Single-cell RNA sequencing (scRNA-seq) is essential for decoding tumor heterogeneity. However, pan-cancer research still faces two key challenges: learning discriminative and efficient single-cell representations, and establishing a comprehensive evaluation benchmark. In this paper, we introduce \algoname, a lightweight hybrid neural network that combines the strengths of Transformers and state-space models to achieve a balance between performance and efficiency. \algoname consists of a front-end local-context encoder with shared self-attention layers to capture complex, order-independent gene interactions; and a back-end global sequential feature decoder that efficiently integrates global context using a linear-time state-space model. This modular design preserves the expressive power of Transformers while leveraging the scalability of Mamba to enable transcriptome modeling, effectively capturing both local and global regulatory signals. To enable robust evaluation, we also construct a large-scale pan-cancer single-cell benchmark, \algoname Bench, containing over 3.5 million high-quality cells across 33 cancer subtypes, curated through a rigorous preprocessing pipeline. Experimental results show that \algoname outperforms state-of-the-art models on our pan-cancer benchmark (+4.0\%) and across multiple public tasks, including cell type annotation (+7.4\%), batch integration (+4.0\%) and multi-omics integration (+3.1\%).

Knowledge-based Visual Question Answering (KB-VQA) extends general Visual Question Answering by requiring external knowledge beyond the provided visual and textual inputs, facilitating more complex real-world applications. KB-VQA introduces unique challenges, including the alignment of heterogeneous information from diverse modalities and sources, the retrieval of relevant knowledge from large-scale and noisy repositories, and the execution of complex reasoning to infer answers from the combined context. With the advancement of large language models, KB-VQA systems have undergone a notable transformation, where LLMs serve as powerful knowledge repositories, retrieval-augmented generators and strong reasoners. Despite substantial progress, there is a lack of a recent, systematic survey that organizes and reviews the evolving landscape of existing KB-VQA methods. This survey aims to fill this gap by establishing a structured taxonomy of KB-VQA approaches and decomposing mainstream systems into three fundamental stages: knowledge representation, knowledge retrieval, and knowledge reasoning. Through an examination of existing techniques employed at each stage, this survey identifies persistent challenges and outlines promising future research directions, providing a foundation for advancing KB-VQA models and their applications.

Heterogeneous Federated Learning (HtFL) enables collaborative learning across clients with diverse model architectures and non-IID data distributions, which are prevalent in real-world edge computing applications. Existing HtFL approaches typically employ proxy datasets to facilitate knowledge sharing or implement coarse-grained model-level knowledge transfer. However, such approaches not only elevate risks of user privacy leakage but also lead to the loss of fine-grained model-specific knowledge, ultimately creating barriers to effective knowledge sharing. To address these challenges, we propose FedFree, a novel data-free and model-free HtFL framework featuring two key innovations. First, FedFree introduces a reverse layer-wise knowledge transfer mechanism that aggregates heterogeneous client models into a global model solely using Gaussian-based pseudo data, eliminating reliance on proxy datasets. Second, it leverages Knowledge Gain Entropy (KGE) to guide targeted layer-wise knowledge alignment, ensuring that each client receives the most relevant global updates tailored to its specific architecture. We provide rigorous theoretical convergence guarantees for FedFree and conduct extensive experiments on CIFAR-10 and CIFAR-100. Results demonstrate that FedFree achieves substantial performance gains, with relative accuracy improving up to 46.3% over state-of-the-art baselines. The framework consistently excels under highly heterogeneous model/data distributions and in large scale settings.

Recent studies have shifted their focus towards formulating traffic forecasting as a spatio-temporal graph modeling problem. Typically, they constructed a static spatial graph at each time step and then connected each node with itself between adjacent time steps to create a spatio-temporal graph. However, this approach failed to explicitly reflect the correlations between different nodes at different time steps, thus limiting the learning capability of graph neural networks. Additionally, those models overlooked the dynamic spatio-temporal correlations among nodes by using the same adjacency matrix across different time steps. To address these limitations, we propose a novel approach called Spatio-Temporal Joint Graph Convolutional Networks (STJGCN) for accurate traffic forecasting on road networks over multiple future time steps. Specifically, our method encompasses the construction of both pre-defined and adaptive spatio-temporal joint graphs (STJGs) between any two time steps, which represent comprehensive and dynamic spatio-temporal correlations. We further introduce dilated causal spatio-temporal joint graph convolution layers on the STJG to capture spatio-temporal dependencies from distinct perspectives with multiple ranges. To aggregate information from different ranges, we propose a multi-range attention mechanism. Finally, we evaluate our approach on five public traffic datasets and experimental results demonstrate that STJGCN is not only computationally efficient but also outperforms 11 state-of-the-art baseline methods.

This article aims to unify spatial dependency and temporal dependency in a non-Euclidean space while capturing the inner spatial-temporal dependencies for traffic data. For spatial-temporal attribute entities with topological structure, the space-time is consecutive and unified while each node's current status is influenced by its neighbors' past states over variant periods of each neighbor. Most spatial-temporal neural networks for traffic forecasting study spatial dependency and temporal correlation separately in processing, gravely impaired the spatial-temporal integrity, and ignore the fact that the neighbors' temporal dependency period for a node can be delayed and dynamic. To model this actual condition, we propose TraverseNet, a novel spatial-temporal graph neural network, viewing space and time as an inseparable whole, to mine spatial-temporal graphs while exploiting the evolving spatial-temporal dependencies for each node via message traverse mechanisms. Experiments with ablation and parameter studies have validated the effectiveness of the proposed TraverseNet, and the detailed implementation can be found from https://github.com/nnzhan/TraverseNet.

