Tao Zhou

Tao Zhou, Lingyu Shu, Zixing Zhang et al.

Deep learning has shown great promise in physiological signal analysis, yet its progress is hindered by heterogeneous data formats, inconsistent preprocessing strategies, fragmented model pipelines, and non-reproducible experimental setups. To address these limitations, we present Tyee, a unified, modular, and fully-integrated configurable toolkit designed for intelligent physiological healthcare. Tyee introduces three key innovations: (1) a unified data interface and configurable preprocessing pipeline for 12 kinds of signal modalities; (2) a modular and extensible architecture enabling flexible integration and rapid prototyping across tasks; and (3) end-to-end workflow configuration, promoting reproducible and scalable experimentation. Tyee demonstrates consistent practical effectiveness and generalizability, outperforming or matching baselines across all evaluated tasks (with state-of-the-art results on 12 of 13 datasets). The Tyee toolkit is released at https://github.com/SmileHnu/Tyee and actively maintained.

Zhengwang Xia, Tao Zhou, Saqib Mamoon et al.

Brain network provides important insights for the diagnosis of many brain disorders, and how to effectively model the brain structure has become one of the core issues in the domain of brain imaging analysis. Recently, various computational methods have been proposed to estimate the causal relationship (i.e., effective connectivity) between brain regions. Compared with traditional correlation-based methods, effective connectivity can provide the direction of information flow, which may provide additional information for the diagnosis of brain diseases. However, existing methods either ignore the fact that there is a temporal-lag in the information transmission across brain regions, or simply set the temporal-lag value between all brain regions to a fixed value. To overcome these issues, we design an effective temporal-lag neural network (termed ETLN) to simultaneously infer the causal relationships and the temporal-lag values between brain regions, which can be trained in an end-to-end manner. In addition, we also introduce three mechanisms to better guide the modeling of brain networks. The evaluation results on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database demonstrate the effectiveness of the proposed method.

Ruiqi Wu, Chenran Zhang, Jianle Zhang et al.

Current fundus image analysis models are predominantly built for specific tasks relying on individual datasets. The learning process is usually based on data-driven paradigm without prior knowledge, resulting in poor transferability and generalizability. To address this issue, we propose MM-Retinal, a multi-modal dataset that encompasses high-quality image-text pairs collected from professional fundus diagram books. Moreover, enabled by MM-Retinal, we present a novel Knowledge-enhanced foundational pretraining model which incorporates Fundus Image-Text expertise, called KeepFIT. It is designed with image similarity-guided text revision and mixed training strategy to infuse expert knowledge. Our proposed fundus foundation model achieves state-of-the-art performance across six unseen downstream tasks and holds excellent generalization ability in zero-shot and few-shot scenarios. MM-Retinal and KeepFIT are available at https://github.com/lxirich/MM-Retinal.

Ruiqi Wu, Na Su, Chenran Zhang et al.

Vision-language pretraining (VLP) has been investigated to generalize across diverse downstream tasks for fundus image analysis. Although recent methods showcase promising achievements, they significantly rely on large-scale private image-text data but pay less attention to the pretraining manner, which limits their further advancements. In this work, we introduce MM-Retinal V2, a high-quality image-text paired dataset comprising CFP, FFA, and OCT image modalities. Then, we propose a novel fundus vision-language pretraining model, namely KeepFIT V2, which is pretrained by integrating knowledge from the elite data spark into categorical public datasets. Specifically, a preliminary textual pretraining is adopted to equip the text encoder with primarily ophthalmic textual knowledge. Moreover, a hybrid image-text knowledge injection module is designed for knowledge transfer, which is essentially based on a combination of global semantic concepts from contrastive learning and local appearance details from generative learning. Extensive experiments across zero-shot, few-shot, and linear probing settings highlight the generalization and transferability of KeepFIT V2, delivering performance competitive to state-of-the-art fundus VLP models trained on large-scale private image-text datasets. Our dataset and model are publicly available via https://github.com/lxirich/MM-Retinal.

Yuxin Xie, Tao Zhou, Yi Zhou et al.

