Jianzhong He

Jianzhong He, Fan Zhang, Yiang Pan et al.

The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body. Diffusion MRI tractography is the only method that enables the study of the anatomy and variability of the CST pathway in human health. In this work, we explored the performance of six widely used tractography methods for reconstructing the CST and its somatotopic organization. We perform experiments using diffusion MRI data from the Human Connectome Project. Four quantitative measurements including reconstruction rate, the WM-GM interface coverage, anatomical distribution of streamlines, and correlation with cortical volumes to assess the advantages and limitations of each method. Overall, we conclude that while current tractography methods have made progress toward the well-known challenge of improving the reconstruction of the lateral projections of the CST, the overall problem of performing a comprehensive CST reconstruction, including clinically important projections in the lateral (hand and face area) and medial portions (leg area), remains an important challenge for diffusion MRI tractography.

Yuqian Chen, Fan Zhang, Chaoyi Zhang et al.

White matter tract microstructure has been shown to influence neuropsychological scores of cognitive performance. However, prediction of these scores from white matter tract data has not been attempted. In this paper, we propose a deep-learning-based framework for neuropsychological score prediction using microstructure measurements estimated from diffusion magnetic resonance imaging (dMRI) tractography, focusing on predicting performance on a receptive vocabulary assessment task based on a critical fiber tract for language, the arcuate fasciculus (AF). We directly utilize information from all points in a fiber tract, without the need to average data along the fiber as is traditionally required by diffusion MRI tractometry methods. Specifically, we represent the AF as a point cloud with microstructure measurements at each point, enabling adoption of point-based neural networks. We improve prediction performance with the proposed Paired-Siamese Loss that utilizes information about differences between continuous neuropsychological scores. Finally, we propose a Critical Region Localization (CRL) algorithm to localize informative anatomical regions containing points with strong contributions to the prediction results. Our method is evaluated on data from 806 subjects from the Human Connectome Project dataset. Results demonstrate superior neuropsychological score prediction performance compared to baseline methods. We discover that critical regions in the AF are strikingly consistent across subjects, with the highest number of strongly contributing points located in frontal cortical regions (i.e., the rostral middle frontal, pars opercularis, and pars triangularis), which are strongly implicated as critical areas for language processes.

Sipei Li, Jianzhong He, Tengfei Xue et al.

The retinogeniculate pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time-consuming, has high clinical and expert labor costs, and affected by inter-observer variability. In this paper, we present what we believe is the first deep learning framework, namely DeepRGVP, to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure-informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a simple and successful streamline-level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non-RGVP streamlines. We perform comparisons with several state-of-the-art deep learning methods that were designed for tractography parcellation, and we show superior RGVP identification results using DeepRGVP.

Shengsen Wu, Yan Bai, Yihang Lou et al.

Real-world visual search systems involve deployments on multiple platforms with different computing and storage resources. Deploying a unified model that suits the minimal-constrain platforms leads to limited accuracy. It is expected to deploy models with different capacities adapting to the resource constraints, which requires features extracted by these models to be aligned in the metric space. The method to achieve feature alignments is called ``compatible learning''. Existing research mainly focuses on the one-to-one compatible paradigm, which is limited in learning compatibility among multiple models. We propose a Switchable representation learning Framework with Self-Compatibility (SFSC). SFSC generates a series of compatible sub-models with different capacities through one training process. The optimization of sub-models faces gradients conflict, and we mitigate this problem from the perspective of the magnitude and direction. We adjust the priorities of sub-models dynamically through uncertainty estimation to co-optimize sub-models properly. Besides, the gradients with conflicting directions are projected to avoid mutual interference. SFSC achieves state-of-the-art performance on the evaluated datasets.

Jinze Li, Yan Bai, Yihang Lou et al.

Few-shot class-incremental learning(FSCIL) focuses on designing learning algorithms that can continually learn a sequence of new tasks from a few samples without forgetting old ones. The difficulties are that training on a sequence of limited data from new tasks leads to severe overfitting issues and causes the well-known catastrophic forgetting problem. Existing researches mainly utilize the image information, such as storing the image knowledge of previous tasks or limiting classifiers updating. However, they ignore analyzing the informative and less noisy text information of class labels. In this work, we propose leveraging the label-text information by adopting the memory prompt. The memory prompt can learn new data sequentially, and meanwhile store the previous knowledge. Furthermore, to optimize the memory prompt without undermining the stored knowledge, we propose a stimulation-based training strategy. It optimizes the memory prompt depending on the image embedding stimulation, which is the distribution of the image embedding elements. Experiments show that our proposed method outperforms all prior state-of-the-art approaches, significantly mitigating the catastrophic forgetting and overfitting problems.

Xiongkun Linghu, Yan Bai, Yihang Lou et al.