Graph convolutional networks are becoming indispensable for deep learning from graph-structured data. Most of the existing graph convolutional networks share two big shortcomings. First, they are essentially low-pass filters, thus the potentially useful middle and high frequency band of graph signals are ignored. Second, the bandwidth of existing graph convolutional filters is fixed. Parameters of a graph convolutional filter only transform the graph inputs without changing the curvature of a graph convolutional filter function. In reality, we are uncertain about whether we should retain or cut off the frequency at a certain point unless we have expert domain knowledge. In this paper, we propose Automatic Graph Convolutional Networks (AutoGCN) to capture the full spectrum of graph signals and automatically update the bandwidth of graph convolutional filters. While it is based on graph spectral theory, our AutoGCN is also localized in space and has a spatial form. Experimental results show that AutoGCN achieves significant improvement over baseline methods which only work as low-pass filters.

Knowledge sharing and model personalization are two key components in the conceptual framework of personalized federated learning (PFL). Existing PFL methods focus on proposing new model personalization mechanisms while simply implementing knowledge sharing by aggregating models from all clients, regardless of their relation graph. This paper aims to enhance the knowledge-sharing process in PFL by leveraging the graph-based structural information among clients. We propose a novel structured federated learning (SFL) framework to learn both the global and personalized models simultaneously using client-wise relation graphs and clients' private data. We cast SFL with graph into a novel optimization problem that can model the client-wise complex relations and graph-based structural topology by a unified framework. Moreover, in addition to using an existing relation graph, SFL could be expanded to learn the hidden relations among clients. Experiments on traffic and image benchmark datasets can demonstrate the effectiveness of the proposed method.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications, where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on the existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this article, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art GNNs into four categories, namely, recurrent GNNs, convolutional GNNs, graph autoencoders, and spatial-temporal GNNs. We further discuss the applications of GNNs across various domains and summarize the open-source codes, benchmark data sets, and model evaluation of GNNs. Finally, we propose potential research directions in this rapidly growing field.

Modeling multivariate time series has long been a subject that has attracted researchers from a diverse range of fields including economics, finance, and traffic. A basic assumption behind multivariate time series forecasting is that its variables depend on one another but, upon looking closely, it is fair to say that existing methods fail to fully exploit latent spatial dependencies between pairs of variables. In recent years, meanwhile, graph neural networks (GNNs) have shown high capability in handling relational dependencies. GNNs require well-defined graph structures for information propagation which means they cannot be applied directly for multivariate time series where the dependencies are not known in advance. In this paper, we propose a general graph neural network framework designed specifically for multivariate time series data. Our approach automatically extracts the uni-directed relations among variables through a graph learning module, into which external knowledge like variable attributes can be easily integrated. A novel mix-hop propagation layer and a dilated inception layer are further proposed to capture the spatial and temporal dependencies within the time series. The graph learning, graph convolution, and temporal convolution modules are jointly learned in an end-to-end framework. Experimental results show that our proposed model outperforms the state-of-the-art baseline methods on 3 of 4 benchmark datasets and achieves on-par performance with other approaches on two traffic datasets which provide extra structural information.

Cerebrovascular segmentation from time-of-flight magnetic resonance angiography (TOF-MRA) data is of great importance in blood supply structure analysis, diagnosis, and treatment of cerebrovascular pathologies. However, complete and accurate segmentation is still a challenge due to the complex image context and vascular morphology. The existing model-driven methods are often difficult to obtain prominent accuracy and robustness. Deep-learning based technology has achieved unimaginable success, but always faces the problem of insufficient labeled data. In this paper, a novel strategy is proposed to automate cerebrovascular segmentation, which integrates model- and data-driven methods. Firstly, the TOF-MRA data are sparsely labeled by three radiologists. Secondly, a semi-supervised mixture probability model is proposed to fit the cerebrovascular intensity distribution precisely, which starts from the sparse annotations and generates massive labeled points. Thirdly, mislabeled points are corrected by a Clean-Mechanism model, to acquire a well-labeled point-set of good quality. Finally, we construct and train a dilated dense convolution network (DD-CNN) by the resultant labeled point-set. The proposed method is validated on 109 clinical TOR-MRA data from a public dataset. Compared with the other state-of-the-art segmentation methods, our method segments cerebrovascular structure with better completeness and sensibility, especially for slender vascularity. The experimental results show that our method reaches an average dice score of 93.20%, which also indicates that the DD-CNN is very competent for cerebrovascular segmentation from TOF-MRA volume.

Spatial-temporal graph modeling is an important task to analyze the spatial relations and temporal trends of components in a system. Existing approaches mostly capture the spatial dependency on a fixed graph structure, assuming that the underlying relation between entities is pre-determined. However, the explicit graph structure (relation) does not necessarily reflect the true dependency and genuine relation may be missing due to the incomplete connections in the data. Furthermore, existing methods are ineffective to capture the temporal trends as the RNNs or CNNs employed in these methods cannot capture long-range temporal sequences. To overcome these limitations, we propose in this paper a novel graph neural network architecture, {Graph WaveNet}, for spatial-temporal graph modeling. By developing a novel adaptive dependency matrix and learn it through node embedding, our model can precisely capture the hidden spatial dependency in the data. With a stacked dilated 1D convolution component whose receptive field grows exponentially as the number of layers increases, Graph WaveNet is able to handle very long sequences. These two components are integrated seamlessly in a unified framework and the whole framework is learned in an end-to-end manner. Experimental results on two public traffic network datasets, METR-LA and PEMS-BAY, demonstrate the superior performance of our algorithm.