arXiv subjects

Cuntai Guan

Publications and source records attributed to Cuntai Guan.

At least 55 records · Page 3Linked to original sources

arXiv2023

SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Network for Efficient and Generalizable Protein-Protein Interaction Prediction

Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance degradation under complex real-world scenarios due to various factors, e.g., label scarcity and domain shift. In this paper, we propose a self-ensembling multigraph neural network (SemiGNN-PPI) that can effectively predict PPIs while being both efficient and generalizable. In SemiGNN-PPI, we not only model the protein correlations but explore the label dependencies by constructing and processing multiple graphs from the perspectives of both features and labels in the graph learning process. We further marry GNN with Mean Teacher to effectively leverage unlabeled graph-structured PPI data for self-ensemble graph learning. We also design multiple graph consistency constraints to align the student and teacher graphs in the feature embedding space, enabling the student model to better learn from the teacher model by incorporating more relationships. Extensive experiments on PPI datasets of different scales with different evaluation settings demonstrate that SemiGNN-PPI outperforms state-of-the-art PPI prediction methods, particularly in challenging scenarios such as training with limited annotations and testing on unseen data.

q-bio.MN↗

arXiv2023

Meta-hallucinator: Towards Few-Shot Cross-Modality Cardiac Image Segmentation

Domain shift and label scarcity heavily limit deep learning applications to various medical image analysis tasks. Unsupervised domain adaptation (UDA) techniques have recently achieved promising cross-modality medical image segmentation by transferring knowledge from a label-rich source domain to an unlabeled target domain. However, it is also difficult to collect annotations from the source domain in many clinical applications, rendering most prior works suboptimal with the label-scarce source domain, particularly for few-shot scenarios, where only a few source labels are accessible. To achieve efficient few-shot cross-modality segmentation, we propose a novel transformation-consistent meta-hallucination framework, meta-hallucinator, with the goal of learning to diversify data distributions and generate useful examples for enhancing cross-modality performance. In our framework, hallucination and segmentation models are jointly trained with the gradient-based meta-learning strategy to synthesize examples that lead to good segmentation performance on the target domain. To further facilitate data hallucination and cross-domain knowledge transfer, we develop a self-ensembling model with a hallucination-consistent property. Our meta-hallucinator can seamlessly collaborate with the meta-segmenter for learning to hallucinate with mutual benefits from a combined view of meta-learning and self-ensembling learning. Extensive studies on MM-WHS 2017 dataset for cross-modality cardiac segmentation demonstrate that our method performs favorably against various approaches by a lot in the few-shot UDA scenario.

cs.CV↗

arXiv2023

Multimodal Continuous Emotion Recognition: A Technical Report for ABAW5

We used two multimodal models for continuous valence-arousal recognition using visual, audio, and linguistic information. The first model is the same as we used in ABAW2 and ABAW3, which employs the leader-follower attention. The second model has the same architecture for spatial and temporal encoding. As for the fusion block, it employs a compact and straightforward channel attention, borrowed from the End2You toolkit. Unlike our previous attempts that use Vggish feature directly as the audio feature, this time we feed the pre-trained VGG model using logmel-spectrogram and finetune it during the training. To make full use of the data and alleviate over-fitting, cross-validation is carried out. The code is available at https://github.com/sucv/ABAW3.

cs.MM↗

arXiv2023

MS-MT: Multi-Scale Mean Teacher with Contrastive Unpaired Translation for Cross-Modality Vestibular Schwannoma and Cochlea Segmentation

Domain shift has been a long-standing issue for medical image segmentation. Recently, unsupervised domain adaptation (UDA) methods have achieved promising cross-modality segmentation performance by distilling knowledge from a label-rich source domain to a target domain without labels. In this work, we propose a multi-scale self-ensembling based UDA framework for automatic segmentation of two key brain structures i.e., Vestibular Schwannoma (VS) and Cochlea on high-resolution T2 images. First, a segmentation-enhanced contrastive unpaired image translation module is designed for image-level domain adaptation from source T1 to target T2. Next, multi-scale deep supervision and consistency regularization are introduced to a mean teacher network for self-ensemble learning to further close the domain gap. Furthermore, self-training and intensity augmentation techniques are utilized to mitigate label scarcity and boost cross-modality segmentation performance. Our method demonstrates promising segmentation performance with a mean Dice score of 83.8% and 81.4% and an average asymmetric surface distance (ASSD) of 0.55 mm and 0.26 mm for the VS and Cochlea, respectively in the validation phase of the crossMoDA 2022 challenge.

