Anatomical Tracings of Lesions After Stroke (ATLAS). The experimental results demonstrate that the proposed network achieves superior segmentation performance. In semi-supervised segmentation task, the proposed CPGAN using only two-fifths of labeled samples outperforms some approaches using full labeled samples.

Wei Wang, Xiang-Gen Xia, Chuanjiang He et al.

In this paper, we first propose a variational model for the limited-angle computed tomography (CT) image reconstruction and then convert the model into an end-to-end deep network.We use the penalty method to solve the model and divide it into three iterative subproblems, where the first subproblem completes the sinograms by utilizing the prior information of sinograms in the frequency domain and the second refines the CT images by using the prior information of CT images in the spatial domain, and the last merges the outputs of the first two subproblems. In each iteration, we use the convolutional neural networks (CNNs) to approxiamte the solutions of the first two subproblems and, thus, obtain an end-to-end deep network for the limited-angle CT image reconstruction. Our network tackles both the sinograms and the CT images, and can simultaneously suppress the artifacts caused by the incomplete data and recover fine structural information in the CT images. Experimental results show that our method outperforms the existing algorithms for the limited-angle CT image reconstruction.

Shengye Hu, Baiying Lei, Yong Wang et al.

Fusing multi-modality medical images, such as MR and PET, can provide various anatomical or functional information about human body. But PET data is always unavailable due to different reasons such as cost, radiation, or other limitations. In this paper, we propose a 3D end-to-end synthesis network, called Bidirectional Mapping Generative Adversarial Networks (BMGAN), where image contexts and latent vector are effectively used and jointly optimized for brain MR-to-PET synthesis. Concretely, a bidirectional mapping mechanism is designed to embed the semantic information of PET images into the high dimensional latent space. And the 3D DenseU-Net generator architecture and the extensive objective functions are further utilized to improve the visual quality of synthetic results. The most appealing part is that the proposed method can synthesize the perceptually realistic PET images while preserving the diverse brain structures of different subjects. Experimental results demonstrate that the performance of the proposed method outperforms other competitive cross-modality synthesis methods in terms of quantitative measures, qualitative displays, and classification evaluation.

Wen Yu, Baiying Lei, Michael K. Ng et al.

It is of great significance to apply deep learning for the early diagnosis of Alzheimer's Disease (AD). In this work, a novel tensorizing GAN with high-order pooling is proposed to assess Mild Cognitive Impairment (MCI) and AD. By tensorizing a three-player cooperative game based framework, the proposed model can benefit from the structural information of the brain. By incorporating the high-order pooling scheme into the classifier, the proposed model can make full use of the second-order statistics of the holistic Magnetic Resonance Imaging (MRI) images. To the best of our knowledge, the proposed Tensor-train, High-pooling and Semi-supervised learning based GAN (THS-GAN) is the first work to deal with classification on MRI images for AD diagnosis. Extensive experimental results on Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset are reported to demonstrate that the proposed THS-GAN achieves superior performance compared with existing methods, and to show that both tensor-train and high-order pooling can enhance classification performance. The visualization of generated samples also shows that the proposed model can generate plausible samples for semi-supervised learning purpose.

Feng Zhou, Tao Chen, Baiying Lei

Amid the ongoing COVID-19 pandemic, whether COVID-19 patients with high risks can be recovered or not depends, to a large extent, on how early they will be treated appropriately before irreversible consequences are caused to the patients by the virus. In this research, we reported an explainable, intuitive, and accurate machine learning model based on logistic regression to predict the fatality rate of COVID-19 patients using only three important blood biomarkers, including lactic dehydrogenase, lymphocyte (%) and high-sensitivity C-reactive protein, and their interactions. We found that when the fatality probability produced by the logistic regression model was over 0.8, the model had the optimal performance in that it was able to predict patient fatalities more than 11.30 days on average with maximally 34.91 days in advance, an accumulative f1-score of 93.76% and and an accumulative accuracy score of 93.92%. Such a model can be used to identify COVID-19 patients with high risks with three blood biomarkers and help the medical systems around the world plan critical medical resources amid this pandemic.

Mohammad Hamghalam, Baiying Lei, Tianfu Wang

Magnetic resonance imaging (MRI) provides varying tissue contrast images of internal organs based on a strong magnetic field. Despite the non-invasive advantage of MRI in frequent imaging, the low contrast MR images in the target area make tissue segmentation a challenging problem. This paper demonstrates the potential benefits of image-to-image translation techniques to generate synthetic high tissue contrast (HTC) images. Notably, we adopt a new cycle generative adversarial network (CycleGAN) with an attention mechanism to increase the contrast within underlying tissues. The attention block, as well as training on HTC images, guides our model to converge on certain tissues. To increase the resolution of HTC images, we employ multi-stage architecture to focus on one particular tissue as a foreground and filter out the irrelevant background in each stage. This multi-stage structure also alleviates the common artifacts of the synthetic images by decreasing the gap between source and target domains. We show the application of our method for synthesizing HTC images on brain MR scans, including glioma tumor. We also employ HTC MR images in both the end-to-end and two-stage segmentation structure to confirm the effectiveness of these images. The experiments over three competitive segmentation baselines on BraTS 2018 dataset indicate that incorporating the synthetic HTC images in the multi-modal segmentation framework improves the average Dice scores 0.8%, 0.6%, and 0.5% on the whole tumor, tumor core, and enhancing tumor, respectively, while eliminating one real MRI sequence from the segmentation procedure.

Youyi Song, Lei Zhu, Baiying Lei et al.

