Understanding how chemical perturbations propagate through biological systems is essential for robust molecular property prediction. While most existing methods focus on chemical structures alone, recent advances highlight the crucial role of cellular responses such as morphology and gene expression in shaping drug effects. However, current cell-aware approaches face two key limitations: (1) modality incompleteness in external biological data, and (2) insufficient modeling of hierarchical dependencies across molecular, cellular, and genomic levels. We propose CHMR (Cell-aware Hierarchical Multi-Modal Representations), a robust framework that jointly models local-global dependencies between molecules and cellular responses and captures latent biological hierarchies via a novel tree-structured vector quantization module. Evaluated on public benchmarks spanning 696 tasks, CHMR outperforms state-of-the-art baselines, yielding average improvements of 3.6% on classification and 17.2% on regression tasks. These results demonstrate the advantage of hierarchy-aware, multi-modal learning for reliable and biologically grounded molecular representations, offering a generalizable framework for integrative biomedical modeling.

In real-world graphs, node attributes are often incomplete due to acquisition costs or privacy restrictions, reducing representation quality and harming downstream predictions in graph neural networks (GNNs). A common remedy is feature-propagation-based imputation. However, cold-start effects arising from attribute resetting and low-degree nodes impede effective propagation and convergence in these methods. To address these challenges, we propose AttriReBoost (ARB), a propagation-based method that mitigates cold-start issues in attribute-missing graphs. ARB enhances global feature propagation (FP) by redefining initial boundary conditions and strategically integrating virtual edges, thereby improving node connectivity and ensuring stable and efficient convergence. The method supports gradient-free attribute reconstruction with low computational overhead, and we provide a rigorous convergence analysis. Extensive experiments on several real-world benchmark datasets demonstrate the effectiveness of ARB, achieving an average accuracy improvement of 5.11% over state-of-the-art methods. In addition, ARB exhibits remarkable computational efficiency, processing a large-scale graph with 2.44 million nodes in just 16 s on a single GPU. Our code is available at https://github.com/limengran98/ARB.

The data sparsity problem significantly hinders the performance of recommender systems, as traditional models rely on limited historical interactions to learn user preferences and item properties. While incorporating multimodal information can explicitly represent these preferences and properties, existing works often use it only as side information, failing to fully leverage its potential. In this paper, we propose MDVT, a model-agnostic approach that constructs multimodal-driven virtual triplets to provide valuable supervision signals, effectively mitigating the data sparsity problem in multimodal recommendation systems. To ensure high-quality virtual triplets, we introduce three tailored warm-up threshold strategies: static, dynamic, and hybrid. The static warm-up threshold strategy exhaustively searches for the optimal number of warm-up epochs but is time-consuming and computationally intensive. The dynamic warm-up threshold strategy adjusts the warm-up period based on loss trends, improving efficiency but potentially missing optimal performance. The hybrid strategy combines both, using the dynamic strategy to find the approximate optimal number of warm-up epochs and then refining it with the static strategy in a narrow hyper-parameter space. Once the warm-up threshold is satisfied, the virtual triplets are used for joint model optimization by our enhanced pair-wise loss function without causing significant gradient skew. Extensive experiments on multiple real-world datasets demonstrate that integrating MDVT into advanced multimodal recommendation models effectively alleviates the data sparsity problem and improves recommendation performance, particularly in sparse data scenarios.

With the advancement of information technology, the Social Internet of Things (SIoT) has fostered the integration of physical devices and social networks, deepening the study of complex interaction patterns. Text attribute graphs (TAGs) capture both topological structures and semantic attributes, enhancing the analysis of complex interactions within the SIoT. However, existing graph learning methods are typically designed for complete attributed graphs, and the common issue of missing attributes in attribute missing graphs (AMGs) increases the difficulty of analysis tasks. To address this, we propose the topology-driven attribute recovery (TDAR) framework, which leverages topological data for AMG learning. TDAR introduces an improved prefilling method for initial attribute recovery using native graph topology. Additionally, it dynamically adjusts propagation weights and incorporates homogeneity strategies within the embedding space to suit AMGs’ unique topological structures, effectively reducing noise during information propagation. Extensive experiments on public datasets demonstrate that TDAR significantly outperforms state-of-the-art methods in attribute reconstruction and downstream tasks, offering a robust solution to the challenges posed by AMGs. The code is available athttps://github.com/limengran98/TDAR.