eess.IV↗

arXiv2022

Federated Graph Neural Networks: Overview, Techniques and Challenges

With its capability to deal with graph data, which is widely found in practical applications, graph neural networks (GNNs) have attracted significant research attention in recent years. As societies become increasingly concerned with the need for data privacy protection, GNNs face the need to adapt to this new normal. Besides, as clients in Federated Learning (FL) may have relationships, more powerful tools are required to utilize such implicit information to boost performance. This has led to the rapid development of the emerging research field of federated graph neural networks (FedGNNs). This promising interdisciplinary field is highly challenging for interested researchers to grasp. The lack of an insightful survey on this topic further exacerbates the entry difficulty. In this paper, we bridge this gap by offering a comprehensive survey of this emerging field. We propose a 2-dimensional taxonomy of the FedGNNs literature: 1) the main taxonomy provides a clear perspective on the integration of GNNs and FL by analyzing how GNNs enhance FL training as well as how FL assists GNNs training, and 2) the auxiliary taxonomy provides a view on how FedGNNs deal with heterogeneity across FL clients. Through discussions of key ideas, challenges, and limitations of existing works, we envision future research directions that can help build more robust, explainable, efficient, fair, inductive, and comprehensive FedGNNs.

cs.DC↗

arXiv2022

Quantifying Explainability of Saliency Methods in Deep Neural Networks with a Synthetic Dataset

Post-hoc analysis is a popular category in eXplainable artificial intelligence (XAI) study. In particular, methods that generate heatmaps have been used to explain the deep neural network (DNN), a black-box model. Heatmaps can be appealing due to the intuitive and visual ways to understand them but assessing their qualities might not be straightforward. Different ways to assess heatmaps' quality have their own merits and shortcomings. This paper introduces a synthetic dataset that can be generated adhoc along with the ground-truth heatmaps for more objective quantitative assessment. Each sample data is an image of a cell with easily recognized features that are distinguished from localization ground-truth mask, hence facilitating a more transparent assessment of different XAI methods. Comparison and recommendations are made, shortcomings are clarified along with suggestions for future research directions to handle the finer details of select post-hoc analysis methods. Furthermore, mabCAM is introduced as the heatmap generation method compatible with our ground-truth heatmaps. The framework is easily generalizable and uses only standard deep learning components.

cs.CV↗

arXiv2022

LGGNet: Learning from Local-Global-Graph Representations for Brain-Computer Interface

Neuropsychological studies suggest that co-operative activities among different brain functional areas drive high-level cognitive processes. To learn the brain activities within and among different functional areas of the brain, we propose LGGNet, a novel neurologically inspired graph neural network, to learn local-global-graph representations of electroencephalography (EEG) for Brain-Computer Interface (BCI). The input layer of LGGNet comprises a series of temporal convolutions with multi-scale 1D convolutional kernels and kernel-level attentive fusion. It captures temporal dynamics of EEG which then serves as input to the proposed local and global graph-filtering layers. Using a defined neurophysiologically meaningful set of local and global graphs, LGGNet models the complex relations within and among functional areas of the brain. Under the robust nested cross-validation settings, the proposed method is evaluated on three publicly available datasets for four types of cognitive classification tasks, namely, the attention, fatigue, emotion, and preference classification tasks. LGGNet is compared with state-of-the-art methods, such as DeepConvNet, EEGNet, R2G-STNN, TSception, RGNN, AMCNN-DGCN, HRNN and GraphNet. The results show that LGGNet outperforms these methods, and the improvements are statistically significant (p<0.05) in most cases. The results show that bringing neuroscience prior knowledge into neural network design yields an improvement of classification performance. The source code can be found at https://github.com/yi-ding-cs/LGG

cs.NE↗

arXiv2022

LE-UDA: Label-efficient unsupervised domain adaptation for medical image segmentation