Weakly-supervised medical image segmentation is a challenging task that aims to reduce the annotation cost while keep the segmentation performance. In this paper, we present a novel framework, SimTxtSeg, that leverages simple text cues to generate high-quality pseudo-labels and study the cross-modal fusion in training segmentation models, simultaneously. Our contribution consists of two key components: an effective Textual-to-Visual Cue Converter that produces visual prompts from text prompts on medical images, and a text-guided segmentation model with Text-Vision Hybrid Attention that fuses text and image features. We evaluate our framework on two medical image segmentation tasks: colonic polyp segmentation and MRI brain tumor segmentation, and achieve consistent state-of-the-art performance. Source code is available at: https://github.com/xyx1024/SimTxtSeg.

Keren Fu, Yao Jiang, Ge-Peng Ji et al.

Salient object detection (SOD) is a long-standing research topic in computer vision and has drawn an increasing amount of research interest in the past decade. This paper provides the first comprehensive review and benchmark for light field SOD, which has long been lacking in the saliency community. Firstly, we introduce preliminary knowledge on light fields, including theory and data forms, and then review existing studies on light field SOD, covering ten traditional models, seven deep learning-based models, one comparative study, and one brief review. Existing datasets for light field SOD are also summarized with detailed information and statistical analyses. Secondly, we benchmark nine representative light field SOD models together with several cutting-edge RGB-D SOD models on four widely used light field datasets, from which insightful discussions and analyses, including a comparison between light field SOD and RGB-D SOD models, are achieved. Besides, due to the inconsistency of datasets in their current forms, we further generate complete data and supplement focal stacks, depth maps and multi-view images for the inconsistent datasets, making them consistent and unified. Our supplemental data makes a universal benchmark possible. Lastly, because light field SOD is quite a special problem attributed to its diverse data representations and high dependency on acquisition hardware, making it differ greatly from other saliency detection tasks, we provide nine hints into the challenges and future directions, and outline several open issues. We hope our review and benchmarking could help advance research in this field. All the materials including collected models, datasets, benchmarking results, and supplemented light field datasets will be publicly available on our project site https://github.com/kerenfu/LFSOD-Survey.

Xiangde Luo, Jia Fu, Yunxin Zhong et al.

Radiation therapy is a primary and effective NasoPharyngeal Carcinoma (NPC) treatment strategy. The precise delineation of Gross Tumor Volumes (GTVs) and Organs-At-Risk (OARs) is crucial in radiation treatment, directly impacting patient prognosis. Previously, the delineation of GTVs and OARs was performed by experienced radiation oncologists. Recently, deep learning has achieved promising results in many medical image segmentation tasks. However, for NPC OARs and GTVs segmentation, few public datasets are available for model development and evaluation. To alleviate this problem, the SegRap2023 challenge was organized in conjunction with MICCAI2023 and presented a large-scale benchmark for OAR and GTV segmentation with 400 Computed Tomography (CT) scans from 200 NPC patients, each with a pair of pre-aligned non-contrast and contrast-enhanced CT scans. The challenge's goal was to segment 45 OARs and 2 GTVs from the paired CT scans. In this paper, we detail the challenge and analyze the solutions of all participants. The average Dice similarity coefficient scores for all submissions ranged from 76.68\% to 86.70\%, and 70.42\% to 73.44\% for OARs and GTVs, respectively. We conclude that the segmentation of large-size OARs is well-addressed, and more efforts are needed for GTVs and small-size or thin-structure OARs. The benchmark will remain publicly available here: https://segrap2023.grand-challenge.org

Zhangyong Tang, Tianyang Xu, Xuefeng Zhu et al.

The development of smart cities has led to the generation of massive amounts of multi-modal data in the context of a range of tasks that enable a comprehensive monitoring of the smart city infrastructure and services. This paper surveys one of the most critical tasks, multi-modal visual object tracking (MMVOT), from the perspective of multimodality analysis. Generally, MMVOT differs from single-modal tracking in four key aspects, data collection, modality alignment and annotation, model designing, and evaluation. Accordingly, we begin with an introduction to the relevant data modalities, laying the groundwork for their integration. This naturally leads to a discussion of challenges of multi-modal data collection, alignment, and annotation. Subsequently, existing MMVOT methods are categorised, based on different ways to deal with visible (RGB) and X modalities: programming the auxiliary X branch with replicated or non-replicated experimental configurations from the RGB branch. Here X can be thermal infrared (T), depth (D), event (E), near infrared (NIR), language (L), or sonar (S). The final part of the paper addresses evaluation and benchmarking. In summary, we undertake an omni survey of all aspects of multi-modal visual object tracking (VOT), covering six MMVOT tasks and featuring 338 references in total. In addition, we discuss the fundamental rhetorical question: Is multi-modal tracking always guaranteed to provide a superior solution to unimodal tracking with the help of information fusion, and if not, in what circumstances its application is beneficial. Furthermore, for the first time in this field, we analyse the distributions of the object categories in the existing MMVOT datasets, revealing their pronounced long-tail nature and a noticeable lack of animal categories when compared with RGB datasets.

