State-of-the-art brain graph analysis methods fail to fully encode the small-world architecture of brain graphs (accompanied by the presence of hubs and functional modules), and therefore lack biological plausibility to some extent. This limitation hinders their ability to accurately represent the brain's structural and functional properties, thereby restricting the effectiveness of machine learning models in tasks such as brain disorder detection. In this work, we propose a novel Biologically Plausible Brain Graph Transformer (BioBGT) that encodes the small-world architecture inherent in brain graphs. Specifically, we present a network entanglement-based node importance encoding technique that captures the structural importance of nodes in global information propagation during brain graph communication, highlighting the biological properties of the brain structure. Furthermore, we introduce a functional module-aware self-attention to preserve the functional segregation and integration characteristics of brain graphs in the learned representations. Hub2 (a) Hubs play essential roles (b) Functional modules in the brain. One Figure 1: Small-world architecture of brain graphs. of the most important characteristics of brain graphs is their small-world architecture, with scientific evidence supporting the presence of hubs and functional modules in brain graphs (Liao et al., 2017; Swanson et al., 2024). First, it is demonstrated that nodes in brain graphs exhibit a high degree of difference in their importance, with certain nodes having more central roles in information propagation (Lynn & Bassett, 2019; Betzel et al., 2024). These nodes are perceived as hubs, as shown in Figure 1 (a) (the visualization is based on findings by Seguin et al. (2023)), which are usually highly connected so as to support efficient communication within the brain. Second, human brain consists of various functional modules (e.g., visual cortex), where ROIs within the same module exhibit high functional coherence, termed functional integration, while ROIs from different modules show lower functional coherence, termed functional segregation (Rubinov & Sporns, 2010; Seguin et al., 2022). Therefore, brain graphs are characterized by community structure, reflecting functional modules. Our code is available at https://github.com/pcyyyy/BioBGT. ROIs in the same module have strong connections (high temporal correlations), while those from different modules show weaker connections. With the significant ability of graph transformers in capturing interactions between nodes (Ma et al., 2023a; Shehzad et al., 2024; Yi et al., 2024), Transformer-based brain graph learning methods have gained prominence (Kan et al., 2022; Bannadabhavi et al., 2023).

Cyber-physical-social systems (CPSSs) have emerged in many applications over recent decades, requiring increased attention to security concerns. The rise of sophisticated threats like Advanced Persistent Threats (APTs) makes ensuring security in CPSSs particularly challenging. Provenance graph analysis has proven effective for tracing and detecting anomalies within systems, but the sheer size and complexity of these graphs hinder the efficiency of existing methods, especially those relying on graph neural networks (GNNs). To address these challenges, we present GraphDART, a modular framework designed to distill provenance graphs into compact yet informative representations, enabling scalable and effective anomaly detection. GraphDART can take advantage of diverse graph distillation techniques, including classic and modern graph distillation methods, to condense large provenance graphs while preserving essential structural and contextual information. This approach significantly reduces computational overhead, allowing GNNs to learn from distilled graphs efficiently and enhance detection performance. Extensive evaluations on benchmark datasets demonstrate the robustness of GraphDART in detecting malicious activities across cyber-physical-social systems. By optimizing computational efficiency, GraphDART provides a scalable and practical solution to safeguard interconnected environments against APTs.

Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility across various graph-related tasks. This survey provides an in-depth review of recent progress and challenges in graph transformer research. We begin with foundational concepts of graphs and transformers. We then explore design perspectives of graph transformers, focusing on how they integrate graph inductive biases and graph attention mechanisms into the transformer architecture. Furthermore, we propose a taxonomy classifying graph transformers based on depth, scalability, and pre-training strategies, summarizing key principles for effective development of graph transformer models. Beyond technical analysis, we discuss the applications of graph transformer models for node-level, edge-level, and graph-level tasks, exploring their potential in other application scenarios as well. Finally, we identify remaining challenges in the field, such as scalability and efficiency, generalization and robustness, interpretability and explainability, dynamic and complex graphs, as well as data quality and diversity, charting future directions for graph transformer research.

Multimodal data pervades various domains, including healthcare, social media, and transportation, where multimodal graphs play a pivotal role. Machine learning on multimodal graphs, referred to as multimodal graph learning (MGL), is essential for successful artificial intelligence (AI) applications. The burgeoning research in this field encompasses diverse graph data types and modalities, learning techniques, and application scenarios. This survey paper conducts a comparative analysis of existing works in multimodal graph learning, elucidating how multimodal learning is achieved across different graph types and exploring the characteristics of prevalent learning techniques. Additionally, we delineate significant applications of multimodal graph learning and offer insights into future directions in this domain. Consequently, this paper serves as a foundational resource for researchers seeking to comprehend existing MGL techniques and their applicability across diverse scenarios.

With the explosive growth of artificial intelligence (AI) and big data, it has become vitally important to organize and represent the enormous volume of knowledge appropriately. As graph data, knowledge graphs accumulate and convey knowledge of the real world. It has been well-recognized that knowledge graphs effectively represent complex information; hence, they rapidly gain the attention of academia and industry in recent years. Thus to develop a deeper understanding of knowledge graphs, this paper presents a systematic overview of this field. Specifically, we focus on the opportunities and challenges of knowledge graphs. We first review the opportunities of knowledge graphs in terms of two aspects: (1) AI systems built upon knowledge graphs; (2) potential application fields of knowledge graphs. Then, we thoroughly discuss severe technical challenges in this field, such as knowledge graph embeddings, knowledge acquisition, knowledge graph completion, knowledge fusion, and knowledge reasoning. We expect that this survey will shed new light on future research and the development of knowledge graphs.

Quantum theory has shown its superiority in enhancing machine learning. However, facilitating quantum theory to enhance graph learning is in its infancy. This survey investigates the current advances in quantum graph learning (QGL) from three perspectives, i.e., underlying theories, methods, and prospects. We first look at QGL and discuss the mutualism of quantum theory and graph learning, the specificity of graph-structured data, and the bottleneck of graph learning, respectively. A new taxonomy of QGL is presented, i.e., quantum computing on graphs, quantum graph representation, and quantum circuits for graph neural networks. Pitfall traps are then highlighted and explained. This survey aims to provide a brief but insightful introduction to this emerging field, along with a detailed discussion of frontiers and outlook yet to be investigated.