While deep learning methods hitherto have achieved considerable success in medical image segmentation, they are still hampered by two limitations: (i) reliance on large-scale well-labeled datasets, which are difficult to curate due to the expert-driven and time-consuming nature of pixel-level annotations in clinical practices, and (ii) failure to generalize from one domain to another, especially when the target domain is a different modality with severe domain shifts. Recent unsupervised domain adaptation~(UDA) techniques leverage abundant labeled source data together with unlabeled target data to reduce the domain gap, but these methods degrade significantly with limited source annotations. In this study, we address this underexplored UDA problem, investigating a challenging but valuable realistic scenario, where the source domain not only exhibits domain shift~w.r.t. the target domain but also suffers from label scarcity. In this regard, we propose a novel and generic framework called ``Label-Efficient Unsupervised Domain Adaptation"~(LE-UDA). In LE-UDA, we construct self-ensembling consistency for knowledge transfer between both domains, as well as a self-ensembling adversarial learning module to achieve better feature alignment for UDA. To assess the effectiveness of our method, we conduct extensive experiments on two different tasks for cross-modality segmentation between MRI and CT images. Experimental results demonstrate that the proposed LE-UDA can efficiently leverage limited source labels to improve cross-domain segmentation performance, outperforming state-of-the-art UDA approaches in the literature. Code is available at: https://github.com/jacobzhaoziyuan/LE-UDA.

eess.IV↗

arXiv2022

Decomposing 3D Neuroimaging into 2+1D Processing for Schizophrenia Recognition

Deep learning has been successfully applied to recognizing both natural images and medical images. However, there remains a gap in recognizing 3D neuroimaging data, especially for psychiatric diseases such as schizophrenia and depression that have no visible alteration in specific slices. In this study, we propose to process the 3D data by a 2+1D framework so that we can exploit the powerful deep 2D Convolutional Neural Network (CNN) networks pre-trained on the huge ImageNet dataset for 3D neuroimaging recognition. Specifically, 3D volumes of Magnetic Resonance Imaging (MRI) metrics (grey matter, white matter, and cerebrospinal fluid) are decomposed to 2D slices according to neighboring voxel positions and inputted to 2D CNN models pre-trained on the ImageNet to extract feature maps from three views (axial, coronal, and sagittal). Global pooling is applied to remove redundant information as the activation patterns are sparsely distributed over feature maps. Channel-wise and slice-wise convolutions are proposed to aggregate the contextual information in the third view dimension unprocessed by the 2D CNN model. Multi-metric and multi-view information are fused for final prediction. Our approach outperforms handcrafted feature-based machine learning, deep feature approach with a support vector machine (SVM) classifier and 3D CNN models trained from scratch with better cross-validation results on publicly available Northwestern University Schizophrenia Dataset and the results are replicated on another independent dataset.

eess.IV↗

arXiv2022

A Transformer-based deep neural network model for SSVEP classification

Steady-state visual evoked potential (SSVEP) is one of the most commonly used control signal in the brain-computer interface (BCI) systems. However, the conventional spatial filtering methods for SSVEP classification highly depend on the subject-specific calibration data. The need for the methods that can alleviate the demand for the calibration data become urgent. In recent years, developing the methods that can work in inter-subject classification scenario has become a promising new direction. As the popular deep learning model nowadays, Transformer has excellent performance and has been used in EEG signal classification tasks. Therefore, in this study, we propose a deep learning model for SSVEP classification based on Transformer structure in inter-subject classification scenario, termed as SSVEPformer, which is the first application of the transformer to the classification of SSVEP. Inspired by previous studies, the model adopts the frequency spectrum of SSVEP data as input, and explores the spectral and spatial domain information for classification. Furthermore, to fully utilize the harmonic information, an extended SSVEPformer based on the filter bank technology (FB-SSVEPformer) is proposed to further improve the classification performance. Experiments were conducted using two open datasets (Dataset 1: 10 subjects, 12-class task; Dataset 2: 35 subjects, 40-class task) in the inter-subject classification scenario. The experimental results show that the proposed models could achieve better results in terms of classification accuracy and information transfer rate, compared with other baseline methods. The proposed model validates the feasibility of deep learning models based on Transformer structure for SSVEP classification task, and could serve as a potential model to alleviate the calibration procedure in the practical application of SSVEP-based BCI systems.

q-bio.NC↗

arXiv2022

Tensor-CSPNet: A Novel Geometric Deep Learning Framework for Motor Imagery Classification