Yu Zhang, Tao Zhou, Wei Wu et al.

Accurate electroencephalogram (EEG) pattern decoding for specific mental tasks is one of the key steps for the development of brain-computer interface (BCI), which is quite challenging due to the considerably low signal-to-noise ratio of EEG collected at the brain scalp. Machine learning provides a promising technique to optimize EEG patterns toward better decoding accuracy. However, existing algorithms do not effectively explore the underlying data structure capturing the true EEG sample distribution, and hence can only yield a suboptimal decoding accuracy. To uncover the intrinsic distribution structure of EEG data, we propose a clustering-based multi-task feature learning algorithm for improved EEG pattern decoding. Specifically, we perform affinity propagation-based clustering to explore the subclasses (i.e., clusters) in each of the original classes, and then assign each subclass a unique label based on a one-versus-all encoding strategy. With the encoded label matrix, we devise a novel multi-task learning algorithm by exploiting the subclass relationship to jointly optimize the EEG pattern features from the uncovered subclasses. We then train a linear support vector machine with the optimized features for EEG pattern decoding. Extensive experimental studies are conducted on three EEG datasets to validate the effectiveness of our algorithm in comparison with other state-of-the-art approaches. The improved experimental results demonstrate the outstanding superiority of our algorithm, suggesting its prominent performance for EEG pattern decoding in BCI applications.

Deng-Ping Fan, Ge-Peng Ji, Tao Zhou et al.

Colonoscopy is an effective technique for detecting colorectal polyps, which are highly related to colorectal cancer. In clinical practice, segmenting polyps from colonoscopy images is of great importance since it provides valuable information for diagnosis and surgery. However, accurate polyp segmentation is a challenging task, for two major reasons: (i) the same type of polyps has a diversity of size, color and texture; and (ii) the boundary between a polyp and its surrounding mucosa is not sharp. To address these challenges, we propose a parallel reverse attention network (PraNet) for accurate polyp segmentation in colonoscopy images. Specifically, we first aggregate the features in high-level layers using a parallel partial decoder (PPD). Based on the combined feature, we then generate a global map as the initial guidance area for the following components. In addition, we mine the boundary cues using a reverse attention (RA) module, which is able to establish the relationship between areas and boundary cues. Thanks to the recurrent cooperation mechanism between areas and boundaries, our PraNet is capable of calibrating any misaligned predictions, improving the segmentation accuracy. Quantitative and qualitative evaluations on five challenging datasets across six metrics show that our PraNet improves the segmentation accuracy significantly, and presents a number of advantages in terms of generalizability, and real-time segmentation efficiency.

Tao Zhou, Huazhu Fu, Yu Zhang et al.

Early and accurate prediction of overall survival (OS) time can help to obtain better treatment planning for brain tumor patients. Although many OS time prediction methods have been developed and obtain promising results, there are still several issues. First, conventional prediction methods rely on radiomic features at the local lesion area of a magnetic resonance (MR) volume, which may not represent the full image or model complex tumor patterns. Second, different types of scanners (i.e., multi-modal data) are sensitive to different brain regions, which makes it challenging to effectively exploit the complementary information across multiple modalities and also preserve the modality-specific properties. Third, existing methods focus on prediction models, ignoring complex data-to-label relationships. To address the above issues, we propose an end-to-end OS time prediction model; namely, Multi-modal Multi-channel Network (M2Net). Specifically, we first project the 3D MR volume onto 2D images in different directions, which reduces computational costs, while preserving important information and enabling pre-trained models to be transferred from other tasks. Then, we use a modality-specific network to extract implicit and high-level features from different MR scans. A multi-modal shared network is built to fuse these features using a bilinear pooling model, exploiting their correlations to provide complementary information. Finally, we integrate the outputs from each modality-specific network and the multi-modal shared network to generate the final prediction result. Experimental results demonstrate the superiority of our M2Net model over other methods.

Deng-Ping Fan, Tao Zhou, Ge-Peng Ji et al.