Few-Shot Classification(FSC) aims to generalize from base classes to novel classes given very limited labeled samples, which is an important step on the path toward human-like machine learning. State-of-the-art solutions involve learning to find a good metric and representation space to compute the distance between samples. Despite the promising accuracy performance, how to model uncertainty for metric-based FSC methods effectively is still a challenge. To model uncertainty, We place a distribution over class probability based on the theory of evidence. As a result, uncertainty modeling and metric learning can be decoupled. To reduce the uncertainty of classification, we propose a Bayesian evidence fusion theorem. Given observed samples, the network learns to get posterior distribution parameters given the prior parameters produced by the pre-trained network. Detailed gradient analysis shows that our method provides a smooth optimization target and can capture the uncertainty. The proposed method is agnostic to metric learning strategies and can be implemented as a plug-and-play module. We integrate our method into several newest FSC methods and demonstrate the improved accuracy and uncertainty quantification on standard FSC benchmarks.

Yuanjing Feng, Lei Xie, Jingqiang Wang et al.

Tractography traces the peak directions extracted from fiber orientation distribution (FOD) suffering from ambiguous spatial correspondences between diffusion directions and fiber geometry, which is prone to producing erroneous tracks while missing true positive connections. The peaks-based tractography methods 'locally' reconstructed streamlines in 'single to single' manner, thus lacking of global information about the trend of the whole fiber bundle. In this work, we propose a novel tractography method based on a bundle-specific tractogram distribution function by using a higher-order streamline differential equation, which reconstructs the streamline bundles in 'cluster to cluster' manner. A unified framework for any higher-order streamline differential equation is presented to describe the fiber bundles with disjoint streamlines defined based on the diffusion tensor vector field. At the global level, the tractography process is simplified as the estimation of bundle-specific tractogram distribution (BTD) coefficients by minimizing the energy optimization model, and is used to characterize the relations between BTD and diffusion tensor vector under the prior guidance by introducing the tractogram bundle information to provide anatomic priors. Experiments are performed on simulated Hough, Sine, Circle data, ISMRM 2015 Tractography Challenge data, FiberCup data, and in vivo data from the Human Connectome Project (HCP) data for qualitative and quantitative evaluation. The results demonstrate that our approach can reconstruct the complex global fiber bundles directly. BTD reduces the error deviation and accumulation at the local level and shows better results in reconstructing long-range, twisting, and large fanning tracts.

Jianzhong He, Shiliang Zhang, Ming Yang et al.

Exploiting multi-scale representations is critical to improve edge detection for objects at different scales. To extract edges at dramatically different scales, we propose a Bi-Directional Cascade Network (BDCN) structure, where an individual layer is supervised by labeled edges at its specific scale, rather than directly applying the same supervision to all CNN outputs. Furthermore, to enrich multi-scale representations learned by BDCN, we introduce a Scale Enhancement Module (SEM) which utilizes dilated convolution to generate multi-scale features, instead of using deeper CNNs or explicitly fusing multi-scale edge maps. These new approaches encourage the learning of multi-scale representations in different layers and detect edges that are well delineated by their scales. Learning scale dedicated layers also results in compact network with a fraction of parameters. We evaluate our method on three datasets, i.e., BSDS500, NYUDv2, and Multicue, and achieve ODS Fmeasure of 0.828, 1.3% higher than current state-of-the art on BSDS500. The code has been available at https://github.com/pkuCactus/BDCN.

Shanshan Wang, Shoujun Yu, Jian Cheng et al.

Diffusion magnetic resonance imaging (dMRI) provides critical insights into the microstructural and connectional organization of the human brain. However, the availability of high-field, open-access datasets that include raw k-space data for advanced research remains limited. To address this gap, we introduce Diff5T, a first comprehensive 5.0 Tesla diffusion MRI dataset focusing on the human brain. This dataset includes raw k-space data and reconstructed diffusion images, acquired using a variety of imaging protocols. Diff5T is designed to support the development and benchmarking of innovative methods in artifact correction, image reconstruction, image preprocessing, diffusion modelling and tractography. The dataset features a wide range of diffusion parameters, including multiple b-values and gradient directions, allowing extensive research applications in studying human brain microstructure and connectivity. With its emphasis on open accessibility and detailed benchmarks, Diff5T serves as a valuable resource for advancing human brain mapping research using diffusion MRI, fostering reproducibility, and enabling collaboration across the neuroscience and medical imaging communities.

Lei Xie, Jiahao Huang, Jiawei Zhang et al.