Deep learning (DL) has been widely investigated in a vast majority of applications in electroencephalography (EEG)-based brain-computer interfaces (BCIs), especially for motor imagery (MI) classification in the past five years. The mainstream DL methodology for the MI-EEG classification exploits the temporospatial patterns of EEG signals using convolutional neural networks (CNNs), which have remarkably succeeded in visual images. However, since the statistical characteristics of visual images depart radically from EEG signals, a natural question arises whether an alternative network architecture exists apart from CNNs. To address this question, we propose a novel geometric deep learning (GDL) framework called Tensor-CSPNet, which characterizes spatial covariance matrices derived from EEG signals on symmetric positive definite (SPD) manifolds and fully captures the temporospatiofrequency patterns using existing deep neural networks on SPD manifolds, integrating with experiences from many successful MI-EEG classifiers to optimize the framework. In the experiments, Tensor-CSPNet attains or slightly outperforms the current state-of-the-art performance on the cross-validation and holdout scenarios in two commonly-used MI-EEG datasets. Moreover, the visualization and interpretability analyses also exhibit the validity of Tensor-CSPNet for the MI-EEG classification. To conclude, in this study, we provide a feasible answer to the question by generalizing the DL methodologies on SPD manifolds, which indicates the start of a specific GDL methodology for the MI-EEG classification.

eess.SP↗

arXiv2022

OCTAve: 2D en face Optical Coherence Tomography Angiography Vessel Segmentation in Weakly-Supervised Learning with Locality Augmentation

While there have been increased researches using deep learning techniques for the extraction of vascular structure from the 2D en face OCTA, for such approach, it is known that the data annotation process on the curvilinear structure like the retinal vasculature is very costly and time consuming, albeit few tried to address the annotation problem. In this work, we propose the application of the scribble-base weakly-supervised learning method to automate the pixel-level annotation. The proposed method, called OCTAve, combines the weakly-supervised learning using scribble-annotated ground truth augmented with an adversarial and a novel self-supervised deep supervision. Our novel mechanism is designed to utilize the discriminative outputs from the discrimination layer of a UNet-like architecture where the Kullback-Liebler Divergence between the aggregate discriminative outputs and the segmentation map predicate is minimized during the training. This combined method leads to the better localization of the vascular structure as shown in our experiments. We validate our proposed method on the large public datasets i.e., ROSE, OCTA-500. The segmentation performance is compared against both state-of-the-art fully-supervised and scribble-based weakly-supervised approaches. The implementation of our work used in the experiments is located at [LINK].

eess.IV↗

arXiv2022

ADAST: Attentive Cross-domain EEG-based Sleep Staging Framework with Iterative Self-Training

Sleep staging is of great importance in the diagnosis and treatment of sleep disorders. Recently, numerous data-driven deep learning models have been proposed for automatic sleep staging. They mainly train the model on a large public labeled sleep dataset and test it on a smaller one with subjects of interest. However, they usually assume that the train and test data are drawn from the same distribution, which may not hold in real-world scenarios. Unsupervised domain adaption (UDA) has been recently developed to handle this domain shift problem. However, previous UDA methods applied for sleep staging have two main limitations. First, they rely on a totally shared model for the domain alignment, which may lose the domain-specific information during feature extraction. Second, they only align the source and target distributions globally without considering the class information in the target domain, which hinders the classification performance of the model while testing. In this work, we propose a novel adversarial learning framework called ADAST to tackle the domain shift problem in the unlabeled target domain. First, we develop an unshared attention mechanism to preserve the domain-specific features in both domains. Second, we design an iterative self-training strategy to improve the classification performance on the target domain via target domain pseudo labels. We also propose dual distinct classifiers to increase the robustness and quality of the pseudo labels. The experimental results on six cross-domain scenarios validate the efficacy of our proposed framework and its advantage over state-of-the-art UDA methods. The source code is available at https://github.com/emadeldeen24/ADAST.

cs.LG↗

arXiv2022

ACT-Net: Asymmetric Co-Teacher Network for Semi-supervised Memory-efficient Medical Image Segmentation

While deep models have shown promising performance in medical image segmentation, they heavily rely on a large amount of well-annotated data, which is difficult to access, especially in clinical practice. On the other hand, high-accuracy deep models usually come in large model sizes, limiting their employment in real scenarios. In this work, we propose a novel asymmetric co-teacher framework, ACT-Net, to alleviate the burden on both expensive annotations and computational costs for semi-supervised knowledge distillation. We advance teacher-student learning with a co-teacher network to facilitate asymmetric knowledge distillation from large models to small ones by alternating student and teacher roles, obtaining tiny but accurate models for clinical employment. To verify the effectiveness of our ACT-Net, we employ the ACDC dataset for cardiac substructure segmentation in our experiments. Extensive experimental results demonstrate that ACT-Net outperforms other knowledge distillation methods and achieves lossless segmentation performance with 250x fewer parameters.