Temporal dynamic graphs (TDGs), representing the dynamic evolution of entities and their relationships over time with intricate temporal features, are widely used in various real-world domains. Existing methods typically rely on mainstream techniques such as transformers and graph neural networks (GNNs) to capture the spatiotemporal information of TDGs. However, despite their advanced capabilities, these methods often struggle with significant computational complexity and limited ability to capture temporal dynamic contextual relationships. Recently, a new model architecture called mamba has emerged, noted for its capability to capture complex dependencies in sequences while significantly reducing computational complexity. Building on this, we propose a novel method, TDG-mamba, which integrates mamba for TDG learning. TDG-mamba introduces deep semantic spatiotemporal embeddings into the mamba architecture through a specially designed spatiotemporal prior tokenization module (SPTM). Furthermore, to better leverage temporal information differences and enhance the modeling of dynamic changes in graph structures, we separately design a bidirectional mamba and a directed GNN for improved spatiotemporal embedding learning. Link prediction experiments on multiple public datasets demonstrate that our method delivers superior performance, with an average improvement of 5.11% over baseline methods across various settings.

With the development of intelligent connected vehicle technology, human-machine shared control has gained popularity in vehicle following due to its effectiveness in driver assistance. However, traditional vehicle following systems struggle to maintain stability when driver reaction time fluctuates, as these variations require different levels of system intervention. To address this issue, the proposed human-machine shared vehicle following assistance system (HM-VFAS) integrates driver outputs under various states with the assistance system. The system employs an intelligent driver model that accounts for reaction time delays, simulating time-varying driver outputs. Acontrol authority allocation strategy is designed to dynamically adjust the level of intervention based on real-time driver state assessment. To handle instability from driver authority switching, the proposed solution includes a two-layer adaptive finite time sliding mode controller (A-FTSMC). The first layer is an integral sliding mode adaptive controller that ensures robustness by compensating for uncertainties in the driver output. The second layer is a fast non-singular terminal sliding mode controller designed to accelerate convergence for rapid stabilization. Based on the driver-in-the-loop experimental results using the intelligent cockpit system, the performance of the HM-VFAS was evaluated. Results show that the proposed control strategy maintains a safe distance under time-varying driver states, with the actual acceleration error relative to the target acceleration maintained within$\pm 0.6\!\ \text {m/s}^{2}$and the maximum acceleration error reduced by$1.3\!\ \text {m/s}^{2}$. Compared to traditional controllers, the A-FTSMC controller offers faster convergence and less vibration, reducing the stabilization time by 26.8%.

Accurate and refined passenger flow prediction is essential for optimizing the collaborative management of multiple collection and distribution modes in large-scale transportation hubs. Traditional methods often focus only on the overall passenger volume, neglecting the interdependence between different modes within the hub. To address this limitation, we propose MM-STFlowNet, a comprehensive multi-mode prediction framework grounded in dynamic spatial-temporal graph modeling. Initially, an integrated temporal feature processing strategy is implemented using signal decomposition and convolution techniques to address data spikes and high volatility. Subsequently, we introduce the Spatial-Temporal Dynamic Graph Convolutional Recurrent Network (STDGCRN) to capture detailed spatial-temporal dependencies across multiple traffic modes, enhanced by an adaptive channel attention mechanism. Finally, the self-attention mechanism is applied to incorporate various external factors, further enhancing prediction accuracy. Experiments on a real-world dataset from Guangzhounan Railway Station in China demonstrate that MM-STFlowNet achieves state-of-the-art performance, with an average improvement of 52.56% in MSE and 36.38% in MAE. Especially during peak hours, it demonstrates excellent forecasting performance, providing valuable insights for transportation hub management. Our model is also demonstrated strong generalization in low-resource scenarios and different traffic scenarios. Our code is available at https://github.com/BMRETURN/MM-STFlowNet