Cranial nerves (CNs) play a crucial role in various essential functions of the human brain, and mapping their pathways from diffusion MRI (dMRI) provides valuable preoperative insights into the spatial relationships between individual CNs and key tissues. However, mapping a comprehensive and detailed CN atlas is challenging because of the unique anatomical structures of each CN pair and the complexity of the skull base environment.In this work, we present what we believe to be the first study to develop a comprehensive diffusion tractography atlas for automated mapping of CN pathways in the human brain. The CN atlas is generated by fiber clustering by using the streamlines generated by multi-parametric fiber tractography for each pair of CNs. Instead of disposable clustering, we explore a new strategy of multi-stage fiber clustering for multiple analysis of approximately 1,000,000 streamlines generated from the 50 subjects from the Human Connectome Project (HCP). Quantitative and visual experiments demonstrate that our CN atlas achieves high spatial correspondence with expert manual annotations on multiple acquisition sites, including the HCP dataset, the Multi-shell Diffusion MRI (MDM) dataset and two clinical cases of pituitary adenoma patients. The proposed CN atlas can automatically identify 8 fiber bundles associated with 5 pairs of CNs, including the optic nerve CN II, oculomotor nerve CN III, trigeminal nerve CN V and facial-vestibulocochlear nerve CN VII/VIII, and its robustness is demonstrated experimentally. This work contributes to the field of diffusion imaging by facilitating more efficient and automated mapping the pathways of multiple pairs of CNs, thereby enhancing the analysis and understanding of complex brain structures through visualization of their spatial relationships with nearby anatomy.

Haotian Yan, Bocheng Guo, Jianzhong He et al.

Streamline classification is essential to identify anatomically meaningful white matter tracts from diffusion MRI (dMRI) tractography. However, current streamline classification methods rely primarily on the geometric features of the streamline trajectory, failing to distinguish between functionally distinct fiber tracts with similar pathways. To address this, we introduce a novel dual-stream streamline classification framework that jointly analyzes dMRI and functional MRI (fMRI) data to enhance the functional coherence of tract parcellation. We design a novel network that performs streamline classification using a pretrained backbone model for full streamline trajectories, while augmenting with an auxiliary network that processes fMRI signals from fiber endpoint regions. We demonstrate our method by parcellating the corticospinal tract (CST) into its four somatotopic subdivisions. Experimental results from ablation studies and comparisons with state-of-the-art methods demonstrate our approach's superior performance.

Lei Xie, Huajun Zhou, Junxiong Huang et al.

The segmentation of cranial nerves (CNs) tract provides a valuable quantitative tool for the analysis of the morphology and trajectory of individual CNs. Multimodal CNs tract segmentation networks, e.g., CNTSeg, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI, have achieved promising segmentation performance. However, it is laborious or even infeasible to collect complete multimodal data in clinical practice due to limitations in equipment, user privacy, and working conditions. In this work, we propose a novel arbitrary-modal fusion network for volumetric CNs tract segmentation, called CNTSeg-v2, which trains one model to handle different combinations of available modalities. Instead of directly combining all the modalities, we select T1-weighted (T1w) images as the primary modality due to its simplicity in data acquisition and contribution most to the results, which supervises the information selection of other auxiliary modalities. Our model encompasses an Arbitrary-Modal Collaboration Module (ACM) designed to effectively extract informative features from other auxiliary modalities, guided by the supervision of T1w images. Meanwhile, we construct a Deep Distance-guided Multi-stage (DDM) decoder to correct small errors and discontinuities through signed distance maps to improve segmentation accuracy. We evaluate our CNTSeg-v2 on the Human Connectome Project (HCP) dataset and the clinical Multi-shell Diffusion MRI (MDM) dataset. Extensive experimental results show that our CNTSeg-v2 achieves state-of-the-art segmentation performance, outperforming all competing methods.

Ruihuang Li, Xu Jia, Jianzhong He et al.

Most existing domain adaptation methods focus on adaptation from only one source domain, however, in practice there are a number of relevant sources that could be leveraged to help improve performance on target domain. We propose a novel approach named T-SVDNet to address the task of Multi-source Domain Adaptation (MDA), which is featured by incorporating Tensor Singular Value Decomposition (T-SVD) into a neural network's training pipeline. Overall, high-order correlations among multiple domains and categories are fully explored so as to better bridge the domain gap. Specifically, we impose Tensor-Low-Rank (TLR) constraint on a tensor obtained by stacking up a group of prototypical similarity matrices, aiming at capturing consistent data structure across different domains. Furthermore, to avoid negative transfer brought by noisy source data, we propose a novel uncertainty-aware weighting strategy to adaptively assign weights to different source domains and samples based on the result of uncertainty estimation. Extensive experiments conducted on public benchmarks demonstrate the superiority of our model in addressing the task of MDA compared to state-of-the-art methods.

Takashi Isobe, Xu Jia, Shuaijun Chen et al.