Coronavirus Disease 2019 (COVID-19) spread globally in early 2020, causing the world to face an existential health crisis. Automated detection of lung infections from computed tomography (CT) images offers a great potential to augment the traditional healthcare strategy for tackling COVID-19. However, segmenting infected regions from CT slices faces several challenges, including high variation in infection characteristics, and low intensity contrast between infections and normal tissues. Further, collecting a large amount of data is impractical within a short time period, inhibiting the training of a deep model. To address these challenges, a novel COVID-19 Lung Infection Segmentation Deep Network (Inf-Net) is proposed to automatically identify infected regions from chest CT slices. In our Inf-Net, a parallel partial decoder is used to aggregate the high-level features and generate a global map. Then, the implicit reverse attention and explicit edge-attention are utilized to model the boundaries and enhance the representations. Moreover, to alleviate the shortage of labeled data, we present a semi-supervised segmentation framework based on a randomly selected propagation strategy, which only requires a few labeled images and leverages primarily unlabeled data. Our semi-supervised framework can improve the learning ability and achieve a higher performance. Extensive experiments on our COVID-SemiSeg and real CT volumes demonstrate that the proposed Inf-Net outperforms most cutting-edge segmentation models and advances the state-of-the-art performance.

Tao Zhou, Huazhu Fu, Geng Chen et al.

Magnetic resonance imaging (MRI) is a widely used neuroimaging technique that can provide images of different contrasts (i.e., modalities). Fusing this multi-modal data has proven particularly effective for boosting model performance in many tasks. However, due to poor data quality and frequent patient dropout, collecting all modalities for every patient remains a challenge. Medical image synthesis has been proposed as an effective solution to this, where any missing modalities are synthesized from the existing ones. In this paper, we propose a novel Hybrid-fusion Network (Hi-Net) for multi-modal MR image synthesis, which learns a mapping from multi-modal source images (i.e., existing modalities) to target images (i.e., missing modalities). In our Hi-Net, a modality-specific network is utilized to learn representations for each individual modality, and a fusion network is employed to learn the common latent representation of multi-modal data. Then, a multi-modal synthesis network is designed to densely combine the latent representation with hierarchical features from each modality, acting as a generator to synthesize the target images. Moreover, a layer-wise multi-modal fusion strategy is presented to effectively exploit the correlations among multiple modalities, in which a Mixed Fusion Block (MFB) is proposed to adaptively weight different fusion strategies (i.e., element-wise summation, product, and maximization). Extensive experiments demonstrate that the proposed model outperforms other state-of-the-art medical image synthesis methods.

Fanghui Liu, Tao Zhou, Irene Y. H. Gu et al.

This paper presents a novel object tracking method based on approximated Locality-constrained Linear Coding (LLC). Rather than using a non-negativity constraint on encoding coefficients to guarantee these elements nonnegative, in this paper, the non-negativity constraint is substituted for a conventional $\ell_2$ norm regularization term in approximated LLC to obtain the similar nonnegative effect. And we provide a detailed and adequate explanation in theoretical analysis to clarify the rationality of this replacement. Instead of specifying fixed K nearest neighbors to construct the local dictionary, a series of different dictionaries with pre-defined numbers of nearest neighbors are selected. Weights of these various dictionaries are also learned from approximated LLC in the similar framework. In order to alleviate tracking drifts, we propose a simple and efficient occlusion detection method. The occlusion detection criterion mainly depends on whether negative templates are selected to represent the severe occluded target. Both qualitative and quantitative evaluations on several challenging sequences show that the proposed tracking algorithm achieves favorable performance compared with other state-of-the-art methods.

Fanghui Liu, Tao Zhou, Keren Fu et al.

The establishment of robust target appearance model over time is an overriding concern in visual tracking. In this paper, we propose an inverse nonnegative matrix factorization (NMF) method for robust appearance modeling. Rather than using a linear combination of nonnegative basis matrices for each target image patch in the conventional NMF, the proposed method is a reverse thought to conventional NMF tracker. It utilizes both the foreground and background information, and imposes a local coordinate constraint, where the basis matrix is sparse matrix from the linear combination of candidates with corresponding nonnegative coefficient vectors. Inverse NMF is used as a feature encoder, where the resulting coefficient vectors are fed into a SVM classifier for separating the target from the background. The proposed method is tested on several videos and compared with seven state-of-the-art methods. Our results have provided further support to the effectiveness and robustness of the proposed method.