Attribute graphs are a crucial data structure for graph communities. However, the presence of redundancy and noise in the attribute graph can impair the aggregation effect of integrating two different heterogeneous distributions of attribute and structural features, resulting in inconsistent and distorted data that ultimately compromises the accuracy and reliability of attribute graph learning. For instance, redundant or irrelevant attributes can result in overfitting, while noisy attributes can lead to underfitting. Similarly, redundant or noisy structural features can affect the accuracy of graph representations, making it challenging to distinguish between different nodes or communities. To address these issues, we propose the embedded fusion graph auto-encoder framework for self-supervised learning (SSL), which leverages multitask learning to fuse node features across different tasks to reduce redundancy. The embedding fusion graph auto-encoder (EFGAE) framework comprises two phases: pretraining (PT) and downstream task learning (DTL). During the PT phase, EFGAE uses a graph auto-encoder (GAE) based on adversarial contrastive learning to learn structural and attribute embeddings separately and then fuses these embeddings to obtain a representation of the entire graph. During the DTL phase, we introduce an adaptive graph convolutional network (AGCN), which is applied to graph neural network (GNN) classifiers to enhance recognition for downstream tasks. The experimental results demonstrate that our approach outperforms state-of-the-art (SOTA) techniques in terms of accuracy, generalization ability, and robustness.

Spatial transcriptomics reveals the spatial distribution of genes in complex tissues, providing crucial insights into biological processes, disease mechanisms, and drug development. The prediction of gene expression based on cost-effective histology images is a promising yet challenging field of research. Existing methods for gene prediction from histology images exhibit two major limitations. First, they ignore the intricate relationship between cell morphological information and gene expression. Second, these methods do not fully utilize the different latent stages of features extracted from the images. To address these limitations, we propose a novel hypergraph neural network model, HGGEP, to predict gene expressions from histology images. HGGEP includes a gradient enhancement module to enhance the model's perception of cell morphological information. A lightweight backbone network extracts multiple latent stage features from the image, followed by attention mechanisms to refine the representation of features at each latent stage and capture their relations with nearby features. To explore higher-order associations among multiple latent stage features, we stack them and feed into the hypergraph to establish associations among features at different scales. Experimental results on multiple datasets from disease samples including cancers and tumor disease, demonstrate the superior performance of our HGGEP model than existing methods.

Community detection aims to identify dense subgroups of nodes within a network. However, in real-world networks, node attributes are often missing, making traditional methods less effective. In networks with missing attributes, the main challenge of community detection is to deal with the missing attribute information efficiently and use network structure information to make accurate predictions. This article proposes an innovative method called contrastive sampling-aggregating transformer (CSAT) for community detection in attribute-missing networks. CSAT incorporates the contrastive learning principle to capture hidden patterns among nodes and to aggregate information from different samples to create a more robust and accurate methodology for community detection. Specifically, CSAT utilizes a sampling and propagation strategy to obtain different samples and smooth attribute features of the network structure and leverages the Transformer architecture to model the pairwise relationships between nodes. Therefore, our method can address the attribute-missing issue by integrating the auxiliary information from both the network structure and other sources. Extensive experiments on several benchmark datasets demonstrate CSAT’s superior performance compared to the state-of-the-art methods for community detection.

Recommender systems have become an indispensable tool in today's digital age, significantly enhancing user engagement on various online platforms by curating personalized item recommendations tailored to individual preferences. While the field has long been dominated by the collaborative filtering technique, which primarily leverages user–item interaction data, it often falls short in encapsulating the rich contextual intricacies and evolving dynamics inherent to these interactions. Recognizing this limitation, our research introduces the contextual semantic interaction graph embedding (CSI-GE) method. This advanced model incorporates a dynamic hop window within a multilayer graph convolutional network, ensuring a comprehensive extraction of both immediate and evolving contextual features. By amalgamating self-supervised contrastive learning, we achieve a refinement of user and item embeddings. Furthermore, our innovative variance–invariance–covariance (VIC) regularization-based loss function fortifies the robustness of these embeddings. Through rigorous testing, CSI-GE consistently outperformed contemporary methods, underscoring its superior accuracy and stability.