Segmenting overlapping cytoplasm of cells in cervical smear images is a clinically essential task, for quantitatively measuring cell-level features in order to diagnose cervical cancer. This task, however, remains rather challenging, mainly due to the deficiency of intensity (or color) information in the overlapping region. Although shape prior-based models that compensate intensity deficiency by introducing prior shape information (shape priors) about cytoplasm are firmly established, they often yield visually implausible results, mainly because they model shape priors only by limited shape hypotheses about cytoplasm, exploit cytoplasm-level shape priors alone, and impose no shape constraint on the resulting shape of the cytoplasm. In this paper, we present a novel and effective shape prior-based approach, called constrained multi-shape evolution, that segments all overlapping cytoplasms in the clump simultaneously by jointly evolving each cytoplasm's shape guided by the modeled shape priors. We model local shape priors (cytoplasm--level) by an infinitely large shape hypothesis set which contains all possible shapes of the cytoplasm. In the shape evolution, we compensate intensity deficiency for the segmentation by introducing not only the modeled local shape priors but also global shape priors (clump--level) modeled by considering mutual shape constraints of cytoplasms in the clump. We also constrain the resulting shape in each evolution to be in the built shape hypothesis set, for further reducing implausible segmentation results. We evaluated the proposed method in two typical cervical smear datasets, and the extensive experimental results show that the proposed method is effective to segment overlapping cytoplasm, consistently outperforming the state-of-the-art methods.

Youyi Song, Zhen Yu, Teng Zhou et al.

Exploiting more information from ground truth (GT) images now is a new research direction for further improving CNN's performance in CT image segmentation. Previous methods focus on devising the loss function for fulfilling such a purpose. However, it is rather difficult to devise a general and optimization-friendly loss function. We here present a novel and practical method that exploits GT images beyond the loss function. Our insight is that feature maps of two CNNs trained respectively on GT and CT images should be similar on some metric space, because they both are used to describe the same objects for the same purpose. We hence exploit GT images by enforcing such two CNNs' feature maps to be consistent. We assess the proposed method on two data sets, and compare its performance to several competitive methods. Extensive experimental results show that the proposed method is effective, outperforming all the compared methods.

Wei Wang, Xiang-Gen Xia, Chuanjiang He et al.

A CT image can be well reconstructed when the sampling rate of the sinogram satisfies the Nyquist criteria and the sampled signal is noise-free. However, in practice, the sinogram is usually contaminated by noise, which degrades the quality of a reconstructed CT image. In this paper, we design a deep network for sinogram and CT image reconstruction. The network consists of two cascaded blocks that are linked by a filter backprojection (FBP) layer, where the former block is responsible for denoising and completing the sinograms while the latter is used to removing the noise and artifacts of the CT images. Experimental results show that the reconstructed CT images by our methods have the highest PSNR and SSIM in average compared to state of the art methods.

Xinzi He, Baiying Lei, Tianfu Wang

The accurate detection of lesion attributes is meaningful for both the computeraid diagnosis system and dermatologists decisions. However, unlike lesion segmentation and melenoma classification, there are few deep learning methods and literatures focusing on this task. Currently, the lesion attribute detection still remains challenging due to the extremely unbalanced class distribution and insufficient samples, as well as large intraclass and low interclass variations. To solve these problems, we propose a deep learning framework named superpixel attention network (SANet). Firstly, we segment input images into small regions and shuffle the obtained regions by the random shuttle mechanism (RSM). Secondly, we apply the SANet to capture discriminative features and reconstruct input images. Specifically, SANet contains two sub modules: superpixel average pooling and superpixel at tention module. We introduce a superpixel average pooling to reformulate the superpixel classification problem as a superpixel segmentation problem and a SAMis utilized to focus on discriminative superpixel regions and feature channels. Finally, we design a novel but effective loss, namely global balancing loss to address the serious data imbalance in ISIC 2018 Task 2 lesion attributes detection dataset. The proposed method achieves quite good performance on the ISIC 2018 Task 2 challenge.

Mohammad Hamghalam, Baiying Lei, Tianfu Wang

The magnetic resonance (MR) analysis of brain tumors is widely used for diagnosis and examination of tumor subregions. The overlapping area among the intensity distribution of healthy, enhancing, non-enhancing, and edema regions makes the automatic segmentation a challenging task. Here, we show that a convolutional neural network trained on high-contrast images can transform the intensity distribution of brain lesions in its internal subregions. Specifically, a generative adversarial network (GAN) is extended to synthesize high-contrast images. A comparison of these synthetic images and real images of brain tumor tissue in MR scans showed significant segmentation improvement and decreased the number of real channels for segmentation. The synthetic images are used as a substitute for real channels and can bypass real modalities in the multimodal brain tumor segmentation framework. Segmentation results on BraTS 2019 dataset demonstrate that our proposed approach can efficiently segment the tumor areas. In the end, we predict patient survival time based on volumetric features of the tumor subregions as well as the age of each case through several regression models.

Feng Zhou, Shu Kong, Charless Fowlkes et al.

Automated facial expression analysis has a variety of applications in human-computer interaction. Traditional methods mainly analyze prototypical facial expressions of no more than eight discrete emotions as a classification task. However, in practice, spontaneous facial expressions in naturalistic environment can represent not only a wide range of emotions, but also different intensities within an emotion family. In such situation, these methods are not reliable or adequate. In this paper, we propose to train deep convolutional neural networks (CNNs) to analyze facial expressions explainable in a dimensional emotion model. The proposed method accommodates not only a set of basic emotion expressions, but also a full range of other emotions and subtle emotion intensities that we both feel in ourselves and perceive in others in our daily life. Specifically, we first mapped facial expressions into dimensional measures so that we transformed facial expression analysis from a classification problem to a regression one. We then tested our CNN-based methods for facial expression regression and these methods demonstrated promising performance. Moreover, we improved our method by a bilinear pooling which encodes second-order statistics of features. We showed such bilinear-CNN models significantly outperformed their respective baselines.