eess.IV↗

arXiv2022

MMGL: Multi-Scale Multi-View Global-Local Contrastive learning for Semi-supervised Cardiac Image Segmentation

With large-scale well-labeled datasets, deep learning has shown significant success in medical image segmentation. However, it is challenging to acquire abundant annotations in clinical practice due to extensive expertise requirements and costly labeling efforts. Recently, contrastive learning has shown a strong capacity for visual representation learning on unlabeled data, achieving impressive performance rivaling supervised learning in many domains. In this work, we propose a novel multi-scale multi-view global-local contrastive learning (MMGL) framework to thoroughly explore global and local features from different scales and views for robust contrastive learning performance, thereby improving segmentation performance with limited annotations. Extensive experiments on the MM-WHS dataset demonstrate the effectiveness of MMGL framework on semi-supervised cardiac image segmentation, outperforming the state-of-the-art contrastive learning methods by a large margin.

eess.IV↗

arXiv2022

Self-supervised Assisted Active Learning for Skin Lesion Segmentation

Label scarcity has been a long-standing issue for biomedical image segmentation, due to high annotation costs and professional requirements. Recently, active learning (AL) strategies strive to reduce annotation costs by querying a small portion of data for annotation, receiving much traction in the field of medical imaging. However, most of the existing AL methods have to initialize models with some randomly selected samples followed by active selection based on various criteria, such as uncertainty and diversity. Such random-start initialization methods inevitably introduce under-value redundant samples and unnecessary annotation costs. For the purpose of addressing the issue, we propose a novel self-supervised assisted active learning framework in the cold-start setting, in which the segmentation model is first warmed up with self-supervised learning (SSL), and then SSL features are used for sample selection via latent feature clustering without accessing labels. We assess our proposed methodology on skin lesions segmentation task. Extensive experiments demonstrate that our approach is capable of achieving promising performance with substantial improvements over existing baselines.

eess.IV↗

arXiv2022

TSception: Capturing Temporal Dynamics and Spatial Asymmetry from EEG for Emotion Recognition

The high temporal resolution and the asymmetric spatial activations are essential attributes of electroencephalogram (EEG) underlying emotional processes in the brain. To learn the temporal dynamics and spatial asymmetry of EEG towards accurate and generalized emotion recognition, we propose TSception, a multi-scale convolutional neural network that can classify emotions from EEG. TSception consists of dynamic temporal, asymmetric spatial, and high-level fusion layers, which learn discriminative representations in the time and channel dimensions simultaneously. The dynamic temporal layer consists of multi-scale 1D convolutional kernels whose lengths are related to the sampling rate of EEG, which learns the dynamic temporal and frequency representations of EEG. The asymmetric spatial layer takes advantage of the asymmetric EEG patterns for emotion, learning the discriminative global and hemisphere representations. The learned spatial representations will be fused by a high-level fusion layer. Using more generalized cross-validation settings, the proposed method is evaluated on two publicly available datasets DEAP and MAHNOB-HCI. The performance of the proposed network is compared with prior reported methods such as SVM, KNN, FBFgMDM, FBTSC, Unsupervised learning, DeepConvNet, ShallowConvNet, and EEGNet. TSception achieves higher classification accuracies and F1 scores than other methods in most of the experiments. The codes are available at https://github.com/yi-ding-cs/TSception

cs.LG↗

arXiv2022

Continuous Emotion Recognition using Visual-audio-linguistic information: A Technical Report for ABAW3

We propose a cross-modal co-attention model for continuous emotion recognition using visual-audio-linguistic information. The model consists of four blocks. The visual, audio, and linguistic blocks are used to learn the spatial-temporal features of the multi-modal input. A co-attention block is designed to fuse the learned features with the multi-head co-attention mechanism. The visual encoding from the visual block is concatenated with the attention feature to emphasize the visual information. To make full use of the data and alleviate over-fitting, cross-validation is carried out on the training and validation set. The concordance correlation coefficient (CCC) centering is used to merge the results from each fold. The achieved CCC on the test set is $0.520$ for valence and $0.602$ for arousal, which significantly outperforms the baseline method with the corresponding CCC of 0.180 and 0.170 for valence and arousal, respectively. The code is available at https://github.com/sucv/ABAW3.

cs.MM↗