Recently unsupervised domain adaptation for the semantic segmentation task has become more and more popular due to high-cost of pixel-level annotation on real-world images. However, most domain adaptation methods are only restricted to single-source-single-target pair, and can not be directly extended to multiple target domains. In this work, we propose a collaborative learning framework to achieve unsupervised multi-target domain adaptation. An unsupervised domain adaptation expert model is first trained for each source-target pair and is further encouraged to collaborate with each other through a bridge built between different target domains. These expert models are further improved by adding the regularization of making the consistent pixel-wise prediction for each sample with the same structured context. To obtain a single model that works across multiple target domains, we propose to simultaneously learn a student model which is trained to not only imitate the output of each expert on the corresponding target domain, but also to pull different expert close to each other with regularization on their weights. Extensive experiments demonstrate that the proposed method can effectively exploit rich structured information contained in both labeled source domain and multiple unlabeled target domains. Not only does it perform well across multiple target domains but also performs favorably against state-of-the-art unsupervised domain adaptation methods specially trained on a single source-target pair

Jianzhong He, Xu Jia, Shuaijun Chen et al.

Multi-source unsupervised domain adaptation~(MSDA) aims at adapting models trained on multiple labeled source domains to an unlabeled target domain. In this paper, we propose a novel multi-source domain adaptation framework based on collaborative learning for semantic segmentation. Firstly, a simple image translation method is introduced to align the pixel value distribution to reduce the gap between source domains and target domain to some extent. Then, to fully exploit the essential semantic information across source domains, we propose a collaborative learning method for domain adaptation without seeing any data from target domain. In addition, similar to the setting of unsupervised domain adaptation, unlabeled target domain data is leveraged to further improve the performance of domain adaptation. This is achieved by additionally constraining the outputs of multiple adaptation models with pseudo labels online generated by an ensembled model. Extensive experiments and ablation studies are conducted on the widely-used domain adaptation benchmark datasets in semantic segmentation. Our proposed method achieves 59.0\% mIoU on the validation set of Cityscapes by training on the labeled Synscapes and GTA5 datasets and unlabeled training set of Cityscapes. It significantly outperforms all previous state-of-the-arts single-source and multi-source unsupervised domain adaptation methods.

Shuaijun Chen, Xu Jia, Jianzhong He et al.

Data-driven based approaches, in spite of great success in many tasks, have poor generalization when applied to unseen image domains, and require expensive cost of annotation especially for dense pixel prediction tasks such as semantic segmentation. Recently, both unsupervised domain adaptation (UDA) from large amounts of synthetic data and semi-supervised learning (SSL) with small set of labeled data have been studied to alleviate this issue. However, there is still a large gap on performance compared to their supervised counterparts. We focus on a more practical setting of semi-supervised domain adaptation (SSDA) where both a small set of labeled target data and large amounts of labeled source data are available. To address the task of SSDA, a novel framework based on dual-level domain mixing is proposed. The proposed framework consists of three stages. First, two kinds of data mixing methods are proposed to reduce domain gap in both region-level and sample-level respectively. We can obtain two complementary domain-mixed teachers based on dual-level mixed data from holistic and partial views respectively. Then, a student model is learned by distilling knowledge from these two teachers. Finally, pseudo labels of unlabeled data are generated in a self-training manner for another few rounds of teachers training. Extensive experimental results have demonstrated the effectiveness of our proposed framework on synthetic-to-real semantic segmentation benchmarks.

Longhui Wei, Lingxi Xie, Jianzhong He et al.

Recently, contrastive learning has largely advanced the progress of unsupervised visual representation learning. Pre-trained on ImageNet, some self-supervised algorithms reported higher transfer learning performance compared to fully-supervised methods, seeming to deliver the message that human labels hardly contribute to learning transferrable visual features. In this paper, we defend the usefulness of semantic labels but point out that fully-supervised and self-supervised methods are pursuing different kinds of features. To alleviate this issue, we present a new algorithm named Supervised Contrastive Adjustment in Neighborhood (SCAN) that maximally prevents the semantic guidance from damaging the appearance feature embedding. In a series of downstream tasks, SCAN achieves superior performance compared to previous fully-supervised and self-supervised methods, and sometimes the gain is significant. More importantly, our study reveals that semantic labels are useful in assisting self-supervised methods, opening a new direction for the community.

Xinyue Huo, Lingxi Xie, Jianzhong He et al.

In medical image analysis, semi-supervised learning is an effective method to extract knowledge from a small amount of labeled data and a large amount of unlabeled data. This paper focuses on a popular pipeline known as self learning, and points out a weakness named lazy learning that refers to the difficulty for a model to learn from the pseudo labels generated by itself. To alleviate this issue, we propose ATSO, an asynchronous version of teacher-student optimization. ATSO partitions the unlabeled data into two subsets and alternately uses one subset to fine-tune the model and updates the label on the other subset. We evaluate ATSO on two popular medical image segmentation datasets and show its superior performance in various semi-supervised settings. With slight modification, ATSO transfers well to natural image segmentation for autonomous driving data.