Social link is an important index to understand master students’ mental health and social ability in educational management. Extracting hidden social strength from students’ rich daily life behaviors has also become an attractive research hotspot. Devices with positioning functions record many students’ spatiotemporal behavior data, which can infer students’ social links. However, under the guidance of school regulations, students’ daily activities have a certain regularity and periodicity. Traditional methods usually compare the co-occurrence frequency of two users to infer social association but do not consider the location-intensive and time-sensitive in campus scenes. Aiming at the campus environment, a Spatiotemporal Entropy-Based Analyzing (S-EBA) model for inferring students’ social strength is proposed. The model is based on students’ multi-source heterogeneous behavioral data to calculate the frequency of co-occurrence under the influence of time intervals. Then, the three features of diversity, spatiotemporal hotspot and behavior similarity are introduced to calculate social strength. Experiments show that our method is superior to the traditional methods under many evaluating criteria. The inferred social strength is used as the weight of the edge to construct a social network further to analyze its important impact on students’ education management.

The exploration of self-supervised information mining of heterogeneous datasets has gained significant traction in recent years. Heterogeneous graph neural networks (HGNNs) have emerged as a highly promising method for handling heterogeneous information networks (HINs) due to their superior performance. These networks leverage aggregation functions to convert pairwise relations-based features from raw heterogeneous graphs into embedding vectors. However, real-world HINs contain valuable higher-order relations that are often overlooked but can provide complementary information. To address this issue, we propose a novel method calledSelf-supervisedNodes-HyperedgesEmbedding (SNHE), which leverages hypergraph structures to incorporate higher-order information into the embedding process of HINs. Our method decomposes the raw graph structure into snapshots based on various meta-paths, which are then transformed into hypergraphs to aggregate high-order information within the data and generate embedding representations. Given the complexity of HINs, we develop a dual self-supervised structure that maximizes mutual information in the enhanced graph data space, guides the overall model update, and reduces redundancy and noise. We evaluate our proposed method on various real-world datasets for node classification and clustering tasks, and compare it against state-of-the-art methods. The experimental results demonstrate the efficacy of our method. Our code is available athttps://github.com/limengran98/SNHE.

Graph neural networks (GNNs) have been widely used for graph structure learning and achieved excellent performance in tasks such as node classification and link prediction. Real-world graph networks imply complex and various semantic information and are often referred to as heterogeneous information networks (HINs). Previous GNNs have laboriously modeled heterogeneous graph networks with pairwise relations, in which the semantic information representation for learning is incomplete and severely hinders node embedded learning. Therefore, the conventional graph structure cannot satisfy the demand for information discovery in HINs. In this article, we propose an end-to-end hypergraph transformer neural network (HGTN) that exploits the communication abilities between different types of nodes and hyperedges to learn higher-order relations and discover semantic information. Specifically, attention mechanisms weigh the importance of semantic information hidden in original HINs to generate useful meta-paths. Meanwhile, our method develops a multi-scale attention module to aggregate node embeddings in higher-order neighborhoods. We evaluate the proposed model with node classification tasks on six datasets: DBLP, ACM, IBDM, Reuters, STUD-BJUT, and Citeseer. Experiments on a large number of benchmarks show the advantages of HGTN.

Clustering is a fundamental and hot issue in the unsupervised learning area. With the rapid development of deep learning and graph neural networks (GNNs) techniques, researchers have proposed a series of effective clustering methods. However, most existing approaches adopt a conventional graph to aggregate the neighborhood information, where only the pairwise relations are considered. Moreover, the redundancy/noise in the raw data samples may result in less accurate sample relations and inferior clustering results. In this paper, we proposed a new GNNs based clustering method, which adopts the hypergraph learning approach to explore the high-order relationship for accurate relation learning. Specifically, we first construct two hypergraph representations based on the topology feature and attribute feature from data samples. Then, a self-supervised structure is integrated to learn a cross-correlation matrix from the original hypergraph to act as a higher-order neighborhood with reduced redundancy and noise. Finally the embedding representation of the clustering space is learned in the graph convolution. The proposed method has been evaluated on six public datasets for clustering tasks. Experimental results show that our proposed method outperforms the state-of-the-art ones.